@article {pmid39351379,
year = {2024},
author = {Leavy, OC and Russell, RJ and Harrison, EM and Lone, NI and Kerr, S and Docherty, AB and Sheikh, A and Richardson, M and Elneima, O and Greening, NJ and Harris, VC and Houchen-Wolloff, L and McAuley, HJC and Saunders, RM and Sereno, M and Shikotra, A and Singapuri, A and Aul, R and Beirne, P and Bolton, CE and Brown, JS and Choudhury, G and Diar Bakerly, N and Easom, N and Echevarria, C and Fuld, J and Hart, N and Hurst, JR and Jones, M and Parekh, D and Pfeffer, P and Rahman, NM and Rowland-Jones, S and Shah, AM and Wootton, DG and Jolley, C and Thompson, AAR and Chalder, T and Davies, MJ and De Soyza, A and Geddes, JR and Greenhalf, W and Heller, S and Howard, L and Jacob, J and Jenkins, RG and Lord, JM and Man, WD and McCann, GP and Neubauer, S and Openshaw, PJM and Porter, J and Rowland, MJ and Scott, JT and Semple, MG and Singh, SJ and Thomas, D and Toshner, M and Lewis, K and Heaney, LG and Briggs, A and Zheng, B and Thorpe, M and Quint, JK and Chalmers, JD and Ho, LP and Horsley, A and Marks, M and Poinasamy, K and Raman, B and Wain, LV and Brightling, CE and Evans, RA},
title = {1-year health outcomes associated with systemic corticosteroids for COVID-19: a longitudinal cohort study.},
journal = {ERJ open research},
volume = {10},
number = {5},
pages = {},
pmid = {39351379},
issn = {2312-0541},
abstract = {BACKGROUND: In patients with coronavirus disease 2019 (COVID-19) requiring supplemental oxygen, dexamethasone reduces acute severity and improves survival, but longer-term effects are unknown. We hypothesised that systemic corticosteroid administration during acute COVID-19 would be associated with improved health-related quality of life (HRQoL) 1 year after discharge.<br><br>METHODS: Adults admitted to hospital between February 2020 and March 2021 for COVID-19 and meeting current guideline recommendations for dexamethasone treatment were included using two prospective UK cohort studies (Post-hospitalisation COVID-19 and the International Severe Acute Respiratory and emerging Infection Consortium). HRQoL, assessed by the EuroQol-Five Dimensions-Five Levels utility index (EQ-5D-5L UI), pre-hospital and 1 year after discharge were compared between those receiving corticosteroids or not after propensity weighting for treatment. Secondary outcomes included patient-reported recovery, physical and mental health status, and measures of organ impairment. Sensitivity analyses were undertaken to account for survival and selection bias.<br><br>FINDINGS: Of the 1888 participants included in the primary analysis, 1149 received corticosteroids. There was no between-group difference in EQ-5D-5L UI at 1 year (mean difference 0.004, 95% CI -0.026-0.034). A similar reduction in EQ-5D-5L UI was seen at 1 year between corticosteroid exposed and nonexposed groups (mean&#xb1;sd change -0.12&#xb1;0.22 versus -0.11&#xb1;0.22). Overall, there were no differences in secondary outcome measures. After sensitivity analyses modelled using a cohort of 109&#x2009;318 patients admitted to hospital with COVID-19, EQ-5D-5L UI at 1 year remained similar between the two groups.<br><br>INTERPRETATION: Systemic corticosteroids for acute COVID-19 have no impact on the large reduction in HRQoL 1 year after hospital discharge. Treatments to address the persistent reduction in HRQoL are urgently needed.},
}
@article {pmid39351031,
year = {2024},
author = {Wei, C and Cai, Y and Liu, J and Guo, Y and Wu, X and He, X and Hu, D},
title = {Factors influencing user's health information discernment abilities in online health communities: based on SEM and fsQCA.},
journal = {Frontiers in public health},
volume = {12},
number = {},
pages = {1379094},
pmid = {39351031},
issn = {2296-2565},
mesh = {Humans ; Surveys and Questionnaires ; Female ; Male ; Adult ; *Internet ; Consumer Health Information ; Latent Class Analysis ; Information Seeking Behavior ; Fuzzy Logic ; Young Adult ; Middle Aged ; },
abstract = {INTRODUCTION: Online health communities have become the main source for people to obtain health information. However, the existence of poor-quality health information, misinformation, and rumors in online health communities increases the challenges in governing information quality. It not only affects users' health decisions but also undermines social stability. It is of great significance to explore the factors that affect users' ability to discern information in online health communities.<br><br>METHODS: This study integrated the Stimulus-Organism-Response Theory, Information Ecology Theory and the Mindsponge Theory to constructed a model of factors influencing users' health information discernment abilities in online health communities. A questionnaire was designed based on the variables in the model, and data was collected. Utilizing Structural Equation Modeling (SEM) in conjunction with fuzzy-set Qualitative Comparative Analysis (fsQCA), the study analyzed the complex causal relationships among stimulus factors, user perception, and the health information discernment abilities.<br><br>RESULTS: The results revealed that the dimensions of information, information environment, information technology, and information people all positively influenced health information discernment abilities. Four distinct configurations were identified as triggers for users' health information discernment abilities. The core conditions included information source, informational support, technological security, technological facilitation, and perceived risk. It was also observed that information quality and emotional support can act as substitutes for one another, as can informational support and emotional support.<br><br>DISCUSSION: This study provides a new perspective to study the influencing factors of health information discernment abilities of online health community users. It can provide experiences and references for online health community information services, information resource construction and the development of users' health information discernment abilities.},
}
@article {pmid39349447,
year = {2024},
author = {Zhou, L and Wu, S and Chen, Y and Huang, R and Cheng, B and Mao, Q and Liu, T and Liu, Y and Zhao, K and Pan, H and Yu, C and Gao, X and Luo, L and Zhang, Q},
title = {Multi-omics analyzes of Rosa gigantea illuminate tea scent biosynthesis and release mechanisms.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8469},
pmid = {39349447},
issn = {2041-1723},
mesh = {*Rosa/genetics/metabolism ; *Volatile Organic Compounds/metabolism ; *Odorants/analysis ; *Genome, Plant ; *Gene Expression Regulation, Plant ; Gene Regulatory Networks ; Genomics/methods ; Eugenol/analogs &amp; derivatives/metabolism ; Plant Proteins/genetics/metabolism ; Pollination ; Multiomics ; },
abstract = {Rose is an important ornamental crop cultivated globally for perfume production. However, our understanding of the mechanisms underlying scent production and molecular breeding for fragrance is hindered by the lack of a reference genome for tea roses. We present the first complete telomere-to-telomere (T2T) genome of Rosa gigantea, with high quality (QV > 60), including detailed characterization of the structural features of repetitive regions. The expansion of genes associated with phenylpropanoid biosynthesis may account for the unique tea scent. We uncover the release rhythm of aromatic volatile organic compounds and their gene regulatory networks through comparative genomics and time-ordered gene co-expression networks. Analyzes of eugenol homologs demonstrate how plants attract pollinators using specialized phenylpropanoids in specific tissues. This study highlights the conservation and utilization of genetic diversity from wild endangered species through multi-omics approaches, providing a scientific foundation for enhancing rose fragrance via de novo domestication.},
}
@article {pmid39346055,
year = {2024},
author = {Knobloch, S and Salimi, F and Buaya, A and Ploch, S and Thines, M},
title = {RAPiD: a rapid and accurate plant pathogen identification pipeline for on-site nanopore sequencing.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17893},
pmid = {39346055},
issn = {2167-8359},
mesh = {*Nanopore Sequencing/methods ; Metagenomics/methods ; Plant Diseases/microbiology ; Bacteria/genetics/isolation &amp; purification/classification ; Sequence Analysis, DNA/methods ; Fungi/genetics/isolation &amp; purification/classification ; Plants/microbiology ; Computational Biology/methods ; },
abstract = {Nanopore sequencing technology has enabled the rapid, on-site taxonomic identification of samples from anything and anywhere. However, sequencing errors, inadequate databases, as well as the need for bioinformatic expertise and powerful computing resources, have hampered the widespread use of the technology for pathogen identification in the agricultural sector. Here we present RAPiD, a lightweight and accurate real-time taxonomic profiling pipeline. Compared to other metagenomic profilers, RAPiD had a higher classification precision achieved through the use of a curated, non-redundant database of common agricultural pathogens and extensive quality filtering of alignments. On a fungal, bacterial and mixed mock community RAPiD was the only pipeline to detect all members of the communities. We also present a protocol for in-field sample processing enabling pathogen identification from plant sample to sequence within 3 h using low-cost equipment. With sequencing costs continuing to decrease and more high-quality reference genomes becoming available, nanopore sequencing provides a viable method for rapid and accurate pathogen identification in the field. A web implementation of the RAPiD pipeline for real-time analysis is available at https://agrifuture.senckenberg.de.},
}
@article {pmid39143756,
year = {2024},
author = {Bauer, IE and Davies, MA and Bona, KA and Hararuk, O and Shaw, CH and Thompson, DK and Kurz, WA and Webster, KL and Garneau, M and McLaughlin, JW and Packalen, MS and Prystupa, E and Sanderson, NK and Tarnocai, C},
title = {Peat profile database from peatlands in Canada.},
journal = {Ecology},
volume = {105},
number = {10},
pages = {e4398},
doi = {10.1002/ecy.4398},
pmid = {39143756},
issn = {1939-9170},
support = {//Government of Canada (Expanding Market Opportunities Program)/ ; },
mesh = {Canada ; *Soil/chemistry ; Databases, Factual ; Ecosystem ; },
abstract = {Peatlands cover approximately 12% of the Canadian landscape and play an important role in the carbon cycle through their centennial- to millennial-scale storage of carbon under waterlogged and anoxic conditions. In recognizing the potential of these ecosystems as natural climate solutions and therefore the need to include them in national greenhouse gas inventories, the Canadian Model for Peatlands module (CaMP v. 2.0) was developed by the Canadian Forest Service. Model parameterization included compiling peat profiles across Canada to calibrate peat decomposition rates from different peatland types, to define typical bulk density profiles, and to describe the hydrological (i.e., water table) response of peatlands to climatic changes. A total of 1217 sites were included in the dataset from published and unpublished sources. The CORESITES table contains site location and summary data for each profile, as well as an estimate of total carbon mass per unit area (in megagrams of C per hectare). Total carbon mass per unit area at each location was calculated using bulk density and carbon content through each profile. The PROFILES table contains data for depth (in centimeters), bulk density (in grams per cubic meter), ash and carbon content (in percentage), and material descriptions for contiguous samples through each peat profile. Data gaps for bulk density and C content were filled using interpolation, regression trees, and assigned values based on material description and/or soil classification to allow for the estimation of total carbon mass per unit area. A subset of the sites (N = 374) also have pH and pore water trace-elemental geochemistry data and are found in the WATER table. The REFERENCES table contains the full citation of each source of the data and is linked to each core location through the SOURCEDATA table. The LOOKUP table defines codes in the database that required more space that what was sufficient in the metadata tables. The data can be accessed on Open Government Canada and will be useful for future work on carbon stock mapping and ecosystem modeling. All metadata and data are provided © Her Majesty the Queen in Right of Canada, 2023 and information contained in this publication may be reproduced for personal or public noncommercial purposes with attribution, whereas commercial reproduction and distribution are prohibited except with written permission from NRCan; complete details are noted in the Supporting Information file Metadata S1 (see Class III.B.3: Copyright restrictions).},
}
@article {pmid39345343,
year = {2024},
author = {Halpern, B and Vörös, J and Mc Cartney, AM and Formenti, G and Mouton, A and , and , and , and , },
title = {The genome sequence of the Hungarian meadow viper, Vipera ursinii rakosiensis Méhely, 1893.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {404},
pmid = {39345343},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Vipera ursinii rakosiensis (the Hungarian meadow viper; Chordata; Lepidosauria; Squamata; Viperidae). The genome sequence is 1,625.0 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 17.38 kilobases in length.},
}
@article {pmid39343505,
year = {2024},
author = {Eneli, I and Heeren, FAN and Cason-Wilkerson, RL and Pratt, KJ},
title = {Metabolic and Bariatric Surgery for Adolescents.},
journal = {Pediatric clinics of North America},
volume = {71},
number = {5},
pages = {981-998},
doi = {10.1016/j.pcl.2024.06.007},
pmid = {39343505},
issn = {1557-8240},
mesh = {Humans ; Adolescent ; *Bariatric Surgery/methods ; *Pediatric Obesity/surgery ; Obesity, Morbid/surgery/psychology ; Gastrectomy/methods ; },
abstract = {Obesity is a chronic, complex, and multifactorial disease. Currently, approximately 6% have severe obesity with higher rates seen among racial/ethnic minority subgroups and in rural communities. Severe obesity is associated with cardiometabolic, psychologic, and musculoskeletal comorbidities. Metabolic and bariatric surgery is an effective treatment option for adolescents endorsed by major pediatric organizations. The most common procedure is the vertical sleeve gastrectomy. Pre-operative evaluation includes an in-depth medical, nutrition, physical activity and psychosocial assessment, with a care plan developed by a multidicplinary team with the adolescent and caregiver. The post-operative plan should include monitoring for surgical complications, weight regain, micronutrient deficiencies, psychologic challenges, and transition to adult care.},
}
@article {pmid39341239,
year = {2024},
author = {Adomako, MO and Jin, L and Li, C and Liu, J and Adu, D and Seshie, VI and Yu, FH},
title = {Mechanisms underpinning microplastic effects on the natural climate solutions of wetland ecosystems.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176491},
doi = {10.1016/j.scitotenv.2024.176491},
pmid = {39341239},
issn = {1879-1026},
abstract = {Wetland ecosystems are vital carbon dioxide (CO2) sinks, offering significant nature-based solutions for global climate mitigation. However, the recent influx of microplastic (MP) into wetlands substantially impacts key drivers (e.g., plants and microorganisms) underpinning these wetland functions. While MP-induced greenhouse gas (GHG) emissions and effects on soil organic carbon (SOC) mineralization potentially threaten the long-term wetland C-climate feedbacks, the exact mechanisms and linkage are unclear. This review provides a conceptual framework to elaborate on the interplay between MPs, wetland ecosystems, and the atmospheric milieu. We also summarize published studies that validate possible MP impacts on natural climate solutions of wetlands, as well as provide extensive elaboration on underlying mechanisms. We briefly highlight the relationships between MP influx, wetland degradation, and climate change and conclude by identifying key gaps for future research priorities. Globally, plastic production, MP entry into aquatic systems, and wetland degradation-related emissions are predicted to increase. This means that MP-related emissions and wetland-climate feedback should be addressed in the context of the UN Paris Climate Agreement on net-zero emissions by 2050. This overview serves as a wake-up call on the alarming impacts of MPs on wetland ecosystems and urges a global reconsideration of nature-based solutions in the context of climate mitigation.},
}
@article {pmid39292721,
year = {2024},
author = {Bastien, GE and Cable, RN and Batterbee, C and Wing, AJ and Zaman, L and Duhaime, MB},
title = {Virus-host interactions predictor (VHIP): Machine learning approach to resolve microbial virus-host interaction networks.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1011649},
doi = {10.1371/journal.pcbi.1011649},
pmid = {39292721},
issn = {1553-7358},
mesh = {*Machine Learning ; Humans ; *Viruses/genetics ; *Computational Biology/methods ; *Host-Pathogen Interactions/genetics/physiology ; Host Microbial Interactions/genetics/physiology ; },
abstract = {Viruses of microbes are ubiquitous biological entities that reprogram their hosts' metabolisms during infection in order to produce viral progeny, impacting the ecology and evolution of microbiomes with broad implications for human and environmental health. Advances in genome sequencing have led to the discovery of millions of novel viruses and an appreciation for the great diversity of viruses on Earth. Yet, with knowledge of only "who is there?" we fall short in our ability to infer the impacts of viruses on microbes at population, community, and ecosystem-scales. To do this, we need a more explicit understanding "who do they infect?" Here, we developed a novel machine learning model (ML), Virus-Host Interaction Predictor (VHIP), to predict virus-host interactions (infection/non-infection) from input virus and host genomes. This ML model was trained and tested on a high-value manually curated set of 8849 virus-host pairs and their corresponding sequence data. The resulting dataset, 'Virus Host Range network' (VHRnet), is core to VHIP functionality. Each data point that underlies the VHIP training and testing represents a lab-tested virus-host pair in VHRnet, from which meaningful signals of viral adaptation to host were computed from genomic sequences. VHIP departs from existing virus-host prediction models in its ability to predict multiple interactions rather than predicting a single most likely host or host clade. As a result, VHIP is able to infer the complexity of virus-host networks in natural systems. VHIP has an 87.8% accuracy rate at predicting interactions between virus-host pairs at the species level and can be applied to novel viral and host population genomes reconstructed from metagenomic datasets.},
}
@article {pmid39292164,
year = {2024},
author = {Sakai, K and Nagata, T and Mori, T and Inoue, S and Fujiwara, H and Odagami, K and Adi, NP and Tatemichi, M and Mori, K},
title = {Research topics in occupational medicine, 1990-2022: A text-mining-applied bibliometric study.},
journal = {Scandinavian journal of work, environment &amp; health},
volume = {50},
number = {7},
pages = {567-576},
doi = {10.5271/sjweh.4177},
pmid = {39292164},
issn = {1795-990X},
mesh = {*Bibliometrics ; *Data Mining ; Humans ; *Occupational Medicine ; Occupational Health ; },
abstract = {OBJECTIVE: Occupational health has been influenced by societal and industrial changes. This study aimed to clarify topic trends in occupational health research in 1990-2022.<br><br>METHODS: We conducted a text-mining-adjusted bibliometric study using research titles in occupational health. Data on research titles and the years of publication were collected from 26 peer-reviewed journals on PubMed. Using morphological and correspondence analyses in text mining, we structured research topics into multiple categories and visualized the relationship between all categories and publication years. Statistical analyses were conducted using the text mining software - KH Coder 3.0.<br><br>RESULTS: We obtained 48 645 articles containing 714 890 words in their titles. The research topics were classified into 4 categories and 17 subcategories, of which those of occupations; countries; non-intervention; psychosocial factors; lifestyle factors; safety; symptoms; therapy and care; and productivity have recently shown an increasing trend. In contrast, the subcategories of risk, chemical factors, disease, and organ damage showed decreasing trends. Chemical factors, which were the main topics in the 1990s, included risk, organ damage, and disease. Productivity, the main topic in the 2020s, co-occurred with lifestyle factors, symptoms, and intervention.<br><br>CONCLUSIONS: Focal areas in occupational-health research shift according to societal trends. Occupational-health research has primarily analyzed issues in developed countries with capitalist values and may not have sufficiently covered issues in developing countries. It is imperative for policymakers and public funding bodies to determine priorities for investigation in the field.},
}
@article {pmid39340701,
year = {2024},
author = {Gang, J and Ping, Y and Du, C},
title = {Anti-Magnaporthe oryzae Activity of Streptomyces bikiniensis HD-087 In Vitro and Bioinformatics Analysis of Polyketide Synthase Gene pksL.},
journal = {Current microbiology},
volume = {81},
number = {11},
pages = {379},
pmid = {39340701},
issn = {1432-0991},
support = {32172468//National Natural Science Foundation of China/ ; },
mesh = {*Polyketide Synthases/genetics/metabolism ; *Streptomyces/genetics/metabolism/enzymology ; *Computational Biology ; *Multigene Family ; Bacterial Proteins/genetics/metabolism ; Erythromycin/pharmacology ; Antifungal Agents/pharmacology/metabolism ; Polyketides/metabolism/pharmacology ; Anti-Bacterial Agents/pharmacology ; Molecular Docking Simulation ; Ascomycota ; },
abstract = {Streptomyces bikiniensis HD-087 is capable of synthesizing various antimicrobial substances to counter the detrimental effects of hazardous microorganisms. To elucidate whether it produces polyketide antibiotics and the synthesis mechanism of antibiotic substances, the metabolites and related genes of S. bikiniensis HD-087 were analyzed through LC-MS, anti-Magnaporthe oryzae activity detection, and bioinformatics approaches. The result indicated that the strain HD-087 could produce erythromycin, a polyketide antibiotic. The inhibitory zones of the fermentation supernatant of strain HD-087 and methanol solution of erythromycin extract against M. oryzae were 40.84 ± 0.68 mm and 33.18 ± 0.81 mm, respectively. The IC50 value of erythromycin extract for inhibiting spore germination of erythromycin extract was 220.43 μg/mL. There are two polyketide synthesis gene clusters in the genome of strain HD-087, namely t1pks-nrps and t3pks-lantipeptide-t1pks-nrps. The key gene pksL in the t3pks-lantipeptide-t1pks-nrps gene cluster was predicted. The results suggested that it encodes a stable, hydrophilic, and acidic protein, mainly composed of α-helix and random coil. The PksL protein contains dehydrogenase (DH), ketone reductase (KR), acyl carrier protein (ACP), and ketone synthase (KS) domains. Moreover, it can form interaction networks with 11 proteins containing domains, such as polyketide synthase and ACP synthase. The molecular docking between PksL and acetyl-CoA is stable and strong, suggesting that PksL protein could catalyze the synthesis of polyketides with CoA as a substrate. This study provides a theoretical basis for further exploring the polyketides synthesis mechanism and developing antifungal metabolites in S. bikiniensis HD-087.},
}
@article {pmid39337302,
year = {2024},
author = {Romano Spica, V and Volpini, V and Valeriani, F and Carotenuto, G and Arcieri, M and Platania, S and Castrignanò, T and Clementi, ME and Michetti, F},
title = {In Silico Predicting the Presence of the S100B Motif in Edible Plants and Detecting Its Immunoreactive Materials: Perspectives for Functional Foods, Dietary Supplements and Phytotherapies.},
journal = {International journal of molecular sciences},
volume = {25},
number = {18},
pages = {},
doi = {10.3390/ijms25189813},
pmid = {39337302},
issn = {1422-0067},
mesh = {*Dietary Supplements ; *S100 Calcium Binding Protein beta Subunit/metabolism ; *Functional Food ; *Plants, Edible/chemistry ; Computer Simulation ; Amino Acid Motifs ; Phytotherapy/methods ; Computational Biology/methods ; Humans ; Fruit/chemistry/metabolism ; Phylogeny ; Plant Proteins/metabolism ; },
abstract = {The protein S100B is a part of the S100 protein family, which consists of at least 25 calcium-binding proteins. S100B is highly conserved across different species, supporting important biological functions. The protein was shown to play a role in gut microbiota eubiosis and is secreted in human breast milk, suggesting a physiological trophic function in newborn development. This study explores the possible presence of the S100B motif in plant genomes, and of S100B-like immunoreactive material in different plant extracts, opening up potential botanical uses for dietary supplementation. To explore the presence of the S100B motif in plants, a bioinformatic workflow was used. In addition, the immunoreactivity of S100B from vegetable and fruit samples was tested using an ELISA assay. The S100B motif was expected in silico in the genome of different edible plants belonging to the Viridiplantae clade, such as Durio zibethinus or Malus domestica and other medicinal species. S100B-like immunoreactive material was also detected in samples from fruits or leaves. The finding of S100B-like molecules in plants sheds new light on their role in phylogenesis and in the food chain. This study lays the foundation to elucidate the possible beneficial effects of plants or derivatives containing the S100B-like principle and their potential use in nutraceuticals.},
}
@article {pmid39328967,
year = {2024},
author = {Dey, B and Ferdous, J and Ahmed, R},
title = {Comprehensive stomata image dataset of Sundarbans Mangrove and Ratargul Swamp forest tree species in Bangladesh.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110908},
pmid = {39328967},
issn = {2352-3409},
abstract = {Plants' leaf stomata are crucial for various scientific research, including identifying species, studying ecology, conserving ecosystems, improving agriculture, and advancing the field of deep learning. This dataset, containing 1083 images, encompasses 11 species from two distinct locations in Bangladesh: nine from the Sundarbans mangrove forest and two from the Ratargul Swamp Forest. It is a valuable tool for refining machine learning algorithms that specialize in detecting stomata and categorizing species accurately. Researchers can explore a deeper understanding of plant physiology, adaptation mechanisms, and environmental interactions by employing pattern recognition, deep learning, and feature extraction techniques. Additionally, this dataset could be a potential tool for enhancing research in macroscopic metamaterials, extending its impact beyond traditional biological studies into interdisciplinary fields of technology and material science.},
}
@article {pmid39181078,
year = {2024},
author = {Wei, Q and Yin, Y and Tong, Q and Gong, Z and Shi, Y},
title = {Multi-omics analysis of excessive nitrogen fertilizer application: Assessing environmental damage and solutions in potato farming.},
journal = {Ecotoxicology and environmental safety},
volume = {284},
number = {},
pages = {116916},
doi = {10.1016/j.ecoenv.2024.116916},
pmid = {39181078},
issn = {1090-2414},
mesh = {*Solanum tuberosum/microbiology ; *Fertilizers ; *Nitrogen/analysis ; *Soil Microbiology ; Transcriptome ; Metabolome/drug effects ; Agriculture/methods ; Metagenomics ; Soil/chemistry ; Multiomics ; },
abstract = {Potatoes (Solanum tuberosum L.) are the third largest food crop globally and are pivotal for global food security. Widespread N fertilizer waste in potato cultivation has caused diverse environmental issues. This study employed microbial metagenomic sequencing to analyze the causes behind the declining N use efficiency (NUE) and escalating greenhouse gas emissions resulting from excessive N fertilizer application. Addressing N fertilizer inefficiency through breeding has emerged as a viable solution for mitigating overuse in potato cultivation. In this study, transcriptome and metabolome analyses were applied to identify N fertilizer-responsive genes. Metagenomic sequencing revealed that excessive N fertilizer application triggered alterations in the population dynamics of 11 major bacterial phyla, consequently affecting soil microbial functions, particularly N metabolism pathways and bacterial secretion systems. Notably, the enzyme levels associated with NO3[-] increased, and those associated with NO and N2O increased. Furthermore, excessive N fertilizer application enhanced soil virulence factors and increased potato susceptibility to diseases. Transcriptome and metabolome sequencing revealed significant impacts of excessive N fertilizer use on lipid and amino acid metabolism pathways. Weighted gene co‑expression network analysis (WGCNA) was adopted to identify two genes associated with N fertilizer response: PGSC0003DMG400021157 and PGSC0003DMG400009544.},
}
@article {pmid39328383,
year = {2023},
author = {Catalàn, N and Campo, RD and Talluto, L and Mendoza-Lera, C and Grandi, G and Bernal, S and Schiller, DV and Singer, G and Bertuzzo, E},
title = {Pulse, Shunt and Storage: Hydrological Contraction Shapes Processing and Export of Particulate Organic Matter in River Networks.},
journal = {Ecosystems (New York, N.Y.)},
volume = {26},
number = {4},
pages = {873-892},
pmid = {39328383},
issn = {1432-9840},
abstract = {UNLABELLED: Streams and rivers act as landscape-scale bioreactors processing large quantities of terrestrial particulate organic matter (POM). This function is linked to their flow regime, which governs residence times, shapes organic matter reactivity and controls the amount of carbon (C) exported to the atmosphere and coastal oceans. Climate change impacts flow regimes by increasing both flash floods and droughts. Here, we used a modelling approach to explore the consequences of lateral hydrological contraction, that is, the reduction of the wet portion of the streambed, for POM decomposition and transport at the river network scale. Our model integrates seasonal leaf litter input as generator of POM, transient storage of POM on wet and dry streambed portions with associated decomposition and ensuing changes in reactivity, and transport dynamics through a dendritic river network. Simulations showed that the amount of POM exported from the river network and its average reactivity increased with lateral hydrological contraction, due to the combination of (1) low processing of POM while stored on dry streambeds, and (2) large shunting during flashy events. The sensitivity analysis further supported that high lateral hydrological contraction leads to higher export of higher reactivity POM, regardless of transport coefficient values, average reactivity of fresh leaf litter and differences between POM reactivity under wet and dry conditions. Our study incorporates storage in dry streambed areas into the pulse-shunt concept (Raymond and others in Ecology 97(1):5-16, 2016. 10.1890/14-1684.1), providing a mechanistic framework and testable predictions about leaf litter storage, transport and decomposition in fluvial networks.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10021-022-00802-4.},
}
@article {pmid39326744,
year = {2024},
author = {Wang, Y and Feng, Z and Ghani, MI and Wang, Q and Zeng, L and Yang, X and Zhang, X and Chen, C and Li, S and Cao, P and Chen, X and Cernava, T},
title = {Co-exposure to microplastics and soil pollutants significantly exacerbates toxicity to crops: Insights from a global meta and machine-learning analysis.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176490},
doi = {10.1016/j.scitotenv.2024.176490},
pmid = {39326744},
issn = {1879-1026},
abstract = {Environmental contamination of microplastics (MPs) is ubiquitous worldwide, and co-contamination of arable soils with MPs and other pollutants is of increasing concern, and may lead to unexpected consequences on crop production. However, the overall implications of this combined effect, whether beneficial or detrimental, remain a subject of current debate. Here, we conducted a global meta and machine-learning analysis to evaluate the effects of co-exposure to MPs and other pollutants on crops, utilizing 3346 biological endpoints derived from 68 different studies. Overall, compared with control groups that only exposure to conventional soil contaminants, co-exposure significantly exacerbated toxicity to crops, particularly with MPs intensifying adverse effects on crop morphology, oxidative damage, and photosynthetic efficiency. Interestingly, our analysis demonstrated a significant reduction in the accumulation of pollutants in the crop due to the presence of MPs. In addition, the results revealed that potential adverse effects were primarily associated with crop species, MPs mass concentration, and exposure duration. Our study reaffirms the substantial repercussions of MPs as emerging pollutants on crops within the context of integrated pollution, providing novel insights into improving sustainability in agro-ecosystems.},
}
@article {pmid39323974,
year = {2022},
author = {Boyes, D and Crowley, LM and , and , and , and , and , and Skojec, C and Plotkin, D and Kawahara, AY and , },
title = {The genome sequence of the 6-spot burnet, Zygaena filipendulae (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {197},
pmid = {39323974},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Zygaena filipendulae (6-spot burnet; Arthropoda; Insecta; Lepidoptera; Zygaenidae). The genome sequence is 365.9 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.6 kilobases in length. Gene annotation of this assembly on Ensembl has identified 12,493 protein coding genes.},
}
@article {pmid39081076,
year = {2024},
author = {Levy, O and Shahar, S},
title = {Artificial Intelligence for Climate Change Biology: From Data Collection to Predictions.},
journal = {Integrative and comparative biology},
volume = {64},
number = {3},
pages = {953-974},
doi = {10.1093/icb/icae127},
pmid = {39081076},
issn = {1557-7023},
support = {300/22//Israeli Science Foundation/ ; NGS-84241T-21//National Geographic Society/ ; IOS-1754949//National Science Foundation/ ; },
mesh = {*Climate Change ; *Artificial Intelligence ; Animals ; Big Data ; Microclimate ; Data Collection/methods ; },
abstract = {In the era of big data, ecological research is experiencing a transformative shift, yet big-data advancements in thermal ecology and the study of animal responses to climate conditions remain limited. This review discusses how big data analytics and artificial intelligence (AI) can significantly enhance our understanding of microclimates and animal behaviors under changing climatic conditions. We explore AI's potential to refine microclimate models and analyze data from advanced sensors and camera technologies, which capture detailed, high-resolution information. This integration can allow researchers to dissect complex ecological and physiological processes with unprecedented precision. We describe how AI can enhance microclimate modeling through improved bias correction and downscaling techniques, providing more accurate estimates of the conditions that animals face under various climate scenarios. Additionally, we explore AI's capabilities in tracking animal responses to these conditions, particularly through innovative classification models that utilize sensors such as accelerometers and acoustic loggers. For example, the widespread usage of camera traps can benefit from AI-driven image classification models to accurately identify thermoregulatory responses, such as shade usage and panting. AI is therefore instrumental in monitoring how animals interact with their environments, offering vital insights into their adaptive behaviors. Finally, we discuss how these advanced data-driven approaches can inform and enhance conservation strategies. In particular, detailed mapping of microhabitats essential for species survival under adverse conditions can guide the design of climate-resilient conservation and restoration programs that prioritize habitat features crucial for biodiversity resilience. In conclusion, the convergence of AI, big data, and ecological science heralds a new era of precision conservation, essential for addressing the global environmental challenges of the 21st century.},
}
@article {pmid39323166,
year = {2024},
author = {Lin, ML and Hu, ZQ and Peng, WH and Ye, WL and Zhang, CL and Huang, XR and Chen, S and Gui, HR},
title = {[Pollution Assessment and Source Apportionment of Heavy Metals in the Surrounding Soil of Typical Mining Areas in Tongling, Anhui Province].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {9},
pages = {5494-5505},
doi = {10.13227/j.hjkx.202307274},
pmid = {39323166},
issn = {0250-3301},
abstract = {To study the level of heavy metal pollution and ecological risks in the soil around typical mining areas in Tongling, a total of 150 soil samples were collected from the study area. The content characteristics of 10 elements, namely, As, Cd, Cr, Cu, Hg, Mn, Ni, Pb, Fe, and Zn, in the soils were analyzed. Methods including enrichment factor, the geo-accumulation index, single-factor pollution index, Nemero comprehensive pollution index, and potential ecological risk index were used to evaluate the pollution status of heavy metals in the soil of the study area. The pollution sources of heavy metals in the soil were also analyzed using correlation analysis, cluster analysis, and principal component analysis. The results showed that except for Cr and Fe, the average contents of the other eight heavy metal elements were higher than the soil background values in the study area. Pb, Zn, As, Cu, and Cd had a high degree of variation and were significantly affected by external interference. The spatial distribution showed that both Cr and Ni showed a decreasing trend from the edge to the central region, whereas the other eight heavy metals showed a decreasing trend from the central region to the surrounding areas. The pollution level of Cd and Cu in the soil of the research area was relatively severe. The overall ecological risk was at a medium to low level. Cd and Hg were the main contributing factors. As, Cd, Cu, Fe, Mn, Pb, and Zn mainly came from agricultural, industrial, and transportation sources, whereas Cr and Ni were mainly from natural sources. However, the sources of Hg were relatively complex. The research results can provide a scientific basis for the prevention and control of soil heavy metal pollution in metal mining areas, as well as the remediation of mine pollution.},
}
@article {pmid39320588,
year = {2024},
author = {Oroud, IM},
title = {The implications of climate change on freshwater resources in the arid and semiarid Mediterranean environments using hydrological modeling, GIS tools, and remote sensing.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {10},
pages = {979},
pmid = {39320588},
issn = {1573-2959},
mesh = {*Climate Change ; *Environmental Monitoring/methods ; *Hydrology ; *Remote Sensing Technology ; *Geographic Information Systems ; Fresh Water/chemistry ; Groundwater/chemistry ; Models, Theoretical ; Mediterranean Region ; Desert Climate ; Water Resources ; },
abstract = {Precipitation partitioning in arid and semiarid environments is not well understood due to scanty precipitation, its temporal distribution, and the lack/absence of adequate measurements of the hydrometeorological components. Simulation methods have the potential to bridge the data gap, thereby providing a window to estimate the water balance components. The present investigation evaluates the water balance components of a typical watershed situated in the southeastern Mediterranean for the period 1979 through 2019 using daily meteorological data and a grid spacing of 250 m. Generated runoff results were commensurate with corresponding values obtained using the SWAT model. Computed groundwater recharge is also compatible with recharge values calculated using the chloride mass balance method. Results show that average runoff and groundwater recharge for the entire period was ⁓24 mm a[-1] and 19 mm a[-1], giving a precipitation ratio of 9.5% and 7.5%, respectively. Substantial interannual variability in the water balance components was observed during the study period which reflected the significant precipitation fluctuations typifying the Eastern Mediterranean. Results show that the period extending from 1998/1999 through 2018/2019 witnessed an 18% drop in annual precipitation, while surface runoff and groundwater recharge experienced a reduction of ⁓34% and ⁓67%, respectively. Although groundwater recharge is a complex function of numerous meteorological and geological factors, the NDVI can provide an excellent indicator of groundwater recharge in marginal Mediterranean environments. This is highly beneficial in areas where climate records are scanty or absent. The presented results emphasize the significant impacts of global warming and aridification on the future availability of water resources in the semiarid marginal climates in the Eastern Mediterranean and point out clearly that water resources in this area will become scarcer, leading to multiple security threats at national and regional levels.},
}
@article {pmid37495016,
year = {2023},
author = {Regmi, PR and Adhikaree, A and Bhattarai, U and Chhetri, S and Shakya, U and Uranw, S and Lamichhane, P and Sharma, SK},
title = {Rheumatic heart disease in school-attending Nepalese children: A descriptive analysis of the national heart screening database.},
journal = {Indian heart journal},
volume = {75},
number = {5},
pages = {363-369},
pmid = {37495016},
issn = {2213-3763},
mesh = {Humans ; *Rheumatic Heart Disease/epidemiology/diagnosis ; Nepal/epidemiology ; Cross-Sectional Studies ; Child ; Male ; Female ; Prevalence ; Adolescent ; *Mass Screening/methods ; Child, Preschool ; Echocardiography ; Databases, Factual ; Schools ; Retrospective Studies ; },
abstract = {OBJECTIVE: Rheumatic Heart Disease (RHD) remains a significant public health problem with high morbidity and mortality in children and young adults from lower-middle income countries like Nepal. However, a nation-wide database of the disease is lacking for designing effective future prevention and control programmes and strategies. The aim of our study is to estimate the prevalence of RHD in school-attending Nepalese children.<br><br>METHODS: We performed a cross-sectional descriptive analysis of a nationally representative database of Nepal Heart Foundation (NHF) national RHD screening programme which included school-attending Nepalese children between five and sixteen years of age. The screening was conducted between May 2015 and March 2020 in 236 schools, representing all seven provinces, across all three ecological zones of Nepal. Transthoracic two-dimensional echocardiography was performed in all eligible children with more than grade one murmur on cardiac auscultation. We estimated the prevalence of RHD among school-attending children as the number of RHD cases per 1000 school-attending children with a 95% confidence interval.<br><br>RESULTS: The database included a total of 107,340 children who were screened clinically, of whom 10,600 (9&#xb7;9%) underwent transthoracic two-dimensional echocardiography. The overall prevalence of RHD was 2.22 cases per 1000 school-attending children (95% CI:1&#xb7;94 - 2&#xb7;50). The highest prevalence was observed among children living in the southern Terai ecological zone (2&#xb7;89 per 1000, 95% CI (2&#xb7;32-3&#xb7;46)) of Nepal. Among the provinces, Karnali had the highest prevalence of RHD (3&#xb7;45 per 1000, 95% CI (2&#xb7;42-4&#xb7;48)). Among the districts screened, Kalikot had the highest RHD prevalence (5.47 per 1000, 95% CI (3.02-7.92)).<br><br>CONCLUSION: Primordial, primary and secondary prevention programmes should pay special attention to southern Terai zone, particularly the under-privileged children from remote districts.},
}
@article {pmid39313745,
year = {2024},
author = {Dabrowski, JK and Yang, EJ and Crofts, SJC and Hillary, RF and Simpson, DJ and McCartney, DL and Marioni, RE and Kirschner, K and Latorre-Crespo, E and Chandra, T},
title = {Probabilistic inference of epigenetic age acceleration from cellular dynamics.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {39313745},
issn = {2662-8465},
abstract = {The emergence of epigenetic predictors was a pivotal moment in geroscience, propelling the measurement and concept of biological aging into a quantitative era; however, while current epigenetic clocks show strong predictive power, they are data-driven in nature and are not based on the underlying biological mechanisms driving methylation dynamics. We show that predictions of these clocks are susceptible to several confounding non-age-related phenomena that make interpretation of these estimates and associations difficult. To address these limitations, we developed a probabilistic model describing methylation transitions at the cellular level. Our approach reveals two measurable components, acceleration and bias, which directly reflect perturbations of the underlying cellular dynamics. Acceleration is the proportional increase in the speed of methylation transitions across CpG sites, whereas bias corresponds to global changes in methylation levels. Using data from 15,900 participants from the Generation Scotland study, we develop a robust inference framework and show that these are two distinct processes confounding current epigenetic predictors. Our results show improved associations of acceleration and bias with physiological traits known to impact healthy aging, such as smoking and alcohol consumption, respectively. Furthermore, a genome-wide association study of epigenetic age acceleration identified seven genomic loci.},
}
@article {pmid39269993,
year = {2024},
author = {Golumbeanu, M and Briët, O and Champagne, C and Lemant, J and Winkel, M and Zogo, B and Gerhards, M and Sinka, M and Chitnis, N and Penny, M and Pothin, E and Smith, T},
title = {AnophelesModel: An R package to interface mosquito bionomics, human exposure and intervention effects with models of malaria intervention impact.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1011609},
doi = {10.1371/journal.pcbi.1011609},
pmid = {39269993},
issn = {1553-7358},
mesh = {Animals ; Humans ; *Malaria/transmission/prevention &amp; control ; *Anopheles/physiology ; *Mosquito Vectors/physiology ; *Mosquito Control/methods ; *Software ; Computational Biology ; Models, Biological ; },
abstract = {In recent decades, field and semi-field studies of malaria transmission have gathered geographic-specific information about mosquito ecology, behaviour and their sensitivity to interventions. Mathematical models of malaria transmission can incorporate such data to infer the likely impact of vector control interventions and hence guide malaria control strategies in various geographies. To facilitate this process and make model predictions of intervention impact available for different geographical regions, we developed AnophelesModel. AnophelesModel is an online, open-access R package that quantifies the impact of vector control interventions depending on mosquito species and location-specific characteristics. In addition, it includes a previously published, comprehensive, curated database of field entomological data from over 50 Anopheles species, field data on mosquito and human behaviour, and estimates of vector control effectiveness. Using the input data, the package parameterizes a discrete-time, state transition model of the mosquito oviposition cycle and infers species-specific impacts of various interventions on vectorial capacity. In addition, it offers formatted outputs ready to use in downstream analyses and by other models of malaria transmission for accurate representation of the vector-specific components. Using AnophelesModel, we show how the key implications for intervention impact change for various vectors and locations. The package facilitates quantitative comparisons of likely intervention impacts in different geographical settings varying in vector compositions, and can thus guide towards more robust and efficient malaria control recommendations. The AnophelesModel R package is available under a GPL-3.0 license at https://github.com/SwissTPH/AnophelesModel.},
}
@article {pmid39269992,
year = {2024},
author = {O'Meara, BC and Beaulieu, JM},
title = {Noise leads to the perceived increase in evolutionary rates over short time scales.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012458},
doi = {10.1371/journal.pcbi.1012458},
pmid = {39269992},
issn = {1553-7358},
mesh = {*Computational Biology/methods ; Models, Genetic ; Biological Evolution ; Evolution, Molecular ; Animals ; Models, Statistical ; Humans ; },
abstract = {Across a variety of biological datasets, from genomes to conservation to the fossil record, evolutionary rates appear to increase toward the present or over short time scales. This has long been seen as an indication of processes operating differently at different time scales, even potentially as an indicator of a need for new theory connecting macroevolution and microevolution. Here we introduce a set of models that assess the relationship between rate and time and demonstrate that these patterns are statistical artifacts of time-independent errors present across ecological and evolutionary datasets, which produce hyperbolic patterns of rates through time. We show that plotting a noisy numerator divided by time versus time leads to the observed hyperbolic pattern; in fact, randomizing the amount of change over time generates patterns functionally identical to observed patterns. Ignoring errors can not only obscure true patterns but create novel patterns that have long misled scientists.},
}
@article {pmid39181462,
year = {2024},
author = {de Vries, P},
title = {ECOTOXr: An R package for reproducible and transparent retrieval of data from EPA's ECOTOX database.},
journal = {Chemosphere},
volume = {364},
number = {},
pages = {143078},
doi = {10.1016/j.chemosphere.2024.143078},
pmid = {39181462},
issn = {1879-1298},
mesh = {*United States Environmental Protection Agency ; *Databases, Factual ; *Software ; United States ; Ecotoxicology/methods ; Risk Assessment/methods ; Reproducibility of Results ; },
abstract = {The US EPA ECOTOX database provides key ecotoxicological data that are crucial in environmental risk assessment. It can be used for computational predictions of toxicity or indications of hazard in a wide range of situations. There is no standardised or formalised method for extracting and subsetting data from the database for these purposes. Consequently, results in such meta-analyses are difficult to reproduce. The present study introduces the software package ECOTOXr, which provides the means to formalise data retrieval from the ECOTOX database in the R scripting language. Three cases are presented to evaluate the performance of the package in relation to earlier data extractions and searches on the website. These cases demonstrate that the package can reproduce data sets relatively well. Furthermore, they illustrate how future studies can further improve traceability and reproducibility by applying the package and adhering to some simple guidelines. This contributes to the FAIR principles, credibility and acceptance of research that uses data from the ECOTOX database.},
}
@article {pmid38972039,
year = {2024},
author = {Nurkolis, F and Wiyarta, E and Taslim, NA and Kurniawan, R and Thibault, R and Fernandez, ML and Yang, Y and Han, J and Tsopmo, A and Mayulu, N and Tjandrawinata, RR and Tallei, TE and Hardinsyah, H},
title = {Unraveling diabetes complexity through natural products, miRNAs modulation, and future paradigms in precision medicine and global health.},
journal = {Clinical nutrition ESPEN},
volume = {63},
number = {},
pages = {283-293},
doi = {10.1016/j.clnesp.2024.06.043},
pmid = {38972039},
issn = {2405-4577},
mesh = {Humans ; *Precision Medicine ; *MicroRNAs/genetics ; *Diabetes Mellitus/therapy/genetics ; *Biological Products/therapeutic use ; *Global Health ; Metabolomics ; Computational Biology ; Biomarkers/blood ; Genomics ; },
abstract = {BACKGROUND AND AIMS: The challenge posed by diabetes necessitates a paradigm shift from conventional diagnostic approaches focusing on glucose and lipid levels to the transformative realm of precision medicine. This approach, leveraging advancements in genomics and proteomics, acknowledges the individualistic genetic variations, dietary preferences, and environmental exposures in diabetes management. The study comprehensively analyzes the evolving diabetes landscape, emphasizing the pivotal role of genomics, proteomics, microRNAs (miRNAs), metabolomics, and bioinformatics.<br><br>RESULTS: Precision medicine revolutionizes diabetes research and treatment by diverging from traditional diagnostic methods, recognizing the heterogeneous nature of the condition. MiRNAs, crucial post-transcriptional gene regulators, emerge as promising therapeutic targets, influencing key facets such as insulin signaling and glucose homeostasis. Metabolomics, an integral component of omics sciences, contributes significantly to diabetes research, elucidating metabolic disruptions, and offering potential biomarkers for early diagnosis and personalized therapies. Bioinformatics unveils dynamic connections between natural substances, miRNAs, and cellular pathways, aiding in the exploration of the intricate molecular terrain in diabetes. The study underscores the imperative for experimental validation in natural product-based diabetes therapy, emphasizing the need for in&#xa0;vitro and in&#xa0;vivo studies leading to clinical trials for assessing effectiveness, safety, and tolerability in real-world applications. Global cooperation and ethical considerations play a pivotal role in addressing diabetes challenges worldwide, necessitating a multifaceted approach that integrates traditional knowledge, cultural competence, and environmental awareness.<br><br>CONCLUSIONS: The key components of diabetes treatment, including precision medicine, metabolomics, bioinformatics, and experimental validation, converge in future strategies, embodying a holistic paradigm for diabetes care anchored in cutting-edge research and global healthcare accessibility.},
}
@article {pmid36002035,
year = {2024},
author = {Polanowska, KE and Iwański, S and Leśniak, MM and Seniów, J},
title = {Computer-assisted training of executive functions in adult patients with non-progressive acquired brain damage - a pilot study on efficacy of a new therapeutic application.},
journal = {Applied neuropsychology. Adult},
volume = {31},
number = {6},
pages = {1180-1191},
doi = {10.1080/23279095.2022.2114354},
pmid = {36002035},
issn = {2327-9109},
mesh = {Humans ; *Executive Function/physiology ; Male ; Pilot Projects ; Female ; Middle Aged ; Adult ; *Brain Injuries/complications/rehabilitation ; *Therapy, Computer-Assisted ; Aged ; Problem Solving/physiology ; Activities of Daily Living ; Social Skills ; },
abstract = {Executive dysfunction is most often caused by post-traumatic or post-stroke damage to the prefrontal regions of the brain. The aim of this study was to compare the efficacy of two computer-assisted therapy programs for executive dysfunctions in patients with acquired brain injury. Patients were trained using either a newly developed application ExeSystem (designed to help improve the ability to manage and control one's own behavior by performing tasks imitating natural, everyday situations) or a combination of two commercial applications RehaCom and CogniPlus. Data collected after a three-week period of therapy conducted in two 15-person groups of participants indicated comparable efficacy of both therapy programs in improving quality of daily functioning, executive attention, as well as planning and problem-solving but not memory. The improvement in social competence (p = .028) was the only advantage of therapy with the ExeSystem. Therapeutic interactions using computer programs were shown to be positively evaluated by patients (p < .01). This study confirmed at least equal efficacy of computer-based executive function therapy using ExeSystem compared to RehaCom and CogniPlus. However, despite the implementation of a more ecological and comprehensive approach to the content of a new application, the benefits of this approach were limited.},
}
@article {pmid39264951,
year = {2024},
author = {Pfennig, T and Kullmann, E and Zavřel, T and Nakielski, A and Ebenhöh, O and Červený, J and Bernát, G and Matuszyńska, AB},
title = {Shedding light on blue-green photosynthesis: A wavelength-dependent mathematical model of photosynthesis in Synechocystis sp. PCC 6803.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012445},
doi = {10.1371/journal.pcbi.1012445},
pmid = {39264951},
issn = {1553-7358},
mesh = {*Photosynthesis/physiology ; *Synechocystis/metabolism/physiology ; *Light ; *Models, Biological ; Computational Biology ; Carbon Dioxide/metabolism ; Carbon Cycle/physiology ; Phycobilisomes/metabolism ; Computer Simulation ; },
abstract = {Cyanobacteria hold great potential to revolutionize conventional industries and farming practices with their light-driven chemical production. To fully exploit their photosynthetic capacity and enhance product yield, it is crucial to investigate their intricate interplay with the environment including the light intensity and spectrum. Mathematical models provide valuable insights for optimizing strategies in this pursuit. In this study, we present an ordinary differential equation-based model for the cyanobacterium Synechocystis sp. PCC 6803 to assess its performance under various light sources, including monochromatic light. Our model can reproduce a variety of physiologically measured quantities, e.g. experimentally reported partitioning of electrons through four main pathways, O2 evolution, and the rate of carbon fixation for ambient and saturated CO2. By capturing the interactions between different components of a photosynthetic system, our model helps in understanding the underlying mechanisms driving system behavior. Our model qualitatively reproduces fluorescence emitted under various light regimes, replicating Pulse-amplitude modulation (PAM) fluorometry experiments with saturating pulses. Using our model, we test four hypothesized mechanisms of cyanobacterial state transitions for ensemble of parameter sets and found no physiological benefit of a model assuming phycobilisome detachment. Moreover, we evaluate metabolic control for biotechnological production under diverse light colors and irradiances. We suggest gene targets for overexpression under different illuminations to increase the yield. By offering a comprehensive computational model of cyanobacterial photosynthesis, our work enhances the basic understanding of light-dependent cyanobacterial behavior and sets the first wavelength-dependent framework to systematically test their producing capacity for biocatalysis.},
}
@article {pmid39213378,
year = {2024},
author = {Wang, M and Li, Z and Wang, H and Zhao, J and Zhang, Y and Lin, K and Zheng, S and Feng, Y and Zhang, Y and Teng, W and Tong, Y and Zhang, W and Xue, Y and Mao, H and Li, H and Zhang, B and Rasheed, A and Bhavani, S and Liu, C and Ling, HQ and Hu, YQ and Zhang, Y},
title = {A Quantitative Computational Framework for Allopolyploid Single-Cell Data Integration and Core Gene Ranking in Development.},
journal = {Molecular biology and evolution},
volume = {41},
number = {9},
pages = {},
doi = {10.1093/molbev/msae178},
pmid = {39213378},
issn = {1537-1719},
support = {//National Natural Science Foundation of China/ ; //National Key R&amp;D Program of China/ ; //Yangfan Project of Shanghai Science and Technology Commission/ ; //State Key Laboratory of Genetic Engineering/ ; //State Key Laboratory of Crop Gene Exploration and Utilization in Southwest/ ; //State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology/ ; //Shanghai Key Laboratory of Agricultural Genetics and Breeding/ ; },
mesh = {*Single-Cell Analysis/methods ; *Polyploidy ; Animals ; Computational Biology/methods ; },
abstract = {Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome-divergent regulation in the context of cellular differentiation. However, analyzing single-cell data suffers from high error rates due to high dimensionality, noise, and sparsity, and the errors stack up in polyploid analysis due to the increased dimensionality of comparisons between subgenomes of each cell, hindering deeper mechanistic understandings. In this study, we develop a quantitative computational framework, called "pseudo-genome divergence quantification" (pgDQ), for quantifying and tracking subgenome divergence directly at the cellular level. Further comparing with cellular differentiation trajectories derived from single-cell RNA sequencing data allows for an examination of the relationship between subgenome divergence and the progression of development. pgDQ produces robust results and is insensitive to data dropout and noise, avoiding high error rates due to multiple comparisons of genes, cells, and subgenomes. A statistical diagnostic approach is proposed to identify genes that are central to subgenome divergence during development, which facilitates the integration of different data modalities, enabling the identification of factors and pathways that mediate subgenome-divergent activity during development. Case studies have demonstrated that applying pgDQ to single-cell and bulk tissue transcriptomic data promotes a systematic and deeper understanding of how dynamic subgenome divergence contributes to developmental trajectories in polyploid evolution.},
}
@article {pmid39309423,
year = {2023},
author = {Boyes, D and Blaxter, ML and , and , and , and , and , and , },
title = {The genome sequence of the Beautiful Hook-tip, Laspeyria flexula (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {529},
pmid = {39309423},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Laspeyria flexula (the Beautiful Hook-tip; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 450.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,281 protein coding genes.},
}
@article {pmid39309224,
year = {2024},
author = {Boyes, D and Lees, DC and Wawman, DC and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Blue-bordered Carpet moth Plemyria rubiginata (Denis &amp; Schiffermüller) 1775.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {271},
pmid = {39309224},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Plemyria rubiginata (the Blue-bordered Carpet moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 356.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.64 kilobases in length.},
}
@article {pmid39309222,
year = {2024},
author = {Boyes, D and Wawman, DC and , and , and , and , and , and , and , },
title = {The genome sequence of the Figure of Eighty moth Tethea ocularis Linnaeus, 1767.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {348},
pmid = {39309222},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Tethea ocularis (the Figure of Eighty; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 339.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.28 kilobases in length.},
}
@article {pmid39304543,
year = {2024},
author = {Hossen, MF and Sultana, N},
title = {Landscape transition-induced ecological risk modeling using GIS and remote sensing techniques: a case of Saint Martin Island, Bangladesh.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {10},
pages = {964},
pmid = {39304543},
issn = {1573-2959},
mesh = {Bangladesh ; *Environmental Monitoring/methods ; *Remote Sensing Technology ; *Geographic Information Systems ; *Conservation of Natural Resources ; *Islands ; *Ecosystem ; Risk Assessment/methods ; Humans ; Bayes Theorem ; },
abstract = {Uncontrolled human activity and nature are causing the deterioration of Saint Martin Island, Bangladesh's only tropical island, necessitating sustainable land use strategies and ecological practices. Therefore, the present study measures the land use/cover transition from 1974 to 2021, predicts 2032 and 2042, and constructs the spatiotemporal features of the Landscape Ecological Risk Index based on land use changes. The study utilized Maximum Likelihood Classification (MLC) on Landsat images from 1974, 1988, 2001, 2013, and Sentinel 2B in 2021, achieving ≥ 80% accuracy. The MLP-MC approach was also used to predict 2032 and 2042 LULC change patterns. The eco-risk index was developed using landscape disturbance and vulnerability indices, Bayesian Kriging interpolation, and spatial autocorrelations to indicate spatial clustering. The research found that settlements increased from 2.06 to 28.62 ha between 1974 and 2021 and would cover 41.22 ha in 2042, causing considerable losses in agricultural areas, waterbodies, sand, coral reefs, and vegetation. The area under study showed a more uniform and homogenous environment as Shannon's diversity and evenness scores decreased. The ecological risk of Saint Martin Island increased from 4.31 to 31.05 ha between 1974 and 2042 due to natural and human factors like erosion, tidal bores, population growth, coral mining, habitat destruction, and intensive agricultural practices and tourism, primarily in Nazrul Para, Galachipa, and Western Dakhin Para. The findings will benefit St. Martin Island stakeholders and policymakers by providing insights into current and potential landscape changes and land eco-management.},
}
@article {pmid39303692,
year = {2024},
author = {Crits-Christoph, A and Levy, JI and Pekar, JE and Goldstein, SA and Singh, R and Hensel, Z and Gangavarapu, K and Rogers, MB and Moshiri, N and Garry, RF and Holmes, EC and Koopmans, MPG and Lemey, P and Peacock, TP and Popescu, S and Rambaut, A and Robertson, DL and Suchard, MA and Wertheim, JO and Rasmussen, AL and Andersen, KG and Worobey, M and Débarre, F},
title = {Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.},
journal = {Cell},
volume = {187},
number = {19},
pages = {5468-5482.e11},
doi = {10.1016/j.cell.2024.08.010},
pmid = {39303692},
issn = {1097-4172},
mesh = {Animals ; *COVID-19/epidemiology/virology ; *SARS-CoV-2/genetics/isolation &amp; purification ; *Animals, Wild/virology ; *Phylogeny ; Humans ; Pandemics ; },
abstract = {Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Seafood Wholesale Market. Here, we analyze environmental qPCR and sequencing data collected in the Huanan market in early 2020. We demonstrate that market-linked severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity is consistent with market emergence and find increased SARS-CoV-2 positivity near and within a wildlife stall. We identify wildlife DNA in all SARS-CoV-2-positive samples from this stall, including species such as civets, bamboo rats, and raccoon dogs, previously identified as possible intermediate hosts. We also detect animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them with those from farms and other markets. This analysis provides the genetic basis for a shortlist of potential intermediate hosts of SARS-CoV-2 to prioritize for serological and viral sampling.},
}
@article {pmid39301440,
year = {2024},
author = {Morales, HE and Groombridge, JJ and Tollington, S and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Gilbert, MTP and , and , and , and , },
title = {The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A.Newton &amp; E. Newton, 1876).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {378},
pmid = {39301440},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Alexandrinus eques, formerly Psittacula eques (the Mauritius Parakeet; Chordata; Aves; Psittaciformes; Psittacidae). The genome sequence is 1203.8 megabases in span. Most of the assembly is scaffolded into 35 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 18.86 kilobases in length.},
}
@article {pmid39151562,
year = {2024},
author = {Rahimian, M and Panahi, B},
title = {Metagenome sequence data mining for viral interaction studies: Review on progress and prospects.},
journal = {Virus research},
volume = {349},
number = {},
pages = {199450},
pmid = {39151562},
issn = {1872-7492},
mesh = {*Metagenomics/methods ; *Metagenome ; *Viruses/genetics/classification ; *Computational Biology/methods ; *Data Mining ; *High-Throughput Nucleotide Sequencing ; Humans ; Animals ; },
abstract = {Metagenomics has been greatly accelerated by the development of next-generation sequencing (NGS) technologies, which allow scientists to discover and describe novel microorganisms without the need for conventional culture techniques. Examining integrative bioinformatics methods used in viral interaction research, this study highlights metagenomic data from various contexts. Accurate viral identification depends on high-purity genetic material extraction, appropriate NGS platform selection, and sophisticated bioinformatics tools like VirPipe and VirFinder. The efficiency and precision of metagenomic analysis are further improved with the advent of AI-based techniques. The diversity and dynamics of viral communities are demonstrated by case studies from a variety of environments, emphasizing the seasonal and geographical variations that influence viral populations. In addition to speeding up the discovery of new viruses, metagenomics offers thorough understanding of virus-host interactions and their ecological effects. This review provides a promising framework for comprehending the complexity of viral communities and their interactions with hosts, highlighting the transformational potential of metagenomics and bioinformatics in viral research.},
}
@article {pmid39255272,
year = {2024},
author = {Sylla, A and Chevillon, C and Djidjiou-Demasse, R and Seydi, O and Campos, CAV and Dogbe, M and Fast, KM and Pechal, JL and Rakestraw, A and Scott, ME and Sandel, MW and Jordan, H and Benbow, ME and Guégan, JF},
title = {Understanding the transmission of bacterial agents of sapronotic diseases using an ecosystem-based approach: A first spatially realistic metacommunity model.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012435},
doi = {10.1371/journal.pcbi.1012435},
pmid = {39255272},
issn = {1553-7358},
mesh = {Humans ; *Ecosystem ; Mycobacterium ulcerans/pathogenicity ; Buruli Ulcer/transmission/microbiology ; Models, Biological ; Computational Biology ; Animals ; },
abstract = {Pathogens such as bacteria, fungi and viruses are important components of soil and aquatic communities, where they can benefit from decaying and living organic matter, and may opportunistically infect human and animal hosts. One-third of human infectious diseases is constituted by sapronotic disease agents that are natural inhabitants of soil or aquatic ecosystems. They are capable of existing and reproducing in the environment outside of the host for extended periods of time. However, as ecological research on sapronosis is infrequent and epidemiological models are even rarer, very little information is currently available. Their importance is overlooked in medical and veterinary research, as well as the relationships between free environmental forms and those that are pathogenic. Here, using dynamical models in realistic aquatic metacommunity systems, we analyze sapronosis transmission, using the human pathogen Mycobacterium ulcerans that is responsible for Buruli ulcer. We show that the persistence of bacilli in aquatic ecosystems is driven by a seasonal upstream supply, and that the attachment and development of cells to aquatic living forms is essential for such pathogen persistence and population dynamics. Our work constitutes the first set of metacommunity models of sapronotic disease transmission, and is highly flexible for adaptation to other types of sapronosis. The importance of sapronotic agents on animal and human disease burden needs better understanding and new models of sapronosis disease ecology to guide the management and prevention of this important group of pathogens.},
}
@article {pmid39295890,
year = {2023},
author = {Boyes, D and Januszczak, I and , and , and , and , and , and , },
title = {The genome sequence of the Lunar-spotted Pinion, Cosmia pyralina (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {545},
pmid = {39295890},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Cosmia pyralina (the Lunar-spotted Pinion; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 803.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,901 protein coding genes.},
}
@article {pmid39294496,
year = {2024},
author = {Khaliq, AM and Rajamohan, M and Saeed, O and Mansouri, K and Adil, A and Zhang, C and Turk, A and Carstens, JL and House, M and Hayat, S and Nagaraju, GP and Pappas, SG and Wang, YA and Zyromski, NJ and Opyrchal, M and Lee, KP and O'Hagan, H and El Rayes, B and Masood, A},
title = {Spatial transcriptomic analysis of primary and metastatic pancreatic cancers highlights tumor microenvironmental heterogeneity.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {39294496},
issn = {1546-1718},
abstract = {Although the spatial, cellular and molecular landscapes of resected pancreatic ductal adenocarcinoma (PDAC) are well documented, the characteristics of its metastatic ecology remain elusive. By applying spatially resolved transcriptomics to matched primary and metastatic PDAC samples, we discovered a conserved continuum of fibrotic, metabolic and immunosuppressive spatial ecotypes across anatomical regions. We observed spatial tumor microenvironment heterogeneity spanning beyond that previously appreciated in PDAC. Through comparative analysis, we show that the spatial ecotypes exhibit distinct enrichment between primary and metastatic sites, implying adaptability to the local environment for survival and progression. The invasive border ecotype exhibits both pro-tumorigenic and anti-tumorigenic cell-type enrichment, suggesting a potential immunotherapy target. The ecotype heterogeneity across patients emphasizes the need to map individual patient landscapes to develop personalized treatment strategies. Collectively, our findings provide critical insights into metastatic PDAC biology and serve as a valuable resource for future therapeutic exploration and molecular investigations.},
}
@article {pmid39292040,
year = {2024},
author = {Vasconcelos, NM and Bernal, RTI and Souza, JB and Bordoni, PHC and Stein, C and Coll, CVN and Murray, J and Malta, DC},
title = {Underreporting of violence against women: an analysis of two data sources.},
journal = {Ciencia &amp; saude coletiva},
volume = {29},
number = {10},
pages = {e07732023},
doi = {10.1590/1413-812320242910.07732023},
pmid = {39292040},
issn = {1678-4561},
mesh = {Humans ; Brazil/epidemiology ; Female ; Adult ; Young Adult ; Adolescent ; *Sex Offenses/statistics &amp; numerical data ; Middle Aged ; Health Surveys ; Gender-Based Violence/statistics &amp; numerical data ; Information Systems/statistics &amp; numerical data ; Information Sources ; },
abstract = {This article aims to estimate the underreporting of violence against women (VAW) in the Notifiable Diseases Information System (SINAN), based on data from the National Survey of Health (NSH), in Brazil and subnational units (SU). This work was an ecological study using SINAN and NSH, both from 2019. In SINAN, reports of sexual, physical, and psychological VAW, aged 18 years or older, were selected. In the NSH, women of the same age group who reported psychological, physical, or sexual violence, and who had sought health care due to consequences of the violence were selected. SINAN underreporting was calculated in reference to the NSH's estimated population, for Brazil and each SU. Underreporting of VAW in Brazil was 98.5%, 75.9%, and 89.4% for psychological, physical, and sexual violence, respectively. The North and Northeast states presented the lowest reporting rates among the states. VAW in Brazil is highly underreported by the health sector, showing the need for adequate training of health professionals to recognize situations of violence and raise awareness of the importance of reporting.},
}
@article {pmid39290666,
year = {2024},
author = {Guclu, C and Luk, CL and Ashton, LA and Abbas, S and Boyle, MJW},
title = {Beta diversity subcomponents of plant species turnover and nestedness reveal drivers of community assembly in a regenerating subtropical forest.},
journal = {Ecology and evolution},
volume = {14},
number = {9},
pages = {e70233},
pmid = {39290666},
issn = {2045-7758},
abstract = {Secondary forests represent a significant proportion of global forest cover, with over 70% of forests in East Asia classified as regenerating. While succession has been studied extensively in temperate systems, trajectories of subtropical succession remain poorly characterized in highly disturbed, urban-adjacent forests. Investigating the additive beta diversity components of turnover and nestedness may reveal community assembly mechanisms driving secondary succession. The present study investigates plant community assembly along a successional gradient from 7 to 70 years following the onset of succession in secondary subtropical forests in Hong Kong, China. Plant survey data for 28 plots were analysed, generating additive Simpsons turnover and nestedness beta diversity metrics. Dissimilarity matrices were generated and modelled as a function of environmental matrices including forest plant community age (years following onset of secondary succession), inter-community distance (metres), and soil moisture saturation (%) across three elevational bands using generalized dissimilarity models. Nonmetric multidimensional scaling of plant communities was conducted with Bray-Curtis dissimilarity matrices. Inter-community distance and successional age differentially influenced plant species turnover between lowland and Montane forest types. Models of nestedness found that plot age and soil moisture saturation were significant drivers of nestedness patterns in plant communities across elevational classes. Turnover represented a higher proportion of Sorensen beta diversity than nestedness, while ANOSIM found significant differentiation between plant communities at different successional stages. Turnover patterns suggest a deterministic model of community assembly, with strong patterns of species replacement between communities at fine spatial scales and successional stages, as well as clear compositional shifts between lowland and montane forest types. NMDS analysis and functional compositional assessments suggested a transition from early successional communities with a high proportion of shrub species, to later successional communities with a higher proportion of tree species, with an increase in species turnover with greater age dissimilarity.},
}
@article {pmid39290433,
year = {2024},
author = {Castrillo, M and Aguilar, F and García-Díaz, D},
title = {Dataset on sub-daily vertical profiles of physicochemical parameters and chlorophyll concentration in El Val reservoir, together with its daily meteorological data, storage state and downstream flow (2018-2022).},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110839},
pmid = {39290433},
issn = {2352-3409},
abstract = {The dataset addressed in this article contains parameters about El Val reservoir (province of Zaragoza, Spain). It includes physicochemical variables, the water level, the stored water volume, its meteorological conditions and the flow rate of its effluent, the Queiles River, a few metres downstream of the dam. The El Val reservoir stores water from the Val River, but it also receives water from the Queiles River through a pipeline and from several ravines. The dam releases on the Queiles River, which is a tributary of the Ebro River (the second one in Spain in length and discharge rate). A multiparametric probe (aquaDam, Adasa Systems), hanging from a structure located in the dam, every 6 h makes a vertical profile taking the measurements at each metre of depth from the surface to approximately 573 m above sea level (m.a.s.l.), in other words, between 2 and 3 m above the bottom outlet. This probe collects data of water temperature, pH, ORP, conductivity, dissolved oxygen, turbidity and chlorophyll concentration. Meteorological data are collected in the nearest weather station, located in the municipality of Los Fayos which is about 500 m downstream of the dam. These include daily accumulated precipitation, daily maximum and average solar irradiance, daily maximum, minimum and average air temperature and daily average wind speed. The water level and volume of stored water and the flow rate of the Queiles River are collected in the El Val monitoring station and the Queiles River gauge station respectively, and are also provided on a daily basis. These data are useful to feed deterministic, data driven or hybrid hydrological models with different purposes, like the identification of the impact of meteorological conditions on the physicochemical properties of the reservoir as well as the assessment of different management strategies in the reservoir. This is a data article that additionally supports the work published in Ecological Informatics [1] where the use of common and readily available open data is promoted through its use to feed data driven models, in particular to infer the depth of the thermocline in reservoirs that are periodically or permanently thermally stratified. In that article a dataset derived from the one presented in this article is used.},
}
@article {pmid39290364,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Red Chestnut moth, Cerastis rubricosa (Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {88},
pmid = {39290364},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Cerastis rubricosa (the Red Chestnut moth; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 678.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,784 protein coding genes.},
}
@article {pmid39290036,
year = {2024},
author = {Monreal-Di Bello, M and González-Bermejo, D and Castillo-Cano, B and Rodriguez-Pascual, A and Montero-Corominas, D},
title = {Impact of Regulatory Interventions on Ulipristal Acetate 5 mg (Esmya) Use in Spain: An Interrupted Time-Series Analysis.},
journal = {Pharmacoepidemiology and drug safety},
volume = {33},
number = {9},
pages = {e70004},
doi = {10.1002/pds.70004},
pmid = {39290036},
issn = {1099-1557},
support = {//Spanish Agency on Medicines and Medical Devices (AEMPS)/ ; },
mesh = {Humans ; Spain/epidemiology ; *Norpregnadienes/administration &amp; dosage/adverse effects/therapeutic use ; *Interrupted Time Series Analysis ; Female ; Databases, Factual ; Electronic Health Records/statistics &amp; numerical data ; Risk Evaluation and Mitigation ; Male ; Adult ; Middle Aged ; },
abstract = {PURPOSE: Since late 2017, the use of ulipristal acetate 5 mg (UPA; Proprietary name: Esmya) has been under review in the European Union, due to an emerging hepatic risk. In February 2018 and in July 2018, the Spanish Agency of Medicines and Medical Devices and the marketing authorization holder put two risk minimization measures (RMM) in place, in order to inform about new safety information and to mitigate this risk. This study aims to assess RMM effectiveness in Spain, by performing an interrupted time-series (ITS) analyses, between 2014 and 2019.<br><br>METHOD: Two quasi-experimental ITS analyses to examine the use of UPA before and after the RMM release were performed: (a) an ecological study using aggregated data from a drug consumption database; and (b) a study using primary healthcare data gathered from electronic clinical records.<br><br>RESULTS: Regulatory interventions were associated with an immediate and significant decrease level of DID (the number of DDD dispensed per 100&#x2009;000 inhabitants and day) and incidence. The DID was 70% less than expected 12&#x2009;months after the interventions. This value was 59% for the incidence. However, a change in the slope was not observed and the use started rising again in the last segment of the study period.<br><br>CONCLUSION: Despite RMM had an immediate strong impact on UPA use, the last segment upward trend in the long-term might have been affected by the lack of comparable therapeutic alternatives. Further studies should be performed to confirm the increase trend observed and analyze subsequent measures and additional data.},
}
@article {pmid39289538,
year = {2024},
author = {Mc Cartney, AM and Formenti, G and Mouton, A and De Panis, D and Marins, LS and Leitão, HG and Diedericks, G and Kirangwa, J and Morselli, M and Salces-Ortiz, J and Escudero, N and Iannucci, A and Natali, C and Svardal, H and Fernández, R and De Pooter, T and Joris, G and Strazisar, M and Wood, JMD and Herron, KE and Seehausen, O and Watts, PC and Shaw, F and Davey, RP and Minotto, A and Fernández, JM and Böhne, A and Alegria, C and Alioto, T and Alves, PC and Amorim, IR and Aury, JM and Backstrom, N and Baldrian, P and Baltrunaite, L and Barta, E and BedHom, B and Belser, C and Bergsten, J and Bertrand, L and Bilandija, H and Binzer-Panchal, M and Bista, I and Blaxter, M and Borges, PAV and Dias, GB and Bosse, M and Brown, T and Bruggmann, R and Buena-Atienza, E and Burgin, J and Buzan, E and Cariani, A and Casadei, N and Chiara, M and Chozas, S and Čiampor, F and Crottini, A and Cruaud, C and Cruz, F and Dalen, L and De Biase, A and Del Campo, J and Delic, T and Dennis, AB and Derks, MFL and Diroma, MA and Djan, M and Duprat, S and Eleftheriadi, K and Feulner, PGD and Flot, JF and Forni, G and Fosso, B and Fournier, P and Fournier-Chambrillon, C and Gabaldon, T and Garg, S and Gissi, C and Giupponi, L and Gomez-Garrido, J and González, J and Grilo, ML and Grüning, B and Guerin, T and Guiglielmoni, N and Gut, M and Haesler, MP and Hahn, C and Halpern, B and Harrison, PW and Heintz, J and Hindrikson, M and Höglund, J and Howe, K and Hughes, GM and Istace, B and Cock, MJ and Janžekovič, F and Jonsson, ZO and Joye-Dind, S and Koskimäki, JJ and Krystufek, B and Kubacka, J and Kuhl, H and Kusza, S and Labadie, K and Lähteenaro, M and Lantz, H and Lavrinienko, A and Leclère, L and Lopes, RJ and Madsen, O and Magdelenat, G and Magoga, G and Manousaki, T and Mappes, T and Marques, JP and Redondo, GIM and Maumus, F and McCarthy, SA and Megens, HJ and Melo-Ferreira, J and Mendes, SL and Montagna, M and Moreno, J and Mosbech, MB and Moura, M and Musilova, Z and Myers, E and Nash, WJ and Nater, A and Nicholson, P and Niell, M and Nijland, R and Noel, B and Noren, K and Oliveira, PH and Olsen, RA and Ometto, L and Oomen, RA and Ossowski, S and Palinauskas, V and Palsson, S and Panibe, JP and Pauperio, J and Pavlek, M and Payen, E and Pawlowska, J and Pellicer, J and Pesole, G and Pimenta, J and Pippel, M and Pirttilä, AM and Poulakakis, N and Rajan, J and M C Rego, R and Resendes, R and Resl, P and Riesgo, A and Rodin-Morch, P and Soares, AER and Fernandes, CR and Romeiras, MM and Roxo, G and Rüber, L and Ruiz-Lopez, MJ and Saarma, U and da Silva, LP and Sim-Sim, M and Soler, L and Sousa, VC and Santos, CS and Spada, A and Stefanovic, M and Steger, V and Stiller, J and Stöck, M and Struck, TH and Sudasinghe, H and Tapanainen, R and Tellgren-Roth, C and Trindade, H and Tukalenko, Y and Urso, I and Vacherie, B and Van Belleghem, SM and Van Oers, K and Vargas-Chavez, C and Velickovic, N and Vella, N and Vella, A and Vernesi, C and Vicente, S and Villa, S and Pettersson, OV and Volckaert, FAM and Voros, J and Wincker, P and Winkler, S and Ciofi, C and Waterhouse, RM and Mazzoni, CJ},
title = {The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.},
journal = {npj biodiversity},
volume = {3},
number = {1},
pages = {28},
pmid = {39289538},
issn = {2731-4243},
abstract = {A genomic database of all Earth's eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.},
}
@article {pmid39287883,
year = {2024},
author = {Stolz, BJ and Dhesi, J and Bull, JA and Harrington, HA and Byrne, HM and Yoon, IHR},
title = {Relational Persistent Homology for Multispecies Data with Application to the Tumor Microenvironment.},
journal = {Bulletin of mathematical biology},
volume = {86},
number = {11},
pages = {128},
doi = {10.1007/s11538-024-01353-6},
pmid = {39287883},
issn = {1522-9602},
support = {EP/R018472/1//EPSRC/ ; EP/R018472/1, EP/K041096/1, EP/R005125/1, EP/T001968/1//EPSRC/ ; EP/R018472/1//EPSRC/ ; EP/R018472/1//EPSRC/ ; RGF EA 201074, UF150238//Royal Society/ ; CTRQQR-2021/100002/CRUK_/Cancer Research UK/United Kingdom ; },
mesh = {*Tumor Microenvironment/immunology ; Humans ; *Mathematical Concepts ; *Models, Biological ; *Neoplasms/pathology/immunology ; Computer Simulation ; Computational Biology ; Macrophages/immunology/pathology ; },
abstract = {Topological data analysis (TDA) is an active field of mathematics for quantifying shape in complex data. Standard methods in TDA such as persistent homology (PH) are typically focused on the analysis of data consisting of a single entity (e.g., cells or molecular species). However, state-of-the-art data collection techniques now generate exquisitely detailed multispecies data, prompting a need for methods that can examine and quantify the relations among them. Such heterogeneous data types arise in many contexts, ranging from biomedical imaging, geospatial analysis, to species ecology. Here, we propose two methods for encoding spatial relations among different data types that are based on Dowker complexes and Witness complexes. We apply the methods to synthetic multispecies data of a tumor microenvironment and analyze topological features that capture relations between different cell types, e.g., blood vessels, macrophages, tumor cells, and necrotic cells. We demonstrate that relational topological features can extract biological insight, including the dominant immune cell phenotype (an important predictor of patient prognosis) and the parameter regimes of a data-generating model. The methods provide a quantitative perspective on the relational analysis of multispecies spatial data, overcome the limits of traditional PH, and are readily computable.},
}
@article {pmid39287032,
year = {2024},
author = {Meaume, S and Senet, P and Thomé, B and Aragno, VA and Serge, B and Fortin, S and Boucley, I and Michon-Pasturel, U and Colboc, H},
title = {Impact of primary dressings on healing of venous leg ulcers: a French cohort study from the healthcare insurance database.},
journal = {Journal of wound care},
volume = {33},
number = {9},
pages = {678-686},
doi = {10.12968/jowc.2024.0189},
pmid = {39287032},
issn = {0969-0700},
mesh = {Humans ; Female ; Male ; *Wound Healing ; France ; *Varicose Ulcer/therapy/economics ; Aged ; *Bandages/economics ; Middle Aged ; Cohort Studies ; Databases, Factual ; Aged, 80 and over ; Insurance, Health/statistics &amp; numerical data ; Treatment Outcome ; Health Care Costs/statistics &amp; numerical data ; },
abstract = {OBJECTIVE: Multicomponent bandages (MCBs) are recommended by the French Authority for Health (Haute Autorité de Santé) as first-line treatment for venous leg ulcers (VLUs). A first analysis of the data collected from the French administrative healthcare database (Système National des Données de Santé (SNDS)) on 25,255 patients with a VLU supported superiority of MCBs versus short stretch bandages when considering the healing outcomes and costs associated with closure of these wounds. The aim of this study was to assess how beneficial the primary dressing (technology lipido-colloid nano-oligosaccharide factor (TLC NOSF) or control dressing group (CDG)) could be, when used in combination with MCBs in the treatment of VLUs.<br><br>METHOD: Data from the SNDS were collected for patients meeting the following inclusion criteria: treatment for a VLU with MCBs and with the same dressing type (TLC-NOSF or CDG) during the whole treatment period. Healing outcomes were documented on the global cohorts and propensity score-matched cohorts. The mean healthcare cost and the ecological impact were calculated for those patients healed within the study period.<br><br>RESULTS: In total, 12,507 patients met the criteria for treatment with both MCBs and TLC-NOSF dressings (n=1134) versus MCBs and CDG (n=11,373); with 1134 and 2268 patients per group following propensity score matching. Healing outcomes were favourable for the TLC-NOSF group in the global cohort and were enhanced in the propensity score-matched cohorts. At every point of the analysis, the adjusted healing rates were significantly higher in the TLC-NOSF group than in the CDG group (p<0.001). In the propensity score-matched cohorts (n=3402), the healing rate at three months was 52% in the TLC-NOSF group versus 37% in the CDG group (p<0.001). The median healing time was 87 days versus 125.5 days in the TLC-NOSF and CDG groups, respectively (p<0.0001). TLC-NOSF dressings significantly reduced the average treatment cost per healed ulcer (&#x20ac;2099) by 23.7% compared with dressings without TLC-NOSF (&#x20ac;2751) (p<0.001), as well as the resources used.<br><br>CONCLUSION: This SNDS analysis confirms, in the largest real-life study performed in VLU management, the superiority of the TLC-NOSF dressings versus those not impregnated with the NOSF compound. Better clinical outcomes associated with cost savings and a positive ecological impact support the combination of MCBs and TLC-NOSF dressings and should be considered as an optimal standard of care for the global management of VLUs. These outcomes reinforce the current positions of the international guidelines on the use of NOSF impregnated dressings (UrgoStart range; Laboratoires Urgo, France) in this pathology.},
}
@article {pmid39257810,
year = {2024},
author = {Hartley, GA and Okhovat, M and Hoyt, SJ and Fuller, E and Pauloski, N and Alexandre, N and Alexandrov, I and Drennan, R and Dubocanin, D and Gilbert, DM and Mao, Y and McCann, C and Neph, S and Ryabov, F and Sasaki, T and Storer, JM and Svendsen, D and Troy, W and Wells, J and Core, L and Stergachis, A and Carbone, L and O'Neill, RJ},
title = {Centromeric transposable elements and epigenetic status drive karyotypic variation in the eastern hoolock gibbon.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39257810},
issn = {2692-8205},
support = {P51 OD011092/OD/NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; R01 HG007352/HG/NHGRI NIH HHS/United States ; R01 HG010333/HG/NHGRI NIH HHS/United States ; },
abstract = {Great apes have maintained a stable karyotype with few large-scale rearrangements; in contrast, gibbons have undergone a high rate of chromosomal rearrangements coincident with rapid centromere turnover. Here we characterize assembled centromeres in the Eastern hoolock gibbon, Hoolock leuconedys (HLE), finding a diverse group of transposable elements (TEs) that differ from the canonical alpha satellites found across centromeres of other apes. We find that HLE centromeres contain a CpG methylation centromere dip region, providing evidence this epigenetic feature is conserved in the absence of satellite arrays; nevertheless, we report a variety of atypical centromeric features, including protein-coding genes and mismatched replication timing. Further, large structural variations define HLE centromeres and distinguish them from other gibbons. Combined with differentially methylated TEs, topologically associated domain boundaries, and segmental duplications at chromosomal breakpoints, we propose that a "perfect storm" of multiple genomic attributes with propensities for chromosome instability shaped gibbon centromere evolution.},
}
@article {pmid39209912,
year = {2024},
author = {Yuan, R and Qu, Q and Lu, Z and Geng, X and Tian, S and Jin, Y and Gong, J and Ye, X and Tang, P and Chen, X},
title = {A chromosome-level genome assembly of the gall maker pest inquiline, Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae).},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {944},
pmid = {39209912},
issn = {2052-4463},
support = {32070467//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31920103005//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Chromosomes, Insect ; Genome Size ; *Genome, Insect ; *Hymenoptera/genetics ; Wasps/parasitology ; Datasets as Topic ; },
abstract = {Diomorus aiolomorphi Kamijo (Hymenoptera: Torymidae) is an inquiline of gall maker Aiolomorphus rhopaloides Walker (Hymenoptera: Eurytomidae). They are of significant economic significance and predominantly inhabit bamboo forest. So far, only four scaffold-level genomes have been published for the family Torymidae. In this study, we present a high-quality genome assembly of D. aiolomorphi at the chromosome level, achieved through the integration of Nanopore (ONT) long-read, Illumina pair-end DNA short-read, and High-through Chromosome Conformation Capture (Hi-C) sequencing methods. The final assembly was 1,084.56 Mb in genome size, with 1,083.41 Mb (99.89%) assigned to five pseudochromosomes. The scaffold N50 length reached 224.87 Mb, and the complete Benchmarking Universal Single-Copy Orthologs (BUSCO) score was 97.3%. The genome contained 762.12 Mb of repetitive elements, accounting for 70.27% of the total genome size. A total of 18,011 protein-coding genes were predicted, with 17,829 genes being functionally annotated. The high-quality genome assembly of D. aiolomorphi presented in this study will serve as a valuable genomic resource for future research on parasitoid wasps. The results of this study may also contribute to the development of biological control strategies for pest management in bamboo forests, enhancing ecological balance and economic sustainability.},
}
@article {pmid39277496,
year = {2024},
author = {van der Feltz-Cornelis, CM and Turk, F and Sweetman, J and Khunti, K and Gabbay, M and Shepherd, J and Montgomery, H and Strain, WD and Lip, GYH and Wootton, D and Watkins, CL and Cuthbertson, DJ and Williams, N and Banerjee, A},
title = {Corrigendum to "Prevalence of mental health conditions and brain fog in people with long COVID: A systematic review and meta-analysis" [General Hospital Psychiatry volume 88 (2024)10-22 10.1016/j.genhosppsych.2024.02.009].},
journal = {General hospital psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.genhosppsych.2024.09.006},
pmid = {39277496},
issn = {1873-7714},
}
@article {pmid39275913,
year = {2024},
author = {Takada, K and Nakagawa, S and Kryukov, K and Ozawa, M and Watanabe, T},
title = {Metagenomic analysis of the gut microbiota of hooded cranes (Grus monacha) on the Izumi plain in Japan.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.13881},
pmid = {39275913},
issn = {2211-5463},
support = {//Crane Conservation by the City of Izumi/ ; //Tokyo Biochemical Research Foundation/ ; JPMJCR20H6//Core Research for Evolutional Science and Technology/ ; //2020 Tokai University School of Medicine Research Aid/ ; 22gm1610010h0001//Japan Agency for Medical Research and Development/ ; JP223fa627002h//Japan Agency for Medical Research and Development/ ; //Takeda Science Foundation/ ; 16H06429//Japan Society for the Promotion of Science/ ; 16H06434//Japan Society for the Promotion of Science/ ; 16K21723//Japan Society for the Promotion of Science/ ; 19H04843//Japan Society for the Promotion of Science/ ; 19fk0108171//Japan Society for the Promotion of Science/ ; 21J01036//Japan Society for the Promotion of Science/ ; 22K15469//Japan Society for the Promotion of Science/ ; JP19fk0108113//Japan Society for the Promotion of Science/ ; JP22H02521//Japan Society for the Promotion of Science/ ; },
abstract = {Recent advances in DNA sequencing technology have dramatically improved our understanding of the gut microbiota of various animal species. However, research on the gut microbiota of birds lags behind that of many other vertebrates, and information about the gut microbiota of wild birds such as migratory waterfowl is particularly lacking. Because the ecology of migratory waterfowl (e.g., lifestyle, diet, physiological characteristics) differs from that of other birds, the gut microbiota of migratory waterfowl likely also differs, but much is still unknown. The hooded crane (Grus monacha) is an important representative migratory waterbird species and is listed as endangered on the International Union for Conservation of Nature and Natural Resources Red List of Threatened Species. In this study, we analyzed the bacterial and viral microbiota in the gut of hooded cranes by using deep sequencing data from fecal samples of hooded cranes that winter on the Izumi plain in Japan, and found that Cetobacterium, Clupeiformes, and Pbunavirus were clearly present in the fecal samples of hooded cranes. These findings advance our understanding of the ecology of hooded cranes.},
}
@article {pmid39274728,
year = {2024},
author = {Sąsiadek-Andrzejczak, E and Maras, P and Kozicki, M},
title = {Flexible and Ecological Cotton-Based Dosimeter for 2D UV Surface Dose Distribution Measurements.},
journal = {Materials (Basel, Switzerland)},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/ma17174339},
pmid = {39274728},
issn = {1996-1944},
abstract = {This work presents a 2D radiochromic dosimeter for ultraviolet (UV) radiation measurements, based on cotton fabric volume-modified with nitroblue tetrazolium chloride (NBT) as a radiation-sensitive compound. The developed dosimeter is flexible, which allows it to adapt to various shapes and show a color change from yellowish to purple-brown during irradiation. The intensity of the color change depends on the type of UV radiation and is the highest for UVC (253.7 nm). It has been shown that the developed dosimeters (i) can be used for UVC radiation dose measurements in the range of up to 10 J/cm[2]; (ii) can be measured in 2D using a flatbed scanner; and (iii) can have the obtained images after scanning be filtered with a medium filter to improve their quality by reducing noise from the fabric structure. The developed cotton-NBT dosimeters can measure UVC-absorbed radiation doses on objects of various shapes, and when combined with a dedicated computer software package and a data processing method, they form a comprehensive system for measuring dose distributions for objects with complex shapes. The developed system can also serve as a comprehensive method for assessing the quality and control of UV radiation sources used in various industrial processes.},
}
@article {pmid39273837,
year = {2024},
author = {Gatina, E and Zinicovscaia, I and Yushin, N and Chaligava, O and Frontasyeva, M and Sharipova, A},
title = {Assessment of the Atmospheric Deposition of Potentially Toxic Elements Using Moss Pleurozium schreberi in an Urban Area: The Perm (Perm Region, Russia) Case Study.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {17},
pages = {},
doi = {10.3390/plants13172353},
pmid = {39273837},
issn = {2223-7747},
abstract = {Assessment of air quality in urban areas is very important because pollutants affect both the environment and human health. In Perm (Russia), a moss biomonitoring method was used to assess the level of air pollution. The concentrations of 15 elements in 87 samples of moss Pleurozium schreberi in the city territory were determined using a direct mercury analyzer and an inductively coupled plasma atomic emission spectroscopy. Using factor and correlation analyses, the grouping of elements and their relationship with emission sources were established. The main sources of emissions of potentially toxic elements are the transportation (road and rail), metallurgical, and chemical industries. The level of atmospheric air pollution was assessed by calculating the environmental risk index, pollutant load index, and pollution coefficient. Based on the values of the pollution index, the level of atmospheric air pollution in Perm varies from unpolluted to highly polluted, with moderate environmental risk.},
}
@article {pmid39273245,
year = {2024},
author = {Damarov, IS and Korbolina, EE and Rykova, EY and Merkulova, TI},
title = {Multi-Omics Analysis Revealed the rSNPs Potentially Involved in T2DM Pathogenic Mechanism and Metformin Response.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
doi = {10.3390/ijms25179297},
pmid = {39273245},
issn = {1422-0067},
support = {23-15-00113//Russian Science Foundation/ ; },
mesh = {Humans ; *Metformin/pharmacology/therapeutic use ; *Diabetes Mellitus, Type 2/genetics/drug therapy/metabolism ; *Polymorphism, Single Nucleotide ; *Genome-Wide Association Study ; Hypoglycemic Agents/therapeutic use/pharmacology ; Quantitative Trait Loci ; Computational Biology/methods ; Leukocytes, Mononuclear/metabolism/drug effects ; Gene Expression Regulation/drug effects ; Promoter Regions, Genetic ; Multiomics ; },
abstract = {The goal of our study was to identify and assess the functionally significant SNPs with potentially important roles in the development of type 2 diabetes mellitus (T2DM) and/or their effect on individual response to antihyperglycemic medication with metformin. We applied a bioinformatics approach to identify the regulatory SNPs (rSNPs) associated with allele-asymmetric binding and expression events in our paired ChIP-seq and RNA-seq data for peripheral blood mononuclear cells (PBMCs) of nine healthy individuals. The rSNP outcomes were analyzed using public data from the GWAS (Genome-Wide Association Studies) and Genotype-Tissue Expression (GTEx). The differentially expressed genes (DEGs) between healthy and T2DM individuals (GSE221521), including metformin responders and non-responders (GSE153315), were searched for in GEO RNA-seq data. The DEGs harboring rSNPs were analyzed using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). We identified 14,796 rSNPs in the promoters of 5132 genes of human PBMCs. We found 4280 rSNPs to associate with both phenotypic traits (GWAS) and expression quantitative trait loci (eQTLs) from GTEx. Between T2DM patients and controls, 3810 rSNPs were detected in the promoters of 1284 DEGs. Based on the protein-protein interaction (PPI) network, we identified 31 upregulated hub genes, including the genes involved in inflammation, obesity, and insulin resistance. The top-ranked 10 enriched KEGG pathways for these hubs included insulin, AMPK, and FoxO signaling pathways. Between metformin responders and non-responders, 367 rSNPs were found in the promoters of 131 DEGs. Genes encoding transcription factors and transcription regulators were the most widely represented group and many were shown to be involved in the T2DM pathogenesis. We have formed a list of human rSNPs that add functional interpretation to the T2DM-association signals identified in GWAS. The results suggest candidate causal regulatory variants for T2DM, with strong enrichment in the pathways related to glucose metabolism, inflammation, and the effects of metformin.},
}
@article {pmid39271937,
year = {2024},
author = {Hansen, AJ and Burns, P and Ervin, J and Goetz, SJ and Hansen, M and Venter, O and Watson, JEM and Jantz, PA and Virnig, ALS and Barnett, K and Pillay, R and Atkinson, S and Supples, C and Rodríguez-Buritica, S and Armenteras, D},
title = {Author Correction: A policy-driven framework for conserving the best of Earth's remaining moist tropical forests.},
journal = {Nature ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41559-024-02557-8},
pmid = {39271937},
issn = {2397-334X},
}
@article {pmid39271747,
year = {2024},
author = {Shin, S and Baker, AJ and Enk, J and McKenna, DD and Foquet, B and Vandergast, AG and Weissman, DB and Song, H},
title = {Orthoptera-specific target enrichment (OR-TE) probes resolve relationships over broad phylogenetic scales.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21377},
pmid = {39271747},
issn = {2045-2322},
support = {DEB-1937815//National Science Foundation/ ; IOS-1253493//National Science Foundation/ ; DEB-1064082//National Science Foundation/ ; Hatch Grant TEX0-2-6584//U.S. Department of Agriculture/ ; },
mesh = {Animals ; *Phylogeny ; *Orthoptera/genetics/classification ; Transcriptome/genetics ; Computational Biology/methods ; DNA Probes/genetics ; Evolution, Molecular ; },
abstract = {Phylogenomic data are revolutionizing the field of insect phylogenetics. One of the most tenable and cost-effective methods of generating phylogenomic data is target enrichment, which has resulted in novel phylogenetic hypotheses and revealed new insights into insect evolution. Orthoptera is the most diverse insect order within polyneoptera and includes many evolutionarily and ecologically interesting species. Still, the order as a whole has lagged behind other major insect orders in terms of transitioning to phylogenomics. In this study, we developed an Orthoptera-specific target enrichment (OR-TE) probe set from 80 transcriptomes across Orthoptera. The probe set targets 1828 loci from genes exhibiting a wide range of evolutionary rates. The utility of this new probe set was validated by generating phylogenomic data from 36 orthopteran species that had not previously been subjected to phylogenomic studies. The OR-TE probe set captured an average of 1037 loci across the tested taxa, resolving relationships across broad phylogenetic scales. Our detailed documentation of the probe design and bioinformatics process is intended to facilitate the widespread adoption of this tool.},
}
@article {pmid39103035,
year = {2024},
author = {Shi, C and Cheng, L and Yu, Y and Chen, S and Dai, Y and Yang, J and Zhang, H and Chen, J and Geng, N},
title = {Multi-omics integration analysis: Tools and applications in environmental toxicology.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {360},
number = {},
pages = {124675},
doi = {10.1016/j.envpol.2024.124675},
pmid = {39103035},
issn = {1873-6424},
mesh = {*Environmental Pollutants/toxicity ; *Ecotoxicology/methods ; *Proteomics ; Genomics ; Metabolomics ; Animals ; Humans ; Multiomics ; },
abstract = {Nowadays, traditional single-omics study is not enough to explain the causality between molecular alterations and toxicity endpoints for environmental pollutants. With the development of high-throughput sequencing technology and high-resolution mass spectrometry technology, the integrative analysis of multi-omics has become an efficient strategy to understand holistic biological mechanisms and to uncover the regulation network in specific biological processes. This review summarized sample preparation methods, integration analysis tools and the application of multi-omics integration analyses in environmental toxicology field. Currently, omics methods have been widely applied being as the sensitivity of early biological response, especially for low-dose and long-term exposure to environmental pollutants. Integrative omics can reveal the overall changes of genes, proteins, and/or metabolites in the cells, tissues or organisms, which provide new insights into revealing the overall toxicity effects, screening the toxic targets, and exploring the underlying molecular mechanism of pollutants.},
}
@article {pmid39268176,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the White Satin, Leucoma salicis (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {323},
pmid = {39268176},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Leucoma salicis (the White Satin; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 733.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.73 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,222 protein coding genes.},
}
@article {pmid39267994,
year = {2024},
author = {Boyes, D and Broad, GR and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Oak Nycteoline moth, Nycteola revayana (Scopoli, 1772).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {258},
pmid = {39267994},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Nycteola revayana (the Oak Nycteoline moth; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 621.0 megabases in span. Most of the assembly is scaffolded into 26 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.25 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,235 protein-coding genes.},
}
@article {pmid39226337,
year = {2024},
author = {Rahman, AU and Tikhonov, G and Oksanen, J and Rossi, T and Ovaskainen, O},
title = {Accelerating joint species distribution modelling with Hmsc-HPC by GPU porting.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1011914},
doi = {10.1371/journal.pcbi.1011914},
pmid = {39226337},
issn = {1553-7358},
mesh = {*Algorithms ; *Computational Biology/methods ; *Software ; Models, Biological ; Machine Learning ; Computer Graphics ; Models, Statistical ; Humans ; },
abstract = {Joint species distribution modelling (JSDM) is a widely used statistical method that analyzes combined patterns of all species in a community, linking empirical data to ecological theory and enhancing community-wide prediction tasks. However, fitting JSDMs to large datasets is often computationally demanding and time-consuming. Recent studies have introduced new statistical and machine learning techniques to provide more scalable fitting algorithms, but extending these to complex JSDM structures that account for spatial dependencies or multi-level sampling designs remains challenging. In this study, we aim to enhance JSDM scalability by leveraging high-performance computing (HPC) resources for an existing fitting method. Our work focuses on the Hmsc R-package, a widely used JSDM framework that supports the integration of various dataset types into a single comprehensive model. We developed a GPU-compatible implementation of its model-fitting algorithm using Python and the TensorFlow library. Despite these changes, our enhanced framework retains the original user interface of the Hmsc R-package. We evaluated the performance of the proposed implementation across various model configurations and dataset sizes. Our results show a significant increase in model fitting speed for most models compared to the baseline Hmsc R-package. For the largest datasets, we achieved speed-ups of over 1000 times, demonstrating the substantial potential of GPU porting for previously CPU-bound JSDM software. This advancement opens promising opportunities for better utilizing the rapidly accumulating new biodiversity data resources for inference and prediction.},
}
@article {pmid39266599,
year = {2024},
author = {He, H and Boehringer, T and Schäfer, B and Heppell, K and Beck, C},
title = {Analyzing spatio-temporal dynamics of dissolved oxygen for the River Thames using superstatistical methods and machine learning.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {21288},
pmid = {39266599},
issn = {2045-2322},
support = {VH-NG-1727//Helmholtz Association and the Networking Fund/ ; },
abstract = {By employing superstatistical methods and machine learning, we analyze time series data of water quality indicators for the River Thames (UK). The indicators analyzed include dissolved oxygen, temperature, electrical conductivity, pH, ammonium, turbidity, and rainfall, with a specific focus on the dynamics of dissolved oxygen. After detrending, the probability density functions of dissolved oxygen fluctuations exhibit heavy tails that are effectively modeled using q-Gaussian distributions. Our findings indicate that the multiplicative Empirical Mode Decomposition method stands out as the most effective detrending technique, yielding the highest log-likelihood in nearly all fittings. We also observe that the optimally fitted width parameter of the q-Gaussian shows a negative correlation with the distance to the sea, highlighting the influence of geographical factors on water quality dynamics. In the context of same-time prediction of dissolved oxygen, regression analysis incorporating various water quality indicators and temporal features identify the Light Gradient Boosting Machine as the best model. SHapley Additive exPlanations reveal that temperature, pH, and time of year play crucial roles in the predictions. Furthermore, we use the Transformer, a state-of-the-art machine learning model, to forecast dissolved oxygen concentrations. For long-term forecasting, the Informer model consistently delivers superior performance, achieving the lowest Mean Absolute Error (0.15) and Symmetric Mean Absolute Percentage Error (21.96%) with the 192 historical time steps that we used. This performance is attributed to the Informer's ProbSparse self-attention mechanism, which allows it to capture long-range dependencies in time-series data more effectively than other machine learning models. It effectively recognizes the half-life cycle of dissolved oxygen, with particular attention to critical periods such as morning to early afternoon, late evening to early morning, and key intervals between the 16th and 26th quarter-hours of the previous half-day. Our findings provide valuable insights for policymakers involved in ecological health assessments, aiding in accurate predictions of river water quality and the maintenance of healthy aquatic ecosystems.},
}
@article {pmid39264914,
year = {2024},
author = {Zhang, K and Cao, Y and Guo, X and Kong, F and Sun, H and Jing, T and Zhan, Y and Qi, F},
title = {Comparative transcriptome analysis of differentially expressed genes and pathways in male and female flowers of Fraxinus mandshurica.},
journal = {PloS one},
volume = {19},
number = {9},
pages = {e0308013},
doi = {10.1371/journal.pone.0308013},
pmid = {39264914},
issn = {1932-6203},
mesh = {*Flowers/genetics/metabolism/growth &amp; development ; *Gene Expression Regulation, Plant ; *Gene Expression Profiling ; *Fraxinus/genetics ; *Transcriptome ; Signal Transduction/genetics ; Plant Proteins/genetics/metabolism ; Gene Ontology ; Genes, Plant ; },
abstract = {Fraxinus mandshurica Rupr. (F. mandshurica) is a dioecious tree species with important ecological and application values. To delve deeper into the regulatory pathways and genes responsible for male and female flowers in F. mandshurica, we conducted transcriptome sequencing on male and female flowers at four distinct stages. The analysis revealed that the female database generated 38,319,967 reads while the male database generated 43,320,907 reads, resulting in 2930 differentially expressed genes with 1441 were up-regulated and 1489 down-regulated in males compared to females. Following an analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), four distinct pathways (hormone signal transduction, energy metabolism, flavonoid biosynthesis, and photoperiod) linked to female and male flowers were identified. Subsequently, qRT-PCR verification revealed that FmAUX/IAA, FmEIN3, and FmA-ARR genes in hormone signal transduction pathway are related to female flower development. Meanwhile, FmABF genes in hormone signal transduction pathway, FmGS and FmGDH genes in energy metabolism pathway, FmFLS genes in flavonoid biosynthesis pathway, and FmCaM, FmCRY, and FmPKA genes in photoperiod pathway are related to male flower development. This study was the first to analyze the transcriptome of male and female flowers of F. mandshurica, providing a reference for the developmental pathways and gene expression levels of male and female plants.},
}
@article {pmid39264239,
year = {2024},
author = {Silva, M and Capps, S and London, JK},
title = {Community-Engaged Research and the Use of Open Access ToxVal/ToxRef In Vivo Databases and New Approach Methodologies (NAM) to Address Human Health Risks From Environmental Contaminants.},
journal = {Birth defects research},
volume = {116},
number = {9},
pages = {e2395},
doi = {10.1002/bdr2.2395},
pmid = {39264239},
issn = {2472-1727},
support = {P30 ES023513/ES/NIEHS NIH HHS/United States ; },
mesh = {Humans ; *Environmental Pollutants ; *Databases, Factual ; Risk Assessment/methods ; Environmental Exposure/adverse effects ; United States ; United States Environmental Protection Agency ; Pesticides/adverse effects/toxicity ; },
abstract = {BACKGROUND: The paper analyzes opportunities for integrating Open access resources (Abstract Sifter, US EPA and NTP Toxicity Value and Toxicity Reference [ToxVal/ToxRefDB]) and New Approach Methodologies (NAM) integration into Community Engaged Research (CEnR).<br><br>METHODS: CompTox Chemicals Dashboard and Integrated Chemical Environment with in vivo ToxVal/ToxRef and NAMs (in vitro) databases are presented in three case studies to show how these resources could be used in Pilot Projects involving Community Engaged Research (CEnR) from the University of California, Davis, Environmental Health Sciences Center.<br><br>RESULTS: Case #1 developed a novel assay methodology for testing pesticide toxicity. Case #2 involved detection of water contaminants from wildfire ash and Case #3 involved contaminants on Tribal Lands. Abstract Sifter/ToxVal/ToxRefDB regulatory data and NAMs could be used to screen/prioritize risks from exposure to metals, PAHs and PFAS from wildfire ash leached into water and to investigate activities of environmental toxins (e.g., pesticides) on Tribal lands. Open access NAMs and computational tools can apply to detection of sensitive biological activities in potential or known adverse outcome pathways to predict points of departure (POD) for comparison with regulatory values for hazard identification. Open access Systematic Empirical Evaluation of Models or biomonitoring exposures are available for human subpopulations and can be used to determine bioactivity (POD) to exposure ratio to facilitate mitigation.<br><br>CONCLUSIONS: These resources help prioritize chemical toxicity and facilitate regulatory decisions and health protective policies that can aid stakeholders in deciding on needed research. Insights into exposure risks can aid environmental justice and health equity advocates.},
}
@article {pmid39263387,
year = {2024},
author = {Deeleman-Reinhold, CL and Addink, W and Miller, JA},
title = {The genera Chrysillaand Phintelloidesrevisited with the description of a new species (Araneae, Salticidae) using digital specimen DOIs and nanopublications.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e129438},
doi = {10.3897/BDJ.12.e129438},
pmid = {39263387},
issn = {1314-2828},
abstract = {BACKGROUND: Two Southeast Asian spider collections: that of Frances and John Murphy, now in the Manchester University Museum and the Deeleman collection, now at the Naturalis Biodiversity Center in Leiden constituted the basis of this analysis of Chrysilla Thorell, 1887 and related genera. The latter collection also includes many thousands of spiders obtained by canopy fogging for an ecological project in Borneo by A. Floren.<br><br>NEW INFORMATION: Some incongruences within the genera of the tribe Chrysillini are disentangled. The transfer of C.jesudasi Caleb &amp; Mathai, 2014 from Chrysilla as type species of Phintelloides Kanesharatnam &amp; Benjamin, 2019, based on analysis of molecular data is validated by morphology. An interesting new species known only from the forest canopy in Borneo, Phintelloidesscandens sp. nov, is described based on both male and female specimens. Distinguishing chrysilline genera is mostly based on traditional somatic characters, e.g., habitus, carapace and abdomen patterns, mouthparts, and genital organs. The utility of two character systems for distinguishing chrysilline genera is highlighted: 1) the presence of a flexible, articulating embolic tegular branch (etb) in combination with the conformation of the characteristic construction of the epigyne in Chrysilla and Phintelloides; 2) presence of red colour on carapace and abdomen of live males and females, in combination with abundant blue/violet/white iridescent scales such as inChrysilla and Siler. The red colour usually gets lost in alcohol, hampering species identification of alcohol material. The genera Chrysilla andPhintelloidesare redefined. Specimens of the heretofore unknown female of Chrysilla deelemani Pr&#xf3;szy&#x144;ski &amp; Deeleman-Reinhold, 2010 are described. The male and female ofChrysillalauta and male of C.volupe are redescribed. The genus Chrysilla is diagnosed and discriminated from PhintellaB&#xf6;senberg &amp; Strand, 1906, SilerSimon, 1889, Phintelloides Kanesharatnam &amp; Benjamin, 2019 andProszynskiaKanesharatnam &amp; Benjamin, 2019. The structure of the female genital organ of Phintelloidesflavumi Kanesharatnam &amp; Benjamin, 2019 is scrutinized and the generic placement of Phintelloides is discussed. Males and females of one of the most variable species, Phintelloidesversicolor (C. L. Koch, 1846) are redescribed.Phintelloidesmunita(B&#xf6;senberg &amp; Strand, 1906) is removed from synonymy with P.versicolor. Phintellaleucaspis Simon 1903 (male, Sumatra) is synonymized withP.versicolor.Biodiversity data are increasingly reliant on digital infrastructure. By linking physical specimens to digital representations of their associated data, we can lower barriers to information flow. Here we demonstrate a workflow whereby persistent identifiers (PIDs) in the form of DOIs issued by DataCite are assigned to specimens. Recognized taxa are identified by their catalog of life identifier, or by registration in ZooBank where no catalog of life identifier is available. We demonstrate the use of nanopublications, creating a series of machine readable, scientifically meaningful assertions regarding the provenance and identification of cited specimens. All human agents associated with the specimen data are linked to a persistent identifier issued by either ORCiD or Wikidata.},
}
@article {pmid39262445,
year = {2023},
author = {Borry, M and Forsythe, A and Andrades Valtueña, A and Hübner, A and Ibrahim, A and Quagliariello, A and White, AE and Kocher, A and Vågene, &#xc5;J and Bartholdy, BP and Spurīte, D and Ponce-Soto, GY and Neumann, G and Huang, IT and Light, I and Velsko, IM and Jackson, I and Frangenberg, J and Serrano, JG and Fumey, J and Özdoğan, KT and Blevins, KE and Daly, KG and Lopopolo, M and Moraitou, M and Michel, M and van Os, M and Bravo-Lopez, MJ and Sarhan, MS and Dagtas, ND and Oskolkov, N and Smith, OS and Lebrasseur, O and Rozwalak, P and Eisenhofer, R and Wasef, S and Ramachandran, SL and Vanghi, V and Warinner, C and Fellows Yates, JA},
title = {Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {926},
doi = {10.12688/f1000research.134798.2},
pmid = {39262445},
issn = {2046-1402},
mesh = {*Metagenomics/methods ; Humans ; *Metadata ; High-Throughput Nucleotide Sequencing/methods ; Software ; Metagenome ; Computational Biology/methods ; DNA, Ancient/analysis ; },
abstract = {BACKGROUND: Access to sample-level metadata is important when selecting public metagenomic sequencing datasets for reuse in new biological analyses. The Standards, Precautions, and Advances in Ancient Metagenomics community (SPAAM, https://spaam-community.org) has previously published AncientMetagenomeDir, a collection of curated and standardised sample metadata tables for metagenomic and microbial genome datasets generated from ancient samples. However, while sample-level information is useful for identifying relevant samples for inclusion in new projects, Next Generation Sequencing (NGS) library construction and sequencing metadata are also essential for appropriately reprocessing ancient metagenomic data. Currently, recovering information for downloading and preparing such data is difficult when laboratory and bioinformatic metadata is heterogeneously recorded in prose-based publications.<br><br>METHODS: Through a series of community-based hackathon events, AncientMetagenomeDir was updated to provide standardised library-level metadata of existing and new ancient metagenomic samples. In tandem, the companion tool 'AMDirT' was developed to facilitate rapid data filtering and downloading of ancient metagenomic data, as well as improving automated metadata curation and validation for AncientMetagenomeDir.<br><br>RESULTS: AncientMetagenomeDir was extended to include standardised metadata of over 6000 ancient metagenomic libraries. The companion tool 'AMDirT' provides both graphical- and command-line interface based access to such metadata for users from a wide range of computational backgrounds. We also report on errors with metadata reporting that appear to commonly occur during data upload and provide suggestions on how to improve the quality of data sharing by the community.<br><br>CONCLUSIONS: Together, both standardised metadata reporting and tooling will help towards easier incorporation and reuse of public ancient metagenomic datasets into future analyses.},
}
@article {pmid39262678,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Brindled Flat-body, Agonopterix arenella (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {214},
doi = {10.12688/wellcomeopenres.19252.1},
pmid = {39262678},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Agonopterix arenella (the Brindled Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 545.8 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length.},
}
@article {pmid39257624,
year = {2024},
author = {Lohse, K and Vila, R and Hayward, A and , and , and , and , and , },
title = {The genome sequence of the Lulworth Skipper, Thymelicus acteon (Rottemburg, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {266},
doi = {10.12688/wellcomeopenres.21627.1},
pmid = {39257624},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Thymelicus acteon (the Lulworth Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 537.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,813 protein-coding genes.},
}
@article {pmid39257623,
year = {2024},
author = {Boyes, D and Januszczak, I and Lees, DC and , and , and , and , and , and , and , },
title = {The genome sequence of the White-pinion Spotted, Lomographa bimaculata (Fabricius, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {96},
doi = {10.12688/wellcomeopenres.20841.1},
pmid = {39257623},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Lomographa bimaculata (the White-pinion Spotted; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 554.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.66 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,749 protein coding genes.},
}
@article {pmid39257281,
year = {2024},
author = {Calabrese, JM and Schüler, L and Fu, X and Gawel, E and Zozmann, H and Bumberger, J and Quaas, M and Wolf, G and Attinger, S},
title = {A novel, scenario-based approach to comparing non-pharmaceutical intervention strategies across nations.},
journal = {Journal of the Royal Society, Interface},
volume = {21},
number = {218},
pages = {20240301},
doi = {10.1098/rsif.2024.0301},
pmid = {39257281},
issn = {1742-5662},
support = {//Helmholtz-Gemeinschaft/ ; //Bundesministerium f&#xfc;r Bildung und Forschung/ ; //S&#xe4;chsisches Staatsministerium f&#xfc;r Wissenschaft und Kunst/ ; },
mesh = {*COVID-19/epidemiology/prevention &amp; control ; Humans ; New Zealand/epidemiology ; Switzerland/epidemiology ; Germany/epidemiology ; *SARS-CoV-2 ; Pandemics/prevention &amp; control ; },
abstract = {Comparing COVID-19 response strategies across nations is a key step in preparing for future pandemics. Conventional comparisons, which rank individual non-pharmaceutical intervention (NPI) effects, are limited by: (i) a focus on epidemiological outcomes; (ii) NPIs typically being applied as packages of interventions; and (iii) different political, economic and social conditions among nations. Here, we develop a coupled epidemiological-behavioural-macroeconomic model that can transfer NPI effects from a reference nation to a focal nation. This approach quantifies epidemiological, behavioural and economic outcomes while accounting for both packaged NPIs and differing conditions among nations. As a first proof of concept, we take Germany as our focal nation during Spring 2020, and New Zealand and Switzerland as reference nations with contrasting NPI strategies. Our results suggest that, while New Zealand's more aggressive strategy would have yielded modest epidemiological gains in Germany, it would have resulted in substantially higher economic costs while dramatically reducing social contacts. In contrast, Switzerland's more lenient strategy would have prolonged the first wave in Germany, but would also have increased relative costs. More generally, these findings indicate that our approach can provide novel, multifaceted insights on the efficacy of pandemic response strategies, and therefore merits further exploration and development.},
}
@article {pmid39253482,
year = {2024},
author = {Mortzfeld, BM and Bhattarai, SK and Bucci, V},
title = {Expanding the toolbox: Novel class IIb microcins show activity against Gram-negative ESKAPE and plant pathogens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2023.12.05.570296},
pmid = {39253482},
issn = {2692-8205},
abstract = {Interspecies interactions involving direct competition via bacteriocin production play a vital role in shaping ecological dynamics within microbial ecosystems. For instance, the ribosomally-produced siderophore bacteriocins, known as class IIb microcins, affect the colonization of host-associated pathogenic Enterobacteriaceae species. Notably, to date, only five of these antimicrobials have been identified, all derived from specific Escherichia coli and Klebsiella pneumoniae strains. We hypothesized that class IIb microcin production extends beyond these specific compounds and organisms. With a customized informatics-driven approach, screening bacterial genomes in public databases with BLAST and manual curation, we have discovered twelve previously unknown class IIb microcins in seven additional Enterobacteriaceae species, encompassing phytopathogens and environmental isolates. We introduce three novel clades of microcins (MccW, MccX, and MccZ), while also identifying eight new variants of the five known class IIb microcins. To validate their antimicrobial potential, we heterologously expressed these microcins in E. coli and demonstrated efficacy against a variety of bacterial isolates, including plant pathogens from the genera Brenneria, Gibbsiella, and Rahnella . Two newly discovered microcins exhibit activity against Gram-negative ESKAPE pathogens, i.e. Acinetobacter baumannii or Pseudomonas aeruginosa , providing the first evidence that class IIb microcins can target bacteria outside of the Enterobacteriaceae family. This study underscores that class IIb microcin genes are more prevalent in the microbial world than previously recognized and that synthetic hybrid microcins can be a viable tool to target clinically relevant drug-resistant pathogens. Our findings hold significant promise for the development of innovative engineered live biotherapeutic products tailored to combat these resilient bacteria.},
}
@article {pmid39250076,
year = {2024},
author = {Zancolli, G and von Reumont, BM and Anderluh, G and Caliskan, F and Chiusano, ML and Fröhlich, J and Hapeshi, E and Hempel, BF and Ikonomopoulou, MP and Jungo, F and Marchot, P and de Farias, TM and Modica, MV and Moran, Y and Nalbantsoy, A and Procházka, J and Tarallo, A and Tonello, F and Vitorino, R and Zammit, ML and Antunes, A},
title = {Web of venom: exploration of big data resources in animal toxin research.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
doi = {10.1093/gigascience/giae054},
pmid = {39250076},
issn = {2047-217X},
support = {//European Cooperation in Science and Technology/ ; //Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; },
mesh = {Animals ; *Venoms ; *Internet ; *Computational Biology/methods ; *Big Data ; Databases, Factual ; },
abstract = {Research on animal venoms and their components spans multiple disciplines, including biology, biochemistry, bioinformatics, pharmacology, medicine, and more. Manipulating and analyzing the diverse array of data required for venom research can be challenging, and relevant tools and resources are often dispersed across different online platforms, making them less accessible to nonexperts. In this article, we address the multifaceted needs of the scientific community involved in venom and toxin-related research by identifying and discussing web resources, databases, and tools commonly used in this field. We have compiled these resources into a comprehensive table available on the VenomZone website (https://venomzone.expasy.org/10897). Furthermore, we highlight the challenges currently faced by researchers in accessing and using these resources and emphasize the importance of community-driven interdisciplinary approaches. We conclude by underscoring the significance of enhancing standards, promoting interoperability, and encouraging data and method sharing within the venom research community.},
}
@article {pmid39233286,
year = {2024},
author = {Long, XB and Yao, CR and Li, SY and Zhang, JG and Lu, ZJ and Ma, DD and Jiang, YX and Ying, GG and Shi, WJ},
title = {Multiomics analysis reveal the impact of 17α-Ethinylestradiol on mortality in juvenile zebrafish.},
journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP},
volume = {286},
number = {},
pages = {110027},
doi = {10.1016/j.cbpc.2024.110027},
pmid = {39233286},
issn = {1532-0456},
mesh = {Animals ; *Zebrafish ; *Ethinyl Estradiol/toxicity ; *Water Pollutants, Chemical/toxicity ; Endocrine Disruptors/toxicity ; Transcriptome/drug effects ; Multiomics ; },
abstract = {17α-Ethinylestradiol (EE2) is known for its endocrine-disrupting effects on embryonic and adult fish. However, its impact on juvenile zebrafish has not been well established. In this study, juvenile zebrafish were exposed to EE2 at concentrations of 5 ng/L (low dose, L), 10 ng/L (medium dose, M), and 50 ng/L (high dose, H) from 21 days post-fertilization (dpf) to 49 dpf. We assessed their growth, development, behavior, transcriptome, and metabolome. The findings showed that the survival rate in the EE2-H group was 66.8 %, with all surviving fish displaying stunted growth and swollen, transparent abdomens by 49 dpf. Moreover, severe organ deformities were observed in the gills, kidneys, intestines, and heart of fish in both the EE2-H and EE2-M groups. Co-expression analysis of mRNA and lncRNA revealed that EE2 downregulated the transcription of key genes involved in the cell cycle, DNA replication, and Fanconi anemia signaling pathways. Additionally, metabolomic analysis indicated that EE2 influenced metabolism and development-related signaling pathways. These pathways were also significantly identified based on the genes regulated by lncRNA. Consequently, EE2 induced organ deformities and mortality in juvenile zebrafish by disrupting signaling pathways associated with development and metabolism. The results of this study offer new mechanistic insights into the adverse effects of EE2 on juvenile zebrafish based on multiomics analysis. The juvenile zebrafish are highly sensitive to EE2 exposure, which is not limited to adult and embryonic stages. It is a potential model for studying developmental toxicity.},
}
@article {pmid39178805,
year = {2024},
author = {Bravo-Ortiz, MA and Guevara-Navarro, E and Holguín-García, SA and Rivera-Garcia, M and Cardona-Morales, O and Ruz, GA and Tabares-Soto, R},
title = {SpectroCVT-Net: A convolutional vision transformer architecture and channel attention for classifying Alzheimer's disease using spectrograms.},
journal = {Computers in biology and medicine},
volume = {181},
number = {},
pages = {109022},
doi = {10.1016/j.compbiomed.2024.109022},
pmid = {39178805},
issn = {1879-0534},
mesh = {*Alzheimer Disease/classification/physiopathology/diagnosis ; Humans ; *Electroencephalography/methods ; *Signal Processing, Computer-Assisted ; Male ; Female ; Databases, Factual ; Aged ; },
abstract = {Dementia arises from various brain-affecting diseases and injuries, with Alzheimer's disease being the most prevalent, impacting around 55 million people globally. Current clinical diagnosis often relies on biomarkers indicative of Alzheimer's distinctive features. Electroencephalography (EEG) serves as a cost-effective, user-friendly, and safe biomarker for early Alzheimer's detection. This study utilizes EEG signals processed with Short-Time Fourier Transform (STFT) to generate spectrograms, facilitating visualization of EEG signal properties. Leveraging the Brainlat database, we propose SpectroCVT-Net, a novel convolutional vision transformer architecture incorporating channel attention mechanisms. SpectroCVT-Net integrates convolutional and attention mechanisms to capture local and global dependencies within spectrograms. Comprising feature extraction and classification stages, the model enhances Alzheimer's disease classification accuracy compared to transfer learning methods, achieving 92.59 ± 2.3% accuracy across Alzheimer's, healthy controls, and behavioral variant frontotemporal dementia (bvFTD). This article introduces a new architecture and evaluates its efficacy with unconventional data for Alzheimer's diagnosis, contributing: SpectroCVT-Net, tailored for EEG spectrogram classification without reliance on transfer learning; a convolutional vision transformer (CVT) module in the classification stage, integrating local feature extraction with attention heads for global context analysis; Grad-CAM analysis for network decision insight, identifying critical layers, frequencies, and electrodes influencing classification; and enhanced interpretability through spectrograms, illuminating key brain wave contributions to Alzheimer's, frontotemporal dementia, and healthy control classifications, potentially aiding clinical diagnosis and management.},
}
@article {pmid39242865,
year = {2023},
author = {Karakulak, A and Tepe, B and Dimitrova, R and Abdelrahman, M and Akaliyski, P and Alaseel, R and Alkamali, YA and Amin, A and Lizarzaburu Aguinaga, DA and Andres, A and Aruta, JJBR and Assiotis, M and Avanesyan, H and Ayub, N and Bacikova-Sleskova, M and Baikanova, R and Bakkar, B and Bartoluci, S and Benitez, D and Bodnar, I and Bolatov, A and Borchet, J and Bosnar, K and Broche-Pérez, Y and Buzea, C and Cassibba, R and Carbonell, MM and Chen, BB and Dimitrovska, GR and Công Doanh, D and Dominguez Espinosa, ADC and Edine, WG and Ferenczi, N and Fernández-Morales, R and Gaete, J and Gan, Y and Giolo, S and Giordani, RCF and Friehs, MT and Gindi, S and Gjoneska, B and Godoy, JC and Del Pilar Grazioso, M and Hancheva, C and Hapunda, G and Hihara, S and Husain, MS and Islam, MS and Janovská, A and Javakhishvili, N and Jovanović, V and Kabir, RS and Abdul Kadir, NB and Karl, J and Katović, D and Kauyzbay, Z and Kawashima, TD and Kazmierczak, M and Khanna, R and Khosla, M and Klicperová-Baker, M and Kozina, A and Krauss, SE and Landabur, R and Lefringhausen, K and Lewandowska-Walter, A and Liang, YH and Makashvili, A and Malik, S and Manrique-Millones, D and Mastrotheodoros, S and McGrath, B and Mechili, EA and Mejía, M and Mhizha, S and Michalek-Kwiecien, J and Miconi, D and Mohsen, F and Moreta-Herrera, R and Muhl, C and Muradyan, M and Musso, P and Naterer, A and Nemat, A and Neto, F and Neto, J and Palacio, LMA and Okati-Aliabad, H and Orellana, CI and Orellana, LM and Mishra, SK and Park, J and Pavlova, I and Peralta, E and Petrytsa, P and Pišot, S and Prot, F and Rasia, J and Rivera, R and Riyanti, BPD and Samekin, A and Seisembekov, T and Serapinas, D and Silletti, F and Sharma, P and Shukla, S and Skrzypińska, K and Šolcová, IP and Solomontos-Kountouri, O and Stanciu, A and Stefenel, D and Steinmetz, LCL and Stogianni, M and Stuart, J and Sudarnoto, LF and Sugimura, K and Sultana, S and Suryani, AO and Tair, E and Tavitian-Elmadjan, L and Thome, LD and Uka, F and Valickienė, RP and Walter, B and Wendt, GW and Yang, PJ and Yıldırım, E and Yu, Y and Yunes, MAM and Zanoni da Silva, M and Rudnev, M},
title = {Trust in government moderates the association between fear of COVID-19 as well as empathic concern and preventive behaviour.},
journal = {Communications psychology},
volume = {1},
number = {1},
pages = {43},
pmid = {39242865},
issn = {2731-9121},
abstract = {With the COVID-19 pandemic, behavioural scientists aimed to illuminate reasons why people comply with (or not) large-scale cooperative activities. Here we investigated the motives that underlie support for COVID-19 preventive behaviours in a sample of 12,758 individuals from 34 countries. We hypothesized that the associations of empathic prosocial concern and fear of disease with support towards preventive COVID-19 behaviours would be moderated by trust in the government. Results suggest that the association between fear of disease and support for COVID-19 preventive behaviours was strongest when trust in the government was weak (both at individual- and country-level). Conversely, the association with empathic prosocial concern was strongest when trust in the government was high, but this moderation was only found at individual-level scores of governmental trust. We discuss how motivations may be shaped by socio-cultural context, and outline how findings may contribute to a better understanding of collective action during global crises.},
}
@article {pmid39242702,
year = {2023},
author = {Santangeli, A and Haukka, A and Morris, W and Arkkila, S and Delhey, K and Kempenaers, B and Valcu, M and Dale, J and Lehikoinen, A and Mammola, S},
title = {What drives our aesthetic attraction to birds?.},
journal = {npj biodiversity},
volume = {2},
number = {1},
pages = {20},
pmid = {39242702},
issn = {2731-4243},
abstract = {In the Anthropocene, the era when the imprint of humans on nature is pervasive across the planet, it is of utmost importance to understand human relationships with other species. The aesthetics of nature, and of species, is one of the values that plays a role in shaping human-nature relationships. Birds are ubiquitous across the world. The beauty of birds exerts a powerful tug on human emotions, and bird-rich areas attract scores of eco-tourists. People naturally find some birds more beautiful or interesting than others, but we currently lack a global understanding of the specifics of what makes a species aesthetically attractive. Here, we used a global citizen-science database on bird attractiveness covering nearly all extant bird species, to show that there are specific visual features that drive our aesthetic appeal for some bird species over others. First, our aesthetic attraction is highest for smaller birds with specific, vivid colors (e.g., blue and red, and departing from brown-grey) and extreme ornaments (a long crest or tail). Second, our aesthetic attraction is highest for species with broad ranges, possibly because such species may be more familiar to us. The features that make us attracted to a particular bird strongly align with broad human visual aesthetic preferences in modern society. Unveiling the visual features underpinning our aesthetic attraction to birds is a critical step towards optimizing conservation (e.g., via conservation marketing) and education campaigns, and leverage the cultural ecosystem service potential of birds.},
}
@article {pmid39154477,
year = {2024},
author = {Bai, Z and He, Y and Hu, G and Cheng, L and Wang, M},
title = {Microplastics at an environmentally relevant dose enhance mercury toxicity in a marine copepod under multigenerational exposure: Multi-omics perspective.},
journal = {Journal of hazardous materials},
volume = {478},
number = {},
pages = {135529},
doi = {10.1016/j.jhazmat.2024.135529},
pmid = {39154477},
issn = {1873-3336},
mesh = {Animals ; *Copepoda/drug effects ; *Mercury/toxicity ; *Water Pollutants, Chemical/toxicity ; *Microplastics/toxicity ; Reproduction/drug effects ; Apoptosis/drug effects ; Proteomics ; Multiomics ; },
abstract = {Here, we subjected the marine copepod Tigriopus japonicus to environmentally-relevant concentrations of microplastics (MPs) and mercury (Hg) for three generations (F0-F2) to investigate their physiological and molecular responses. Hg accumulation and phenotypic traits were measured in each generation, with multi-omics analysis conducted in F2. The results showed that MPs insignificantly impacted the copepod's development and reproduction, however, which were significantly compromised by Hg exposure. Interestingly, MPs significantly increased Hg accumulation and consequently aggravated this metal toxicity in T. japonicus, demonstrating their carrier role. Multi-omics analysis indicated that Hg pollution produced numerous toxic events, e.g., induction of apoptosis, damage to cell/organ morphogenesis, and disordered energy metabolism, ultimately resulting in retarded development and decreased fecundity. Importantly, MPs enhanced Hg toxicity mainly via increased oxidative apoptosis, compromised cell/organ morphogenesis, and energy depletion. Additionally, phosphoproteomic analysis revealed extensive regulation of the above processes, and also impaired neuron activity under combined MPs and Hg exposure. These alterations adversely affected development and reproduction of T. japonicus. Overall, our findings should offer novel molecular insights into the response of T. japonicus to long-term exposure to MPs and Hg, with a particular emphasis on the carrier role of MPs on Hg toxicity.},
}
@article {pmid39242656,
year = {2023},
author = {Hui, C and Pyšek, P and Richardson, DM},
title = {Disentangling the relationships among abundance, invasiveness and invasibility in trait space.},
journal = {npj biodiversity},
volume = {2},
number = {1},
pages = {13},
pmid = {39242656},
issn = {2731-4243},
support = {89967//National Research Foundation/ ; NE/V007548/1//Natural Environment Research Council/ ; DP200101680//Australian Research Council/ ; 101059592//HORIZON EUROPE European Research Council/ ; EXPRO 19-28807X//Czech Science Foundation/ ; RVO 67985939//Czech Academy of Sciences/ ; RVO 67985939//Czech Academy of Sciences/ ; CZ.02.2.69/0.0/0.0/18_053/0017850//Ministry of Education, Youth, and Sports of the Czech Republic/ ; },
abstract = {Identifying conditions and traits that allow an introduced species to grow and spread, from being initially rare to becoming abundant (defined as invasiveness), is the crux of invasion ecology. Invasiveness and abundance are related but not the same, and we need to differentiate these concepts. Predicting both species abundance and invasiveness and their relationship in an invaded community is highly contextual, being contingent on the community trait profile and its invasibility. We operationalised a three-pronged invasion framework that considers traits, environmental context, and propagule pressure. Specifically, we measure the invasiveness of an alien species by combining three components (performance reflecting environmental suitability, product of species richness and the covariance between interaction strength and species abundance, and community-level interaction pressure); the expected population growth rate of alien species simply reflects the total effect of propagule pressure and the product of their population size and invasiveness. The invasibility of a community reflects the size of opportunity niches (the integral of positive invasiveness in the trait space) under the given abiotic conditions of the environment. Both species abundance and the surface of invasiveness over the trait space can be dynamic and variable. Whether an introduced species with functional traits similar to those of an abundant species in the community exhibits high or low invasiveness depends largely on the kernel functions of performance and interaction strength with respect to traits and environmental conditions. Knowledge of the covariance between interaction strength and species abundance and these kernel functions, thus, holds the key to accurate prediction of invasion dynamics.},
}
@article {pmid39240878,
year = {2024},
author = {Shipley, ON and Dabrowski, AJ and Bowen, GJ and Hayden, B and Pauli, JN and Jordan, C and Anderson, L and Bailey, A and Bataille, CP and Cicero, C and Close, HG and Cook, C and Cook, JA and Desai, AR and Evaristo, J and Filley, TR and France, CAM and Jackson, AL and Kim, SL and Kopf, S and Loisel, J and Manlick, PJ and McFarlin, JM and McMeans, BC and O'Connell, TC and Pilaar Birch, SE and Putman, AL and Semmens, BX and Stantis, C and Stricker, CA and Szejner, P and Trammell, TLE and Uhen, MD and Weintraub-Leff, S and Wooller, MJ and Williams, JW and Yarnes, CT and Vander Zanden, HB and Newsome, SD},
title = {Design, development, and implementation of IsoBank: A centralized repository for isotopic data.},
journal = {PloS one},
volume = {19},
number = {9},
pages = {e0295662},
doi = {10.1371/journal.pone.0295662},
pmid = {39240878},
issn = {1932-6203},
mesh = {*Databases, Factual ; *Metadata ; Isotopes ; Internet ; },
abstract = {Stable isotope data have made pivotal contributions to nearly every discipline of the physical and natural sciences. As the generation and application of stable isotope data continues to grow exponentially, so does the need for a unifying data repository to improve accessibility and promote collaborative engagement. This paper provides an overview of the design, development, and implementation of IsoBank (www.isobank.org), a community-driven initiative to create an open-access repository for stable isotope data implemented online in 2021. A central goal of IsoBank is to provide a web-accessible database supporting interdisciplinary stable isotope research and educational opportunities. To achieve this goal, we convened a multi-disciplinary group of over 40 analytical experts, stable isotope researchers, database managers, and web developers to collaboratively design the database. This paper outlines the main features of IsoBank and provides a focused description of the core metadata structure. We present plans for future database and tool development and engagement across the scientific community. These efforts will help facilitate interdisciplinary collaboration among the many users of stable isotopic data while also offering useful data resources and standardization of metadata reporting across eco-geoinformatics landscapes.},
}
@article {pmid39239169,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Elephant Hawk-moth, Deilephila elpenor (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {104},
pmid = {39239169},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Deilephila elpenor (the Elephant Hawk-moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 414.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,748 protein coding genes.},
}
@article {pmid39238468,
year = {2024},
author = {Liu, L and Liu, Y and Min, L and Zhou, Z and He, X and Xie, Y and Cao, W and Deng, S and Lin, X and He, X and Chen, X},
title = {Most pleiotropic effects of gene knockouts are evolutionarily transient in yeasts.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae189},
pmid = {39238468},
issn = {1537-1719},
abstract = {Pleiotropy, the phenomenon in which a single gene influences multiple traits, is a fundamental concept in genetics. However, the evolutionary mechanisms underlying pleiotropy require further investigation. In this study, we conducted parallel gene knockouts targeting 100 transcription factors in two strains of Saccharomyces cerevisiae. We systematically examined and quantified the pleiotropic effects of these knockouts on gene expression levels for each transcription factor. Our results showed that the knockout of a single gene generally affected the expression levels of multiple genes in both strains, indicating various degrees of pleiotropic effects. Strikingly, the pleiotropic effects of the knockouts change rapidly between strains in different genetic backgrounds, and ∼85% of them were non-conserved. Further analysis revealed that the conserved effects tended to be functionally associated with the deleted transcription factors, while the non-conserved effects appeared to be more ad hoc responses. In addition, we measured 184 yeast cell morphological traits in these knockouts and found consistent patterns. In order to investigate the evolutionary processes underlying pleiotropy, we examined the pleiotropic effects of standing genetic variations in a population consisting of ∼1000 hybrid progenies of the two strains. We observed that newly evolved expression quantitative trait loci (eQTLs) impacted the expression of a greater number of genes than did old eQTLs, suggesting that natural selection is gradually eliminating maladaptive or slightly deleterious pleiotropic responses. Overall, our results show that, although being prevalent for new mutations, the majority of pleiotropic effects observed are evolutionarily transient, which explains how evolution proceeds despite complicated pleiotropic effects.},
}
@article {pmid39235751,
year = {2025},
author = {Lemée, P and Bridier, A},
title = {Bioinformatic Pipeline for Profiling Foodborne Bacterial Ecology and Resistome from Short-Read Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2852},
number = {},
pages = {289-309},
pmid = {39235751},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Food Microbiology/methods ; *Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Microbiota/genetics ; },
abstract = {Next-generation sequencing revolutionized food safety management these last years providing access to a huge quantity of valuable data to identify, characterize, and monitor bacterial pathogens on the food chain. Shotgun metagenomics emerged as a particularly promising approach as it enables in-depth taxonomic profiling and functional investigation of food microbial communities. In this chapter, we provide a comprehensive step-by-step bioinformatical workflow to characterize bacterial ecology and resistome composition from metagenomic short-reads obtained by shotgun sequencing.},
}
@article {pmid39233902,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Green Silver-lines, Pseudoips prasinana (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {117},
pmid = {39233902},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Pseudoips prasinana (the Green Silver-lines; Arthropoda; Insecta; Lepidoptera; Nolidae). The genome sequence is 1,125.7 megabases in span. Most of the assembly is scaffolded into 33 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,065 protein coding genes.},
}
@article {pmid39233899,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Scarlet Tiger moth, Callimorpha dominula (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {31},
pmid = {39233899},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Callimorpha dominula (the Scarlet Tiger moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 658.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.45 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,234 protein coding genes.},
}
@article {pmid39233418,
year = {2024},
author = {Li, X and Zhang, LY and Wu, C},
title = {Vegetation changes and influencing factors in different watersheds of Henan Province based on GEE and geographic detectors.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {7},
pages = {1887-1896},
doi = {10.13287/j.1001-9332.202407.021},
pmid = {39233418},
issn = {1001-9332},
mesh = {China ; *Rivers ; *Ecosystem ; *Environmental Monitoring/methods ; Conservation of Natural Resources ; Plant Development ; Geographic Information Systems ; Plants ; },
abstract = {Clarifying vegetation changes and the driving factors can provide references for ecological restoration and sustainable social development. We analyzed vegetation distribution and trend changes in Henan Province and its basin zoning (Haihe River basin zoning, Yellow River basin zoning, Huaihe River basin zoning, Yangtze River basin zoning), with fractional vegetation cover data from 2000 to 2020 based on the Google Earth Engine platform, and by combining Theil-Sen Median trend analysis, Mann-Kendall test, and Hurst index. We also utilized factor detection and factor interaction to explore the individual and mutual influences of natural and anthropogenic factors on vegetation at different scales. The results showed that the fractional vegetation cover (FVC) in Henan Province exhibited a distribution pattern of higher coverage in the south and lower in the north during the study period, predominantly characterized by moderate to high vegetation coverage. The Yangtze River basin zoning had the highest coverage. FVC in Henan Province and its zoning exhibited a consistent pattern of fluctuating upward trends, with all areas showing significant improvement. Particularly, the Yangtze River basin zoning had the largest area of improvement. According to the Hurst index, apart from the possibility of continued improvement in the Huaihe River basin zoning, other zoning would be likely to shift from improvement to degradation in the future. Vegetation changes in Henan Province and its zoning were the result of combined effects of anthropogenic and natural factors, with the influence of these factors changing over time and the dominant factors varying by region. Anthropogenic factors such as land use/cover type and nighttime lighting had a stronger impact on vegetation than natural factors like elevation, slope, and annual mean low temperature. The interaction between factors, particularly between anthropogenic and natural factors, exhibited a nonlinear enhancing pattern.},
}
@article {pmid39233066,
year = {2024},
author = {Wen, J and Chuai, X and Xiang, A and Liu, Y and Wang, T and Xu, Y and Miao, L and Zhang, L and Li, J and Zhao, R},
title = {Re-identifying farmland carbon neutrality gap under a new carbon counting and the framework of regional interactions in China.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {175996},
doi = {10.1016/j.scitotenv.2024.175996},
pmid = {39233066},
issn = {1879-1026},
abstract = {The farmland ecosystem, with its numerous material cycles and energy flows, is an important part of the carbon cycle in terrestrial ecosystems. Focusing on the carbon neutrality of farmland is meaningful for mitigating global warming and serving national low-carbon strategies. This study enriches the carbon accounting items of farmland and establishes a new research framework to check the carbon neutrality of farmland from the aspect of regional interactions and, subsequently, the inequality among China's provinces. The results revealed that there is still a great gap in the capability of China[']s farmland to reach carbon neutrality, with a gap value of up to 10,503 × 10[4] t C. All of the provinces presented net carbon emissions, and the per unit area carbon neutrality gaps showed spatial regularity decreasing from the coastal regions to the inland areas. Anthropogenic carbon emissions on farmland played a dominant role compared with soil organic carbon. Five provinces had reduced interior-regional carbon emissions through grain trade, and the amounts were especially high for developed regions, such as Guangdong, Zhejiang, Beijing, Shanghai and Jiangsu. Sixteen provinces gained external carbon emissions through trade; these were the less developed regions located mainly in the north, such as Inner Mongolia, Hebei, Jilin, Heilongjiang and Xinjiang. Under regional inequality, 15 provinces added to the net amount of the carbon emissions generated in external regions, with China's megacities adding the highest percentage, especially Beijing, with 389.95 % compared with its original emissions. Inequality showed that most provinces had a moderate status. Sichuan and Hunan experienced weak advantages, and six provinces had disadvantages. Therefore, constructing compensation and trade-based rights and responsibilities traceability mechanisms is important.},
}
@article {pmid39178313,
year = {2024},
author = {Du, J and Liu, W and Li, M and Li, Z and Li, X and Dai, Y and Liu, G and Wang, X and Zhu, P and Gladyshev, VN and Zhou, X},
title = {Comparative time-series multi-omics analyses suggest H1.2 involvement in anoxic adaptation and cancer resistance.},
journal = {PLoS biology},
volume = {22},
number = {8},
pages = {e3002778},
doi = {10.1371/journal.pbio.3002778},
pmid = {39178313},
issn = {1545-7885},
mesh = {Animals ; Mice ; *Histones/metabolism ; Humans ; Neoplasms/genetics/metabolism/pathology ; Mole Rats/genetics ; Hypoxia-Inducible Factor 1, alpha Subunit/metabolism/genetics ; Proteomics/methods ; Fibroblasts/metabolism ; Autophagy/genetics ; Adaptation, Physiological/genetics ; Transcriptome/genetics ; Cell Hypoxia/genetics ; Cell Line, Tumor ; Signal Transduction ; Multiomics ; },
abstract = {The naked mole rat (NMR), Heterocephalus glaber, is known as the longest-lived rodent and is extraordinarily resistant to hypoxia and cancer. Here, both NMR embryonic fibroblasts (NEFs) and their mouse counterparts (MEFs) were subjected to anoxic conditions (0% O2, 5% CO2). A combination of comparative transcriptomics and proteomics was then employed to identify differentially expressed genes (DEGs). Notably, we observed distinct levels of histone H1.2 (encoded by HIST1H1C) accumulation between NEFs and MEFs. Subsequent mechanistic analyses showed that higher H1.2 expression in NEFs was associated with the lower expression of its inhibitor, PARP1. Additionally, we discovered that H1.2 can directly interact with HIF-1α PAS domains, thereby promoting the expression of HIF-1α through facilitating the dimerization with HIF-1β. The overexpression of H1.2 was also found to trigger autophagy and to suppress the migration of cancer cells, as well as the formation of xenograft tumors, via the NRF2/P62 signaling pathway. Moreover, an engineered H1.2 knock-in mouse model exhibited significantly extended survival in hypoxic conditions (4% O2) and showed a reduced rate of tumor formation. Collectively, our results indicate a potential mechanistic link between H1.2 and the dual phenomena of anoxic adaptation and cancer resistance.},
}
@article {pmid39145536,
year = {2024},
author = {Pipes, L and Nielsen, R},
title = {A rapid phylogeny-based method for accurate community profiling of large-scale metabarcoding datasets.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.85794},
pmid = {39145536},
issn = {2050-084X},
support = {1R01GM138634-01/GM/NIGMS NIH HHS/United States ; 1K99GM144747-01/GM/NIGMS NIH HHS/United States ; BIO180028//Advanced Cyberinfrastructure Coordination Ecosystem: Services &amp; Support/ ; 1R01GM138634-01/GM/NIGMS NIH HHS/United States ; 1K99GM144747-01/GM/NIGMS NIH HHS/United States ; BIO180028//Pittsburgh Supercomputing Center/ ; },
mesh = {*Phylogeny ; *DNA Barcoding, Taxonomic/methods ; Computational Biology/methods ; DNA, Environmental/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Environmental DNA (eDNA) is becoming an increasingly important tool in diverse scientific fields from ecological biomonitoring to wastewater surveillance of viruses. The fundamental challenge in eDNA analyses has been the bioinformatical assignment of reads to taxonomic groups. It has long been known that full probabilistic methods for phylogenetic assignment are preferable, but unfortunately, such methods are computationally intensive and are typically inapplicable to modern next-generation sequencing data. We present a fast approximate likelihood method for phylogenetic assignment of DNA sequences. Applying the new method to several mock communities and simulated datasets, we show that it identifies more reads at both high and low taxonomic levels more accurately than other leading methods. The advantage of the method is particularly apparent in the presence of polymorphisms and/or sequencing errors and when the true species is not represented in the reference database.},
}
@article {pmid39137474,
year = {2024},
author = {Tanaka, S and Uraguchi, K and Suzuki, E and Matsumoto, N and Tsumura, M and Fujimoto, S and Miyamoto, S and Yorifuji, T and Ando, M},
title = {Survey of pharyngeal foreign bodies in Japan: An ecological study using the nationwide claims data.},
journal = {International journal of pediatric otorhinolaryngology},
volume = {184},
number = {},
pages = {112055},
doi = {10.1016/j.ijporl.2024.112055},
pmid = {39137474},
issn = {1872-8464},
mesh = {Humans ; *Foreign Bodies/epidemiology ; Japan/epidemiology ; Female ; Male ; Child ; Child, Preschool ; Adolescent ; Infant ; Adult ; *Pharynx ; Young Adult ; Feeding Behavior ; Middle Aged ; Incidence ; Databases, Factual ; Seasons ; Aged ; Sex Distribution ; Age Distribution ; },
abstract = {OBJECTIVE: Pharyngeal foreign bodies (PFBs) are a prevalent disease affected by food culture and dietary habits, with fish bones as the leading cause. Most studies were limited to specific regions, and a nationwide survey was not conducted in Japan. In this ecological study, we aimed to conduct a nationwide analysis of outpatient PFB cases in Japan over three years, focusing on seasonal trends, sex- and age-stratified cases, and regional differences.<br><br>METHODS: We used the National Database of Health Insurance Claims and Specific Health Checkups of Japan open data from April 2019 to March 2022. The case data were analyzed by month, age, sex, and prefecture. Additionally, we calculated the standardized claim ratios (SCRs) for each prefecture and investigated the association between dietary habits, food culture, and SCR of PFBs using a two-level linear regression model.<br><br>RESULTS: We analyzed a total of 164,337 outpatient PFB cases in Japan, revealing an average incidence rate of 45.6 per 100,000 persons. The seasonal trend revealed a peak in July each year from 2019 to 2021, confirming seasonality in PFB incidents. Children reported a higher incidence rate. Living west of Japan and expenditure on fish and shellfish had a strongly positive association with the SCR of PFBs.<br><br>CONCLUSION: Our nationwide survey reveals that, even within Japan, there were regional variations influenced by food culture and dietary habits. The data showed that PFB incidence was higher among children, highlighting the need for preventive education.<br><br>LEVEL OF EVIDENCE: Level 3.},
}
@article {pmid39230451,
year = {2024},
author = {Hendrix, JG and Robitaille, AL and Kusch, JM and Webber, QMR and Vander Wal, E},
title = {Faithful pals and familiar locales: differentiating social and spatial site fidelity during reproduction.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1912},
pages = {20220525},
doi = {10.1098/rstb.2022.0525},
pmid = {39230451},
issn = {1471-2970},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {Animals ; Female ; *Reproduction ; *Reindeer/physiology ; Newfoundland and Labrador ; Social Behavior ; Geographic Information Systems ; },
abstract = {Site fidelity-the tendency to reuse familiar spaces-is expected to improve fitness. Familiarity with the local environment is particularly crucial when resource demands or predation risk are high. Consequently, site fidelity often peaks during reproduction when energetic costs are high and offspring are vulnerable. For many species, the environment they experience is not solely a function of geography but also of the social environment. Social fidelity, the selection for familiar social environments, could constitute an independent or parallel strategy to spatial fidelity when considering behaviour at the spatial-social interface. Using global positioning system locations from caribou across Newfoundland, we tested whether females selected calving sites based on proximity to familiar conspecifics, in addition to geographical (spatial) fidelity. These strategies were synergistic, not alternative, and correlated across the population but more variable within individuals. We also tested whether either form of fidelity affected reproductive success. We failed to detect an effect of spatial or social fidelity on reproductive success in this population. Nevertheless, given the association between social and spatial fidelity and the demonstrated fitness consequences of site fidelity in other systems, familiar conspecifics and the potential benefits these social partners provide may be an underappreciated component driving site fidelity.This article is part of the theme issue 'The spatial-social interface: a theoretical and empirical integration'.},
}
@article {pmid39229001,
year = {2024},
author = {Obbard, DJ and , and , and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Drosophila limbata von Roser 1840.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {365},
pmid = {39229001},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Drosophila limbata (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 233.5 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 16.09 kilobases in length.},
}
@article {pmid39225619,
year = {2024},
author = {Liu, Z and Sun, Y and Li, Y and Ma, A and Willaims, NF and Jahanbahkshi, S and Hoyd, R and Wang, X and Zhang, S and Zhu, J and Xu, D and Spakowicz, D and Ma, Q and Liu, B},
title = {An Explainable Graph Neural Framework to Identify Cancer-Associated Intratumoral Microbial Communities.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2403393},
doi = {10.1002/advs.202403393},
pmid = {39225619},
issn = {2198-3844},
support = {2020YFA0712400//National Key Research and Development Program of China/ ; 62272270//National Nature Science Foundation of China/ ; 11931008//National Nature Science Foundation of China/ ; ZR2023JQ002//Shandong Provincial Natural Science Foundation for Distinguished Young Scholars/ ; },
abstract = {Microbes are extensively present among various cancer tissues and play critical roles in carcinogenesis and treatment responses. However, the underlying relationships between intratumoral microbes and tumors remain poorly understood. Here, a MIcrobial Cancer-association Analysis using a Heterogeneous graph transformer (MICAH) to identify intratumoral cancer-associated microbial communities is presented. MICAH integrates metabolic and phylogenetic relationships among microbes into a heterogeneous graph representation. It uses a graph transformer to holistically capture relationships between intratumoral microbes and cancer tissues, which improves the explainability of the associations between identified microbial communities and cancers. MICAH is applied to intratumoral bacterial data across 5 cancer types and 5 fungi datasets, and its generalizability and reproducibility are demonstrated. After experimentally testing a representative observation using a mouse model of tumor-microbe-immune interactions, a result consistent with MICAH's identified relationship is observed. Source tracking analysis reveals that the primary known contributor to a cancer-associated microbial community is the organs affected by the type of cancer. Overall, this graph neural network framework refines the number of microbes that can be used for follow-up experimental validation from thousands to tens, thereby helping to accelerate the understanding of the relationship between tumors and intratumoral microbiomes.},
}
@article {pmid39224879,
year = {2023},
author = {Boyes, D and Mulley, JF and , and , and , and , and , and , },
title = {The genome sequence of the Small Emerald, Hemistola chrysoprasaria (Esper, 1795).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {441},
pmid = {39224879},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Hemistola chrysoprasaria (the Small Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 438.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.63 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,512 protein coding genes.},
}
@article {pmid39224768,
year = {2024},
author = {Jentoft, S and Tørresen, OK and Tooming-Klunderud, A and Skage, M and Kollias, S and Jakobsen, KS and , and , and , and , and , },
title = {The genome sequence of the Atlantic cod, Gadus morhua (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {189},
pmid = {39224768},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Gadus morhua (the Atlantic cod; Chordata; Actinopteri; Gadiformes; Gadidae). The genome sequence is 669.9 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules. Gene annotation of this assembly on Ensembl identified 23,515 protein coding genes.},
}
@article {pmid39224703,
year = {2024},
author = {Shi, Y and Zhang, W and Li, L and Wu, W and Li, M and Xiao, K and Wang, K and Sheng, Z and Xie, F and Wang, X and Shi, X and Tong, Y and Xie, L},
title = {Evaluation of phage-based decontamination in respiratory intensive care unit environments using ddPCR and 16S rRNA targeted sequencing techniques.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1442062},
pmid = {39224703},
issn = {2235-2988},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Klebsiella pneumoniae/virology/genetics ; *Intensive Care Units ; *Decontamination/methods ; *Bacteriophages/genetics ; Humans ; Polymerase Chain Reaction/methods ; Cross Infection/prevention &amp; control/microbiology ; Disinfectants/pharmacology ; Klebsiella Infections/prevention &amp; control/microbiology ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Klebsiella pneumoniae is a major cause of hospital-acquired infections (HAIs), primarily spread through environmental contamination in hospitals. The effectiveness of current chemical disinfectants is waning due to emerging resistance, which poses environmental hazards and fosters new resistance in pathogens. Developing environmentally friendly and effective disinfectants against multidrug-resistant organisms is increasingly important.<br><br>METHODS: This study developed a bacteriophage cocktail targeting two common carbapenem-resistant Klebsiella pneumoniae (CRKP) strains, ST11 KL47 and ST11 KL64. The cocktail was used as an adjunctive disinfectant in a hospital's respiratory intensive care unit (RICU) via ultrasonic nebulization. Digital PCR was used to quantify CRKP levels post-intervention. The microbial community composition was analyzed via 16S rRNA sequencing to assess the intervention's impact on overall diversity.<br><br>RESULTS: The phage cocktail significantly reduced CRKP levels within the first 24 hours post-treatment. While a slight increase in pathogen levels was observed after 24 hours, they remained significantly lower than those treated with conventional disinfectants. 16S rRNA sequencing showed a decrease in the target pathogens' relative abundance, while overall species diversity remained stable, confirming that phages selectively target CRKP without disrupting ecological balance.<br><br>DISCUSSION: The findings highlight the efficacy and safety of phage-based biocleaners as a sustainable alternative to conventional disinfectants. Phages selectively reduce multidrug-resistant pathogens while preserving microbial diversity, making them a promising tool for infection control.},
}
@article {pmid39222768,
year = {2024},
author = {Yushin, N and Jakhu, R and Chaligava, O and Grozdov, D and Zinicovscaia, I},
title = {Evaluation of the potentially toxic elements and radionuclides in the soil sample of Novaya Zemlya in the Arctic Circle.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {124871},
doi = {10.1016/j.envpol.2024.124871},
pmid = {39222768},
issn = {1873-6424},
abstract = {The study presented here elucidate the concentrations of radionuclides and potentially toxic elements in the soil samples around the Novaya Zemlya in the Russian Arctic zone, determined using HPGe gamma spectrometry, inductively coupled plasma optical emission spectrometry and direct mercury analyzer. The average detected concentrations for [226]Ra, [232]Th, [40]K, [235]U and [137]Cs were 36.40, 46.06, 768, 2.06 and 4.71 Bq/kg, respectively. At many sampling sites, the concentrations of potentially toxic elements (Zn, Cu, Pb, Cd, Ni, and Cr) were higher than the natural levels. Positive Matrix Factorization analysis revealed the contribution of oil dumps (32%), natural sources (16%), bird colonies (32%) and atmospheric deposition (20%) for elevated elements content. In the case of radionuclides, the natural occurring contamination (38%) was primary source followed by dumped material (32%) and bird colonies (30%). The radiological risk from radionuclides was relatively high, yet still under permissible levels. For potentially toxic elements, Fe was predominant non-carcinogenic pollutant and Ni emerged as major carcinogenic contaminant. Keeping in view the high content of some elements, future studies are required to keep the human and ecological risk low, and to establish scientific grounds for the contribution of settled bird species. The findings of the study advance the present knowledge about the contamination of the study area and lays the path for further effort.},
}
@article {pmid39222062,
year = {2024},
author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Kurilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I},
title = {CAIM: coverage-based analysis for identification of microbiome.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {5},
pages = {},
doi = {10.1093/bib/bbae424},
pmid = {39222062},
issn = {1477-4054},
support = {P20GM125503//National Institute of General Medical Sciences of the National Institutes of Health/ ; R01CA143130/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; Computational Biology/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Software ; Algorithms ; Sequence Analysis, DNA/methods ; },
abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic approach. In this study, we developed a new bioinformatics tool, coverage-based analysis for identification of microbiome (CAIM), for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count-based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consistently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similarity of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and 44 primary liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.},
}
@article {pmid39221442,
year = {2024},
author = {Morales, HE and Norris, K and Henshaw, S and Tatayah, V and Ruhomaun, K and van Oosterhout, C and Groombridge, JJ and Gilbert, MTP and , and , and , and , },
title = {The genome sequence of the Mauritius kestrel, Falco punctatus (Temminck, 1821).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {312},
pmid = {39221442},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Falco punctatus (the Mauritius kestrel; Chordata; Aves; Falconiformes; Falconidae). The genome sequence is 1,279.3 megabases in span. Most of the assembly is scaffolded into 23 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.34 kilobases in length.},
}
@article {pmid39219129,
year = {2024},
author = {Xie, Z and Hu, D and Jiang, F and Fu, X and Li, R and Zheng, D and Zhao, L and Xu, J and Yuan, X and Bao, Y and Zhou, H and Wang, B and Wang, Q},
title = {Assessment of urban flood resilience based on the socio-ecological composite index model: a case study in Wuhua District, Kunming City, China.},
journal = {Water science and technology : a journal of the International Association on Water Pollution Research},
volume = {89},
number = {2},
pages = {252-270},
doi = {10.2166/wst.2023.413},
pmid = {39219129},
issn = {0273-1223},
mesh = {China ; *Floods ; *Cities ; Models, Theoretical ; Geographic Information Systems ; Socioeconomic Factors ; },
abstract = {Global climate change and rapid urbanization have increased the frequency of flooding, making urban flood resilience a critical objective. This article introduces a methodology for assessing urban flood resilience, utilizing a social-ecological synthesis index that integrates geographical and temporal data with Geographic Information System (GIS). The study focuses on ten administrative subdistricts in Wuhua District, Kunming City, China, and selects 18 social-ecological indicators. These indicators, chosen from social and ecological perspectives, are weighted using the entropy weight method to determine their significance in the assessment system. By combining scores for each subdistrict, the study quantifies flood resilience and creates a spatial distribution map using ArcGIS. Key findings reveal that out of the ten administrative subdistricts, five in Wuhua District, particularly in the core urban area of Kunming, demonstrate strong overall flood resilience. Influenced by social-ecological indicators, there is significant spatial differentiation in flood resilience within Wuhua District, with a decreasing trend radiating from the city center to areas farther from the urban core. The research indicates that regions with well-established transportation infrastructure, a wide distribution of government institutions, improved water management facilities, and a substantial population with higher education levels contribute significantly to enhancing urban flood resilience.},
}
@article {pmid39147186,
year = {2024},
author = {Song, J and Zhou, S and Zou, D and Kwan, MP and Cai, J and Lu, J},
title = {Non-linear associations between noise level and people's short-term noise annoyance in different activity contexts.},
journal = {Environmental research},
volume = {260},
number = {},
pages = {119772},
doi = {10.1016/j.envres.2024.119772},
pmid = {39147186},
issn = {1096-0953},
mesh = {Humans ; Male ; Female ; Adult ; *Noise/adverse effects ; Young Adult ; Ecological Momentary Assessment ; Environmental Exposure ; Middle Aged ; Noise, Transportation/adverse effects ; Geographic Information Systems ; Nonlinear Dynamics ; },
abstract = {Recent research has become increasingly interested in the on-linear associations between noise levels and people's short-term noise annoyance. However, there has been limited investigation into measuring short-term noise annoyance and how different activity contexts may affect these non-linear associations. To address this research gap, this study measured people's short-term noise annoyance using real-time Ecological Momentary Assessment (EMA) data and the Day Reconstruction Method's (DRM) recalled data. Corresponding noise levels were captured using Global Positioning Systems and portable noise sensors. Employing the Shapley additive explanations method, we examined the non-linear associations between noise level and people's real-time and recalled noise annoyance across different activity contexts. The results indicated that 1) People had greater sensitivity to noise levels in real-time annoyance (non-linear association threshold: 60 dB) compared to recalled annoyance, which had a higher non-linear association threshold of 70 dB. 2) The non-linear associations between noise level and people's real-time/recalled noise annoyance varied between different activity contexts. People tended to be more sensitive to noise in real-time annoyance than recalled annoyance on travel routes and at workplaces. 3) Among the factors examined, the contribution of noise level varied across activity contexts. Noise level contributed more significantly to people's real-time noise annoyance in outdoor recreational sites and on travel routes. These findings enhance our understanding of the non-linear association between noise level and people's short-term noise annoyance, moving beyond the linear paradigm. Policymakers should consider the non-linear relationships and different activity contexts when implementing noise control measures.},
}
@article {pmid38630866,
year = {2024},
author = {Ma, L and Hu, Z and Shen, W and Zhang, Y and Wang, G and Chang, B and Lu, J and Cui, Y and Xu, H and Feng, Y and Jin, B and Zhang, X and Wang, L and Lin, J},
title = {Three-dimensional reconstruction and multiomics analysis reveal a unique pattern of embryogenesis in Ginkgo biloba.},
journal = {Plant physiology},
volume = {196},
number = {1},
pages = {95-111},
doi = {10.1093/plphys/kiae219},
pmid = {38630866},
issn = {1532-2548},
support = {5232016//Beijing Municipal Natural Science Foundation/ ; 32000558//National Natural Science Foundation of China/ ; BLX202116//Fundamental Research Funds for the Central Universities/ ; B13007//Program of Introducing Talents of Discipline to Universities/ ; },
mesh = {*Ginkgo biloba/genetics/embryology ; *Seeds/genetics/growth &amp; development ; Imaging, Three-Dimensional/methods ; Gene Expression Regulation, Plant ; Plant Proteins/metabolism/genetics ; X-Ray Microtomography ; Cotyledon/genetics ; Multiomics ; },
abstract = {Ginkgo (Ginkgo biloba L.) is one of the earliest extant species in seed plant phylogeny. Embryo development patterns can provide fundamental evidence for the origin, evolution, and adaptation of seeds. However, the architectural and morphological dynamics during embryogenesis in G. biloba remain elusive. Herein, we obtained over 2,200 visual slices from 3 stages of embryo development using micro-computed tomography imaging with improved staining methods. Based on 3-dimensional (3D) spatiotemporal pattern analysis, we found that a shoot apical meristem with 7 highly differentiated leaf primordia, including apical and axillary leaf buds, is present in mature Ginkgo embryos. 3D rendering from the front, top, and side views showed 2 separate transport systems of tracheids located in the hypocotyl and cotyledon, representing a unique pattern of embryogenesis. Furthermore, the morphological dynamic analysis of secretory cavities indicated their strong association with cotyledons during development. In addition, we identified genes GbLBD25a (lateral organ boundaries domain 25a), GbCESA2a (cellulose synthase 2a), GbMYB74c (myeloblastosis 74c), GbPIN2 (PIN-FORMED 2) associated with vascular development regulation, and GbWRKY1 (WRKYGOK 1), GbbHLH12a (basic helix-loop-helix 12a), and GbJAZ4 (jasmonate zim-domain 4) potentially involved in the formation of secretory cavities. Moreover, we found that flavonoid accumulation in mature embryos could enhance postgerminative growth and seedling establishment in harsh environments. Our 3D spatial reconstruction technique combined with multiomics analysis opens avenues for investigating developmental architecture and molecular mechanisms during embryogenesis and lays the foundation for evolutionary studies of embryo development and maturation.},
}
@article {pmid39219859,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Ruby Tiger, Phragmatobia fuliginosa (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {124},
pmid = {39219859},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Phragmatobia fuliginosa (the Ruby Tiger; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 629.4 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,338 protein coding genes.},
}
@article {pmid39213392,
year = {2024},
author = {Du, Q and Zhang, Z and Yang, W and Zhou, X and Zhou, N and Wu, C and Bao, J},
title = {CBGDA: a manually curated resource for gene-disease associations based on genome-wide CRISPR.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
doi = {10.1093/database/baae077},
pmid = {39213392},
issn = {1758-0463},
support = {31971162 32071275 U20A20410//National Nature Science Foundation of China/ ; 31971162 32071275 U20A20410//National Nature Science Foundation of China/ ; },
mesh = {Humans ; *Databases, Genetic ; *Data Curation/methods ; Genome-Wide Association Study/methods ; Genetic Predisposition to Disease ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; CRISPR-Cas Systems ; Disease/genetics ; },
abstract = {The field of understanding the association between genes and diseases is rapidly expanding, making it challenging for researchers to keep up with the influx of new publications and genetic datasets. Fortunately, there are now several regularly updated databases available that focus on cataloging gene-disease relationships. The development of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 system has revolutionized the field of gene editing, providing a highly efficient, accurate, and reliable method for exploring gene-disease associations. However, currently, there is no resource specifically dedicated to collecting and integrating the latest experimentally supported gene-disease association data derived from genome-wide CRISPR screening. To address this gap, we have developed the CRISPR-Based Gene-Disease Associations (CBGDA) database, which includes over 200 manually curated gene-disease association data derived from genome-wide CRISPR screening studies. Through CBGDA, users can explore gene-disease association data derived from genome-wide CRISPR screening, gaining insights into the expression patterns of genes in different diseases, associated chemical data, and variant information. This provides a novel perspective on understanding the associations between genes and diseases. What is more, CBGDA integrates data from several other databases and resources, enhancing its comprehensiveness and utility. In summary, CBGDA offers a fresh perspective and comprehensive insights into the research on gene-disease associations. It fills the gap by providing a dedicated resource for accessing up-to-date, experimentally supported gene-disease association data derived from genome-wide CRISPR screening. Database URL: http://cbgda.zhounan.org/main.},
}
@article {pmid39211527,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Small Square-spot, Diarsia rubi (Vieweg, 1790).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {210},
doi = {10.12688/wellcomeopenres.19299.1},
pmid = {39211527},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Diarsia rubi (the Small Square-spot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 624.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,173 protein coding genes.},
}
@article {pmid39209853,
year = {2024},
author = {Mi, J and Jing, X and Ma, C and Yang, Y and Li, Y and Zhang, Y and Long, R and Zheng, H},
title = {Massive expansion of the pig gut virome based on global metagenomic mining.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {76},
pmid = {39209853},
issn = {2055-5008},
mesh = {Animals ; Swine ; *Virome/genetics ; *Metagenomics/methods ; *Gastrointestinal Microbiome ; *Viruses/genetics/classification/isolation &amp; purification ; *Genome, Viral ; Data Mining ; Metagenome ; Phylogeny ; },
abstract = {The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.},
}
@article {pmid39209112,
year = {2024},
author = {Ji, N and Kumar, A and Joe, W and Kuriyan, R and Sethi, V and Finkelstein, JL and Mehta, S},
title = {Prevalence and Correlates of Double and Triple Burden of Malnutrition Among Children and Adolescents in India: Comprehensive National Nutrition Survey.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2024.08.021},
pmid = {39209112},
issn = {1541-6100},
abstract = {BACKGROUND: Limited information on the co-prevalence of undernutrition, micronutrient deficiencies, overnutrition, and abnormal levels of noncommunicable disease biomarkers at the same time in children and adolescents in India hinders efforts to comprehensively address their health. This study aims to examine the prevalence and correlates of double and triple burden of malnutrition (DBM, TBM) among children and adolescents (5-19 y) to inform policies and programs.<br><br>METHODS: A total of 17,599 children (5-9 y) and 16,184 adolescents (10-19 y) with available biomarker data from the Comprehensive National Nutrition Survey were included. Malnutrition was defined based on either undernutrition based on anthropometry, overnutrition/abnormal metabolic markers, and anemia/micronutrient deficiency. DBM was defined as the coexistence of any two forms of malnutrition. DBM+ was defined as the coexistence of undernutrition and/or micronutrient deficiency along with overnutrition. TBM was defined as having the coexistence of all three forms of malnutrition. The prevalence of DBM, DBM+ and TBM was estimated accounting for probabilistic selection. We used mixed effects binomial regression to determine correlates of DBM/TBM in children and adolescents separately.<br><br>RESULTS: The prevalence of DBM, DBM+ and TBM was 50.8%, 37.2%, and 14.4%, respectively, in children, and 53.4%, 36.1%, and 12.7%, respectively, in adolescents. The prevalence of DBM+ was significantly higher in children girls compared to boys. In children, being in a disadvantaged caste group, having a lower wealth index, having inadequate diet diversity, having no maternal schooling and having a recent history of acute illness were associated with DBM. In adolescents, being in a disadvantaged caste group, maternal occupation, and lower paternal age were correlated with DBM. A similar set of variables was associated with TBM in both age groups.<br><br>CONCLUSION: The prevalence of DBM and TBM is substantial in children and adolescents in India and varies across states. Socioeconomic factors and acute illness were the main correlates for DBM and TBM.},
}
@article {pmid39208288,
year = {2024},
author = {Ishigohoka, J and Bascón-Cardozo, K and Bours, A and Fuß, J and Rhie, A and Mountcastle, J and Haase, B and Chow, W and Collins, J and Howe, K and Uliano-Silva, M and Fedrigo, O and Jarvis, ED and Pérez-Tris, J and Illera, JC and Liedvogel, M},
title = {Distinct patterns of genetic variation at low-recombining genomic regions represent haplotype structure.},
journal = {Evolution; international journal of organic evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/evolut/qpae117},
pmid = {39208288},
issn = {1558-5646},
abstract = {Genomic regions sometimes show patterns of genetic variation distinct from the genome-wide population structure. Such deviations have often been interpreted to represent effects of selection. However, systematic investigation of whether and how non-selective factors, such as recombination rates, can affect distinct patterns has been limited. Here, we associate distinct patterns of genetic variation with reduced recombination rates in a songbird, the Eurasian blackcap (Sylvia atricapilla), using a new reference genome assembly, whole-genome resequenc- ing data and recombination maps. We find that distinct patterns of genetic variation reflect haplotype structure at genomic regions with different prevalence of reduced recombination rate across populations. At low-recombining regions shared in most populations, distinct patterns reflect conspicuous haplotypes segregating in multiple populations. At low-recombining regions found only in a few populations, distinct patterns represent variance among cryptic haplotypes within the low-recombining populations. With simulations, we confirm that these distinct patterns evolve neutrally by reduced recombination rate, on which the effects of selection can be overlaid. Our results highlight that distinct patterns of genetic variation can emerge through evolutionary reduction of local recombination rate. The recombination landscape as an evolvable trait therefore plays an important role determining the heterogeneous distribution of genetic variation along the genome.},
}
@article {pmid39208193,
year = {2024},
author = {Naser, AY},
title = {Insights into hospitalization pattern for drug, medicament, and biological substance poisoning, adverse effect, and underdosing in Australia: An ecological study between 1998 and 2019.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0309362},
doi = {10.1371/journal.pone.0309362},
pmid = {39208193},
issn = {1932-6203},
mesh = {Humans ; *Hospitalization/statistics &amp; numerical data/trends ; Australia/epidemiology ; Female ; Male ; Adult ; Middle Aged ; Adolescent ; Aged ; Child ; Young Adult ; Poisoning/epidemiology ; Child, Preschool ; Infant ; Drug-Related Side Effects and Adverse Reactions/epidemiology ; Aged, 80 and over ; Databases, Factual ; },
abstract = {BACKGROUND: Drug, medicament, and biological substance poisoning, adverse effects, and underdosing are significant public health concerns. Gaining insight into the patterns and trends in hospitalizations caused by these occurrences is essential for the development of preventative initiatives, optimization of treatment regimens, and improvement of patient safety. The aim of this study is to examine the trend of hospitalisation related to poisoning by, adverse effect of and underdosing of drugs, medicaments and biological substances in Australia between 1998 and 2019.<br><br>METHODS: This is an ecological descriptive study that examined hospitalisation related to poisoning by, adverse effect of and underdosing of drugs, medicaments and biological substances in Australia between 1998 and 2019. A nationwide hospital admissions database was used for this study.<br><br>RESULTS: Between 1998 and 2019, a total of 683,869 hospital admission episodes were recorded in Australia. The overall annual number of hospital admissions for various reasons increased by 20.5% from 29,854 in 1998 to 35,960 in 2019, representing a decrease in hospital admission rate of 10.6% [from 158.69 (95% CI 156.90-160.49) in 1998 to 141.91 (95% CI 140.44-143.37) in 2019 per 100,000 persons, trend test, p<0.05]. Overnight-stay admissions accounted for 69.2% of the total number of hospital admissions, and 30.8% were same-day admissions. Rates of same-day hospital admission decreased by 13.3% [from 50.55 (95%CI 49.54-51.57) in 1998 to 43.81 (95%CI 43.00-44.63) in 2019 per 100,000 persons]. Rates of overnight-stay hospital admission decreased by 11.1% [from 108.14 (95%CI 106.66-109.63) in 1998 to 96.17 (95%CI 94.96-97.38) in 2019 per 100,000 persons]. Admissions related to antiepileptic, sedative-hypnotic and antiparkinsonism drugs was the most prevalent hospital admissions type accounting for 26.8%. Females were responsible for 418,751 hospital admission episodes, representing 61.5% of the total number of hospital admission.<br><br>CONCLUSION: This study found that while the overall annual number of admissions increased, the rate of admission decreased over the same period. The most common reasons for admissions were antiepileptic, sedative-hypnotic, and anti-parkinsonism drugs. The study also noted increases in admissions related to anaesthetics, therapeutic gases, hormones, and their synthetic substitutes. These findings suggest a concerning rise in the suboptimal use of these medications. In order to combat the increasing incidence of this type of admissions, it is imperative to strengthen public awareness initiatives on medicine safety and abuse.},
}
@article {pmid39205176,
year = {2024},
author = {Vanslembrouck, A and Jansen, S and De Witte, J and Janssens, C and Vereecken, S and Helms, M and Lange, U and Lühken, R and Schmidt-Chanasit, J and Heitmann, A and Müller, R},
title = {Larval Competition between Aedes and Culex Mosquitoes Carries over to Higher Arboviral Infection during Their Adult Stage.},
journal = {Viruses},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/v16081202},
pmid = {39205176},
issn = {1999-4915},
support = {G0G2319N//BiodivERsA/ ; CA17108//European Cooperation in Science and Technology/ ; 653316//European Union's Horizon 2020 research and innovation program/ ; Dubois-Brigu&#xe9; scholarship//Doctor Albert Dubois Foundation for tropical pathology/ ; },
mesh = {Animals ; *Culex/virology/growth &amp; development ; *Aedes/virology/growth &amp; development/physiology ; *Larva/virology ; *Mosquito Vectors/virology/growth &amp; development ; Arbovirus Infections/transmission/virology ; Arboviruses/physiology ; West Nile virus/physiology ; Female ; Chikungunya virus/physiology ; Encephalitis Virus, Japanese/physiology ; },
abstract = {The common house mosquito (Culex pipiens) is a native vector for West Nile virus (WNV). Invasive species like the tiger mosquito (Aedes albopictus) and Asian bush mosquito (Aedes japonicus) are rapidly spreading through Europe, posing a major threat as vectors for dengue, chikungunya (CHIKV), and Japanese encephalitis virus (JEV). These mosquitoes share a similar ecological niche as larvae, but the carry-over effects of aquatic larval interactions to the terrestrial adult stage remain largely unknown and their medical relevance requires further investigation. This study examines the context dependency of larval interactions among Aedes albopictus, Aedes japonicus, and Culex pipiens. The survival, development time, growth, and energetic storage were measured in different European populations within density-response (intraspecific) experiments and replacement (interspecific) experiments at 20 °C and 26 °C. Overall, Ae. japonicus was the weakest competitor, while competition between Ae. albopictus and Cx. pipiens varied with temperature. Adults emerging from this larval competition were infected as follows: Culex pipiens with WNV, Ae. albopictus with CHIKV, and Ae. japonicus with JEV. While no JEV infection was observed, mosquitoes experiencing interspecific interactions during their larval stages exhibited higher infection rates and viral RNA titers for CHIKV and WNV. This increased susceptibility to viral infection after larval competition suggests a higher risk of arbovirus transmission in co-occurring populations.},
}
@article {pmid39202353,
year = {2024},
author = {Maltseva, PY and Plotnitskaya, NA and Krivoruchko, AV and Beletskiy, AV and Rakitin, AL and Mardanov, AV and Ivshina, IB},
title = {Bioinformatics Analysis of the Genome of Rhodococcus rhodochrous IEGM 1362, an (-)-Isopulegol Biotransformer.},
journal = {Genes},
volume = {15},
number = {8},
pages = {},
doi = {10.3390/genes15080992},
pmid = {39202353},
issn = {2073-4425},
support = {24-14-20015//the Russian Science Foundation/ ; },
mesh = {*Rhodococcus/genetics/metabolism ; *Genome, Bacterial ; *Computational Biology/methods ; *Biotransformation/genetics ; Cytochrome P-450 Enzyme System/genetics/metabolism ; Monoterpenes/metabolism ; },
abstract = {A genome of Rhodococcus rhodochrous IEGM 1362 was sequenced and annotated. This strain can transform monoterpene alcohol (-)-isopulegol with the formation of two novel pharmacologically promising metabolites. Nine genes encoding cytochrome P450, presumably involved in (-)-isopulegol transformation, were found in the genome of R. rhodochrous IEGM 1362. Primers and PCR conditions for their detection were selected. The obtained data can be used for the further investigation of genes encoding enzymes involved in monoterpene biotransformation.},
}
@article {pmid39202178,
year = {2024},
author = {de Llanza Varona, M and Martínez, M},
title = {Synergy Makes Direct Perception Inefficient.},
journal = {Entropy (Basel, Switzerland)},
volume = {26},
number = {8},
pages = {},
doi = {10.3390/e26080708},
pmid = {39202178},
issn = {1099-4300},
support = {PID2021-127046NA-I00//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; CEX2021-001169-M MCIN/AEI/10.13039/501100011033)//Ministerio de Ciencia, Innovaci&#xf3;n y Universidades/ ; 2021-SGR-00276//Government of Catalonia/ ; },
abstract = {A typical claim in anti-representationalist approaches to cognition such as ecological psychology or radical embodied cognitive science is that ecological information is sufficient for guiding behavior. According to this view, affordances are immediately perceptually available to the agent (in the so-called "ambient energy array"), so sensory data does not require much further inner processing. As a consequence, mental representations are explanatorily idle: perception is immediate and direct. Here we offer one way to formalize this direct-perception claim and identify some important limits to it. We argue that the claim should be read as saying that successful behavior just implies picking out affordance-related information from the ambient energy array. By relying on the Partial Information Decomposition framework, and more concretely on its development of the notion of synergy, we show that in multimodal perception, where various energy arrays carry affordance-related information, the "just pick out affordance-related information" approach is very inefficient, as it is bound to miss all synergistic components. Efficient multimodal information combination requires transmitting sensory-specific (and not affordance-specific) information to wherever it is that the various information streams are combined. The upshot is that some amount of computation is necessary for efficient affordance reconstruction.},
}
@article {pmid39198944,
year = {2024},
author = {Wang, HT and Li, HY and Lu, QW and He, SL},
title = {[Determination of eight neonicotinoid pesticides in wastewater by solid phase extraction combined with liquid chromatography-tandem mass spectrometry].},
journal = {Se pu = Chinese journal of chromatography},
volume = {42},
number = {9},
pages = {856-865},
doi = {10.3724/SP.J.1123.2023.11010},
pmid = {39198944},
issn = {1872-2059},
mesh = {*Tandem Mass Spectrometry/methods ; *Solid Phase Extraction/methods ; *Wastewater/chemistry/analysis ; *Neonicotinoids/analysis ; *Water Pollutants, Chemical/analysis ; Chromatography, Liquid/methods ; *Nitro Compounds/analysis ; Thiamethoxam/analysis ; Guanidines/analysis ; Thiazoles/analysis ; Pesticides/analysis ; Thiazines/analysis ; Oxazines/analysis ; },
abstract = {Neonicotinoid pesticides are a relatively new class of pesticides that have garnered significant attention owing to their potential ecological risks to nontarget organisms. A method combining solid phase extraction with liquid chromatography-tandem mass spectrometry (SPE-LC-MS/MS) was developed for the rapid and accurate detection of eight neonicotinoid pesticides (dinotefuran, E-nitenpyram, thiamethoxam, clothianidin, imidacloprid, imidaclothiz, acetamiprid, and thiacloprid) in wastewater. The chromatographic mobile phase and MS parameters were selected, and a single-factor method was used to determine the optimal column type, extraction volume, sample loading speed, and pH for SPE. The optimal parameters were as follows: column type, HLB column (500 mg/6 mL); sample extraction volume, 500 mL; sample loading speed, 10 mL/min; and sample pH, 6-8. The matrix effects of the wastewater samples were reduced by optimizing the chromatographic gradient-elution program, examining the dilution factor of the samples, and using the isotope internal standard calibration method. Prior to analysis, the wastewater samples were diluted 5-fold with ultrapure water for pretreatment. Subsequently, 2 mmol/L ammonium acetate aqueous solution containing 0.1% (v/v) formic acid and methanol was used as mobile phases for gradient elution on a ZORBAX Eclipse Plus C18 column (100 mm×2.1 mm, 1.8 μm). The samples were quantified using positive-ion multiple reaction monitoring (MRM) mode for 10 min. Imidacloprid-d4 was used as the isotope internal standard. The SPE process was further optimized by applying response surface methodology to select the type and mass of rinsing and elution solvents. The optimal pretreatment of the SPE column included rinsing with 10% methanol aqueous solution and elution with methanol-acetonitrile (1∶1, v/v) mixture (7 mL). The eight neonicotinoid pesticides showed satisfactory linearity within the relevant range, with linear correlation coefficients (r) all greater than 0.9990. The method detection limits (MDLs) ranged from 0.2 to 1.2 ng/L, and the method quantification limits (MQLs) ranged from 0.8 to 4.8 ng/L. The average recoveries of the eight neonicotinoid pesticides were in the range of 82.6%-94.2% at three spiked levels, with relative standard deviations (RSDs) ranging from 3.9% to 9.4%. Finally, the optimized method was successfully applied to analyze wastewater samples collected from four sewage treatment plants. The results indicated that the eight neonicotinoid pesticides could be generally detected at concentrations ranging from not detected (ND) to 256 ng/L. The developed method has a low MDL and high accuracy, rendering it a suitable choice for the trace detection of the eight neonicotinoid pesticides in wastewater when compared with other similar methods. The proposed method can be utilized to monitor the environmental impact and assess the potential risks of neonicotinoid pesticides in wastewater, thus promoting the protection of nontarget organisms and the sustainable use of these pesticides in agriculture.},
}
@article {pmid39198489,
year = {2024},
author = {Chanda, MM and Campbell, L and Walke, H and Salzer, JS and Hemadri, D and Patil, SS and Purse, BV and Shivachandra, SB},
title = {A thirty-year time series analyses identifies coherence between oscillations in Anthrax outbreaks and El Niño in Karnataka, India.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {19928},
pmid = {39198489},
issn = {2045-2322},
mesh = {*Anthrax/epidemiology ; India/epidemiology ; *Disease Outbreaks ; Animals ; *El Nino-Southern Oscillation ; Bayes Theorem ; Bacillus anthracis/isolation &amp; purification/pathogenicity ; Humans ; Livestock/microbiology ; },
abstract = {Anthrax is an economically important zoonotic disease affecting both livestock and humans. The disease is caused by a spore forming bacterium, Bacillus anthracis, and is considered endemic to the state of Karnataka, India. It is critical to quantify the role of climatic factors in determining the temporal pattern of anthrax outbreaks, so that reliable forecasting models can be developed. These models will aid in establishing public health surveillance and guide strategic vaccination programs, which will reduce the economic loss to farmers, and prevent the spill-over of anthrax from livestock to humans. In this study, correlation and coherence between time series of anthrax outbreaks in livestock (1987-2016) and meteorological variables and Sea Surface Temperature anomalies (SST) were identified using a combination of cross-correlation analyses, spectral analyses (wavelets and empirical mode decomposition) and further quantified using a Bayesian time series regression model accounting for temporal autocorrelation. Monthly numbers of anthrax outbreaks were positively associated with a lagged effect of rainfall and wet day frequency. Long-term periodicity in anthrax outbreaks (approximately 6-8 years) was coherent with the periodicity in SST anomalies and outbreak numbers increased with decrease in SST anomalies. These findings will be useful in planning long-term anthrax prevention and control strategies in Karnataka state of India.},
}
@article {pmid39116194,
year = {2024},
author = {Guseva, K and Mohrlok, M and Alteio, L and Schmidt, H and Pollak, S and Kaiser, C},
title = {Bacteria face trade-offs in the decomposition of complex biopolymers.},
journal = {PLoS computational biology},
volume = {20},
number = {8},
pages = {e1012320},
pmid = {39116194},
issn = {1553-7358},
mesh = {Biopolymers/metabolism/chemistry ; *Bacteria/metabolism/enzymology ; Models, Biological ; Computational Biology ; },
abstract = {Although depolymerization of complex carbohydrates is a growth-limiting bottleneck for microbial decomposers, we still lack understanding about how the production of different types of extracellular enzymes affect individual microbes and in turn the performance of whole decomposer communities. In this work we use a theoretical model to evaluate the potential trade-offs faced by microorganisms in biopolymer decomposition which arise due to the varied biochemistry of different depolymerizing enzyme classes. We specifically consider two broad classes of depolymerizing extracellular enzymes, which are widespread across microbial taxa: exo-enzymes that cleave small units from the ends of polymer chains and endo-enzymes that act at random positions generating degradation products of varied sizes. Our results demonstrate a fundamental trade-off in the production of these enzymes, which is independent of system's complexity and which appears solely from the intrinsically different temporal depolymerization dynamics. As a consequence, specialists that produce either exo- or only endo-enzymes limit their growth to high or low substrate conditions, respectively. Conversely, generalists that produce both enzymes in an optimal ratio expand their niche and benefit from the synergy between the two enzymes. Finally, our results show that, in spatially-explicit environments, consortia composed of endo- and exo-specialists can only exist under oligotrophic conditions. In summary, our analysis demonstrates that the (evolutionary or ecological) selection of a depolymerization pathway will affect microbial fitness under low or high substrate conditions, with impacts on the ecological dynamics of microbial communities. It provides a possible explanation why many polysaccharide degraders in nature show the genetic potential to produce both of these enzyme classes.},
}
@article {pmid39004446,
year = {2024},
author = {Fummey, E and Navarro, P and Plazzer, JP and Frayling, IM and Knott, S and Tenesa, A},
title = {Estimating cancer risk in carriers of Lynch syndrome variants in UK Biobank.},
journal = {Journal of medical genetics},
volume = {61},
number = {9},
pages = {861-869},
doi = {10.1136/jmg-2023-109791},
pmid = {39004446},
issn = {1468-6244},
mesh = {Humans ; *Colorectal Neoplasms, Hereditary Nonpolyposis/genetics/epidemiology ; Female ; United Kingdom/epidemiology ; Male ; *Biological Specimen Banks ; Middle Aged ; *DNA Mismatch Repair/genetics ; *Genetic Predisposition to Disease ; Aged ; Heterozygote ; Exome Sequencing ; Incidence ; Adult ; Breast Neoplasms/genetics/epidemiology ; Endometrial Neoplasms/genetics/epidemiology ; DNA-Binding Proteins/genetics ; MutL Protein Homolog 1/genetics ; UK Biobank ; MutS Homolog 2 Protein ; },
abstract = {UNLABELLED: BackgroundLynch syndrome (LS) is an inherited cancer predisposition syndrome caused by genetic variants affecting DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6 and PMS2 Cancer risk in LS is estimated from cohorts of individuals ascertained by individual or family history of cancer, which may upwardly bias estimates.<br><br>METHODS: 830 carriers of pathogenic or likely pathogenic (path_MMR) MMR gene variants classified by InSiGHT were identified in 454&#x2009;756 UK Biobank (UKB) participants using whole-exome sequence. Nelson-Aalen survival analysis was used to estimate cumulative incidence of colorectal, endometrial and breast cancer (BC).<br><br>RESULTS: Cumulative incidence of colorectal and endometrial cancer (EC) by age 70 years was elevated in path_MMR carriers compared with non-carriers (colorectal: 11.8% (95% confidence interval (CI): 9.5% to 14.6%) vs 1.7% (95% CI: 1.6% to 1.7%), endometrial: 13.4% (95% CI: 10.2% to 17.6%) vs 1.0% (95% CI: 0.9% to 1.0%)), but the magnitude of this increase differed between genes. Cumulative BC incidence by age 70 years was not elevated in path_MMR carriers compared with non-carriers (8.9% (95% CI: 6.3% to 12.4%) vs 7.5% (95% CI: 7.4% to 7.6%)). Cumulative cancer incidence estimates in UKB were similar to estimates from the Prospective Lynch Syndrome Database for all genes and cancers, except there was no evidence for elevated EC risk in carriers of pathogenic PMS2 variants in UKB.<br><br>CONCLUSION: These results support offering incidentally identified carriers of any path_MMR surveillance to manage colorectal cancer risk. Incidentally identified carriers of pathogenic variants in MLH1, MSH2 and MSH6 would also benefit from interventions to reduce EC risk. The results suggest that BC is not an LS-related cancer.},
}
@article {pmid38917931,
year = {2024},
author = {Wang, H and Li, Y and Huang, G and Ma, Y and Zhang, Q and Li, Y},
title = {Analyzing variation of water inflow to inland lakes under climate change: Integrating deep learning and time series data mining.},
journal = {Environmental research},
volume = {259},
number = {},
pages = {119478},
doi = {10.1016/j.envres.2024.119478},
pmid = {38917931},
issn = {1096-0953},
mesh = {*Lakes/chemistry ; *Climate Change ; *Deep Learning ; Data Mining ; Environmental Monitoring/methods ; },
abstract = {The alarming depletion of global inland lakes in recent decades makes it essential to predict water inflow from rivers to lakes (WIRL) trend and unveil the dominant influencing driver, particularly in the context of climate change. The raw time series data contains multiple components (i.e., long-term trend, seasonal periodicity, and random noise), which makes it challenging for traditional machine/deep learning techniques to effectively capture long-term trend information. In this study, a novel FactorConvSTLnet (FCS) method is developed through integrating STL decomposition, convolutional neural networks (CNN), and factorial analysis into a general framework. FCS is more robust in long-term WIRL trend prediction through separating trend information as a modeling predictor, as well as unveiling predominant drivers. FCS is applied to typical inland lakes (the Aral Sea and the Lake Balkhash) in Central Asia, and results indicate that FCS (Nash-Sutcliffe efficiency = 0.88, root mean squared error = 67m[3]/s, mean relative error = 10%) outperforms the traditional CNN. Some main findings are: (i) during 1960-1990, reservoir water storage (WSR) was the dominant driver for the two lakes, respectively contributing to 71% and 49%; during 1991-2014 and 2015-2099, evaporation (EVAP) would be the dominant driver, with the contribution of 30% and 47%; (ii) climate change would shift the dominant driver from human activities to natural factors, where EVAP and surface snow amount (SNW) have an increasing influence on WIRL; (iii) compared to SSP1-2.6, the SNW contribution would decrease by 26% under SSP5-8.5, while the EVAP contribution would increase by 9%. The findings reveal the main drivers of shrinkage of the inland lakes and provide the scientific basis for promoting regional ecological sustainability.},
}
@article {pmid39196880,
year = {2024},
author = {Tsigeman, E and Zemliak, V and Likhanov, M and Papageorgiou, KA and Kovas, Y},
title = {AI can see you: Machiavellianism and extraversion are reflected in eye-movements.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0308631},
doi = {10.1371/journal.pone.0308631},
pmid = {39196880},
issn = {1932-6203},
mesh = {Humans ; *Eye Movements/physiology ; Male ; Female ; Adolescent ; *Extraversion, Psychological ; *Machine Learning ; *Machiavellianism ; Surveys and Questionnaires ; Algorithms ; Personality/physiology ; Eye-Tracking Technology ; },
abstract = {INTRODUCTION: Recent studies showed an association between personality traits and individual patterns of visual behaviour in laboratory and other settings. The current study extends previous research by measuring multiple personality traits in natural settings; and by comparing accuracy of prediction of multiple machine learning algorithms.<br><br>METHODS: Adolescent participants (N = 35) completed personality questionnaires (Big Five Inventory and Short Dark Triad Questionnaire) and visited an interactive museum while their eye movements were recorded with head-mounted eye tracking. To predict personality traits the eye-movement data was analysed using eight machine-learning methods: Random Forest, Adaboost, Naive Bayes, Support Vector Machine, Logistic Regression, k Nearest Neighbours, Decision Tree and a three-layer Perceptron.<br><br>RESULTS AND DISCUSSION: Extracted eye movement features introduced to machine learning algorithms predicted personality traits with above 33% chance accuracy (34%-48%). This result is comparable to previous ecologically valid studies, but lower than in laboratory-based research. Better prediction was achieved for Machiavellianism and Extraversion compared to other traits (10 and 9 predictions above the chance level by different algorithms from different parts of the recording). Conscientiousness, Narcissism and Psychopathy were not reliably predicted from eye movements. These differences in predictability across traits might be explained by differential activation of different traits in different situations, such as new vs. familiar, exciting vs. boring, and complex vs. simple settings. In turn, different machine learning approaches seem to be better at capturing specific gaze patterns (e.g. saccades), associated with specific traits evoked by the situation. Further research is needed to gain better insights into trait-situation-algorithm interactions.},
}
@article {pmid39193916,
year = {2024},
author = {Spöri, Y and Flot, JF},
title = {Haxe as a Swiss knife for bioinformatic applications: the SeqPHASE case story.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {5},
pages = {},
doi = {10.1093/bib/bbae367},
pmid = {39193916},
issn = {1477-4054},
support = {T.0078.23//Fonds de la Recherche Scientifique - FNRS/ ; },
mesh = {*Computational Biology/methods ; *Programming Languages ; *Software ; },
abstract = {Haxe is a general purpose, object-oriented programming language supporting syntactic macros. The Haxe compiler is well known for its ability to translate the source code of Haxe programs into the source code of a variety of other programming languages including Java, C++, JavaScript, and Python. Although Haxe is more and more used for a variety of purposes, including games, it has not yet attracted much attention from bioinformaticians. This is surprising, as Haxe allows generating different versions of the same program (e.g. a graphical user interface version in JavaScript running in a web browser for beginners and a command-line version in C++ or Python for increased performance) while maintaining a single code, a feature that should be of interest for many bioinformatic applications. To demonstrate the usefulness of Haxe in bioinformatics, we present here the case story of the program SeqPHASE, written originally in Perl (with a CGI version running on a server) and published in 2010. As Perl+CGI is not desirable anymore for security purposes, we decided to rewrite the SeqPHASE program in Haxe and to host it at Github Pages (https://eeg-ebe.github.io/SeqPHASE), thereby alleviating the need to configure and maintain a dedicated server. Using SeqPHASE as an example, we discuss the advantages and disadvantages of Haxe's source code conversion functionality when it comes to implementing bioinformatic software.},
}
@article {pmid39193399,
year = {2024},
author = {Boyes, D and Crowley, LM and Hutchinson, F and Wawman, DC and , and , and , and , and , and , and , },
title = {The genome sequence of the Lesser Yellow Underwing, Noctua comes Hübner, 1813.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {200},
doi = {10.12688/wellcomeopenres.21223.1},
pmid = {39193399},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Noctua comes (the Lesser Yellow Underwing; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 540.7 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,001 protein coding genes.},
}
@article {pmid39193313,
year = {2024},
author = {Kang, B and Ma, J and Jeong, I and Yoon, S and Kim, JI and Heo, SJ and Oh, SS},
title = {Behavioral marker-based predictive modeling of functional status for older adults with subjective cognitive decline and mild cognitive impairment: Study protocol.},
journal = {Digital health},
volume = {10},
number = {},
pages = {20552076241269555},
doi = {10.1177/20552076241269555},
pmid = {39193313},
issn = {2055-2076},
abstract = {OBJECTIVE: This study describes a research protocol for a behavioral marker-based predictive model that examines the functional status of older adults with subjective cognitive decline and mild cognitive impairment.<br><br>METHODS: A total of 130 older adults aged &#x2265;65 years with subjective cognitive decline or mild cognitive impairment will be recruited from the Dementia Relief Centers or the Community Service Centers. Data on behavioral and psychosocial markers (e.g. physical activity, mobility, sleep/wake patterns, social interaction, and mild behavioral impairment) will be collected using passive wearable actigraphy, in-person questionnaires, and smartphone-based ecological momentary assessments. Two follow-up assessments will be performed at 12 and 24 months after baseline. Mixed-effect machine learning models: MErf, MEgbm, MEmod, and MEctree, and standard machine learning models without random effects [random forest, gradient boosting machine] will be employed in our analyses to predict functional status over time.<br><br>RESULTS: The results of this study will be fundamental for developing tailored digital interventions that apply deep learning techniques to behavioral data to predict, identify, and aid in the management of functional decline in older adults with subjective cognitive decline and mild cognitive impairment. These older adults are considered the optimal target population for preventive interventions and will benefit from such tailored strategies.<br><br>CONCLUSIONS: Our study will contribute to the development of self-care interventions that utilize behavioral data and machine learning techniques to provide automated analyses of the functional decline of older adults who are at risk for dementia.},
}
@article {pmid39193090,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Small Angle Shades, Euplexia lucipara (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {509},
doi = {10.12688/wellcomeopenres.20242.1},
pmid = {39193090},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Euplexia lucipara (the Small Angle Shades; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 661.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.37 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,395 protein coding genes.},
}
@article {pmid39192185,
year = {2024},
author = {Donthu, R and Marcelino, JAP and Giordano, R and Tao, Y and Weber, E and Avalos, A and Band, M and Akraiko, T and Chen, SC and Reyes, MP and Hao, H and Ortiz-Alvarado, Y and Cuff, CA and Claudio, EP and Soto-Adames, F and Smith-Pardo, AH and Meikle, WG and Evans, JD and Giray, T and Abdelkader, FB and Allsopp, M and Ball, D and Morgado, SB and Barjadze, S and Correa-Benitez, A and Chakir, A and Báez, DR and Chavez, NHM and Dalmon, A and Douglas, AB and Fraccica, C and Fernández-Marín, H and Galindo-Cardona, A and Guzman-Novoa, E and Horsburgh, R and Kence, M and Kilonzo, J and Kükrer, M and Le Conte, Y and Mazzeo, G and Mota, F and Muli, E and Oskay, D and Ruiz-Martínez, JA and Oliveri, E and Pichkhaia, I and Romane, A and Sanchez, CG and Sikombwa, E and Satta, A and Scannapieco, AA and Stanford, B and Soroker, V and Velarde, RA and Vercelli, M and Huang, Z},
title = {HBeeID: a molecular tool that identifies honey bee subspecies from different geographic populations.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {278},
pmid = {39192185},
issn = {1471-2105},
support = {PRSTRT # 2020-00081//Puerto Rico Science, Technology and Research Trust, United States of America/ ; PRSTRT # 2020-00081//Puerto Rico Science, Technology and Research Trust, United States of America/ ; USDA-APHIS #AP20PPQS &amp; T00C009//United States Dept. of Agriculture - Animal and Plant Health Inspection Service (APHIS), United States of America/ ; USDA-APHIS #AP20PPQS &amp; T00C009//United States Dept. of Agriculture - Animal and Plant Health Inspection Service (APHIS), United States of America/ ; NSF-OISE #1545803//National Science Foundation, United States of America/ ; },
mesh = {Bees/genetics/classification ; Animals ; *Polymorphism, Single Nucleotide/genetics ; Genomics/methods ; },
abstract = {BACKGROUND: Honey bees are the principal commercial pollinators. Along with other arthropods, they are increasingly under threat from anthropogenic factors such as the incursion of invasive honey bee subspecies, pathogens and parasites. Better tools are needed to identify bee subspecies. Genomic data for economic and ecologically important organisms is increasing, but in its basic form its practical application to address ecological problems is limited.<br><br>RESULTS: We introduce HBeeID a means to identify honey bees. The tool utilizes a knowledge-based network and diagnostic SNPs identified by discriminant analysis of principle components and hierarchical agglomerative clustering. Tests of HBeeID showed that it identifies African, Americas-Africanized, Asian, and European honey bees with a high degree of certainty even when samples lack the full 272 SNPs of HBeeID. Its prediction capacity decreases with highly admixed samples.<br><br>CONCLUSION: HBeeID is a high-resolution genomic, SNP based tool, that can be used to identify honey bees and screen species that are invasive. Its flexible design allows for future improvements via sample data additions from other localities.},
}
@article {pmid39184546,
year = {2024},
author = {Yuan, H and Mancuso, CA and Johnson, K and Braasch, I and Krishnan, A},
title = {Computational strategies for cross-species knowledge transfer and translational biomedicine.},
journal = {ArXiv},
volume = {},
number = {},
pages = {},
pmid = {39184546},
issn = {2331-8422},
support = {R01 OD011116/OD/NIH HHS/United States ; R35 GM128765/GM/NIGMS NIH HHS/United States ; },
abstract = {Research organisms provide invaluable insights into human biology and diseases, serving as essential tools for functional experiments, disease modeling, and drug testing. However, evolutionary divergence between humans and research organisms hinders effective knowledge transfer across species. Here, we review state-of-the-art methods for computationally transferring knowledge across species, primarily focusing on methods that utilize transcriptome data and/or molecular networks. We introduce the term "agnology" to describe the functional equivalence of molecular components regardless of evolutionary origin, as this concept is becoming pervasive in integrative data-driven models where the role of evolutionary origin can become unclear. Our review addresses four key areas of information and knowledge transfer across species: (1) transferring disease and gene annotation knowledge, (2) identifying agnologous molecular components, (3) inferring equivalent perturbed genes or gene sets, and (4) identifying agnologous cell types. We conclude with an outlook on future directions and several key challenges that remain in cross-species knowledge transfer.},
}
@article {pmid39188222,
year = {2024},
author = {Koracevic, G and Stojanovic, M and Zdravkovic, M and Lovic, D and Simic, D and Mladenovic, K},
title = {Proposal of a Modified Classification of Hypertensive Crises: Urgency, Impending Emergency, and Emergency.},
journal = {Current vascular pharmacology},
volume = {22},
number = {3},
pages = {180-186},
pmid = {39188222},
issn = {1875-6212},
mesh = {Humans ; *Hypertension/diagnosis/physiopathology/drug therapy/classification ; *Antihypertensive Agents/therapeutic use/adverse effects ; Risk Assessment ; Risk Factors ; *Blood Pressure/drug effects ; *Emergencies ; Prognosis ; Predictive Value of Tests ; Decision Support Techniques ; Clinical Decision-Making ; Hypertensive Crisis ; },
abstract = {Systemic arterial hypertension (HTN) is the main cause of morbidity and mortality, and HTN crises contribute significantly to an unfavourable clinical course. For decades, HTN crises have been dichotomized into hypertensive emergency (HTN-E) and hypertensive urgency (HTN-U). The main difference between the two is the presence of acute hypertension-mediated organ damage (HMOD) - if HMOD is present, HTN crisis is HTN-E; if not, it is HTN-U. Patients with HTN-E are in a life-threatening situation. They are hospitalized and receive antihypertensive drugs intravenously (IV). On the other hand, patients with HTN-U are usually not hospitalized and receive their antihypertensives orally. We suggest a modification of the current risk stratification scheme for patients with HTN crises. The new category would be the intermediate risk group, more precisely the 'impending HTN-E' group, with a higher risk in comparison to HTN-U and a lower risk than HTN-E. 'Impending HMOD' means that HMOD has not occurred (yet), and the prognosis is, therefore, better than in patients with ongoing HMOD. There are three main reasons to classify patients as having impending HTN-E: excessively elevated BP, high-risk comorbidities, and ongoing bleeding/high bleeding risk. Their combinations are probable. This approach may enable us to prevent some HTNEs by avoiding acute HMOD using a timely blood pressure treatment. This treatment should be prompt but controlled.},
}
@article {pmid39146377,
year = {2024},
author = {Nuismer, SL and Basinski, AJ and Schreiner, CL and Eskew, EA and Fichet-Calvet, E and Remien, CH},
title = {Quantifying the risk of spillover reduction programs for human health.},
journal = {PLoS computational biology},
volume = {20},
number = {8},
pages = {e1012358},
doi = {10.1371/journal.pcbi.1012358},
pmid = {39146377},
issn = {1553-7358},
mesh = {Humans ; Animals ; *Computer Simulation ; *Zoonoses/transmission/epidemiology/prevention &amp; control/virology ; Computational Biology ; Public Health ; Lassa Fever/epidemiology/prevention &amp; control/transmission ; Disease Outbreaks/prevention &amp; control/statistics &amp; numerical data ; Risk Assessment ; Africa, Western/epidemiology ; },
abstract = {Reducing spillover of zoonotic pathogens is an appealing approach to preventing human disease and minimizing the risk of future epidemics and pandemics. Although the immediate human health benefit of reducing spillover is clear, over time, spillover reduction could lead to counterintuitive negative consequences for human health. Here, we use mathematical models and computer simulations to explore the conditions under which unanticipated consequences of spillover reduction can occur in systems where the severity of disease increases with age at infection. Our results demonstrate that, because the average age at infection increases as spillover is reduced, programs that reduce spillover can actually increase population-level disease burden if the clinical severity of infection increases sufficiently rapidly with age. If, however, immunity wanes over time and reinfection is possible, our results reveal that negative health impacts of spillover reduction become substantially less likely. When our model is parameterized using published data on Lassa virus in West Africa, it predicts that negative health outcomes are possible, but likely to be restricted to a small subset of populations where spillover is unusually intense. Together, our results suggest that adverse consequences of spillover reduction programs are unlikely but that the public health gains observed immediately after spillover reduction may fade over time as the age structure of immunity gradually re-equilibrates to a reduced force of infection.},
}
@article {pmid39186487,
year = {2024},
author = {Raj, U and Banerjee, A and Ray, S and Bhattacharya, S},
title = {Structure of higher-order interactions in social-ecological networks through Q-analysis of their neighbourhood and clique complex.},
journal = {PloS one},
volume = {19},
number = {8},
pages = {e0306409},
doi = {10.1371/journal.pone.0306409},
pmid = {39186487},
issn = {1932-6203},
abstract = {This paper studies higher-order interactions in social-ecological networks, which formally represent interactions within the social and ecological units of an ecosystem. Many real-world social ecosystems exhibit not only pairwise interactions but also higher-order interactions among their units. Therefore, the conventional graph-theoretic description of networks falls short of capturing these higher-order interactions due to the inherent limitations of the graph definition. In this work, a mathematical framework for capturing the higher-order interactions of a social-ecological system has been given by incorporating notions from combinatorial algebraic topology. In order to achieve this, two different simplicial complexes, the clique and the neighbourhood complex, have been constructed from a pairwise social-ecological network. As a case study, the Q-analysis and a structural study of the interactions in the rural agricultural system of southern Madagascar have been done at various structural levels denoted by q. The results obtained by calculating all the structural vectors for both simplicial complexes, along with exciting results about the participation of facets of the clique complex at different q-levels, have been discussed. This work also establishes significant theorems concerning the dimension of the neighbourhood complex and clique complex obtained from the parent pairwise network.},
}
@article {pmid39185327,
year = {2024},
author = {Panyushkina, IP and Jull, AJT and Molnár, M and Varga, T and Kontul', I and Hantemirov, R and Kukarskih, V and Sljusarenko, I and Myglan, V and Livina, V},
title = {The timing of the ca-660 BCE Miyake solar-proton event constrained to between 664 and 663 BCE.},
journal = {Communications earth &amp; environment},
volume = {5},
number = {1},
pages = {454},
doi = {10.1038/s43247-024-01618-x},
pmid = {39185327},
issn = {2662-4435},
abstract = {Extreme solar energetic particle events, known as Miyake events, are rare phenomena observed by cosmogenic isotopes, with only six documented. The timing of the ca. 660 BCE Miyake event remains undefined until now. Here, we assign its occurrence to 664-663 BCE through new radiocarbon measurements in gymnosperm larch tree rings from arctic-alpine biomes (Yamal and Altai). Using a 22-box carbon cycle model and Bayesian statistics, we calculate the radiocarbon production rate during the event that is 3.2-4.8 times higher than the average solar modulation, and comparable to the 774-775 CE solar-proton event. The prolonged radiocarbon signature manifests a 12‰ rise over two years. The non-uniform signal in the tree rings is likely driven by the low rate of CO2 gas exchange between the trees and the ambient atmosphere, and the high residence time of radiocarbon in the post-event stratosphere. We caution about using the event's pronounced signature for precise single-year-dating.},
}
@article {pmid39180071,
year = {2024},
author = {Zhuang, M and Qiao, C and Han, L and Bi, Y and Cao, M and Wang, S and Guo, L and Pang, R and Xie, H},
title = {Multi-omics analyses reveal the responses of wheat (Triticum aestivum L.) and rhizosphere bacterial community to nano(micro)plastics stress.},
journal = {Journal of nanobiotechnology},
volume = {22},
number = {1},
pages = {507},
pmid = {39180071},
issn = {1477-3155},
support = {2023YFD1400902//National Key Research and Development Program of China/ ; J210019//Beijing Municipal Natural Science Foundation/ ; C2021204190//Natural Science Foundation of Hebei Province/ ; 21JCZXJC00110//Natural Science Foundation of Tianjin Municipality/ ; },
mesh = {*Triticum ; *Rhizosphere ; *Bacteria/genetics/metabolism/drug effects ; *Microplastics ; *Soil Microbiology ; Nanoparticles/chemistry ; Stress, Physiological ; Microbiota ; Soil Pollutants ; Particle Size ; Polystyrenes/chemistry ; Multiomics ; },
abstract = {The pervasive existence of nanoplastics (NPs) and microplastics (MPs) in soil has become a worldwide environmental concern. N/MPs exist in the environment in a variety of forms, sizes, and concentrations, while multi-omics studies on the comprehensive impact of N/MPs with different properties (e.g. type and size) on plants remain limited. Therefore, this study utilized multi-omics analysis methods to investigate the effects of three common polymers [polyethylene-NPs (PE-NPs, 50 nm), PE-MPs (PE-MPs, 10 μm), and polystyrene-MPs (PS-MPs, 10 μm)] on the growth and stress response of wheat, as well as the rhizosphere microbial community at two concentrations (0.05 and 0.5 g/kg). PS and PE exhibited different effects for the same particle size and concentration. PE-NPs had the most severe stress effects, resulting in reduced rhizosphere bacteria diversity, plant biomass, and antioxidant enzyme activity while increasing beneficial bacteria richness. N/MPs altered the expression of nitrogen-, phosphorus-, and sulfur-related functional genes in rhizosphere bacteria, thereby affecting photosynthesis, as well as metabolite and gene levels in wheat leaves. Partial least squares pathway models (PLSPMs) indicated that concentration, size, and type play important roles in the impact of N/MPs on the plant ecological environment, which could have essential implications for assessing the environmental risk of N/MPs.},
}
@article {pmid39176874,
year = {2024},
author = {Knak, AK and Roheger, M and Wulff, A},
title = {Challenges in Daily Computerized Assessment of Cognitive Functions of Post-COVID Patients.},
journal = {Studies in health technology and informatics},
volume = {316},
number = {},
pages = {1950-1954},
doi = {10.3233/SHTI240815},
pmid = {39176874},
issn = {1879-8365},
mesh = {Humans ; *COVID-19 ; Cognitive Dysfunction ; Diagnosis, Computer-Assisted/methods ; SARS-CoV-2 ; Fatigue ; Post-Acute COVID-19 Syndrome ; Cognition ; },
abstract = {While it would be quite helpful to learn more about the daily fluctuations of fatigue and cognitive impairments of post-COVID patients, their condition can make investigating these especially challenging. By discussing these issues with post-COVID patients and clinical practitioners, we identified six challenges that specifically apply to daily computerized assessment of cognitive functions of post-COVID patients. We proposed solutions for each of the challenges which can be summarized as offering a carefully planned and flexible study design to participants and monitoring their well-being throughout the assessments. We argue that when the proposed precautions are taken, it is feasible to conduct a study that will generate valuable insights into the trajectories of (cognitive) post-COVID symptoms.},
}
@article {pmid39176504,
year = {2024},
author = {Kokolakis, S and Kokinou, E and Chronaki, C and Moen, A and Datta, G},
title = {Earth Observation and Geoinformatics to Monitoring the Environmental Status of Urban Streams Inextricably Linked to People's Mental Health.},
journal = {Studies in health technology and informatics},
volume = {316},
number = {},
pages = {1560-1564},
doi = {10.3233/SHTI240716},
pmid = {39176504},
issn = {1879-8365},
mesh = {*Environmental Monitoring/methods ; Humans ; *Mental Health ; Rivers ; Geographic Information Systems ; Cities ; },
abstract = {The general condition of urban watercourses is inextricably linked to ecological balance and public health (physical and mental well-being). Given the vulnerability of these systems to climate change and human pollution, this work aims to demonstrate the effective use of environmental indicators to: a) rapidly assess soil and water conditions near urban streams and b) highlight the importance of geoinformatics and earth observation supported by ground-based techniques. There is a great need for new technology and methods for spatial and temporal monitoring and further quantification of environmental quality in urban streams and the land surrounding them to sensitize policymakers and the public to the environmental degradation of these exceptional habitats and to further protect people's mental health.},
}
@article {pmid39175988,
year = {2021},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the bramble shoot moth, Notocelia uddmanniana (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {6},
number = {},
pages = {348},
doi = {10.12688/wellcomeopenres.17488.1},
pmid = {39175988},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Notocelia uddmanniana (the bramble shoot moth; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 794 megabases in span. The majority of the assembly, 99.96%, is scaffolded into 28 chromosomal pseudomolecules, with the Z sex chromosome assembled.},
}
@article {pmid39173171,
year = {2024},
author = {Barahona, M and Alegría, A and Amstein, C and Cárcamo, M and Barahona, M},
title = {Epidemiology of high-energy trauma in Chile: An ecological analysis using public registries.},
journal = {Medwave},
volume = {24},
number = {7},
pages = {e2929},
doi = {10.5867/medwave.2024.07.2929},
pmid = {39173171},
issn = {0717-6384},
mesh = {Chile/epidemiology ; Humans ; *Accidents, Traffic/statistics &amp; numerical data/mortality ; Male ; Adult ; *Databases, Factual ; *Registries ; Female ; Young Adult ; Middle Aged ; *Multiple Trauma/epidemiology/mortality ; Wounds and Injuries/epidemiology/mortality ; Public Health ; Sex Distribution ; Adolescent ; Age Distribution ; World Health Organization ; Aged ; },
abstract = {High-energy trauma is defined as severe organic injuries resulting from events that generate a large amount of kinetic, electrical, or thermal energy. It represents a significant public health concern, accounting for 10% of global mortality. This article aims to describe the epidemiology of high-energy trauma in Chile. Specifically, it seeks to compare the mortality rate per 100 000 inhabitants among member countries of the World Health Organization (WHO), provide a descriptive analysis of notifications under the Explicit Health Guarantees (GES) for the health issue of polytraumatized patients, and analyze the trend in the mortality rate due to external causes in Chile. This study employs an ecological design using three open-access databases. First, the WHO database on deaths from traffic accidents in 2019 was used. Then, the GES database was consulted for the "Polytraumatized" issue between 2018 and 2022. Finally, the Chilean Department of Health Statistics database on causes of death between 1997 and 2020 was utilized. In 2019, Chile ranked in the middle regarding the mortality rate per 100 000 inhabitants due to traffic accidents. GES notifications for polytrauma predominantly involved men aged 20 to 40 years and those affiliated with the public health system, highlighting a primary focus for prevention efforts. Mortality from accidents showed a decreasing trend, with significant structural changes identified in 2000 and 2007.},
}
@article {pmid39170344,
year = {2024},
author = {D, S and Vellaturi, G and Shaik Ibrahim, SH and Molugu, S and Desanamukula, VS and Kocherla, R and Vatambeti, R},
title = {Enhanced deep learning models for automatic fish species identification in underwater imagery.},
journal = {Heliyon},
volume = {10},
number = {15},
pages = {e35217},
pmid = {39170344},
issn = {2405-8440},
abstract = {Underwater cameras are crucial in marine ecology, but their data management needs automatic species identification. This study proposes a two-stage deep learning approach. First, the Unsharp Mask Filter (UMF) preprocesses images. Then, an enhanced region-based fully convolutional network (R-FCN) detects fish using two-order integrals for position-sensitive score maps and precise region of interest (PS-Pr-RoI) pooling for accuracy. The second stage integrates ShuffleNetV2 with the Squeeze and Excitation (SE) module, forming the Improved ShuffleNetV2 model, enhancing classification focus. Hyperparameters are optimized with the Enhanced Northern Goshawk Optimization Algorithm (ENGO). The improved R-FCN model achieves 99.94 % accuracy, 99.58 % precision and recall, and a 99.27 % F-measure on the Fish4knowledge dataset. Similarly, the ENGO-based ShuffleNetV2 model, evaluated on the same dataset, shows 99.93 % accuracy, 99.19 % precision, 98.29 % recall, and a 98.71 % F-measure, highlighting its superior classification accuracy.},
}
@article {pmid39169276,
year = {2024},
author = {Arcioni, L and Arcieri, M and Martino, JD and Liberati, F and Bottoni, P and Castrignanò, T},
title = {HPC-T-Annotator: an HPC tool for de novo transcriptome assembly annotation.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {272},
pmid = {39169276},
issn = {1471-2105},
support = {B87G22000450001//Ministry of University and Research, Italy/ ; },
mesh = {*Software ; *Transcriptome/genetics ; *Molecular Sequence Annotation/methods ; Gene Expression Profiling/methods ; Computational Biology/methods ; Databases, Genetic ; },
abstract = {BACKGROUND: The availability of transcriptomic data for species without a reference genome enables the construction of de novo transcriptome assemblies as alternative reference resources from RNA-Seq data. A transcriptome provides direct information about a species' protein-coding genes under specific experimental conditions. The de novo assembly process produces a unigenes file in FASTA format, subsequently targeted for the annotation. Homology-based annotation, a method to infer the function of sequences by estimating similarity with other sequences in a reference database, is a computationally demanding procedure.<br><br>RESULTS: To mitigate the computational burden, we introduce HPC-T-Annotator, a tool for de novo transcriptome homology annotation on high performance computing (HPC) infrastructures, designed for straightforward configuration via a Web interface. Once the configuration data are given, the entire parallel computing software for annotation is automatically generated and can be launched on a supercomputer using a simple command line. The output data can then be easily viewed using post-processing utilities in the form of Python notebooks integrated in the proposed software.<br><br>CONCLUSIONS: HPC-T-Annotator expedites homology-based annotation in de novo transcriptome assemblies. Its efficient parallelization strategy on HPC infrastructures significantly reduces computational load and execution times, enabling large-scale transcriptome analysis and comparison projects, while its intuitive graphical interface extends accessibility to users without IT skills.},
}
@article {pmid39167718,
year = {2024},
author = {Zass, L and Mwapagha, LM and Louis-Jacques, AF and Allali, I and Mulindwa, J and Kiran, A and Hanachi, M and Souiai, O and Mulder, N and Oduaran, OH},
title = {Advancing microbiome research through standardized data and metadata collection: introducing the Microbiome Research Data Toolkit.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
doi = {10.1093/database/baae062},
pmid = {39167718},
issn = {1758-0463},
support = {1U24HG009780/NH/NIH HHS/United States ; 1U24HG009780/NH/NIH HHS/United States ; },
mesh = {*Metadata ; *Microbiota ; Humans ; Databases, Factual ; },
abstract = {Microbiome research has made significant gains with the evolution of sequencing technologies. Ensuring comparability between studies and enhancing the findability, accessibility, interoperability and reproducibility of microbiome data are crucial for maximizing the value of this growing body of research. Addressing the challenges of standardized metadata reporting, collection and curation, the Microbiome Working Group of the Human Hereditary and Health in Africa (H3Africa) consortium aimed to develop a comprehensive solution. In this paper, we present the Microbiome Research Data Toolkit, a versatile tool designed to standardize microbiome research metadata, facilitate MIxS-MIMS and PhenX reporting, standardize prospective collection of participant biological and lifestyle data, and retrospectively harmonize such data. This toolkit enables past, present and future microbiome research endeavors to collaborate effectively, fostering novel collaborations and accelerating knowledge discovery in the field. Database URL: https://doi.org/10.25375/uct.24218999.v2.},
}
@article {pmid39079269,
year = {2024},
author = {Tian, Y and Liu, Y and Yue, L and Zhao, X and Zhou, Q and Uwaremwe, C and Wang, Y and Chen, G and Sha, Y and Zhang, Y and Wang, R},
title = {Multi-omics analysis reveals the effects of three application modes of plant growth promoting microbes biofertilizer on potato (Solanum tuberosum L.) growth under alkaline loess conditions.},
journal = {Microbiological research},
volume = {287},
number = {},
pages = {127855},
doi = {10.1016/j.micres.2024.127855},
pmid = {39079269},
issn = {1618-0623},
mesh = {*Solanum tuberosum/microbiology/growth &amp; development ; *Fertilizers/analysis ; *Soil Microbiology ; Bacillus amyloliquefaciens/growth &amp; development ; Transcriptome ; Plant Tubers/microbiology/growth &amp; development ; Microbiota ; Soil/chemistry ; Metabolome ; Rhizosphere ; Sucrose/metabolism ; Plant Development ; Metabolomics/methods ; Multiomics ; },
abstract = {Potato is an important crop due to its high contents of starch, protein, and various vitamins and minerals. Biofertilizers are composed of plant growth promoting microbes (PGPMs) which are essential for improving the growth and resistance of potato. However, little information has focused on the modes of inoculation of biofertilizers on plant growth and microecology. This study aims to reveal the response mechanism of the potato to three modes of inoculation of biofertilizers all containing PGPM Bacillus amyloliquefaciens EZ99, i.e. scattered mode of 5 kg/ha biofertilizer (M5), soaking seed tubers with dissolved 5 kg/ha biofertilizer (MZG), and scattered mode of 3 kg/ha biofertilizer + 2 kg/ha sucrose (MY34) in alkaline loess field through multi-omics analysis of transcriptome, metabolome and microbiome. The physiological result revealed that two application modes of equal amount of biofertilizer M5 and MZG significantly improved the growth and yield of potatoes. Furthermore, the transcriptome of potato exhibited sets of differentially expressed genes enriched in photosynthesis, sugar metabolism, and phenylpropanoid biosynthesis among the three modes, with the M5 mode exhibiting overall up-regulation of 828 genes. Based on the untargeted metabolomic analysis of potato tuber, M5 mode significantly accumulated sucrose, while MZG and MY34 mode significantly accumulated the stress metabolites euchrenone b6 and mannobiose, respectively. Besides, the microbial structure of potato rhizosphere showed that the diversity of bacteria and fungi was similar in all soils, but their abundances varied significantly. Specifically, beneficial Penicillium was enriched in M5 and MZG soils, whereas MY34 soil accumulated potential pathogens Plectosphaerella and saccharophilic Mortierella. Collectively, these e findings highlight that MZG is the most effective mode to promote potato growth and stimulate rhizosphere effect. The present study not only encourages sustainable agriculture through agroecological practices, but also provides broad prospects for the application of PGPM biofertilizer in staple foods.},
}
@article {pmid38971026,
year = {2024},
author = {Ou, X and Chen, J and Li, B and Yang, Y and Liu, X and Xu, Z and Xiang, X and Wang, Q},
title = {Multiomics reveals the ameliorating effect and underlying mechanism of aqueous extracts of polygonatum sibiricum rhizome on obesity and liver fat accumulation in high-fat diet-fed mice.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {132},
number = {},
pages = {155843},
doi = {10.1016/j.phymed.2024.155843},
pmid = {38971026},
issn = {1618-095X},
mesh = {Animals ; *Polygonatum/chemistry ; Male ; *Diet, High-Fat/adverse effects ; *Plant Extracts/pharmacology ; *Liver/drug effects/metabolism ; *Obesity/drug therapy ; Mice ; *Rhizome/chemistry ; Mice, Inbred C57BL ; Lipid Metabolism/drug effects ; Gastrointestinal Microbiome/drug effects ; Non-alcoholic Fatty Liver Disease/drug therapy ; Orlistat/pharmacology ; Multiomics ; Akkermansia ; },
abstract = {BACKGROUND: Polygonatum sibiricum polysaccharides protect against obesity and NAFLD. However, the potential effects of PS rhizome aqueous extracts (PSRwe) on adiposity and hepatic lipid accumulation remains unexplored.<br><br>PURPOSE: Elucidating the impact and underlying mechanism of PSRwe on HFD-induced obesity and liver fat depostition.<br><br>STUDY DESIGN: 56 male mice, aged eight weeks, were divided into seven groups: Positive, four doses of PSRwe, Model, and Control. HFD was fed for eight weeks, followed by alternate-day gavage of orlistat and PSRwe for an additional eight-week period. Integrative analysis encompassing multiomics, physiological and histopathological, and biochemical indexes was employed.<br><br>METHODS: Body weight (BW); liver, fat and Lee's indexes; TC, TG, LDL-C, HDL-C, AST, ALT, FFA, leptin, and adiponectin in the liver and blood; TNF&#x3b1;, IL-6, and LPS in the colon, plasma, and liver; H&amp;E, PAS and oil red O staining on adipose and liver samples were examined. OGTT and ITT were conducted The gut microbiome, microbial metabolome, colonic and liver transcriptome, plasma and liver metabolites were investigated.<br><br>RESULTS: PSRwe at the dosage of 7.5 mg/kg demonstrated significant and consistent reduction in BW and hepatic fat deposition than orlistat. PSRwe significantly decreased TC, TG, LDL-C, LEP, FFA levels in blood and liver. PSRwe significantly enhanced the relative abundance of probiotics including Akkermansia muciniphila, Bifidobacterium pseudolongum, Lactobacillus reuteri, and metabolic pathways including glycolysis and fatty acids &#x3b2;-oxidation. The 70 up-regulated microbial metabolites in PSRwe-treated mice mainly involved in nucleotides and amino acids metabolism, while 40 decreased metabolites primarily associated with lipid metabolism. The up-regulated colonic differentially expressed genes (DEGs) participate in JAK-STAT/PI3K-Akt/FoxO signaling pathway, serotonergic/cholinergic/glutamatergic synapses, while the down-regulated DEGs predominantly focused on fat absorption and transport. The up-regulated liver DEGs mainly concentrated on fatty acid oxidation and metabolism. Liver metabolisms revealed 131 differential metabolites, among which carnitine and oxidized lipids significantly increased in PSRwe-treated mice. In plasma, the 58 up-regulated metabolites mainly participate in co-factors/vitamins metabolism while 154 down-regulated ones in fatty acids biosynthesis. Comprehensive multiomics association analysis revealed significant associations between gut microbiota and colonic/liver gene expression, and suggested exogenous and endogenous betaine may be active compound in alleviating HFD-induced symptoms.<br><br>CONCLUSION: PSRwe effectively mitigate HFD-induced obesity and hepatic steatosis by increasing beneficial bacteria, reducing colonic fat digestion/absorption, increasing hepatic lipid metabolism, and elevating betaine levels.},
}
@article {pmid39155119,
year = {2024},
author = {Reitz, ZL},
title = {Predicting metallophore structure and function through genome mining.},
journal = {Methods in enzymology},
volume = {702},
number = {},
pages = {371-401},
doi = {10.1016/bs.mie.2024.06.007},
pmid = {39155119},
issn = {1557-7988},
mesh = {*Genomics/methods ; Genome, Bacterial ; Computational Biology/methods ; Siderophores/metabolism/chemistry/genetics ; Data Mining/methods ; },
abstract = {Metallophores are small molecule chelators that many microbes use to obtain trace metals from their environment. Through genome mining, where genomes are scanned for metallophore biosynthesis genes, one can not only identify which organisms are likely to produce a metallophore, but also predict the metallophore structure, thus preventing undesired reisolation of known compounds and accelerating characterization. Furthermore, the presence of accessory genes for the transport, utilization, and regulation can suggest the biological function and fate of a metallophore. Modern, user-friendly tools have made powerful genomic analyses accessible to scientists with no bioinformatics experience, but these tools are often not utilized to their full potential. This chapter provides an introduction to metallophore genomics and demonstrates how to use the free, publicly available antiSMASH platform to infer metallophore function and structure.},
}
@article {pmid39154763,
year = {2024},
author = {Lin, X and Sun, B and Wang, P and Zhao, M and Liu, D and Zhang, Q and Wu, B and Liu, D},
title = {Enhanced Low-Concentration Phosphate Adsorption Using Magnetic UiO-66@Fe3O4 Composite with Potential Linker Exchange.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {143126},
doi = {10.1016/j.chemosphere.2024.143126},
pmid = {39154763},
issn = {1879-1298},
abstract = {A magnetic FenUiO-66 adsorbent was created to achieve high phosphate adsorption capacity. The incorporation of Fe3O4 facilitated the precipitation and growth of UiO-66 during crystallization, resulting in a shift towards a multilayer heterogeneous distribution of adsorption sites. The increased Fe3O4 content notably enhanced the magnetic properties of FenUiO-66, while negligibly affecting its adsorption performance. The Fe1.5UiO-66 demonstrated exceptional phosphate adsorption capacity (136.54 mg/g), outstanding selectivity, and sustained reusability, with an 80% removal efficiency after nine cycles of treating actual water. The mechanism of phosphate adsorption by FenUiO-66 involved electrostatic attraction, ligand exchange, and linker exchange. Notably, while linker exchange significantly contributed to high adsorption capacity, it resulted in irreversible damage to the FenUiO-66 crystal. These unequivocal findings will serve as a solid foundation for further research and underline the critical role of linkers in the process of phosphate adsorption.},
}
@article {pmid38688803,
year = {2024},
author = {Binion, KE and Perreira, KM and Villa Torres, L and White, JT and Hernandez, GC and Kaefer, M and Misseri, R and Ross, S and Chan, KH},
title = {A multi-site cultural and linguistic adaptation of a hypospadias decision aid for Latinx communities.},
journal = {Journal of pediatric urology},
volume = {20},
number = {4},
pages = {674.e1-674.e9},
doi = {10.1016/j.jpurol.2024.04.002},
pmid = {38688803},
issn = {1873-4898},
support = {UL1 TR002489/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; Male ; *Hispanic or Latino/psychology ; *Hypospadias/ethnology/surgery/psychology ; *Decision Support Techniques ; Focus Groups ; Parents/psychology ; Child, Preschool ; Female ; Language ; Linguistics ; Cultural Characteristics ; },
abstract = {INTRODUCTION: Latinx, Spanish-speaking (LSS) patients are more likely to experience decisional conflict and regret about healthcare decisions than non-Hispanic, white, English-speaking patients.<br><br>OBJECTIVE: To adapt the Hypospadias Hub (Hub), a rigorously developed and tested web-based decision aid (DA), for LSS parents.<br><br>METHODS: Guided by the Ecological Validity Model (EVM), a heuristic framework was followed to culturally adapt the Hub (see Extended Summary Figure). In stage 1, recommendations were obtained from a focus group with members of the institution's Latinx Community Review Board (Latinx CRB) and semi-structured interviews with pediatricians with Latinx-focused practices. In stage 2, preliminary cultural modifications were made, the Hub was translated into Spanish, and a second focus group with the Latinx CRB was convened to review the revised Hub. In stage 3, semi-structured interviews with LSS parents of healthy boys (i.e., without hypospadias)&#xa0;&#x2264;&#xa0;5 years old were conducted to identify any cultural adaptations and/or usability issues regarding the revised Hub. In stage 4, based on parents' feedback, final revisions to the Hub were made. The focus groups and parent interviews were conducted in Spanish; then, the recordings were professionally transcribed in Spanish and translated into English. Interviews with pediatricians were conducted in English; then, the recordings were professionally transcribed. Three coders conducted a qualitative content analysis to identify areas for revision. Changes were applied iteratively.<br><br>RESULTS: Participants included 3 Latinx CRB members (2 women, 1 did not disclose gender; mean age&#xa0;=&#xa0;48.3, SD&#xa0;=&#xa0;21.2), 3 non-Latinx pediatricians (2 women, 1 man; mean age&#xa0;=&#xa0;49.6, SD&#xa0;=&#xa0;9.1), and 5 Latinx mothers (mean age&#xa0;=&#xa0;34.0, SD&#xa0;=&#xa0;1.26). Participants recommended: 1) featuring video testimonials from Latinx families or including Spanish voice-overs/subtitles; 2) diversifying racial/ethnic/geographic representation and including extended families in photographs/illustrations; 3) adding information about health insurance coverage and circumcision, 4) reassuring parents that the condition is not their fault, 5) considering cultural values (e.g., reliance on expert advice), and 6) clarifying medical terminology. Feedback related to seven EVM dimensions: concepts, content, context, goals, language, metaphors, and methods.<br><br>DISCUSSION: Participants perceived the Hub to be informative in guiding parents' treatment decisions. Revisions were reasonable and acceptable for a linguistic and cultural adaptation for LSS parents.<br><br>CONCLUSIONS: We identified and implemented preliminary cultural modifications to the Hub and applied user-centered design methods to test and revise the website. The product is a culturally appropriate DA for LSS parents. Next, English and Spanish-versions of the Hub will be tested in a randomized controlled trial.},
}
@article {pmid39131363,
year = {2024},
author = {Martin, C and Gitter, A and Anantharaman, K},
title = {Protein Set Transformer: A protein-based genome language model to power high diversity viromics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39131363},
issn = {2692-8205},
support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; },
abstract = {Exponential increases in microbial and viral genomic data demand transformational advances in scalable, generalizable frameworks for their interpretation. Standard homology-based functional analyses are hindered by the rapid divergence of microbial and especially viral genomes and proteins that significantly decreases the volume of usable data. Here, we present Protein Set Transformer (PST), a protein-based genome language model that models genomes as sets of proteins without considering sparsely available functional labels. Trained on >100k viruses, PST outperformed other homology- and language model-based approaches for relating viral genomes based on shared protein content. Further, PST demonstrated protein structural and functional awareness by clustering capsid-fold-containing proteins with known capsid proteins and uniquely clustering late gene proteins within related viruses. Our data establish PST as a valuable method for diverse viral genomics, ecology, and evolutionary applications. We posit that the PST framework can be a foundation model for microbial genomics when trained on suitable data.},
}
@article {pmid39131277,
year = {2024},
author = {Yoo, D and Rhie, A and Hebbar, P and Antonacci, F and Logsdon, GA and Solar, SJ and Antipov, D and Pickett, BD and Safonova, Y and Montinaro, F and Luo, Y and Malukiewicz, J and Storer, JM and Lin, J and Sequeira, AN and Mangan, RJ and Hickey, G and Anez, GM and Balachandran, P and Bankevich, A and Beck, CR and Biddanda, A and Borchers, M and Bouffard, GG and Brannan, E and Brooks, SY and Carbone, L and Carrel, L and Chan, AP and Crawford, J and Diekhans, M and Engelbrecht, E and Feschotte, C and Formenti, G and Garcia, GH and de Gennaro, L and Gilbert, D and Green, RE and Guarracino, A and Gupta, I and Haddad, D and Han, J and Harris, RS and Hartley, GA and Harvey, WT and Hiller, M and Hoekzema, K and Houck, ML and Jeong, H and Kamali, K and Kellis, M and Kille, B and Lee, C and Lee, Y and Lees, W and Lewis, AP and Li, Q and Loftus, M and Loh, YHE and Loucks, H and Ma, J and Mao, Y and Martinez, JFI and Masterson, P and McCoy, RC and McGrath, B and McKinney, S and Meyer, BS and Miga, KH and Mohanty, SK and Munson, KM and Pal, K and Pennell, M and Pevzner, PA and Porubsky, D and Potapova, T and Ringeling, FR and Rocha, JL and Ryder, OA and Sacco, S and Saha, S and Sasaki, T and Schatz, MC and Schork, NJ and Shanks, C and Smeds, L and Son, DR and Steiner, C and Sweeten, AP and Tassia, MG and Thibaud-Nissen, F and Torres-González, E and Trivedi, M and Wei, W and Wertz, J and Yang, M and Zhang, P and Zhang, S and Zhang, Y and Zhang, Z and Zhao, SA and Zhu, Y and Jarvis, ED and Gerton, JL and Rivas-González, I and Paten, B and Szpiech, ZA and Huber, CD and Lenz, TL and Konkel, MK and Yi, SV and Canzar, S and Watson, CT and Sudmant, PH and Molloy, E and Garrison, E and Lowe, CB and Ventura, M and O'Neill, RJ and Koren, S and Makova, KD and Phillippy, AM and Eichler, EE},
title = {Complete sequencing of ape genomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39131277},
issn = {2692-8205},
support = {R56 AG056169/AG/NIA NIH HHS/United States ; R01 MH120295/MH/NIMH NIH HHS/United States ; R35 GM142916/GM/NIGMS NIH HHS/United States ; UH3 AG064706/AG/NIA NIH HHS/United States ; R35 GM146886/GM/NIGMS NIH HHS/United States ; R01 HG010329/HG/NHGRI NIH HHS/United States ; R01 AG056169/AG/NIA NIH HHS/United States ; R01 GM123312/GM/NIGMS NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; U24 HG007497/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; P20 GM139769/GM/NIGMS NIH HHS/United States ; U24 HG010263/HG/NHGRI NIH HHS/United States ; R35 GM133747/GM/NIGMS NIH HHS/United States ; P01 AI152999/AI/NIAID NIH HHS/United States ; R35 HG011332/HG/NHGRI NIH HHS/United States ; R35 GM133600/GM/NIGMS NIH HHS/United States ; U19 AG023122/AG/NIA NIH HHS/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; U41 HG007234/HG/NHGRI NIH HHS/United States ; R35 GM146926/GM/NIGMS NIH HHS/United States ; R35 GM151945/GM/NIGMS NIH HHS/United States ; },
abstract = {We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled sequence accuracy (<1 error in 500,000 base pairs), completely sequencing 215 gapless chromosomes telomere-to-telomere. We resolve challenging regions, such as the major histocompatibility complex and immunoglobulin loci, providing more in-depth evolutionary insights. Comparative analyses, including human, allow us to investigate the evolution and diversity of regions previously uncharacterized or incompletely studied without bias from mapping to the human reference. This includes newly minted gene families within lineage-specific segmental duplications, centromeric DNA, acrocentric chromosomes, and subterminal heterochromatin. This resource should serve as a definitive baseline for all future evolutionary studies of humans and our closest living ape relatives.},
}
@article {pmid39148947,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Holland, PWH and , },
title = {The genome sequence of the Green-brindled Crescent, Allophyes oxyacanthae (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {53},
doi = {10.12688/wellcomeopenres.18935.1},
pmid = {39148947},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Allophyes oxyacanthae (the Green-brindled Crescent; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 458 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 17,301 protein coding genes.},
}
@article {pmid39146316,
year = {2024},
author = {He, YJ and Liao, H and Yang, G and Qiu, W and Xuan, R and Zheng, G and Xu, B and Yang, X and Magnuson, JT and Schlenk, D and Zheng, C},
title = {Perfluorohexanesulfonic Acid (PFHxS) Impairs Lipid Homeostasis in Zebrafish Larvae through Activation of PPARα.},
journal = {Environmental science &amp; technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c03053},
pmid = {39146316},
issn = {1520-5851},
abstract = {Perfluorohexanesulfonic acid (PFHxS), an emerging short-chain per- and polyfluoroalkyl substance, has been frequently detected in aquatic environments. Adverse outcome pathway studies have shown that perfluorinated compounds impair lipid homeostasis through peroxisome proliferator activated receptors (PPARs). However, many of these studies were performed at high concentrations and may thus be a result of overt toxicity. To better characterize the molecular and key events of PFHxS to biota, early life-stage zebrafish (Danio rerio) were exposed to concentrations detected in the environment (0.01, 0.1, 1, and 10 μg/L). Lipidomic and transcriptomic evaluations were integrated to predict potential molecular targets. PFHxS significantly impaired lipid homeostasis by the dysregulation of glycerophospholipids, fatty acyls, glycerolipids, sphingolipids, prenol lipids, and sterol lipids. Informatic analyses of the lipidome and transcriptome indicated alterations of the PPAR signaling pathway, with downstream changes to retinol, linoleic acid, and glycerophospholipid metabolism. To assess the role of PPARs, potential binding of PFHxS to PPARs was predicted and animals were coexposed to a PPAR antagonist (GW6471). Molecular simulation indicated PFHxS had a 27.1% better binding affinity than oleic acid, an endogenous agonist of PPARα. Antagonist coexposures rescued impaired glycerophosphocholine concentrations altered by PFHxS. These data indicate PPARα activation may be an important molecular initiating event for PFHxS.},
}
@article {pmid39145283,
year = {2023},
author = {Boyes, D and Skojec, C and Kawahara, AY and , and , and , and , and , and , },
title = {The genome sequence of the Buff Footman, Eilema depressum (Esper, 1787).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {342},
pmid = {39145283},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Eilema depressum (the Buff Footman; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 622.0 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.46 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,038 protein coding genes.},
}
@article {pmid38959816,
year = {2024},
author = {Zhang, Y and Li, D and Li, X and Zhou, X and Newman, G},
title = {The integration of geographic methods and ecological momentary assessment in public health research: A systematic review of methods and applications.},
journal = {Social science &amp; medicine (1982)},
volume = {354},
number = {},
pages = {117075},
doi = {10.1016/j.socscimed.2024.117075},
pmid = {38959816},
issn = {1873-5347},
mesh = {Humans ; *Ecological Momentary Assessment ; *Geographic Information Systems ; *Public Health/methods ; },
abstract = {With the widespread prevalence of mobile devices, ecological momentary assessment (EMA) can be combined with geospatial data acquired through geographic techniques like global positioning system (GPS) and geographic information system. This technique enables the consideration of individuals' health and behavior outcomes of momentary exposures in spatial contexts, mostly referred to as "geographic ecological momentary assessment" or "geographically explicit EMA" (GEMA). However, the definition, scope, methods, and applications of GEMA remain unclear and unconsolidated. To fill this research gap, we conducted a systematic review to synthesize the methodological insights, identify common research interests and applications, and furnish recommendations for future GEMA studies. We followed the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines to systematically search peer-reviewed studies from six electronic databases in 2022. Screening and eligibility were conducted following inclusion criteria. The risk of bias assessment was performed, and narrative synthesis was presented for all studies. From the initial search of 957 publications, we identified 47 articles included in the review. In public health, GEMA was utilized to measure various outcomes, such as psychological health, physical and physiological health, substance use, social behavior, and physical activity. GEMA serves multiple research purposes: 1) enabling location-based EMA sampling, 2) quantifying participants' mobility patterns, 3) deriving exposure variables, 4) describing spatial patterns of outcome variables, and 5) performing data linkage or triangulation. GEMA has advanced traditional EMA sampling strategies and enabled location-based sampling by detecting location changes and specified geofences. Furthermore, advances in mobile technology have prompted considerations of additional sensor-based data in GEMA. Our results highlight the efficacy and feasibility of GEMA in public health research. Finally, we discuss sampling strategy, data privacy and confidentiality, measurement validity, mobile applications and technologies, and GPS accuracy and missing data in the context of current and future public health research that uses GEMA.},
}
@article {pmid39144291,
year = {2022},
author = {Fitzhugh, B and Brown, WA and Misarti, N and Takase, K and Tremayne, AH},
title = {Human Paleodemography and Paleoecology of the North Pacific Rim from the Mid to Late Holocene.},
journal = {Quaternary research},
volume = {108},
number = {PESAS},
pages = {123-149},
pmid = {39144291},
issn = {0033-5894},
abstract = {Using 14 proxy human population time series from around the North Pacific (Alaska, Hokkaido and the Kuril Islands), we evaluate the possibility that the North Pacific climate and marine ecosystem includes a millennial-scale regime shift cycle affecting subsistence and migration. We develop both visual and statistical methods for addressing questions about relative population growth and movement in the past. We introduce and explore the use of a Time Iterative Moran I (TIMI) spatial autocorrelation method to compare time series trends quantitatively - a method that could prove useful in other paleoecological analyses. Results reveal considerable population dynamism around the North Pacific in the last 5000 years and strengthen a previously reported inverse correlation between Northeast and Northwest Pacific proxy population indices. Visual and TIMI analyses suggest multiple, overlapping explanations for the variability, including the potential that oscillating ecological regime shifts affect the North Pacific basin. These results provide an opening for coordinated research to unpack the interrelated social, cultural and environmental dynamics around the subarctic and arctic North Pacific at different spatial and temporal scales by international teams of archaeologists, historians, paleoecologists, paleoceanographers, paleoclimatologists, modelers and data management specialists.},
}
@article {pmid39140146,
year = {2024},
author = {Yang, F and Han, QL and Zhao, WD and Zhao, Y},
title = {EC number prediction of protein sequences based on combination of hierarchical and global features.},
journal = {Yi chuan = Hereditas},
volume = {46},
number = {8},
pages = {661-669},
doi = {10.16288/j.yczz.24-102},
pmid = {39140146},
issn = {0253-9772},
mesh = {*Computational Biology/methods ; Amino Acid Sequence ; Proteins/chemistry ; Algorithms ; Sequence Analysis, Protein/methods ; Enzymes/chemistry/metabolism ; },
abstract = {The identification of enzyme functions plays a crucial role in understanding the mechanisms of biological activities and advancing the development of life sciences. However, existing enzyme EC number prediction methods did not fully utilize protein sequence information and still had shortcomings in identification accuracy. To address this issue, we proposed an EC number prediction network using hierarchical features and global features (ECPN-HFGF). This method first utilized residual networks to extract generic features from protein sequences, and then employed hierarchical feature extraction modules and global feature extraction modules to further extract hierarchical and global features of protein sequences. Subsequently, the prediction results of both feature types were combined, and a multitask learning framework was utilized to achieve accurate prediction of enzyme EC numbers. Experimental results indicated that the ECPN-HFGF method performed best in the task of predicting EC numbers for protein sequences, achieving macro F1 and micro F1 scores of 95.5% and 99.0%, respectively. The ECPN-HFGF method effectively combined hierarchical and global features of protein sequences, allowing for rapid and accurate EC number prediction. Compared to current commonly used methods, this method offers significantly higher prediction accuracy, providing an efficient approach for the advancement of enzymology research and enzyme engineering applications.},
}
@article {pmid39139763,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Acer Sober, Anarsia innoxiella (Gregersen &amp; Karsholt, 2017).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {357},
pmid = {39139763},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Anarsia innoxiella (the Acer Sober; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 302.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length.},
}
@article {pmid39139615,
year = {2024},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Crescent Groundling, Teleiodes luculella (Hübner, 1813).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {143},
pmid = {39139615},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Teleiodes luculella (the Crescent Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 454.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,943 protein coding genes.},
}
@article {pmid39139614,
year = {2024},
author = {Boyes, D and Crowley, LM and McCulloch, J and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Elm Groundling moth, Carpatolechia fugitivella (Zeller, 1839).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {211},
pmid = {39139614},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Carpatolechia fugitivella (the Elm Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 493.1 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.26 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,721 protein coding genes.},
}
@article {pmid37735266,
year = {2024},
author = {Camargo, AP and Roux, S and Schulz, F and Babinski, M and Xu, Y and Hu, B and Chain, PSG and Nayfach, S and Kyrpides, NC},
title = {Identification of mobile genetic elements with geNomad.},
journal = {Nature biotechnology},
volume = {42},
number = {8},
pages = {1303-1312},
pmid = {37735266},
issn = {1546-1696},
mesh = {*Interspersed Repetitive Sequences/genetics ; *Plasmids/genetics ; Software ; Databases, Genetic ; Molecular Sequence Annotation ; Genome, Viral/genetics ; Viruses/genetics ; Neural Networks, Computer ; Computational Biology/methods ; },
abstract = {Identifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications and impact on public health. Here we introduce geNomad, a classification and annotation framework that combines information from gene content and a deep neural network to identify sequences of plasmids and viruses. geNomad uses a dataset of more than 200,000 marker protein profiles to provide functional gene annotation and taxonomic assignment of viral genomes. Using a conditional random field model, geNomad also detects proviruses integrated into host genomes with high precision. In benchmarks, geNomad achieved high classification performance for diverse plasmids and viruses (Matthews correlation coefficient of 77.8% and 95.3%, respectively), substantially outperforming other tools. Leveraging geNomad's speed and scalability, we processed over 2.7 trillion base pairs of sequencing data, leading to the discovery of millions of viruses and plasmids that are available through the IMG/VR and IMG/PR databases. geNomad is available at https://portal.nersc.gov/genomad .},
}
@article {pmid39133313,
year = {2024},
author = {Kuchař, M and Kotěrová, AP and Morávek, A and Santos, F and Harnádková, K and Henyš, P and Cunha, E and Brůžek, J},
title = {Correction to: Automatic variable extraction from 3D coxal bone models for sex estimation using the DSP2 method.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00414-024-03311-2},
pmid = {39133313},
issn = {1437-1596},
}
@article {pmid39132840,
year = {2024},
author = {Vale, FF and Roberts, RJ and Kobayashi, I and Camargo, MC and Rabkin, CS},
title = {Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the Helicobacter pylori Genome Project.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2379440},
doi = {10.1080/19490976.2024.2379440},
pmid = {39132840},
issn = {1949-0984},
mesh = {*Helicobacter pylori/genetics/virology ; *Prophages/genetics/physiology ; *Genome, Bacterial ; Humans ; *Phylogeny ; *Genomics ; Helicobacter Infections/microbiology ; },
abstract = {Prophages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of Helicobacter pylori, a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Helicobacter pylori Genome Project (HpGP) dataset comprises 1011 H. pylori complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the H. pylori prophage genomic content in the HpGP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29.5% (298) of the HpGP genomes contain prophages, of which only 32.2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of H. pylori prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in H. pylori. We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for H. pylori prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages.},
}
@article {pmid39131439,
year = {2024},
author = {Menger, J and Magagna, B and Henle, K and Harpke, A and Frenzel, M and Rick, J and Wiltshire, K and Grimm-Seyfarth, A},
title = {FAIR-EuMon: a FAIR-enabling resource for biodiversity monitoring schemes.},
journal = {Biodiversity data journal},
volume = {12},
number = {},
pages = {e125132},
pmid = {39131439},
issn = {1314-2828},
abstract = {BACKGROUND: Within the scope of the Helmholtz Metadata Collaboration (HMC), the ADVANCE project - Advanced metadata standards for biodiversity survey and monitoring data: supporting of research and conservation - aimed at supporting rich metadata generation with interoperable metadata standards and semantic artefacts that facilitate data access, integration and reuse across terrestrial, freshwater and marine realms. HMC's mission is to facilitate the discovery, access, machine-readability, and reuse of research data across and beyond the Helmholtz Association.<br><br>NEW INFORMATION: We revised, adapted and expanded existing metadata schemas, vocabularies and thesauri to build a FAIR metadata schema and a metadata entry form built on it for users to provide their metadata instances focused on biodiversity monitoring data. The schema is FAIR because it is both machine-interpretable and follows domain-relevant community standards. This report provides a general overview of the project results and instructions on how to access, re-use and complete the metadata form.},
}
@article {pmid39129912,
year = {2023},
author = {Boyes, D and Hutchinson, F and , and , and , and , and , and , },
title = {The genome sequence of the Brown Rustic, Charanyca ferruginea (Esper, 1785).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {547},
pmid = {39129912},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Charanyca ferruginea (the Brown Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 854.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 23,126 protein coding genes.},
}
@article {pmid38977855,
year = {2024},
author = {Sharaf, A and Nesengani, LT and Hayah, I and Kuja, JO and Mdyogolo, S and Omotoriogun, TC and Odogwu, BA and Beedessee, G and Smith, RM and Barakat, A and Moila, AM and El Hamouchi, A and Benkahla, A and Boukteb, A and Elmouhtadi, A and Mafwila, AL and Abushady, AM and Elsherif, AK and Ahmed, B and Wairuri, C and Ndiribe, CC and Ebuzome, C and Kinnear, CJ and Ndlovu, DF and Iraqi, D and El Fahime, E and Assefa, E and Ouardi, F and Belharfi, FZ and Tmimi, FZ and Markey, FB and Radouani, F and Zeukeng, F and Mvumbi, GL and Ganesan, H and Hanachi, M and Nigussie, H and Charoute, H and Benamri, I and Mkedder, I and Haddadi, I and Meftah-Kadmiri, I and Mubiru, JF and Domelevo Entfellner, JK and Rokani, JB and Ogwang, J and Daiga, JB and Omumbo, J and Ideozu, JE and Errafii, K and Labuschagne, K and Komi, KK and Tonfack, LB and Hadjeras, L and Ramantswana, M and Chaisi, M and Botes, MW and Kilian, M and Kvas, M and Melloul, M and Chaouch, M and Khyatti, M and Abdo, M and Phasha-Muchemenye, M and Hijri, M and Mediouni, MR and Hassan, MA and Piro, M and Mwale, M and Maaloum, M and Mavhunga, M and Olivier, NA and Aminou, O and Arbani, O and Souiai, O and Djocgoue, PF and Mentag, R and Zipfel, RD and Tata, RB and Megnekou, R and Muzemil, S and Paez, S and Salifu, SP and Kagame, SP and Selka, S and Edwards, S and Gaouar, SBS and Reda, SRA and Fellahi, S and Khayi, S and Ayed, S and Madisha, T and Sahil, T and Udensi, OU and Ras, V and Ezebuiro, V and Duru, VC and David, X and Geberemichael, Y and Tchiechoua, YH and Mungloo-Dilmohamud, Z and Chen, Z and Happi, C and Kariuki, T and Ziyomo, C and Djikeng, A and Badaoui, B and Mapholi, N and Muigai, A and Osuji, JO and Ebenezer, TE},
title = {Establishing African genomics and bioinformatics programs through annual regional workshops.},
journal = {Nature genetics},
volume = {56},
number = {8},
pages = {1556-1565},
pmid = {38977855},
issn = {1546-1718},
mesh = {*Genomics/education ; *Computational Biology/methods/education ; Africa ; Humans ; Biodiversity ; },
abstract = {The African BioGenome Project (AfricaBP) Open Institute for Genomics and Bioinformatics aims to overcome barriers to capacity building through its distributed African regional workshops and prioritizes the exchange of grassroots knowledge and innovation in biodiversity genomics and bioinformatics. In 2023, we implemented 28 workshops on biodiversity genomics and bioinformatics, covering 11 African countries across the 5 African geographical regions. These regional workshops trained 408 African scientists in hands-on molecular biology, genomics and bioinformatics techniques as well as the ethical, legal and social issues associated with acquiring genetic resources. Here, we discuss the implementation of transformative strategies, such as expanding the regional workshop model of AfricaBP to involve multiple countries, institutions and partners, including the proposed creation of an African digital database with sequence information relating to both biodiversity and agriculture. This will ultimately help create a critical mass of skilled genomics and bioinformatics scientists across Africa.},
}
@article {pmid38155557,
year = {2024},
author = {Forbes, VE and Accolla, C and Banitz, T and Crouse, K and Galic, N and Grimm, V and Raimondo, S and Schmolke, A and Vaugeois, M},
title = {Mechanistic population models for ecological risk assessment and decision support: The importance of good conceptual model diagrams.},
journal = {Integrated environmental assessment and management},
volume = {20},
number = {5},
pages = {1566-1574},
doi = {10.1002/ieam.4886},
pmid = {38155557},
issn = {1551-3793},
support = {//Helmholtz/ ; 2018-06139//Svenska Forskningsr&#xe5;det Formas/ ; },
mesh = {Risk Assessment/methods ; *Ecology ; *Decision Support Techniques ; Models, Theoretical ; Environmental Monitoring/methods ; },
abstract = {The use of mechanistic population models as research and decision-support tools in ecology and ecological risk assessment (ERA) is increasing. This growth has been facilitated by advances in technology, allowing the simulation of more complex systems, as well as by standardized approaches for model development, documentation, and evaluation. Mechanistic population models are particularly useful for simulating complex systems, but the required model complexity can make them challenging to communicate. Conceptual diagrams that summarize key model elements, as well as elements that were considered but not included, can facilitate communication and understanding of models and increase their acceptance as decision-support tools. Currently, however, there are no consistent standards for creating or presenting conceptual model diagrams (CMDs), and both terminology and content vary widely. Here, we argue that greater consistency in CMD development and presentation is an important component of good modeling practice, and we provide recommendations, examples, and a free web app (pop-cmd.com) for achieving this for population models used for decision support in ERAs. Integr Environ Assess Manag 2024;20:1566-1574. © 2023 SETAC.},
}
@article {pmid39129913,
year = {2023},
author = {Boyes, D and , and , and , and , and , and Mulley, JF and , },
title = {The genome sequence of the Dark Arches Apamea monoglypha (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {63},
pmid = {39129913},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Apamea monoglypha (the Dark Arches, Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 576 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length. Gene annotation of this assembly on Ensembl has identified 17,963 protein coding genes.},
}
@article {pmid39127755,
year = {2024},
author = {Pekár, S},
title = {Datasets of traits of zodariid spiders (Araneae: Zodariidae).},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {862},
pmid = {39127755},
issn = {2052-4463},
mesh = {*Spiders/classification/anatomy &amp; histology/physiology ; Animals ; Ecosystem ; Databases, Factual ; Australia ; },
abstract = {Species traits are essential for inferences on ecology and the evolution of organisms. Spiders are the most abundant and diversified terrestrial predators, playing an important role in a range of ecosystem services. Here, I present datasetse on all traits of zodariid spiders, which are known to be free-living ground-dwellers occurring on all continents (except Antarctica) with the highest species diversity in Australia. I collated the data from published resources. The datasets includes nearly 100 000 trait records on all (90) genera and almost all species (1249) of the family. The majority of the 88 traits collected are morphometric, followed by those relating to ecology, reproduction, and physiology. Morphometric traits were available for the majority of species. Other trait classes were only available for some species. I provide a standardized classification of selected categorical traits (habitat, microhabitat, retreat type, circadian activity, prey, primary defensive, and predators). This is the first complete database of traits of a whole spider family, which is available through the World Spider Trait database.},
}
@article {pmid39122728,
year = {2024},
author = {Hixon, SW and Fernandes, R and Andriamahaihavana, A and Baden, AL and Blanco, MB and Caulier, G and Dammhahn, M and Eeckhaut, I and Eppley, TM and Frédérich, B and Ganzhorn, JU and Garbaras, A and Gibson, D and Goodman, SM and Irwin, M and Kelley, EA and Michel, LN and Lepoint, G and Loudon, JE and Mittelheiser, L and Rakotondranary, J and Rasamisoa, DC and Rasolofonirina, R and Ratovonamana, Y and Razafindramanana, J and Reisdorff, C and Sponheimer, M and Terrana, L and Vasey, N and Crowley, BE},
title = {Introducing IsoMad, a compilation of isotopic datasets for Madagascar.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {857},
pmid = {39122728},
issn = {2052-4463},
mesh = {Madagascar ; *Databases, Factual ; Animals ; Carbon Isotopes/analysis ; Nitrogen Isotopes/analysis ; },
abstract = {We present the first open-access, island-wide isotopic database (IsoMad) for modern biologically relevant materials collected on Madagascar within the past 150 years from both terrestrial and nearshore marine environments. Isotopic research on the island has increasingly helped with biological studies of endemic organisms, including evaluating foraging niches and investigating factors that affect the spatial distribution and abundance of species. The IsoMad database should facilitate future work by making it easy for researchers to access existing data (even for those who are relatively unfamiliar with the literature) and identify both research gaps and opportunities for using various isotope systems to answer research questions. We also hope that this database will encourage full data reporting in future publications.},
}
@article {pmid39122322,
year = {2024},
author = {Martín, G and Erinjery, JJ and Ediriweera, D and Goldstein, E and Somaweera, R and de Silva, HJ and Lalloo, DG and Iwamura, T and Murray, KA},
title = {Effects of global change on snakebite envenoming incidence up to 2050: a modelling assessment.},
journal = {The Lancet. Planetary health},
volume = {8},
number = {8},
pages = {e533-e544},
doi = {10.1016/S2542-5196(24)00141-4},
pmid = {39122322},
issn = {2542-5196},
mesh = {*Snake Bites/epidemiology ; Incidence ; Sri Lanka/epidemiology ; Humans ; *Climate Change ; Models, Theoretical ; Forecasting ; Animals ; Snakes ; },
abstract = {BACKGROUND: Human activities are driving climate, land cover, and population change (global change), and shifting the baseline geographical distribution of snakebite. The interacting effects of global change on snakes and communities at risk of snakebite are poorly understood, limiting capacity to anticipate and manage future changes in snakebite risk.<br><br>METHODS: In this modelling study, we projected how global change will affect snakebite envenoming incidence in Sri Lanka, as a model system that has a high incidence of snakebite. We used the shared socioeconomic pathway (SSP) scenario analysis framework to integrate forecasts across the domains of: climate change (historical trend from WorldClim plus three underlying regional circulation models [RCMs] in the Coordinated Regional Downscaling Experiment-South Asia repository, with two emissions pathways [representative concentration pathways RCP4.5 and RCP8.5]); land cover change (Dyna-CLUE model); and human population density change (based on Gridded Population of the World data) from Jan 1, 2010 to Dec 31, 2050. Forecasts were integrated under three different development scenarios: a sustainability pathway (SSP1 and no further emissions), a middle-of-the-road pathway (SSP2 and RCP4.5), and a fossil-fuelled pathway (SSP5 and RCP8.5). For SSP2 and SSP5, we nested three different RCMs (CNRM-CM5, GFDL-CCM3, and MPI-ESM-LR; mean averaged to represent consensus) to account for variability in climate predictions. Data were used as inputs to a mechanistic model that predicted snakebite envenoming incidence based on human-snake contact patterns.<br><br>FINDINGS: From 2010 to 2050, at the national level, envenoming incidence in Sri Lanka was projected to decrease by 12&#xb7;0-23&#xb7;0%, depending on the scenario. The rate of decrease in envenoming incidence was higher in SSP5-RCP8.5 than in SSP1 and SSP2-RCP4.5. Change in envenoming incidence was heterogenous across the country. In SSP1, incidence decreased in urban areas expected to have population growth, and with land cover changes towards anthropised classes. In SSP2-RCP4.5 and SSP5-RCP8.5, most areas were projected to have decreases in incidence (SSP5-RCP8.5 showing the largest area with incidence reductions), while areas such as the central highlands and the north of the country showed localised increases. In the model, decreases occurred with human population growth, land use change towards anthropised classes (potentially shifting occupational risk factors), and decreasing abundance of some snake species, potentially due to global warming and reduced climatic and habitat suitability, with displacement of some snake species.<br><br>INTERPRETATION: Snakebite envenoming incidence was projected to decrease overall in the coming decades in Sri Lanka, but with an apparent emerging conflict with sustainability objectives. Therefore, efforts to mitigate snakebite envenoming incidence will need to consider the potential impacts of sustainability interventions, particularly related to climate and land use change and in areas where increases in incidence are projected. In view of global change, neglected tropical diseases and public health issues related to biodiversity, such as snakebite, should be managed collaboratively by both environment and health stakeholders.<br><br>FUNDING: UK Medical Research Council.},
}
@article {pmid39114815,
year = {2023},
author = {Lohse, K and Ebdon, S and Mackintosh, A and Martin, S and Saccheri, IJ and Bourn, NAD and Vila, R and , and , and , and , },
title = {The genome sequence of the Arctic Skipper, Carterocephalus palaemon (Pallas, 1771).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {369},
pmid = {39114815},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Carterocephalus palaemon (the Arctic Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 394.5 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.78 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,032 protein coding genes.},
}
@article {pmid39114490,
year = {2024},
author = {Butlin, R and Mérot, C and , and , and , and , and , },
title = {The genome sequence of a kelp fly, Coelopa pilipes Haliday, 1838.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {197},
pmid = {39114490},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Coelopa pilipes (kelp fly; Arthropoda; Insecta; Diptera; Coelopidae). The genome sequence is 263.0 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.86 kilobases in length.},
}
@article {pmid39074140,
year = {2024},
author = {Melo, D and Pallares, LF and Ayroles, JF},
title = {Reassessing the modularity of gene co-expression networks using the Stochastic Block Model.},
journal = {PLoS computational biology},
volume = {20},
number = {7},
pages = {e1012300},
doi = {10.1371/journal.pcbi.1012300},
pmid = {39074140},
issn = {1553-7358},
mesh = {*Drosophila melanogaster/genetics ; Animals ; *Gene Regulatory Networks/genetics ; *Stochastic Processes ; *Algorithms ; *Computational Biology/methods ; Models, Genetic ; Gene Expression Profiling/methods ; },
abstract = {Finding communities in gene co-expression networks is a common first step toward extracting biological insight from these complex datasets. Most community detection algorithms expect genes to be organized into assortative modules, that is, groups of genes that are more associated with each other than with genes in other groups. While it is reasonable to expect that these modules exist, using methods that assume they exist a priori is risky, as it guarantees that alternative organizations of gene interactions will be ignored. Here, we ask: can we find meaningful communities without imposing a modular organization on gene co-expression networks, and how modular are these communities? For this, we use a recently developed community detection method, the weighted degree corrected stochastic block model (SBM), that does not assume that assortative modules exist. Instead, the SBM attempts to efficiently use all information contained in the co-expression network to separate the genes into hierarchically organized blocks of genes. Using RNAseq gene expression data measured in two tissues derived from an outbred population of Drosophila melanogaster, we show that (a) the SBM is able to find ten times as many groups as competing methods, that (b) several of those gene groups are not modular, and that (c) the functional enrichment for non-modular groups is as strong as for modular communities. These results show that the transcriptome is structured in more complex ways than traditionally thought and that we should revisit the long-standing assumption that modularity is the main driver of the structuring of gene co-expression networks.},
}
@article {pmid38936185,
year = {2024},
author = {Hu, CJ and Lv, YQ and Xian, WD and Jiao, JY and Lian, ZH and Tan, S and Li, MM and Luo, ZH and Liu, ZT and Lv, AP and Liu, L and Ali, M and Liu, WQ and Li, WJ},
title = {Multi-omics insights into the function and evolution of sodium benzoate biodegradation pathway in Benzoatithermus flavus gen. nov., sp. nov. from hot spring.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {135017},
doi = {10.1016/j.jhazmat.2024.135017},
pmid = {38936185},
issn = {1873-3336},
mesh = {*Sodium Benzoate/metabolism ; *Biodegradation, Environmental ; *Hot Springs/microbiology ; *Phylogeny ; Water Pollutants, Chemical/metabolism ; Multiomics ; },
abstract = {Biodegradation stands as an eco-friendly and effective approach for organic contaminant remediation. However, research on microorganisms degrading sodium benzoate contaminants in extreme environments remains limited. In this study, we report to display the isolation of a novel hot spring enriched cultures with sodium benzoate (400 mg/L) as the sole carbon source. The results revealed that the phylum Pseudomonadota was the potential sodium benzoate degrader and a novel genus within the family Geminicoccaceae of this phylum. The isolated strain was named Benzoatithermus flavus SYSU G07066[T] and was isolated from HNT-2 hot spring samples. Genomic analysis revealed that SYSU G07066[T] carried benABC genes and physiological experiments indicated the ability to utilize sodium benzoate as a sole carbon source for growth, which was further confirmed by transcriptomic data with expression of benABC. Phylogenetic analysis suggested that Horizontal Gene Transfer (HGT) plays a significant role in acquiring sodium benzoate degradation capability among prokaryotes, and SYSU G07066[T] might have acquired benABC genes through HGT from the family Acetobacteraceae. The discovery of the first microorganism with sodium benzoate degradation function from a hot spring enhances our understanding of the diverse functions within the family Geminicoccaceae. This study unearths the first novel genus capable of efficiently degrading sodium benzoate and its evolution history at high temperatures, holding promising industrial applications, and provides a new perspective for further exploring the application potential of hot spring "microbial dark matter".},
}
@article {pmid38926582,
year = {2024},
author = {Tian, SY and Yasuhara, M and Condamine, FL and Huang, HM and Fernando, AGS and Aguilar, YM and Pandita, H and Irizuki, T and Iwatani, H and Shin, CP and Renema, W and Kase, T},
title = {Cenozoic history of the tropical marine biodiversity hotspot.},
journal = {Nature},
volume = {632},
number = {8024},
pages = {343-349},
pmid = {38926582},
issn = {1476-4687},
mesh = {Animals ; *Aquatic Organisms/classification/isolation &amp; purification ; *Biodiversity ; Climate Change ; Datasets as Topic ; Extinction, Biological ; *Fossils ; Genetic Speciation ; History, Ancient ; Time Factors ; *Tropical Climate ; Pacific Ocean ; Coral Reefs ; },
abstract = {The region with the highest marine biodiversity on our planet is known as the Coral Triangle or Indo-Australian Archipelago (IAA)[1,2]. Its enormous biodiversity has long attracted the interest of biologists; however, the detailed evolutionary history of the IAA biodiversity hotspot remains poorly understood[3]. Here we present a high-resolution reconstruction of the Cenozoic diversity history of the IAA by inferring speciation-extinction dynamics using a comprehensive fossil dataset. We found that the IAA has exhibited a unidirectional diversification trend since about 25 million years ago, following a roughly logistic increase until a diversity plateau beginning about 2.6 million years ago. The growth of diversity was primarily controlled by diversity dependency and habitat size, and also facilitated by the alleviation of thermal stress after 13.9 million years ago. Distinct net diversification peaks were recorded at about 25, 20, 16, 12 and 5 million years ago, which were probably related to major tectonic events in addition to climate transitions. Key biogeographic processes had far-reaching effects on the IAA diversity as shown by the long-term waning of the Tethyan descendants versus the waxing of cosmopolitan and IAA taxa. Finally, it seems that the absence of major extinctions and the Cenozoic cooling have been essential in making the IAA the richest marine biodiversity hotspot on Earth.},
}
@article {pmid38917628,
year = {2024},
author = {Li, Q and Ma, Q and Zhou, Y and Jiang, X and Parales, RE and Zhao, S and Zhuang, Y and Ruan, Z},
title = {Isolation, identification, and degradation mechanism by multi-omics of mesotrione-degrading Amycolatopsis nivea La24.},
journal = {Journal of hazardous materials},
volume = {476},
number = {},
pages = {134951},
doi = {10.1016/j.jhazmat.2024.134951},
pmid = {38917628},
issn = {1873-3336},
mesh = {*Herbicides/metabolism/chemistry ; *Cyclohexanones/metabolism ; *Biodegradation, Environmental ; *Amycolatopsis/metabolism/genetics ; Metabolomics ; Sulfonylurea Compounds/metabolism ; Soil Pollutants/metabolism ; Multiomics ; },
abstract = {Mesotrione is a herbicide used in agricultural production; however, its stability and long-term residues pose ecological risks to soil health and subsequent crops. In this research, the strain Amycolatopsis nivea La24 was identified as capable of completely degrading 50 mg∙L[-1] mesotrione within 48 h. It exhibited a broad adaptability to various environment and could degrade three sulfonylurea herbicides (nicosulfuron, chlorimuron-methyl, and cinosulfuron). Non-target metabonomic and mass spectrometry demonstrated that La24 strain broke down the mesotrione parent molecule by targeting the β-diketone bond and nitro group, resulting in the production of five possible degradation products. The differentially expressed genes were significantly enriched in fatty acid degradation, amino acid metabolism, and other pathways, and the differentially metabolites in glutathione metabolism, arginine/proline metabolism, cysteine/methionine metabolism, and other pathways. Additionally, it was confirmed by heterologous expression that nitroreductase was directly involved in the mesotrione degradation, and NDMA-dependent methanol dehydrogenase would increase the resistance to mesotrione. Finally, the intracellular response of La24 during mesotrione degradation was proposed. This work provides insight for a comprehensive understanding of the mesotrione biodegradation mechanism, significantly expands the resources for pollutant degradation, and offers the potential for a more sustainable solution to address herbicide pollution in soil.},
}
@article {pmid38729197,
year = {2024},
author = {Caini, S and Meijer, A and Nunes, MC and Henaff, L and Zounon, M and Boudewijns, B and Del Riccio, M and Paget, J},
title = {Probable extinction of influenza B/Yamagata and its public health implications: a systematic literature review and assessment of global surveillance databases.},
journal = {The Lancet. Microbe},
volume = {5},
number = {8},
pages = {100851},
doi = {10.1016/S2666-5247(24)00066-1},
pmid = {38729197},
issn = {2666-5247},
mesh = {Humans ; *Influenza, Human/epidemiology/virology ; *Influenza B virus/genetics/isolation &amp; purification ; *Public Health ; Global Health ; COVID-19/epidemiology/prevention &amp; control ; Databases, Factual ; SARS-CoV-2 ; Pandemics ; },
abstract = {Early after the start of the COVID-19 pandemic, the detection of influenza B/Yamagata cases decreased globally. Given the potential public health implications of this decline, in this Review, we systematically analysed data on influenza B/Yamagata virus circulation (for 2020-23) from multiple complementary sources of information. We identified relevant articles published in PubMed and Embase, and data from the FluNet, Global Initiative on Sharing All Influenza Data, and GenBank databases, webpages of respiratory virus surveillance systems from countries worldwide, and the Global Influenza Hospital Surveillance Network. A progressive decline of influenza B/Yamagata detections was reported across all sources, in absolute terms (total number of cases), as positivity rate, and as a proportion of influenza B detections. Sporadically reported influenza B/Yamagata cases since March, 2020 were mostly vaccine-derived, attributed to data entry errors, or have yet to be definitively confirmed. The likelihood of extinction necessitates a rapid response in terms of reassessing the composition of influenza vaccines, enhanced surveillance for B/Yamagata, and a possible change in the biosafety level when handling B/Yamagata viruses in laboratories.},
}
@article {pmid39114813,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Thicket Knot-horn, Acrobasis suavella (Zincken, 1818).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {252},
pmid = {39114813},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Acrobasis suavella (the Thicket Knot-horn; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 647.3 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,101 protein coding genes.},
}
@article {pmid39112823,
year = {2024},
author = {Darabi, H and Bazhdar, Y and Ehsani, AH},
title = {Modeling the spatial relationship between landscape services and vulnerability assessment.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {9},
pages = {797},
pmid = {39112823},
issn = {1573-2959},
mesh = {*Geographic Information Systems ; *Environmental Monitoring/methods ; *Conservation of Natural Resources ; *Ecosystem ; Iran ; Remote Sensing Technology ; Models, Theoretical ; Spatial Analysis ; },
abstract = {Even though many studies have been thus far devoted to landscape services (LS) or vulnerability assessment (VA) alone, the relationship between these two concepts has been less investigated. The current study attempts to model the spatial relationship between LS and VA in the Tarhan area (west of Iran). For this purpose, a combination of the analytic hierarchy process (AHP), remote sensing (RS), and geographic information system (GIS) techniques are applied to assess vulnerability. Variogram models and geostatistical simulations are used for mapping and evaluating landscape services. Moreover, the geographically weighted regression (GWR) is operated to predict the relationship between LS and VA. The results indicate that landform and socioeconomic variables are also two main factors shaping variations in VA. As well, the levels of services provided in the possible landscape are affected by the vulnerability. The assessment accordingly establishes that natural and cultural values have significant effects on services, in terms of their spatial distribution and nature. Exploring the relationship between LS and VA correspondingly depicts that VA has a direct influence on the capacity and entity of LS provision (adjusted R[2] = 0.67). The outcomes of the study provide a foundation for nature management and conservation, although it is less able to analyze the trade-off between ecosystem degradation and future development trends. The nexus of LS and future ecological processes in an integrated system can be thus the subject of further research.},
}
@article {pmid39109333,
year = {2024},
author = {Boyes, D and Mulhair, PO and , and , and , and , and , and , and , },
title = {The genome sequence of the Beautiful China-mark moth Nymphula nitidulata (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {135},
pmid = {39109333},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Nymphula nitidulata (the Beautiful China-mark moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 635.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,031 protein coding genes.},
}
@article {pmid39109332,
year = {2024},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Brown Ash Ermine moth, Zelleria hepariella Stainton, 1849.},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {242},
pmid = {39109332},
issn = {2398-502X},
abstract = {We present a genome assembly from a male Zelleria hepariella (the Brown Ash Ermine; Arthropoda; Insecta; Lepidoptera; Yponomeutidae). The genome sequence is 428.8 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.31 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,718 protein coding genes.},
}
@article {pmid39108663,
year = {2023},
author = {Taylor, SC and Crowley, LM and Luker, S and Harvey, M and , and , and , and , and , and , and , },
title = {The genome sequence of the Downland Villa bee-fly, Villa cingulata (Meigen, 1804).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {526},
pmid = {39108663},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Villa cingulata (the Downland Villa bee-fly; Arthropoda; Insecta; Diptera; Bombyliidae). The genome sequence is 412.6 megabases in span. Most of the assembly is scaffolded into 10 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 22.43 kilobases in length.},
}
@article {pmid38961615,
year = {2024},
author = {Papageorgiou, D and Cherono, W and Gall, G and Nyaguthii, B and Farine, DR},
title = {Testing the information centre hypothesis in a multilevel society.},
journal = {The Journal of animal ecology},
volume = {93},
number = {8},
pages = {1147-1159},
doi = {10.1111/1365-2656.14131},
pmid = {38961615},
issn = {1365-2656},
support = {//Max Planck Society/ ; //Wissenschaftskolleg zu Berlin/ ; 422037984//Deutsche Forschungsgemeinschaft/ ; //Deutscher Akademischer Austauschdienst/ ; WW-175ER-17//National Geographic Society/ ; PCEFP3_187058/SNSF_/Swiss National Science Foundation/Switzerland ; 850859/ERC_/European Research Council/International ; },
mesh = {Animals ; *Social Behavior ; *Galliformes/physiology ; Geographic Information Systems ; Female ; Male ; },
abstract = {In various animal species conspecifics aggregate at sleeping sites. Such aggregations can act as information centres where individuals acquire up-to-date knowledge about their environment. In some species, communal sleeping sites comprise individuals from multiple groups, where each group maintains stable membership over time. We used GPS tracking to simultaneously record group movement in a population of wild vulturine guineafowl (Acryllium vulturinum) to investigate whether communal sleeping sites can facilitate the transfer of information among individuals across distinct groups. These birds live in large and stable groups that move both together and apart, often forming communal roosts containing up to five groups. We first test whether roosts provide the opportunity for individuals to acquire information from members of other groups by examining the spatial organization at roosts. The GPS data reveal that groups intermix, thereby providing an opportunity for individuals to acquire out-group information. We next conduct a field experiment to test whether naïve groups can locate novel food patches when co-roosting with knowledgeable groups. We find that co-roosting substantially increases the chances for the members of a naïve group to discover a patch known to individuals from other groups at the shared roost. Further, we find that the discovery of food patches by naïve groups subsequently shapes their space use and inter-group associations. We also draw on our long-term tracking to provide examples that demonstrate natural cases where communal roosting has preceded large-scale multi-group collective movements that extend into areas beyond the groups' normal ranges. Our findings support the extension of the information centre hypothesis to communal sleeping sites that consist of distinct social groups.},
}
@article {pmid38398847,
year = {2024},
author = {Navratilova, HF and Lanham-New, S and Whetton, AD and Geifman, N},
title = {Associations of Diet with Health Outcomes in the UK Biobank: A Systematic Review.},
journal = {Nutrients},
volume = {16},
number = {4},
pages = {},
pmid = {38398847},
issn = {2072-6643},
mesh = {Humans ; United Kingdom/epidemiology ; *Diabetes Mellitus, Type 2/epidemiology/etiology ; *Biological Specimen Banks ; *Cardiovascular Diseases/epidemiology/etiology ; *Diet/statistics &amp; numerical data/adverse effects ; Diet, Healthy/statistics &amp; numerical data ; Female ; Male ; Neoplasms/epidemiology/etiology ; Risk Factors ; Middle Aged ; Colorectal Neoplasms/epidemiology/etiology/prevention &amp; control ; UK Biobank ; },
abstract = {The UK Biobank is a cohort study that collects data on diet, lifestyle, biomarkers, and health to examine diet-disease associations. Based on the UK Biobank, we reviewed 36 studies on diet and three health conditions: type 2 diabetes (T2DM), cardiovascular disease (CVD), and cancer. Most studies used one-time dietary data instead of repeated 24 h recalls, which may lead to measurement errors and bias in estimating diet-disease associations. We also found that most studies focused on single food groups or macronutrients, while few studies adopted a dietary pattern approach. Several studies consistently showed that eating more red and processed meat led to a higher risk of lung and colorectal cancer. The results suggest that high adherence to "healthy" dietary patterns (consuming various food types, with at least three servings/day of whole grain, fruits, and vegetables, and meat and processed meat less than twice a week) slightly lowers the risk of T2DM, CVD, and colorectal cancer. Future research should use multi-omics data and machine learning models to account for the complexity and interactions of dietary components and their effects on disease risk.},
}
@article {pmid39032255,
year = {2024},
author = {Hossain, M and Wiegand, B and Reza, A and Chaudhuri, H and Mukhopadhyay, A and Yadav, A and Patra, PK},
title = {A machine learning approach to investigate the impact of land use land cover (LULC) changes on groundwater quality, health risks and ecological risks through GIS and response surface methodology (RSM).},
journal = {Journal of environmental management},
volume = {366},
number = {},
pages = {121911},
doi = {10.1016/j.jenvman.2024.121911},
pmid = {39032255},
issn = {1095-8630},
mesh = {*Groundwater/analysis ; *Machine Learning ; *Water Quality ; *Geographic Information Systems ; India ; Environmental Monitoring/methods ; Bayes Theorem ; Humans ; Agriculture ; },
abstract = {Groundwater resources are enormously affected by land use land cover (LULC) dynamics caused by increasing urbanisation, agricultural and household discharge as a result of global population growth. This study investigates the impact of decadal LULC changes in groundwater quality, human and ecological health from 2009 to 2021 in a diverse landscape, West Bengal, India. Using groundwater quality data from 479 wells in 2009 and 734 well in 2021, a recently proposed Water Pollution Index (WPI) was computed, and its geospatial distribution by a machine learning-based 'Empirical Bayesian Kriging' (EBK) tool manifested a decline in water quality since the number of excellent water category decreased from 30.5% to 28% and polluted water increased from 44% to 45%. ANOVA and Friedman tests revealed statistically significant differences (p < 0.0001) in year-wise water quality parameters as well as group comparisons for both years. Landsat 7 and 8 satellite images were used to classify the LULC types applying machine learning tools for both years, and were coupled with response surface methodology (RSM) for the first time, which revealed that the alteration of groundwater quality were attributed to LULC changes, e.g. WPI showed a positive correlation with built-up areas, village-vegetation cover, agricultural lands, and a negative correlation with surface water, barren lands, and forest cover. Expansion in built-up areas by 0.7%, and village-vegetation orchards by 2.3%, accompanied by a reduction in surface water coverage by 0.6%, and 2.4% in croplands caused a 1.5% drop in excellent water and 1% increase in polluted water category. However, ecological risks through the ecological risk index (ERI) exhibited a lower risk in 2021 attributed to reduced high-risk potential zones. This study highlights the potentiality in linking LULC and water quality changes using some advanced statistical tools like GIS and RSM for better management of water quality and landscape ecology.},
}
@article {pmid38819974,
year = {2024},
author = {Tang, Z and Tang, S and Wang, H and Li, R and Zhang, X and Zhang, W and Yuan, X and Zang, Y and Li, Y and Zhou, T and Li, Y},
title = {S2VQ-VAE: Semi-Supervised Vector Quantised-Variational AutoEncoder for Automatic Evaluation of Trail Making Test.},
journal = {IEEE journal of biomedical and health informatics},
volume = {28},
number = {8},
pages = {4456-4470},
doi = {10.1109/JBHI.2024.3407881},
pmid = {38819974},
issn = {2168-2208},
mesh = {Humans ; *Cognitive Dysfunction/diagnosis ; Aged ; Male ; Female ; *Trail Making Test ; Supervised Machine Learning ; Aged, 80 and over ; Algorithms ; Deep Learning ; Diagnosis, Computer-Assisted/methods ; Signal Processing, Computer-Assisted ; },
abstract = {BACKGROUND: Computer-aided detection of cognitive impairment garnered increasing attention, offering older adults in the community access to more objective, ecologically valid, and convenient cognitive assessments using multimodal sensing technology on digital devices.<br><br>METHODOLOGY: In this study, we aimed to develop an automated method for screening cognitive impairment, building on paper- and electronic TMTs. We proposed a novel deep representation learning approach named Semi-Supervised Vector Quantised-Variational AutoEncoder (S2VQ-VAE). Within S2VQ-VAE, we incorporated intra- and inter-class correlation losses to disentangle class-related factors. These factors were then combined with various real-time obtainable features (including demographic, time-related, pressure-related, and jerk-related features) to create a robust feature engineering block. Finally, we identified the light gradient boosting machine as the optimal classifier. The experiments were conducted on a dataset collected from older adults in the community.<br><br>RESULTS: The experimental results showed that the proposed multi-type feature fusion method outperformed the conventional method used in paper-based TMTs and the existing VAE-based feature extraction in terms of screening performance.<br><br>CONCLUSIONS: In conclusion, the proposed deep representation learning method significantly enhances the cognitive diagnosis capabilities of behavior-based TMTs and streamlines large-scale community-based cognitive impairment screening while reducing the workload of professional healthcare staff.},
}
@article {pmid39103962,
year = {2024},
author = {Prakofjewa, J and Sartori, M and Kalle, R and Łuczaj, &#x141; and Karbarz, M and Mattalia, G and Šarka, P and Prūse, B and Stryamets, N and Anegg, M and Kuznetsova, N and Kolosova, V and Belichenko, O and Aziz, MA and Pieroni, A and Sõukand, R},
title = {"But how true that is, I do not know": the influence of written sources on the medicinal use of fungi across the western borderlands of the former Soviet Union.},
journal = {IMA fungus},
volume = {15},
number = {1},
pages = {22},
pmid = {39103962},
issn = {2210-6340},
support = {714874//HORIZON EUROPE European Research Council/ ; },
abstract = {Fungi have been used for medicinal purposes for many centuries. This study, based on 35 historical written sources and 581 in-depth semi-structured interviews from eight countries in the western borderlands of the former Soviet Union, investigates the medicinal use of fungi by local communities. We compared the taxa and uses obtained from fieldwork and historical sources with works that advocated fungi use within Soviet herbals, representing the centralised medical system. During fieldwork, we identified eight locally used fungi and one lichen. The highest numbers of medicinal uses were documented in Russia, Estonia and Ukraine. Studies published before the Soviet era listed 21 fungal taxa and one lichen species used in the study region. However, only six of these taxa were mentioned as used by people in our field studies (Amanita muscaria, Boletus edulis, Lycoperdon, Morchella, Phallus impudicus and Cetraria islandica). Notably, these same six taxa were consistently endorsed in Soviet herbals. Of the remaining three taxa recorded in the fieldwork, none were mentioned in historical written sources. However, they were promoted either in Soviet herbals (Inonotus obliquus, Kombucha) or later popular publications (Cantharellus cibarius). This highlights the significant influence of written sources on the use of fungi for medicinal purposes within the studied local communities.},
}
@article {pmid39102402,
year = {2024},
author = {Saad-Roy, CM and Morris, SE and Boots, M and Baker, RE and Lewis, BL and Farrar, J and Marathe, MV and Graham, AL and Levin, SA and Wagner, CE and Metcalf, CJE and Grenfell, BT},
title = {Impact of waning immunity against SARS-CoV-2 severity exacerbated by vaccine hesitancy.},
journal = {PLoS computational biology},
volume = {20},
number = {8},
pages = {e1012211},
doi = {10.1371/journal.pcbi.1012211},
pmid = {39102402},
issn = {1553-7358},
mesh = {Humans ; *COVID-19/immunology/prevention &amp; control/epidemiology ; *SARS-CoV-2/immunology ; *COVID-19 Vaccines/immunology ; Vaccination Hesitancy/statistics &amp; numerical data ; Severity of Illness Index ; Vaccination/statistics &amp; numerical data ; Pandemics/prevention &amp; control ; Computational Biology ; },
abstract = {The SARS-CoV-2 pandemic has generated a considerable number of infections and associated morbidity and mortality across the world. Recovery from these infections, combined with the onset of large-scale vaccination, have led to rapidly-changing population-level immunological landscapes. In turn, these complexities have highlighted a number of important unknowns related to the breadth and strength of immunity following recovery or vaccination. Using simple mathematical models, we investigate the medium-term impacts of waning immunity against severe disease on immuno-epidemiological dynamics. We find that uncertainties in the duration of severity-blocking immunity (imparted by either infection or vaccination) can lead to a large range of medium-term population-level outcomes (i.e. infection characteristics and immune landscapes). Furthermore, we show that epidemiological dynamics are sensitive to the strength and duration of underlying host immune responses; this implies that determining infection levels from hospitalizations requires accurate estimates of these immune parameters. More durable vaccines both reduce these uncertainties and alleviate the burden of SARS-CoV-2 in pessimistic outcomes. However, heterogeneity in vaccine uptake drastically changes immune landscapes toward larger fractions of individuals with waned severity-blocking immunity. In particular, if hesitancy is substantial, more robust vaccines have almost no effects on population-level immuno-epidemiology, even if vaccination rates are compensatorily high among vaccine-adopters. This pessimistic scenario for vaccination heterogeneity arises because those few individuals that are vaccine-adopters are so readily re-vaccinated that the duration of vaccinal immunity has no appreciable consequences on their immune status. Furthermore, we find that this effect is heightened if vaccine-hesitants have increased transmissibility (e.g. due to riskier behavior). Overall, our results illustrate the necessity to characterize both transmission-blocking and severity-blocking immune time scales. Our findings also underline the importance of developing robust next-generation vaccines with equitable mass vaccine deployment.},
}
@article {pmid39102091,
year = {2024},
author = {Michal, K and Anežka, PK and Alexander, M and Frédéric, S and Harnádková, K and Petr, H and Eugénia, C and Jaroslav, B},
title = {Automatic variable extraction from 3D coxal bone models for sex estimation using the DSP2 method.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {39102091},
issn = {1437-1596},
abstract = {Thanks to technical progress and the availability of virtual data, sex estimation methods as part of a biological profile are undergoing an inevitable evolution. Further reductions in subjectivity, but potentially also in measurement errors, can be brought by approaches that automate the extraction of variables. Such automatization also significantly accelerates and facilitates the specialist's work. The aim of this study is (1) to apply a previously proposed algorithm (Kuchař et al. 2021) to automatically extract 10 variables used for the DSP2 sex estimation method, and (2) to test the robustness of the new automatic approach in a current heterogeneous population. For the first aim, we used a sample of 240 3D scans of pelvic bones from the same individuals, which were measured manually for the DSP database. For the second aim a sample of 108 pelvic bones from the New Mexico Decedent Image Database was used. The results showed high agreement between automatic and manual measurements with rTEM below 5% for all dimensions except two. The accuracy of final sex estimates based on all 10 variables was excellent (error rate 0.3%). However, we observed a higher number of undetermined individuals in the Portuguese sample (25% of males) and the New Mexican sample (36.5% of females). In conclusion, the procedure for automatic dimension extraction was successfully applied both to a different type of data and to a heterogeneous population.},
}
@article {pmid39101049,
year = {2024},
author = {Boyes, D and Lees, DC and Holland, PWH and , and , and , and , and , and , and , and , },
title = {The genome sequence of the Oak Beauty, Biston strataria (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {35},
pmid = {39101049},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Biston strataria (the Oak Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 424.0 megabases in span. Most of the assembly is scaffolded into 16 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,406 protein coding genes.},
}
@article {pmid39100235,
year = {2024},
author = {Ciach, MA and Pawłowska, J and Górecki, P and Muszewska, A},
title = {The interkingdom horizontal gene transfer in 44 early diverging fungi boosted their metabolic, adaptive, and immune capabilities.},
journal = {Evolution letters},
volume = {8},
number = {4},
pages = {526-538},
pmid = {39100235},
issn = {2056-3744},
abstract = {Numerous studies have been devoted to individual cases of horizontally acquired genes in fungi. It has been shown that such genes expand the hosts' metabolic capabilities and contribute to their adaptations as parasites or symbionts. Some studies have provided an extensive characterization of the horizontal gene transfer (HGT) in Dikarya. However, in the early diverging fungi (EDF), a similar characterization is still missing. In order to fill this gap, we have designed a computational pipeline to obtain a statistical sample of reliable HGT events with a low false discovery rate. We have analyzed 44 EDF proteomes and identified 829 xenologs in fungi ranging from Chytridiomycota to Mucoromycota. We have identified several patterns and statistical properties of EDF HGT. We show that HGT is driven by bursts of gene exchange and duplication, resulting in highly divergent numbers and molecular properties of xenologs between fungal lineages. Ancestrally aquatic fungi are generally more likely to acquire foreign genetic material than terrestrial ones. Endosymbiotic bacteria can be a source of useful xenologs, as exemplified by NOD-like receptors transferred to Mortierellomycota. Closely related fungi have similar rates of intronization of xenologs. Posttransfer gene fusions and losses of protein domains are common and may influence the encoded proteins' functions. We argue that there is no universal approach for HGT identification and inter- and intra-kingdom transfers require tailored identification methods. Our results help to better understand how and to what extent HGT has shaped the metabolic, adaptive, and immune capabilities of fungi.},
}
@article {pmid39099847,
year = {2024},
author = {Kapsetaki, SE and Compton, ZT and Dolan, J and Harris, V&#x39a; and Mellon, W and Rupp, SM and Duke, EG and Harrison, TM and Aksoy, S and Giraudeau, M and Vincze, O and McGraw, KJ and Aktipis, A and Tollis, M and Boddy, A&#x39c; and Maley, CC},
title = {Life history traits and cancer prevalence in birds.},
journal = {Evolution, medicine, and public health},
volume = {12},
number = {1},
pages = {105-116},
pmid = {39099847},
issn = {2050-6201},
abstract = {BACKGROUND AND OBJECTIVES: Cancer is a disease that affects nearly all multicellular life, including the broad and diverse taxa of Aves. While little is known about the factors that contribute to cancer risk across Aves, life history trade-offs may explain some of this variability in cancer prevalence. We predict birds with high investment in reproduction may have a higher likelihood of developing cancer. In this study, we tested whether life history traits are associated with cancer prevalence in 108 species of birds.<br><br>METHODOLOGY: We obtained life history data from published databases and cancer data from 5,729 necropsies from 108 species of birds across 24 taxonomic orders from 25 different zoological facilities. We performed phylogenetically controlled regression analyses between adult body mass, lifespan, incubation length, clutch size, sexually dimorphic traits, and both neoplasia and malignancy prevalence. We also compared the neoplasia and malignancy prevalence of female and male birds.<br><br>RESULTS: Providing support for a life history trade-off between somatic maintenance and reproduction, we found a positive relationship between clutch size and cancer prevalence across Aves. There was no significant association with body mass, lifespan, incubation length, sexual dimorphism, and cancer.<br><br>CONCLUSIONS AND IMPLICATIONS: Life history theory presents an important framework for understanding differences in cancer defenses across various species. These results suggest a trade-off between reproduction and somatic maintenance, where Aves with small clutch sizes get less cancer.},
}
@article {pmid39099645,
year = {2023},
author = {Obbard, DJ and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Chymomyza fuscimana (Drosophilidae) (Zetterstedt, 1838).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {477},
pmid = {39099645},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Chymomyza fuscimana (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 338.0 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.47 kilobases in length.},
}
@article {pmid38632210,
year = {2024},
author = {Griesberger, P and Kunz, F and Hackländer, K and Mattsson, B},
title = {Building a decision-support tool to inform sustainability approaches under complexity: Case study on managing wild ruminants.},
journal = {Ambio},
volume = {53},
number = {9},
pages = {1307-1322},
pmid = {38632210},
issn = {1654-7209},
mesh = {Animals ; *Conservation of Natural Resources/methods ; *Animals, Wild ; *Decision Support Techniques ; *Bayes Theorem ; *Ruminants ; Austria ; Decision Making ; },
abstract = {In wildlife management, differing perspectives among stakeholders generate conflicts about how to achieve disparate sustainability goals that include ecological, economic, and sociocultural dimensions. To mitigate such conflicts, decisions regarding wildlife management must be taken thoughtfully. To our knowledge, there exists no integrative modeling framework to inform these decisions, considering all dimensions of sustainability. We constructed a decision-support tool based on stakeholder workshops and a Bayesian decision network to inform management of wild ruminants in the federal state of Lower Austria. We use collaborative decision analysis to compare resource allocations while accounting for trade-offs among dimensions of sustainability. The tool is designed for application by non-technical users across diverse decision-making contexts with particular sets of wildlife management actions, objectives, and uncertainties. Our tool represents an important step toward developing and evaluating a transparent and replicable approach for mitigating wildlife-based conflicts in Europe and beyond.},
}
@article {pmid38583934,
year = {2024},
author = {Swanson, SA and Miller, M},
title = {Toward a clearer understanding of what works to reduce gun violence: the role of falsification strategies.},
journal = {American journal of epidemiology},
volume = {193},
number = {8},
pages = {1061-1065},
doi = {10.1093/aje/kwae036},
pmid = {38583934},
issn = {1476-6256},
mesh = {Humans ; *Gun Violence/prevention &amp; control/statistics &amp; numerical data ; United States ; *Firearms/legislation &amp; jurisprudence ; Data Interpretation, Statistical ; Homicide/prevention &amp; control/statistics &amp; numerical data ; Wounds, Gunshot/prevention &amp; control/epidemiology ; },
abstract = {Strong epidemiologic evidence from ecological and individual-level studies in the United States supports the claim that access to firearms substantially increases the risk of dying by suicide, homicide, and firearm accidents. Less certain is how well particular interventions work to prevent these deaths and other firearm-related harms. Given the limits of existing data to study firearm violence and the infeasibility of conducting randomized trials of firearm access, it is important to do the best we can with the data we already have. We argue that falsification strategies are a critical-yet underutilized-component of any such analytical approach. The falsification strategies we focus on are versions of "negative controls" analyses in which we expect that an analysis should yield a null causal effect, and thus where not obtaining a null effect estimate raises questions about the assumptions underlying causal interpretation of a study's findings. We illustrate the saliency of this issue today with examples drawn from studies published in leading peer-reviewed journals within the last 5 years. Collecting rich, high-quality data always takes time, urgent as the need may be. On the other hand, doing better with the data we already have can start right now.},
}
@article {pmid37731336,
year = {2024},
author = {Aizpurua, O and Dunn, RR and Hansen, LH and Gilbert, MTP and Alberdi, A},
title = {Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data.},
journal = {Critical reviews in biotechnology},
volume = {44},
number = {6},
pages = {1164-1182},
doi = {10.1080/07388551.2023.2254933},
pmid = {37731336},
issn = {1549-7801},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; *Bacteria/genetics/classification ; Guidelines as Topic ; Microbiota/genetics ; Humans ; Data Interpretation, Statistical ; Reproducibility of Results ; },
abstract = {Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.},
}
@article {pmid39092794,
year = {2024},
author = {Ma, X and Huete, A and Liu, Y and Zhu, X and Nguyen, H and Miura, T and Chen, M and Li, X and Asrar, G},
title = {A holistic big data approach to understand and manage increasing pollen-induced respiratory allergies under global change.},
journal = {Global change biology},
volume = {30},
number = {8},
pages = {e17451},
doi = {10.1111/gcb.17451},
pmid = {39092794},
issn = {1365-2486},
support = {1027576//National Institute of Food and Agriculture/ ; DP210100347//Australian Research Council/ ; 42171305//National Natural Science Foundation of China/ ; },
mesh = {*Pollen/immunology ; *Big Data ; *Climate Change ; Humans ; Respiratory Hypersensitivity/etiology ; },
}
@article {pmid39092001,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Orange-tailed Clearwing, Synanthedon andrenaeformis (Laspeyres, 1801).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {160},
doi = {10.12688/wellcomeopenres.21110.1},
pmid = {39092001},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Synanthedon andrenaeformis (the Orange-tailed Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 348.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.65 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,867 protein coding genes.},
}
@article {pmid39029911,
year = {2024},
author = {Tyagi, S and Katara, P},
title = {Metatranscriptomics: A Tool for Clinical Metagenomics.},
journal = {Omics : a journal of integrative biology},
volume = {28},
number = {8},
pages = {394-407},
doi = {10.1089/omi.2024.0130},
pmid = {39029911},
issn = {1557-8100},
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Humans ; *Computational Biology/methods ; *Transcriptome/genetics ; Gene Expression Profiling/methods ; RNA, Ribosomal, 16S/genetics ; Metagenome/genetics ; },
abstract = {In the field of bioinformatics, amplicon sequencing of 16S rRNA genes has long been used to investigate community membership and taxonomic abundance in microbiome studies. As we can observe, shotgun metagenomics has become the dominant method in this field. This is largely owing to advancements in sequencing technology, which now allow for random sequencing of the entire genetic content of a microbiome. Furthermore, this method allows profiling both genes and the microbiome's membership. Although these methods have provided extensive insights into various microbiomes, they solely assess the existence of organisms or genes, without determining their active role within the microbiome. Microbiome scholarship now includes metatranscriptomics to decipher how a community of microorganisms responds to changing environmental conditions over a period of time. Metagenomic studies identify the microbes that make up a community but metatranscriptomics explores the diversity of active genes within that community, understanding their expression profile and observing how these genes respond to changes in environmental conditions. This expert review article offers a critical examination of the computational metatranscriptomics tools for studying the transcriptomes of microbial communities. First, we unpack the reasons behind the need for community transcriptomics. Second, we explore the prospects and challenges of metatranscriptomic workflows, starting with isolation and sequencing of the RNA community, then moving on to bioinformatics approaches for quantifying RNA features, and statistical techniques for detecting differential expression in a community. Finally, we discuss strengths and shortcomings in relation to other microbiome analysis approaches, pipelines, use cases and limitations, and contextualize metatranscriptomics as a tool for clinical metagenomics.},
}
@article {pmid38822152,
year = {2024},
author = {Li, X and Bai, Y and Xu, C and Liu, S and Yu, H and Kong, L and Du, S and Li, Q},
title = {OysterDB: A Genome Database for Ostreidae.},
journal = {Marine biotechnology (New York, N.Y.)},
volume = {26},
number = {4},
pages = {827-834},
pmid = {38822152},
issn = {1436-2236},
support = {2022LZGCQY010, 2021ZLGX03 and 2021TSGC1240//Shandong Province Agriculture Research System Project/ ; CARS-49//China Agriculture Research System Project/ ; },
mesh = {Animals ; *Databases, Genetic ; *Ostreidae/genetics ; *Genome ; Molecular Sequence Annotation ; Computational Biology ; Genomics ; },
abstract = {The molluscan family Ostreidae, commonly known as oysters, is an important molluscan group due to its economic and ecological importance. In recent years, an abundance of genomic data of Ostreidae species has been generated and available in public domain. However, there is still a lack of a high-efficiency database platform to store and distribute these data with comprehensive tools. In this study, we developed an oyster genome database (OysterDB) to consolidate oyster genomic data. This database includes eight oyster genomes and 208,923 protein-coding gene annotations. Bioinformatic tools, such as BLAST and JBrowse, are integrated into the database to provide a user-friendly platform for homologous sequence searching, visualization of genomes, and screen for candidate gene information. Moreover, OysterDB will be continuously updated with ever-growing oyster genomic resources and facilitate future studies for comparative and functional genomic analysis of oysters (http://oysterdb.com.cn/).},
}
@article {pmid37994038,
year = {2024},
author = {Nahas, C and Gandit, M and Quillion-Dupré, L and Monfort, E},
title = {How to engage patients in computerized cognitive training: a cognitive rehabilitation expert's perspective.},
journal = {Disability and rehabilitation. Assistive technology},
volume = {19},
number = {6},
pages = {2306-2318},
doi = {10.1080/17483107.2023.2284879},
pmid = {37994038},
issn = {1748-3115},
mesh = {Humans ; Male ; Female ; Adult ; Middle Aged ; *Software ; Interviews as Topic ; Patient Participation ; Qualitative Research ; Therapy, Computer-Assisted ; Cognitive Training ; },
abstract = {PURPOSE: The relationship between a patient and their therapist plays a crucial role in patient engagement. While Computerized Cognitive Training (CCT) may assist in preserving cognitive skills in cases of aging, dementia or acquired brain injuries, its effectiveness has not been definitively proven. Improving user engagement, acceptance, and software usability could aid in addressing this issue. The present study aims to identify potential obstacles and facilitators by examining the perspectives of rehabilitation professionals on the current usage of CCT software.<br><br>METHODS: Semi-structured interviews were conducted with 16 rehabilitation professionals, familiar with a CCT software. The data were transcribed and followed by an independent iterative thematic analysis.<br><br>RESULTS: Two major themes were identified: (1) facilitating factors and (2) difficulties related to use. The main obstacles were difficulties related to the computerized nature of the exercises, technology use, understanding the software and general learning difficulties. The main facilitators were the ecological and novel nature of the exercises, and the adaptability of the difficulty levels.<br><br>CONCLUSION: The complexity of the CCT presents challenges for its usage by rehabilitation professionals, which in turn can impede patient utilization as well. To address this issue and promote sustainable use of the software, providing instruction delivery to facilitate learning and understanding of the CCT is essential. Additionally, creating a standardized foundation that therapists can refer to for guidance may also aid in optimizing the software's usage. It is recommended to utilize a model for CCT acceptability and acceptance in developing these solutions to enhance patient engagement.},
}
@article {pmid39090383,
year = {2024},
author = {Manubens-Gil, L and Zhou, Z and Chen, H and Ramanathan, A and Liu, X and Liu, Y and Bria, A and Gillette, T and Ruan, Z and Yang, J and Radojević, M and Zhao, T and Cheng, L and Qu, L and Liu, S and Bouchard, KE and Gu, L and Cai, W and Ji, S and Roysam, B and Wang, CW and Yu, H and Sironi, A and Iascone, DM and Zhou, J and Bas, E and Conde-Sousa, E and Aguiar, P and Li, X and Li, Y and Nanda, S and Wang, Y and Muresan, L and Fua, P and Ye, B and He, HY and Staiger, JF and Peter, M and Cox, DN and Simonneau, M and Oberlaender, M and Jefferis, G and Ito, K and Gonzalez-Bellido, P and Kim, J and Rubel, E and Cline, HT and Zeng, H and Nern, A and Chiang, AS and Yao, J and Roskams, J and Livesey, R and Stevens, J and Liu, T and Dang, C and Guo, Y and Zhong, N and Tourassi, G and Hill, S and Hawrylycz, M and Koch, C and Meijering, E and Ascoli, GA and Peng, H},
title = {Author Correction: BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41592-024-02395-3},
pmid = {39090383},
issn = {1548-7105},
}
@article {pmid39089617,
year = {2024},
author = {Chen, SH and Chen, CH and Lin, HC and Yeh, SA and Hwang, TL and Chen, PJ},
title = {Drug repurposing of cyclin-dependent kinase inhibitors for neutrophilic acute respiratory distress syndrome and psoriasis.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.07.026},
pmid = {39089617},
issn = {2090-1224},
abstract = {BACKGROUND: Neutrophilic inflammation, characterized by dysregulated neutrophil activation, triggers a variety of inflammatory responses such as chemotactic infiltration, oxidative bursts, degranulation, neutrophil extracellular traps (NETs) formation, and delayed turnover. This type of inflammation is pivotal in the pathogenesis of acute respiratory distress syndrome (ARDS) and psoriasis. Despite current treatments, managing neutrophil-associated inflammatory symptoms remains a significant challenge.<br><br>AIM OF REVIEW: This review emphasizes the role of cyclin-dependent kinases (CDKs) in neutrophil activation and inflammation. It aims to highlight the therapeutic potential of repurposing CDK inhibitors to manage neutrophilic inflammation, particularly in ARDS and psoriasis. Additionally, it discusses the necessary precautions for the clinical application of these inhibitors due to potential off-target effects and the need for dose optimization.<br><br>CDKs regulate key neutrophilic functions, including chemotactic responses, degranulation, NET formation, and apoptosis. Repurposing CDK inhibitors, originally developed for cancer treatment, shows promise in controlling neutrophilic inflammation. Clinical anticancer drugs, palbociclib and ribociclib, have demonstrated efficacy in treating neutrophilic ARDS and psoriasis by targeting off-label pathways, phosphoinositide 3-kinase (PI3K) and phosphodiesterase 4 (PDE4), respectively. While CDK inhibitors offer promising therapeutic benefits, their clinical repurposing requires careful consideration of off-target effects and dose optimization. Further exploration and clinical trials are necessary to ensure their safety and efficacy in treating inflammatory conditions.},
}
@article {pmid39086664,
year = {2023},
author = {Boyes, D and Eljounaidi, K and , and , and , and , and , and , },
title = {The genome sequence of the Rose-flounced Tabby, Endotricha flammealis (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {516},
pmid = {39086664},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Endotricha flammealis (the Rose-flounced Tabby; Arthropoda; Insecta; Lepidoptera; Pyralidae). The genome sequence is 473.9 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,578 protein coding genes.},
}
@article {pmid38949108,
year = {2024},
author = {Bahl, A and Halappanavar, S and Wohlleben, W and Nymark, P and Kohonen, P and Wallin, H and Vogel, U and Haase, A},
title = {Bioinformatics and machine learning to support nanomaterial grouping.},
journal = {Nanotoxicology},
volume = {18},
number = {4},
pages = {373-400},
doi = {10.1080/17435390.2024.2368005},
pmid = {38949108},
issn = {1743-5404},
mesh = {*Machine Learning ; *Nanostructures/chemistry/toxicity ; *Computational Biology/methods ; Humans ; Risk Assessment ; Animals ; },
abstract = {Nanomaterials (NMs) offer plenty of novel functionalities. Moreover, their physicochemical properties can be fine-tuned to meet the needs of specific applications, leading to virtually unlimited numbers of NM variants. Hence, efficient hazard and risk assessment strategies building on New Approach Methodologies (NAMs) become indispensable. Indeed, the design, the development and implementation of NAMs has been a major topic in a substantial number of research projects. One of the promising strategies that can help to deal with the high number of NMs variants is grouping and read-across. Based on demonstrated structural and physicochemical similarity, NMs can be grouped and assessed together. Within an established NM group, read-across may be performed to fill in data gaps for data-poor variants using existing data for NMs within the group. Establishing a group requires a sound justification, usually based on a grouping hypothesis that links specific physicochemical properties to well-defined hazard endpoints. However, for NMs these interrelationships are only beginning to be understood. The aim of this review is to demonstrate the power of bioinformatics with a specific focus on Machine Learning (ML) approaches to unravel the NM Modes-of-Action (MoA) and identify the properties that are relevant to specific hazards, in support of grouping strategies. This review emphasizes the following messages: 1) ML supports identification of the most relevant properties contributing to specific hazards; 2) ML supports analysis of large omics datasets and identification of MoA patterns in support of hypothesis formulation in grouping approaches; 3) omics approaches are useful for shifting away from consideration of single endpoints towards a more mechanistic understanding across multiple endpoints gained from one experiment; and 4) approaches from other fields of Artificial Intelligence (AI) like Natural Language Processing or image analysis may support automated extraction and interlinkage of information related to NM toxicity. Here, existing ML models for predicting NM toxicity and for analyzing omics data in support of NM grouping are reviewed. Various challenges related to building robust models in the field of nanotoxicology exist and are also discussed.},
}
@article {pmid39083325,
year = {2024},
author = {Webb, EK and Stevens, JS and Ely, TD and Lebois, LAM and van Rooij, SJH and Bruce, SE and House, SL and Beaudoin, FL and An, X and Neylan, TC and Clifford, GD and Linnstaedt, SD and Germine, LT and Bollen, KA and Rauch, SL and Haran, JP and Storrow, AB and Lewandowski, C and Musey, PI and Hendry, PL and Sheikh, S and Jones, CW and Punches, BE and Swor, RA and Murty, VP and Hudak, LA and Pascual, JL and Seamon, MJ and Datner, EM and Pearson, C and Peak, DA and Domeier, RM and Rathlev, NK and O'Neil, BJ and Sergot, P and Sanchez, LD and Joormann, J and Pizzagalli, DA and Harte, SE and Kessler, RC and Koenen, KC and Ressler, KJ and McLean, SA and Harnett, NG},
title = {Neighborhood Resources Associated With Psychological Trajectories and Neural Reactivity to Reward After Trauma.},
journal = {JAMA psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1001/jamapsychiatry.2024.2148},
pmid = {39083325},
issn = {2168-6238},
abstract = {IMPORTANCE: Research on resilience after trauma has often focused on individual-level factors (eg, ability to cope with adversity) and overlooked influential neighborhood-level factors that may help mitigate the development of posttraumatic stress disorder (PTSD).<br><br>OBJECTIVE: To investigate whether an interaction between residential greenspace and self-reported individual resources was associated with a resilient PTSD trajectory (ie, low/no symptoms) and to test if the association between greenspace and PTSD trajectory was mediated by neural reactivity to reward.<br><br>As part of a longitudinal cohort study, trauma survivors were recruited from emergency departments across the US. Two weeks after trauma, a subset of participants underwent functional magnetic resonance imaging during a monetary reward task. Study data were analyzed from January to November 2023.<br><br>EXPOSURES: Residential greenspace within a 100-m buffer of each participant's home address was derived from satellite imagery and quantified using the Normalized Difference Vegetation Index and perceived individual resources measured by the Connor-Davidson Resilience Scale (CD-RISC).<br><br>MAIN OUTCOME AND MEASURES: PTSD symptom severity measured at 2 weeks, 8 weeks, 3 months, and 6 months after trauma. Neural responses to monetary reward in reward-related regions (ie, amygdala, nucleus accumbens, orbitofrontal cortex) was a secondary outcome. Covariates included both geocoded (eg, area deprivation index) and self-reported characteristics (eg, childhood maltreatment, income).<br><br>RESULTS: In 2597 trauma survivors (mean [SD] age, 36.5 [13.4] years; 1637 female [63%]; 1304 non-Hispanic Black [50.2%], 289 Hispanic [11.1%], 901 non-Hispanic White [34.7%], 93 non-Hispanic other race [3.6%], and 10 missing/unreported [0.4%]), 6 PTSD trajectories (resilient, nonremitting high, nonremitting moderate, slow recovery, rapid recovery, delayed) were identified through latent-class mixed-effect modeling. Multinominal logistic regressions revealed that for individuals with higher CD-RISC scores, greenspace was associated with a greater likelihood of assignment in a resilient trajectory compared with nonremitting high (Wald z test&#x2009;=&#x2009;-3.92; P&#x2009;<&#x2009;.001), nonremitting moderate (Wald z test&#x2009;=&#x2009;-2.24; P&#x2009;=&#x2009;.03), or slow recovery (Wald z test&#x2009;=&#x2009;-2.27; P&#x2009;=&#x2009;.02) classes. Greenspace was also associated with greater neural reactivity to reward in the amygdala (n&#x2009;=&#x2009;288; t277&#x2009;=&#x2009;2.83; adjusted P value&#x2009;=&#x2009;0.02); however, reward reactivity did not differ by PTSD trajectory.<br><br>CONCLUSIONS AND RELEVANCE: In this cohort study, greenspace and self-reported individual resources were significantly associated with PTSD trajectories. These findings suggest that factors at multiple ecological levels may contribute to the likelihood of resiliency to PTSD after trauma.},
}
@article {pmid39082646,
year = {2024},
author = {Mallawaarachchi, V and Wickramarachchi, A and Xue, H and Papudeshi, B and Grigson, SR and Bouras, G and Prahl, RE and Kaphle, A and Verich, A and Talamantes-Becerra, B and Dinsdale, EA and Edwards, RA},
title = {Solving genomic puzzles: computational methods for metagenomic binning.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {5},
pages = {},
doi = {10.1093/bib/bbae372},
pmid = {39082646},
issn = {1477-4054},
support = {/NH/NIH HHS/United States ; RC2DK116713/DK/NIDDK NIH HHS/United States ; DP220102915//Australian Research Council/ ; },
mesh = {*Metagenomics/methods ; Computational Biology/methods ; Metagenome ; Algorithms ; Genomics/methods ; },
abstract = {Metagenomics involves the study of genetic material obtained directly from communities of microorganisms living in natural environments. The field of metagenomics has provided valuable insights into the structure, diversity and ecology of microbial communities. Once an environmental sample is sequenced and processed, metagenomic binning clusters the sequences into bins representing different taxonomic groups such as species, genera, or higher levels. Several computational tools have been developed to automate the process of metagenomic binning. These tools have enabled the recovery of novel draft genomes of microorganisms allowing us to study their behaviors and functions within microbial communities. This review classifies and analyzes different approaches of metagenomic binning and different refinement, visualization, and evaluation techniques used by these methods. Furthermore, the review highlights the current challenges and areas of improvement present within the field of research.},
}
@article {pmid39082518,
year = {2024},
author = {Cabral, BVB and Sousa, GJB and Cordeiro, LI and Maranhão, TA and Pereira, MLD},
title = {Temporal Pattern and Spatial Distribution of Tuberculosis Prevalence Associated with Multimorbidity in Brazil.},
journal = {Revista da Sociedade Brasileira de Medicina Tropical},
volume = {57},
number = {},
pages = {e00408},
doi = {10.1590/0037-8682-0625-2023},
pmid = {39082518},
issn = {1678-9849},
mesh = {Humans ; Brazil/epidemiology ; Prevalence ; *Tuberculosis/epidemiology ; *Spatio-Temporal Analysis ; Male ; *Multimorbidity ; Female ; Adult ; Middle Aged ; Chronic Disease/epidemiology ; Socioeconomic Factors ; },
abstract = {BACKGROUND: Four main chronic conditions may be involved in the tuberculosis pathogenic process and/or clinical evolution: HIV/AIDS, diabetes mellitus, mental illness, and Chronic Obstructive Pulmonary Disease. This study aimed to determine the spatiotemporal pattern of tuberculosis (TB) associated with multimorbidity in Brazil.<br><br>METHODS: Ecological study use data from the Notifiable Diseases Information System (SINAN), collected from the electronic portal of the Department of Informatics of the SUS (DATASUS). These data included TB cases that were reported between 2007 and 2021 and were associated with two or more chronic clinical health conditions (multimorbidity).<br><br>RESULTS: A total of 7,795 cases of TB associated with multimorbidity were recorded, with an average growth trend of 4.6% per year (95% Confidence Interval (CI): 3.3-5.9; p<0.001) and higher growth in the first temporal segment (2007 to 2011) (8.9%; 95%CI: 4.2-13.9; p=0.002). The spatial analysis, after Bayesian smoothing, highlighted the main municipalities states of the study, namely: S&#xe3;o Paulo (19.8%; n = 297), Porto Alegre (23.6%; n = 354), and Rio de Janeiro (44.8%; n = 672). The proportion of extremely poor (&#x3b2;=-0.002), the bolsa fam&#xed;lia program (&#x3b2;=0.002), the average per-person income (&#x3b2;=0.001), and the percentage of the population living in households with a density of more than 2 people per bedroom (&#x3b2;=0.001) were related to chronic health conditions.<br><br>CONCLUSIONS: These findings will stimulate public action to manage this situation. However, as this is still a recent topic in the literature, we encourage the development of studies on the synergistic characteristics of TB and other clinical conditions.},
}
@article {pmid39082244,
year = {2024},
author = {Farrell, MJ and Le Guillarme, N and Brierley, L and Hunter, B and Scheepens, D and Willoughby, A and Yates, A and Mideo, N},
title = {The changing landscape of text mining: a review of approaches for ecology and evolution.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2027},
pages = {20240423},
doi = {10.1098/rspb.2024.0423},
pmid = {39082244},
issn = {1471-2954},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Data Mining ; *Ecology/methods ; *Biological Evolution ; *Natural Language Processing ; Machine Learning ; },
abstract = {In ecology and evolutionary biology, the synthesis and modelling of data from published literature are commonly used to generate insights and test theories across systems. However, the tasks of searching, screening, and extracting data from literature are often arduous. Researchers may manually process hundreds to thousands of articles for systematic reviews, meta-analyses, and compiling synthetic datasets. As relevant articles expand to tens or hundreds of thousands, computer-based approaches can increase the efficiency, transparency and reproducibility of literature-based research. Methods available for text mining are rapidly changing owing to developments in machine learning-based language models. We review the growing landscape of approaches, mapping them onto three broad paradigms (frequency-based approaches, traditional Natural Language Processing and deep learning-based language models). This serves as an entry point to learn foundational and cutting-edge concepts, vocabularies, and methods to foster integration of these tools into ecological and evolutionary research. We cover approaches for modelling ecological texts, generating training data, developing custom models and interacting with large language models and discuss challenges and possible solutions to implementing these methods in ecology and evolution.},
}
@article {pmid39080706,
year = {2024},
author = {Hamamoto, K and Mizuyama, M and Nishijima, M and Maeda, A and Gibu, K and Poliseno, A and Iguchi, A and Reimer, JD},
title = {Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {54},
pmid = {39080706},
issn = {2524-6372},
support = {20H00653//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: Marine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions.<br><br>RESULTS: The results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation.<br><br>CONCLUSION: Our findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.},
}
@article {pmid38818975,
year = {2024},
author = {Shi, H and Zhu, Y and Wu, X and Jiang, T and Li, X and Liu, J and Di, Y and Chen, F and Gao, J and Xu, X and Xiao, N and Feng, X and Zhang, P and Wu, Y and La, Q and Li, A and Chen, P and Li, X},
title = {CropMetabolome: a comprehensive metabolome database for major crops cross eight categories.},
journal = {The Plant journal : for cell and molecular biology},
volume = {119},
number = {3},
pages = {1613-1626},
doi = {10.1111/tpj.16858},
pmid = {38818975},
issn = {1365-313X},
support = {2023ZD04073//National Key R&amp;D Program of China/ ; XDA24010400//Strategic Priority Research Program of Chinese Academy of Sciences/ ; BE2023336//Key R&amp;D Program of Jiangsu Province Modern Agriculture/ ; 32270719//National Natural Science Foundation of China/ ; 31900470//National Natural Science Foundation of China/ ; 32200093//National Natural Science Foundation of China/ ; CARS-11//Earmarked Fund for China Agriculture Research System/ ; 2022M713144//China Postdoctoral Science Foundation/ ; },
mesh = {*Crops, Agricultural/metabolism/genetics ; *Metabolome ; *Metabolomics/methods ; *Databases, Factual ; Flavonoids/metabolism ; Mass Spectrometry ; },
abstract = {Chemical compositions of crops are of great agronomical importance, as crops serve as resources for nutrition, energy, and medicines for human and livestock. For crop metabolomics research, the lack of crop reference metabolome and high-quality reference compound mass spectra, as well as utilities for metabolic profiling, has hindered the discovery and functional study of phytochemicals in crops. To meet these challenging needs, we have developed the Crop Metabolome database (abbreviated as CropMetabolome) that is dedicated to the construction of crop reference metabolome, repository, and dissemination of crop metabolomic data, and profiling and analytic tools for metabolomics research. CropMetabolome contains a metabolomics database for more than 50 crops (belonging to eight categories) that integrated self-generated raw mass spectral data and public-source datasets. The reference metabolome for 59 crop species was constructed, which have functions that parallel those of reference genome in genomic studies. CropMetabolome also contains 'Standard compound mass spectral library', 'Flavonoids library', 'Pesticide library', and a set of related analytical tools that enable metabolic profiling based on a reference metabolome (CropRefMetaBlast), annotation and identification of new metabolites (CompoundLibBlast), deducing the structure of novel flavonoid derivatives (FlavoDiscover), and detecting possible residual pesticides in crop samples (PesticiDiscover). In addition, CropMetabolome is a repository to share and disseminate metabolomics data and a platform to promote collaborations to develop reference metabolome for more crop species. CropMetabolome is a comprehensive platform that offers important functions in crop metabolomics research and contributes to improve crop breeding, nutrition, and safety. CropMetabolome is freely available at https://www.cropmetabolome.com/.},
}
@article {pmid37881092,
year = {2024},
author = {Wang, S and Ye, H and Shang, S and Li, Z and Peng, Y and Zhou, P},
title = {A Structure-based Data Set of Protein-peptide Affinities and its Nonredundant Benchmark: Potential Applications in Computational Peptidology.},
journal = {Current medicinal chemistry},
volume = {31},
number = {26},
pages = {4127-4137},
pmid = {37881092},
issn = {1875-533X},
mesh = {*Peptides/chemistry/metabolism ; *Databases, Protein ; *Proteins/chemistry/metabolism ; Protein Binding ; Molecular Docking Simulation ; Ligands ; Humans ; Protein Conformation ; },
abstract = {BACKGROUND: Peptides play crucial roles in diverse cellular functions and participate in many biological processes by interacting with a variety of proteins, which have also been exploited as a promising class of therapeutic agents to target druggable proteins over the past decades. Understanding the intrinsic association between the structure and affinity of protein-peptide interactions (PpIs) should be considerably valuable for the computational peptidology area, such as guiding protein-peptide docking calculations, developing protein-peptide affinity scoring functions, and designing peptide ligands for specific protein receptors.<br><br>OBJECTIVE: We attempted to create a data source for relating PpI structure to affinity.<br><br>METHODS: By exhaustively surveying the whole protein data bank (PDB) database as well as the ontologically enriched literature information, we manually curated a structure- based data set of protein-peptide affinities, PpI[S/A]DS, which assembled over 350 PpI complex samples with both the experimentally measured structure and affinity data. The data set was further reduced to a nonredundant benchmark consisting of 102 culled samples, PpI[S/A]BM, which only selected those of structurally reliable, functionally diverse and evolutionarily nonhomologous.<br><br>RESULTS: The collected structures were resolved at a high-resolution level with either Xray crystallography or solution NMR, while the deposited affinities were characterized by dissociation constant, i.e. Kd value, which is a direct biophysical measure of the intermolecular interaction strength between protein and peptide, ranging from subnanomolar to millimolar levels. The PpI samples in the set/benchmark were arbitrarily classified into &#x3b1;-helix, partial &#x3b1;-helix, &#x3b2;-sheet formed through binding, &#x3b2;-strand formed through selffolding, mixed, and other irregular ones, totally resulting in six classes according to the secondary structure of their peptide ligands. In addition, we also categorized these PpIs in terms of their biological function and binding behavior.<br><br>CONCLUSION: The PpI[S/A]DS set and PpI[S/A]BM benchmark can be considered a valuable data source in the computational peptidology community, aiming to relate the affinity to structure for PpIs.},
}
@article {pmid38909735,
year = {2024},
author = {Su, F and Huo, D and Yang, H and Sun, L},
title = {CircRNA8388 functions as the sponge for miR-2392 during intestinal regeneration in sea cucumber Apostichopus japonicus.},
journal = {International journal of biological macromolecules},
volume = {274},
number = {Pt 2},
pages = {133302},
doi = {10.1016/j.ijbiomac.2024.133302},
pmid = {38909735},
issn = {1879-0003},
mesh = {Animals ; Gene Expression Profiling ; Gene Expression Regulation ; Gene Ontology ; *Intestines ; *MicroRNAs/genetics ; *Regeneration/genetics ; *RNA, Circular/genetics ; *Stichopus/genetics ; },
abstract = {The sea cucumber Apostichopus japonicus can expel internal organs under stress and regenerate them subsequently. However, growth is delayed during regeneration, significantly impacting the industry. Circular RNAs (circRNAs) are single-stranded circular RNA molecules produced through alternative splicing of mRNA precursors. They play crucial roles in regulating gene expression via the ceRNA mechanism. In this study, circRNA profiles of control and regenerated intestines were constructed. A total of 15,874 circRNAs were identified, with a length of 300-350 nucleotides (nt) being the most abundant. Sanger sequencing confirmed the circular structure of circRNA398. Compared with the normal intestine, 50 and 83 differentially expressed circRNAs (DE-circRNAs) were identified in the regenerated intestine at 1 and 3 days post evisceration (dpe), respectively. Gene ontology (GO) terms for signal transduction and development regulation were most significantly enriched in 1dpeVScon and 3dpeVScon treatments, respectively. The dual-luciferase assay revealed that circRNA8388 functions as a sponge for miR-2392, participating in the remodeling of the extracellular matrix (ECM). In conclusion, these findings will contribute to the enhancement of the non-coding RNA database for echinoderms and lay the groundwork for future investigations into circRNA regulation during intestinal regeneration.},
}
@article {pmid38850116,
year = {2024},
author = {Yi, X and Kemppainen, P and Merilä, J},
title = {SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering.},
journal = {Molecular ecology resources},
volume = {24},
number = {6},
pages = {e13985},
doi = {10.1111/1755-0998.13985},
pmid = {38850116},
issn = {1755-0998},
support = {N_HKU763/21//National Natural Science Foundation of China/Research Grants Council (RGC) Joint Research Scheme/ ; },
mesh = {*Linkage Disequilibrium ; *Sex Chromosomes/genetics ; Computational Biology/methods ; Animals ; Male ; Female ; Cluster Analysis ; },
abstract = {Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.},
}
@article {pmid38775247,
year = {2024},
author = {Oliveira, S and Marchi, N and Excoffier, L},
title = {Assessing the limits of local ancestry inference from small reference panels.},
journal = {Molecular ecology resources},
volume = {24},
number = {6},
pages = {e13981},
doi = {10.1111/1755-0998.13981},
pmid = {38775247},
issn = {1755-0998},
support = {310030_188883//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Genetics, Population/methods ; Humans ; Computational Biology/methods ; },
abstract = {Admixture is a common biological phenomenon among populations of the same or different species. Identifying admixed tracts within individual genomes can provide valuable information to date admixture events, reconstruct ancestry-specific demographic histories, or detect adaptive introgression, genetic incompatibilities, as well as regions of the genomes affected by (associative-) overdominance. Although many local ancestry inference (LAI) methods have been developed in the last decade, their performance was accessed using large reference panels, which are rarely available for non-model organisms or ancient samples. Moreover, the demographic conditions for which LAI becomes unreliable have not been explicitly outlined. Here, we identify the demographic conditions for which local ancestries can be best estimated using very small reference panels. Furthermore, we compare the performance of two LAI methods (RFMix and MOSAIC) with the performance of a newly developed approach (simpLAI) that can be used even when reference populations consist of single individuals. Based on simulations of various demographic models, we also determine the limits of these LAI tools and propose post-painting filtering steps to reduce false-positive rates and improve the precision and accuracy of the inferred admixed tracts. Besides providing a guide for using LAI, our work shows that reasonable inferences can be obtained from a single diploid genome per reference under demographic conditions that are not uncommon among past human groups and non-model organisms.},
}
@article {pmid38775206,
year = {2024},
author = {Veglia, AJ and Rivera-Vicéns, RE and Grupstra, CGB and Howe-Kerr, LI and Correa, AMS},
title = {vAMPirus: A versatile amplicon processing and analysis program for studying viruses.},
journal = {Molecular ecology resources},
volume = {24},
number = {6},
pages = {e13978},
doi = {10.1111/1755-0998.13978},
pmid = {38775206},
issn = {1755-0998},
support = {OCE 22-24354//Directorate for Biological Sciences/ ; OCE-2145472//Directorate for Biological Sciences/ ; //Wagoner Foreign Study Award/ ; //Kirk W. Dotson Endowed Graduate Fellowship in Ecology and Evolutionary Biology/ ; //Lewis and Clark Grants for Exploration/ ; 100009646//Gulf Research Program of the National Academies of Sciences/ ; },
mesh = {*Software ; Computational Biology/methods ; DNA Viruses/genetics/classification ; Viruses/genetics/classification/isolation &amp; purification ; RNA Viruses/genetics/classification/isolation &amp; purification ; Phylogeny ; },
abstract = {Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a user-friendly, comprehensive, and versatile DNA and RNA virus amplicon sequence analysis program, designed to support investigators in exploring virus amplicon sequencing data and running informed, reproducible analyses. vAMPirus intakes raw virus amplicon libraries and, by default, performs nucleotide- and amino acid-based analyses to produce results such as sequence abundance information, taxonomic classifications, phylogenies and community diversity metrics. The vAMPirus analytical framework leverages 16 different opensource tools and provides optional approaches that can increase the ratio of biological signal-to-noise and thereby reveal patterns that would have otherwise been masked. Here, we validate the vAMPirus analytical framework and illustrate its implementation as a general virus amplicon sequencing workflow by recapitulating findings from two previously published double-stranded DNA virus datasets. As a case study, we also apply the program to explore the diversity and distribution of a coral reef-associated RNA virus. vAMPirus is streamlined within Nextflow, offering straightforward scalability, standardization and communication of virus lineage-specific analyses. The vAMPirus framework is designed to be adaptable; community-driven analytical standards will continue to be incorporated as the field advances. vAMPirus supports researchers in revealing patterns of virus diversity and population dynamics in nature, while promoting study reproducibility and comparability.},
}
@article {pmid39075558,
year = {2024},
author = {Pinheiro-Junior, EL and Alirahimi, E and Peigneur, S and Isensee, J and Schiffmann, S and Erkoc, P and Fürst, R and Vilcinskas, A and Sennoner, T and Koludarov, I and Hempel, BF and Tytgat, J and Hucho, T and von Reumont, BM},
title = {Diversely evolved xibalbin variants from remipede venom inhibit potassium channels and activate PKA-II and Erk1/2 signaling.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {164},
pmid = {39075558},
issn = {1741-7007},
support = {2016/04761-4//S&#xe3;o Paulo Research Foundation/ ; GOC2319 N//F.W.O.-Vlaanderen/ ; GOA4919 N//F.W.O.-Vlaanderen/ ; G0E7120N//F.W.O.-Vlaanderen/ ; PDM/19/164//KU Leuven funding/ ; CA19144 EUVEN//EU COST Action/ ; },
abstract = {BACKGROUND: The identification of novel toxins from overlooked and taxonomically exceptional species bears potential for various pharmacological applications. The remipede Xibalbanus tulumensis, an underwater cave-dwelling crustacean, is the only crustacean for which a venom system has been described. Its venom contains several xibalbin peptides that have an inhibitor cysteine knot (ICK) scaffold.<br><br>RESULTS: Our screenings revealed that all tested xibalbin variants particularly inhibit potassium channels. Xib1 and xib13 with their eight-cysteine domain similar to spider knottins also inhibit voltage-gated sodium channels. No activity was noted on calcium channels. Expanding the functional testing, we demonstrate that xib1 and xib13 increase PKA-II and Erk1/2 sensitization signaling in nociceptive neurons, which may initiate pain sensitization. Our phylogenetic analysis suggests that xib13 either originates from the common ancestor of pancrustaceans or earlier while xib1 is more restricted to remipedes. The ten-cysteine scaffolded xib2 emerged from xib1, a result that is supported by our phylogenetic and machine learning-based analyses.<br><br>CONCLUSIONS: Our functional characterization of synthesized variants of xib1, xib2, and xib13 elucidates their potential as inhibitors of potassium channels in mammalian systems. The specific interaction of xib2 with Kv1.6 channels, which are relevant to treating variants of epilepsy, shows potential for further studies. At higher concentrations, xib1 and xib13 activate the kinases PKA-II and ERK1/2 in mammalian sensory neurons, suggesting pain sensitization and potential applications related to pain research and therapy. While tested insect channels suggest that all probably act as neurotoxins, the biological function of xib1, xib2, and xib13 requires further elucidation. A novel finding on their evolutionary origin is the apparent emergence of X. tulumensis-specific xib2 from xib1. Our study is an important cornerstone for future studies to untangle the origin and function of these enigmatic proteins as important components of remipede but also other pancrustacean and arthropod venoms.},
}
@article {pmid39071792,
year = {2023},
author = {Falk, S and Gorše, I and , and , and , and , and , and , },
title = {The genome sequence of the hawkweed Cheilosia, Cheilosia urbana (Meigen, 1822).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {311},
pmid = {39071792},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Cheilosia urbana (the hawkweed Cheilosia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 546.9 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length.},
}
@article {pmid39068884,
year = {2024},
author = {Fan, Q and Huang, S and Guo, J and Xie, Y and Chen, M and Chen, Y and Qi, W and Liu, H and Jia, Z and Hu, H and Qu, J},
title = {Spatiotemporal distribution and transport flux of organophosphate esters in the sediment of the Yangtze River.},
journal = {Journal of hazardous materials},
volume = {477},
number = {},
pages = {135312},
doi = {10.1016/j.jhazmat.2024.135312},
pmid = {39068884},
issn = {1873-3336},
abstract = {The Yangtze River Basin is an important area for organophosphate esters (OPEs) consumption and emission. Studies proved high OPE detection in Yangtze River water, but there is limited information about the spatiotemporal distribution and transport flux of OPEs in sediment. The present study investigated 16 OPEs in sediment from upstream to mid-downstream of the Yangtze River. The mean concentration of OPEs was 84.30 ng/g, and alkyl-OPEs was the primary component. Great specific surface area and high content of organic carbon significantly increased OPE concentration in Three Gorges Reservoir (TGR) by physical adsorption and chemical bonds (p < 0.05), making TGR the most contaminated area in mainstream. No significant differences in OPE constituents were found in seasonal distribution. Four potential sources of OPEs were identified by principal component analysis and self-organizing maps, and traffic emissions were the dominant source for OPEs. The hazard quotient model results indicated that aryl-OPEs showed moderate risks in the mainstream of Yangtze River, alkyl-OPEs and Cl-OPEs showed low risks. TGR was a significant sink of OPEs in Yangtze River and buried 7.41 tons of OPEs in 2020, a total of 14.87 tons of OPE were transported into the sea by sediment.},
}
@article {pmid39069513,
year = {2024},
author = {Xu, R and Xu, C and Li, Z and Zheng, T and Yu, W and Yang, C},
title = {Boundary guidance network for medical image segmentation.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17345},
pmid = {39069513},
issn = {2045-2322},
support = {2019YFC0117800//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Urinary Bladder Neoplasms/diagnostic imaging/pathology ; Image Processing, Computer-Assisted/methods ; Deep Learning ; Magnetic Resonance Imaging/methods ; Tomography, X-Ray Computed/methods ; Neural Networks, Computer ; Algorithms ; Cystoscopy/methods ; Image Interpretation, Computer-Assisted/methods ; },
abstract = {Accurate segmentation of the tumor area is crucial for the treatment and prognosis of patients with bladder cancer. Cystoscopy is the gold standard for diagnosing bladder tumors. However, The vast majority of current work uses deep learning to identify and segment tumors from CT and MRI findings, and rarely involves cystoscopy findings. Accurately segmenting bladder tumors remains a great challenge due to their diverse morphology and fuzzy boundaries. In order to solve the above problems, this paper proposes a medical image segmentation network with boundary guidance called boundary guidance network. This network combines local features extracted by CNNs and long-range dependencies between different levels inscribed by Parallel ViT, which can capture tumor features more effectively. The Boundary extracted module is designed to extract boundary features and utilize the boundary features to guide the decoding process. Foreground-background dual-channel decoding is performed by boundary integrated module. Experimental results on our proposed new cystoscopic bladder tumor dataset (BTD) show that our method can efficiently perform accurate segmentation of tumors and retain more boundary information, achieving an IoU score of 91.3%, a Hausdorff Distance of 10.43, an mAP score of 85.3%, and a F1 score of 94.8%. On BTD and three other public datasets, our model achieves the best scores compared to state-of-the-art methods, which proves the effectiveness of our model for common medical image segmentation.},
}
@article {pmid39066932,
year = {2024},
author = {Seldeslachts, A and Maurstad, MF and Øyen, JP and Undheim, EAB and Peigneur, S and Tytgat, J},
title = {Exploring oak processionary caterpillar induced lepidopterism (Part 1): unveiling molecular insights through transcriptomics and proteomics.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {81},
number = {1},
pages = {311},
pmid = {39066932},
issn = {1420-9071},
support = {GOC2319N, GOA4919N, and G0E7120N//Fonds Wetenschappelijk Onderzoek/ ; 12W7822N//Fonds Wetenschappelijk Onderzoek/ ; 1S51521N and 1S51523N//Fonds Wetenschappelijk Onderzoek/ ; CA19144 EUVEN//European Cooperation in Science and Technology/ ; FRIPRO-YRT Fellowship no. 287462//Norwegian Research Council/ ; 101039862//H2020 European Research Council/ ; },
mesh = {Animals ; *Proteomics/methods ; *Transcriptome ; *Moths/genetics ; Arthropod Venoms ; Larva/metabolism ; Quercus ; Gene Expression Profiling ; Allergens/immunology ; Insect Proteins/genetics/metabolism ; Proteome/metabolism ; Computational Biology/methods ; },
abstract = {Lepidopterism, a skin inflammation condition caused by direct or airborne exposure to irritating hairs (setae) from processionary caterpillars, is becoming a significant public health concern. Recent outbreaks of the oak processionary caterpillar (Thaumetopoea processionea) have caused noteworthy health and economic consequences, with a rising frequency expected in the future, exacerbated by global warming promoting the survival of the caterpillar. Current medical treatments focus on symptom relief due to the lack of an effective therapy. While the source is known, understanding the precise causes of symptoms remain incomplete understood. In this study, we employed an advanced method to extract venom from the setae and identify the venom components through high-quality de novo transcriptomics, venom proteomics, and bioinformatic analysis. A total of 171 venom components were identified, including allergens, odorant binding proteins, small peptides, enzymes, enzyme inhibitors, and chitin biosynthesis products, potentially responsible for inflammatory and allergic reactions. This work presents the first comprehensive proteotranscriptomic database of T. processionea, contributing to understanding the complexity of lepidopterism. Furthermore, these findings hold promise for advancing therapeutic approaches to mitigate the global health impact of T. processionea and related caterpillars.},
}
@article {pmid39059890,
year = {2024},
author = {Tikhomirov, L and Semmler, C and McCradden, M and Searston, R and Ghassemi, M and Oakden-Rayner, L},
title = {Medical artificial intelligence for clinicians: the lost cognitive perspective.},
journal = {The Lancet. Digital health},
volume = {6},
number = {8},
pages = {e589-e594},
doi = {10.1016/S2589-7500(24)00095-5},
pmid = {39059890},
issn = {2589-7500},
mesh = {*Artificial Intelligence ; Humans ; *Clinical Decision-Making/methods ; Cognition ; Decision Support Systems, Clinical ; Radiology ; },
abstract = {The development and commercialisation of medical decision systems based on artificial intelligence (AI) far outpaces our understanding of their value for clinicians. Although applicable across many forms of medicine, we focus on characterising the diagnostic decisions of radiologists through the concept of ecologically bounded reasoning, review the differences between clinician decision making and medical AI model decision making, and reveal how these differences pose fundamental challenges for integrating AI into radiology. We argue that clinicians are contextually motivated, mentally resourceful decision makers, whereas AI models are contextually stripped, correlational decision makers, and discuss misconceptions about clinician-AI interaction stemming from this misalignment of capabilities. We outline how future research on clinician-AI interaction could better address the cognitive considerations of decision making and be used to enhance the safety and usability of AI models in high-risk medical decision-making contexts.},
}
@article {pmid38507308,
year = {2024},
author = {Sánchez Reyes, LL and McTavish, EJ and O'Meara, B},
title = {DateLife: Leveraging Databases and Analytical Tools to Reveal the Dated Tree of Life.},
journal = {Systematic biology},
volume = {73},
number = {2},
pages = {470-485},
pmid = {38507308},
issn = {1076-836X},
support = {ABI-1458603//National Science Foundation/ ; DBI-0905606//National Evolutionary Synthesis Center/ ; ABI-1759846//Open Tree of Life project/ ; ABI-1458572//Phylotastic project/ ; },
mesh = {*Phylogeny ; *Classification/methods ; *Software ; Databases, Factual ; },
abstract = {Chronograms-phylogenies with branch lengths proportional to time-represent key data on timing of evolutionary events, allowing us to study natural processes in many areas of biological research. Chronograms also provide valuable information that can be used for education, science communication, and conservation policy decisions. Yet, achieving a high-quality reconstruction of a chronogram is a difficult and resource-consuming task. Here we present DateLife, a phylogenetic software implemented as an R package and an R Shiny web application available at www.datelife.org, that provides services for efficient and easy discovery, summary, reuse, and reanalysis of node age data mined from a curated database of expert, peer-reviewed, and openly available chronograms. The main DateLife workflow starts with one or more scientific taxon names provided by a user. Names are processed and standardized to a unified taxonomy, allowing DateLife to run a name match across its local chronogram database that is curated from Open Tree of Life's phylogenetic repository, and extract all chronograms that contain at least two queried taxon names, along with their metadata. Finally, node ages from matching chronograms are mapped using the congruification algorithm to corresponding nodes on a tree topology, either extracted from Open Tree of Life's synthetic phylogeny or one provided by the user. Congruified node ages are used as secondary calibrations to date the chosen topology, with or without initial branch lengths, using different phylogenetic dating methods such as BLADJ, treePL, PATHd8, and MrBayes. We performed a cross-validation test to compare node ages resulting from a DateLife analysis (i.e, phylogenetic dating using secondary calibrations) to those from the original chronograms (i.e, obtained with primary calibrations), and found that DateLife's node age estimates are consistent with the age estimates from the original chronograms, with the largest variation in ages occurring around topologically deeper nodes. Because the results from any software for scientific analysis can only be as good as the data used as input, we highlight the importance of considering the results of a DateLife analysis in the context of the input chronograms. DateLife can help to increase awareness of the existing disparities among alternative hypotheses of dates for the same diversification events, and to support exploration of the effect of alternative chronogram hypotheses on downstream analyses, providing a framework for a more informed interpretation of evolutionary results.},
}
@article {pmid37947402,
year = {2023},
author = {Alexander, H and Hu, SK and Krinos, AI and Pachiadaki, M and Tully, BJ and Neely, CJ and Reiter, T},
title = {Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton.},
journal = {mBio},
volume = {14},
number = {6},
pages = {e0167623},
pmid = {37947402},
issn = {2150-7511},
support = {OCE-1948025//National Science Foundation (NSF)/ ; OCE-0939564, OCE-194777, OCE-2327203//National Science Foundation (NSF)/ ; 931886//Simons Foundation (SF)/ ; DE-SC0020347//U.S. Department of Energy (DOE)/ ; OCE-1924492//National Science Foundation (NSF)/ ; OCE-0939654//National Science Foundation (NSF)/ ; },
mesh = {*Metagenomics/methods ; *Plankton/genetics/classification ; *Eukaryota/genetics/classification ; *Oceans and Seas ; *Metagenome ; Biodiversity ; Computational Biology/methods ; Phylogeny ; Seawater/microbiology ; Phylogeography ; },
abstract = {Single-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.},
}
@article {pmid39060281,
year = {2024},
author = {Khaki, JJ and Meiring, JE and Thindwa, D and Henrion, MYR and Jere, TM and Msuku, H and , and Heyderman, RS and Gordon, MA and Giorgi, E},
title = {Modelling Salmonella Typhi in high-density urban Blantyre neighbourhood, Malawi, using point pattern methods.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17164},
pmid = {39060281},
issn = {2045-2322},
support = {106158/Z/14/Z/WT_/Wellcome Trust/United Kingdom ; 617 OPP1141321//Bill and Melinda Gates Foundation/ ; },
abstract = {Salmonella Typhi is a human-restricted pathogen that is transmitted by the faecal-oral route and causative organism of typhoid fever. Using health facility data from 2016 to 2020, this study focuses on modelling the spatial variation in typhoid risk in Ndirande township in Blantyre. To pursue this objective, we developed a marked inhomogeneous Poisson process model that allows us to incorporate both individual-level and environmental risk factors. The results from our analysis indicate that typhoid cases are spatially clustered, with the incidence decreasing by 54% for a unit increase in the water, sanitation, and hygiene (WASH) score. Typhoid intensity was also higher in children aged below 18 years than in adults. However, our results did not show evidence of a strong temporal variation in typhoid incidence. We also discuss the inferential benefits of using point pattern models to characterise the spatial variation in typhoid risk and outline possible extensions of the proposed modelling framework.},
}
@article {pmid39060268,
year = {2024},
author = {Tagliaferro, S and Maio, S and Pirona, F and Stanisci, I and Sarno, G and Silvi, P and Kermenidou, M and Papaioannou, N and Perchard, R and Prpic, I and Polanska, K and Jerzynska, J and Ramos, E and Rovira, J and Belmonte, J and Snoj Tratnik, JS and Horvat, M and Kocman, D and Spiric, Z and Zickella, J and Fasola, S and La Grutta, S and Malizia, V and Montalbano, L and , and , and Baldacci, S and Annesi-Maesano, I},
title = {Assessing external exposome by implementing an Environmental Data Management System using Open Data.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {17142},
pmid = {39060268},
issn = {2045-2322},
support = {603946//European Commission/ ; },
abstract = {Due to the increasing importance of exposome in environmental epidemiology, feasibility and usefulness of an Environmental Data Management System (EDMS) using Open Data was evaluated. The EDMS includes data from 10 European cities (Celje (Slovenia), Łódź (Poland), Manchester (UK), Palermo (Italy), Paris (France), Porto (Portugal), Regensburg (Germany), Reus (Spain), Rijeka (Croatia), Thessaloniki (Greece)) about external non-specific and specific exposome factors at the city or country level (2017-2020). Findings showed that the highest values of life expectancy were in Reus females (86 years) and Palermo males (81 years). UK had the highest obesity rate (28%), Croatia the highest prescribed drug consumption (62%), Greece and Portugal the highest smoking rates (37%, 42%) and daily alcohol consumption (21%), respectively. The most polluted cities were Thessaloniki for PM10 (38 µg/m[3]), Łódź for PM2.5 (25 µg/m[3]), Porto for NO2 (62 µg/m[3]) and Rijeka for O3 (92 µg/m[3]). Thessaloniki had the highest grey space (98%) and Łódź the highest cumulative amount of pollen (39,041 p/m[3]). The highest daily noise levels ≥ 55 dB was in Reus (81% to traffic) and Regensburg (21% to railway). In drinking water, arsenic had the highest value in Thessaloniki (6.4 µg/L), boron in Celje (24 mg/L) and lead in Paris (46.7 µg/L). Portugal and Greece showed the highest pesticide residues in food (7%). In conclusion, utilizing open-access databases enables the translation of research findings into actionable strategies for public health interventions.},
}
@article {pmid39057817,
year = {2024},
author = {Chanda, MM and Purse, BV and Sedda, L and Benz, D and Prasad, M and Reddy, YN and Yarabolu, KR and Byregowda, SM and Carpenter, S and Prasad, G and Rogers, DJ},
title = {Bluetongue Risk Map for Vaccination and Surveillance Strategies in India.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
doi = {10.3390/pathogens13070590},
pmid = {39057817},
issn = {2076-0817},
support = {BB/H009167/1//BBSRC, DFID, Scottish government/ ; },
abstract = {Bluetongue virus (BTV, Sedoreoviridae: Orbivirus) causes an economically important disease, namely, bluetongue (BT), in domestic and wild ruminants worldwide. BTV is endemic to South India and has occurred with varying severity every year since the virus was first reported in 1963. BT can cause high morbidity and mortality to sheep flocks in this region, resulting in serious economic losses to subsistence farmers, with impacts on food security. The epidemiology of BTV in South India is complex, characterized by an unusually wide diversity of susceptible ruminant hosts, multiple vector species biting midges (Culicoides spp., Diptera: Ceratopogonidae), which have been implicated in the transmission of BTV and numerous co-circulating virus serotypes and strains. BT presence data (1997-2011) for South India were obtained from multiple sources to develop a presence/absence model for the disease. A non-linear discriminant analysis (NLDA) was carried out using temporal Fourier transformed variables that were remotely sensed as potential predictors of BT distribution. Predictive performance was then characterized using a range of different accuracy statistics (sensitivity, specificity, and Kappa). The top ten variables selected to explain BT distribution were primarily thermal metrics (land surface temperature, i.e., LST, and middle infrared, i.e., MIR) and a measure of plant photosynthetic activity (the Normalized Difference Vegetation Index, i.e., NDVI). A model that used pseudo-absence points, with three presence and absence clusters each, outperformed the model that used only the recorded absence points and showed high correspondence with past BTV outbreaks. The resulting risk maps may be suitable for informing disease managers concerned with vaccination, prevention, and control of BT in high-risk areas and for planning future state-wide vector and virus surveillance activities.},
}
@article {pmid39056317,
year = {2024},
author = {Stulberg, EL and Lisabeth, L and Schneider, ALC and Skolarus, L and Kershaw, KN and Zheutlin, AR and Harris, BRE and Sarpong, D and Wong, KH and Sheth, KN and de Havenon, A},
title = {Correlations of Socioeconomic and Clinical Determinants with United States County-Level Stroke Prevalence.},
journal = {Annals of neurology},
volume = {},
number = {},
pages = {},
doi = {10.1002/ana.27039},
pmid = {39056317},
issn = {1531-8249},
support = {1R38HL167282-01/HI/NHLBI NIH HHS/United States ; R01 HL156906/NH/NIH HHS/United States ; R01 HL152741/NH/NIH HHS/United States ; R01 NS038916/NH/NIH HHS/United States ; R01 NS107463/NH/NIH HHS/United States ; K23NS123340/NS/NINDS NIH HHS/United States ; U01NS106513/NS/NINDS NIH HHS/United States ; R01NS110721/NS/NINDS NIH HHS/United States ; R01NR018335/NS/NINDS NIH HHS/United States ; R01EB301114/NS/NINDS NIH HHS/United States ; R01MD016178/NS/NINDS NIH HHS/United States ; U24NS107215/NS/NINDS NIH HHS/United States ; U24NS107136/NS/NINDS NIH HHS/United States ; U24NS129500/NS/NINDS NIH HHS/United States ; K23NS105924/NS/NINDS NIH HHS/United States ; UG3NS130228/NS/NINDS NIH HHS/United States ; R01NS130189/NS/NINDS NIH HHS/United States ; W81XWH-21-1-0590//Department of Defense/ ; HT9425-23-1-0981//Department of Defense/ ; /AG/NIA NIH HHS/United States ; /MD/NIMHD NIH HHS/United States ; //American Heart Association/American Stroke Association/ ; },
abstract = {Socioeconomic status (SES) is a multi-faceted theoretical construct associated with stroke risk and outcomes. Knowing which SES measures best correlate with population stroke metrics would improve its accounting in observational research and inform interventions. Using the Centers for Disease Control and Prevention's (CDC) Population Level Analysis and Community Estimates (PLACES) and other publicly available databases, we conducted an ecological study comparing correlations of different United States county-level SES, health care access and clinical risk factor measures with age-adjusted stroke prevalence. The prevalence of adults living below 150% of the federal poverty level most strongly correlated with stroke prevalence compared to other SES and non-SES measures (correlation coefficient = 0.908, R[2] = 0.825; adjusted partial correlation coefficient: 0.589, R[2] = 0.347). ANN NEUROL 2024.},
}
@article {pmid39056051,
year = {2024},
author = {Navarro-Farfán, MDM and García-Romero, L and Martínez-Cinco, MA and Domínguez-Sánchez, C and Sánchez-Quispe, ST},
title = {Methodology for the assessment of poor-data water resources.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17755},
doi = {10.7717/peerj.17755},
pmid = {39056051},
issn = {2167-8359},
mesh = {*Water Resources ; Models, Theoretical ; Hydrology/methods ; Environmental Monitoring/methods ; },
abstract = {Surface hydrologic modeling becomes a problem when insufficient spatial and temporal information is available. It is common to have useful modeling periods of less than 15 years. The purpose of this work is to develop a methodology that allows the selection of meteorological and hydrometric stations that are suitable for modeling when information is scarce in the area. Based on the scarcity of data, a series of statistical tests are proposed to eliminate stations according to a decision-making process. Although the number of stations decreases drastically, the information used is reliable and of adequate quality, ensuring less uncertainty in the surface simulation models. Individual basin modeling can be carried out considering the poor data. The transfer of parameters can be applied through the nesting of basins to have information distributed over an extensive area. Therefore, temporally and spatially extended modeling can be achieved with information that preserves statistical parameters over time. If data management and validation is performed, the modeled watersheds are well represented; if this is not done, only 26% to 50% of the runoff is represented.},
}
@article {pmid39053536,
year = {2024},
author = {He, M and Cui, J and Yi, Y and Chen, HW and Zhang, Q and Li, L and Huang, L and Hong, S},
title = {Vegetation increases global climate vulnerability risk by shifting climate zones in response to rising atmospheric CO2.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {174810},
doi = {10.1016/j.scitotenv.2024.174810},
pmid = {39053536},
issn = {1879-1026},
abstract = {Global climate zones are experiencing widespread shifts with ongoing rise in atmospheric CO2, influencing vegetation growth and shifting its distributions to challenge ecosystem structure and function, posing threats on ecological and societal safety. However, how rising atmospheric CO2 affects the pace of global climate zone shifts is highly uncertain. More attentions are urgently required on understanding the underlying mechanisms and quantifications of regional climate vulnerability in response to rising CO2. In this study, we employ nine Earth system models from CMIP6 to investigate global climate zone shifts with rising CO2, unravel the effects of vegetation physiological response (PHY), and categorize climate vulnerable regions depending on the extent of climate zone shifts. We find that climate zone reshapes over half of the global land area, 16.8 % of which is contributed by PHY at 4 × CO2. Intriguingly, besides warming, PHY-induced precipitation changes and their interactions with warming manipulate about two-fifths of PHY-forced shifts, providing effective suggestions for model improvement in future predictions in climate zone shifts. Aided with PHY effects, 4 × CO2 imposes substantial climate zone shifts over about one-fifth of the global land area, suggesting substantial changes in local climate and ecosystem structure and functions. Hence, those regions would experience strong climate vulnerability, and face high risk of climate extremes, water scarcity and food production. Our results quantitatively identify the vulnerable regions and unravel the underlying drivers, provide scientific insights to prioritize conservation and restoration efforts to ensure ecological and social safety globally.},
}
@article {pmid39051209,
year = {2024},
author = {de Souza, OF and Araújo, ACB and Vieira, LB and Bachur, JA and Lopez, AGP and Gonçalves, TG and de Abreu, LC},
title = {Sex Disparity in Stroke Mortality among Adults: A Time Series Analysis in the Greater Vitoria Region, Brazil (2000-2021).},
journal = {Epidemiologia (Basel, Switzerland)},
volume = {5},
number = {3},
pages = {402-410},
doi = {10.3390/epidemiologia5030029},
pmid = {39051209},
issn = {2673-3986},
abstract = {The disparity between the sexes in stroke mortality has been demonstrated in people from different locations. The objective of this study was to analyze the disparity between sexes in stroke mortality in adults in the metropolitan area of Greater Vitoria between 2000 and 2021. Ecological time series design was conducted with a database of the Brazilian Health System Informatics Department. The annual percentage change and average annual percentage change were calculated through joinpoint regression. Pairwise comparisons using parallelism and coincidence tests were applied to compare temporal trends between men and women. Men had higher mortality rates in most years between 2000 and 2021. In contrast, women had higher proportional mortality values in all years evaluated from 2000 to 2021. The paired comparison revealed a disparity between the sexes in the proportional mortality time series (parallelism test: p = 0.003; coincidence test: p < 0.001). However, the time series of the mortality rates showed no disparity between the sexes (parallelism test: p = 0.114; coincidence test: p = 0.093). From 2000 to 2021, there was a disparity in proportional mortality from stroke between the sexes of the population in the metropolitan area of Greater Vitoria, Brazil. However, the time series of mortality rates between the sexes did not reveal any disparity in the study period.},
}
@article {pmid39050029,
year = {2024},
author = {Kryukov, K and Nakahama, N and Kuraku, S},
title = {Genome assembly catalog for species in the Japanese Red List: unlocking endangered biodiversity through genomic inventory.},
journal = {F1000Research},
volume = {13},
number = {},
pages = {583},
pmid = {39050029},
issn = {2046-1402},
mesh = {Animals ; *Biodiversity ; *Endangered Species ; Genome ; *Genomics/methods ; Japan ; },
abstract = {Improvements in DNA sequencing technology are allowing the dramatic increase of whole genome data for a wide variety of species. Such genome sequence data can assist the monitoring of intraspecific genetic diversity, but is often lacking for threatened species. In this project, we focused on the national Red List, a catalog of extinct and threatened species, issued by the Japanese government. We combined the data included in it with the record of genome assembly in NCBI and tabulated the assembly availability of the species in the list. The combined data shows a low percentage (2.1%) of the availability of whole genome sequence data for the taxa ranked on the Japanese Red List as well as a strong bias towards mammals and birds in Animalia and vascular plants in Plantae. Our data presentation highlights potential systematic limitations in genome sequencing (e.g., budget for sequencing large genomes of amphibians) and instructs future policies including which taxon needs more effort for genome sequencing. The resultant tables are available in the original website https://treethinkers.nig.ac.jp/redlist/ and are regularly updated.},
}
@article {pmid39049113,
year = {2024},
author = {Yurkov, A and Visagie, CM and Crous, PW and Hashimoto, A and Baschien, C and Begerow, D and Kemler, M and Schoutteten, N and Stadler, M and Wijayawardene, NN and Hyde, KD and Zhang, N and Boekhout, T and , and May, TW and Thines, M and Hawksworth, DL},
title = {Cultures as types and the utility of viable specimens for fungal nomenclature.},
journal = {IMA fungus},
volume = {15},
number = {1},
pages = {20},
pmid = {39049113},
issn = {2210-6340},
abstract = {The debates over the requirement of the International Code of Nomenclature for algae, fungi, and plants (ICNafp) for a viable specimen to represent the name-bearing type material for a species or infraspecific taxon have a long history. Taxonomy of fungi commonly studied as living cultures exemplified by yeasts and moulds, strongly depend on viable reference material. The availability of viable cultures is also particularly useful for several groups of filamentous and dimorphic fungi. While the preservation of metabolically inactive cultures is permitted and recommended by the ICNafp, there is room for improvement. Below, we review the history and current status of cultures as the name-bearing type material under the Code. We also present a roadmap with tasks to be achieved in order to establish a stable nomenclatural system that properly manages taxa typified by viable specimens. Furthermore, we propose setting up rules and defining the nomenclatural status of ex-type cultures under Chapter F, the section of the ICNafp that includes provisions specific to names of fungi.},
}
@article {pmid39048683,
year = {2024},
author = {Gauci, V and Pangala, SR and Shenkin, A and Barba, J and Bastviken, D and Figueiredo, V and Gomez, C and Enrich-Prast, A and Sayer, E and Stauffer, T and Welch, B and Elias, D and McNamara, N and Allen, M and Malhi, Y},
title = {Global atmospheric methane uptake by upland tree woody surfaces.},
journal = {Nature},
volume = {631},
number = {8022},
pages = {796-800},
pmid = {39048683},
issn = {1476-4687},
mesh = {*Methane/metabolism/analysis ; *Atmosphere/chemistry ; *Trees/metabolism ; *Wood/metabolism/chemistry ; *Forests ; Tropical Climate ; Taiga ; },
abstract = {Methane is an important greenhouse gas[1], but the role of trees in the methane budget remains uncertain[2]. Although it has been shown that wetland and some upland trees can emit soil-derived methane at the stem base[3,4], it has also been suggested that upland trees can serve as a net sink for atmospheric methane[5,6]. Here we examine in situ woody surface methane exchange of upland tropical, temperate and boreal forest trees. We find that methane uptake on woody surfaces, in particular at and above about 2 m above the forest floor, can dominate the net ecosystem contribution of trees, resulting in a net tree methane sink. Stable carbon isotope measurement of methane in woody surface chamber air and process-level investigations on extracted wood cores are consistent with methanotrophy, suggesting a microbially mediated drawdown of methane on and in tree woody surfaces and tissues. By applying terrestrial laser scanning-derived allometry to quantify global forest tree woody surface area, a preliminary first estimate suggests that trees may contribute 24.6-49.9 Tg of atmospheric methane uptake globally. Our findings indicate that the climate benefits of tropical and temperate forest protection and reforestation may be greater than previously assumed.},
}
@article {pmid39048062,
year = {2024},
author = {Kondak, S and Kondak, D and Kabadayi, O and Erdei, L and Rónavári, A and Kónya, Z and Galbács, G and Kolbert, Z},
title = {Current insights into the green synthesis, in planta characterization and phytoeffects of nickel nanoparticles and their agricultural implications.},
journal = {Environmental research},
volume = {260},
number = {},
pages = {119665},
doi = {10.1016/j.envres.2024.119665},
pmid = {39048062},
issn = {1096-0953},
abstract = {The intensifying production and release into the environment as well as the increasing potential in agricultural applications make the relationship between plants and nickel nanoparticles (Ni NPs) a relevant and timely topic. The aim of this review is to give an overview and discuss the latest findings about the relationship of Ni NPs and plants. Ni NPs can be synthesized using phytochemicals derived from plant parts in an environmentally friendly manner. There are several ways for these nanoparticles to enter plant cells and tissues. This can be demonstrated through various imaging and chemical mapping approaches (e.g., transmission electron microscopy, X-ray fluorescence spectroscopy etc.). NiO NPs affect plants at multiple levels, including subcellular, cellular, tissue, organ, and whole-plant levels. However, the effects of Ni NPs on plants' ecological partners (e.g., rhizobiome, pollinators) remain largely unknown despite their ecotoxicological significance. The main cause of the Ni NPs-triggered damages is the reactive oxygen species imbalance as a consequence of the modulation of antioxidants. In non-tolerant plants, the toxicity of NiO NPs can be mitigated by exogenous treatments such as the application of silicon, salicylic acid, or jasmonic acid, which induce defense mechanisms whereas Ni-hypertolerant plant species possess endogenous defense systems, such as cell wall modifications and nitrosative signaling against NiO NP stress. Research highlights the role of Ni NPs in managing fungal diseases, showcasing their antifungal properties against specific pathogens. Due to the essentiality of Ni, the application of Ni NPs as nanofertilizers might be promising and has recently started to come into view.},
}
@article {pmid39047578,
year = {2024},
author = {Maxion, A and Gaebler, AJ and Röhrig, R and Mathiak, K and Zweerings, J and Kutafina, E},
title = {Spectral changes in electroencephalography linked to neuroactive medications: A computational pipeline for data mining and analysis.},
journal = {Computer methods and programs in biomedicine},
volume = {255},
number = {},
pages = {108319},
doi = {10.1016/j.cmpb.2024.108319},
pmid = {39047578},
issn = {1872-7565},
abstract = {BACKGROUND AND OBJECTIVES: The increasing amount of open-access medical data provides new opportunities to gain clinically relevant information without recruiting new patients. We developed an open-source computational pipeline, that utilizes the publicly available electroencephalographic (EEG) data of the Temple University Hospital to identify EEG profiles associated with the usage of neuroactive medications. It facilitates access to the data and ensures consistency in data processing and analysis, thus reducing the risk of errors and creating comparable and reproducible results. Using this pipeline, we analyze the influence of common neuroactive medications on brain activity.<br><br>METHODS: The pipeline is constructed using easily controlled modules. The user defines the medications of interest and comparison groups. The data is downloaded and preprocessed, spectral features are extracted, and statistical group comparison with visualization through a topographic EEG map is performed. The pipeline is adjustable to answer a variety of research questions. Here, the effects of carbamazepine and risperidone were statistically compared with control data and with other medications from the same classes (anticonvulsants and antipsychotics).<br><br>RESULTS: The comparison between carbamazepine and the control group showed an increase in absolute and relative power for delta and theta, and a decrease in relative power for alpha, beta, and gamma. Compared to antiseizure medications, carbamazepine showed an increase in alpha and theta for absolute powers, and for relative powers an increase in alpha and theta, and a decrease in gamma and delta. Risperidone compared with the control group showed a decrease in absolute and relative power for alpha and beta and an increase in theta for relative power. Compared to antipsychotic medications, risperidone showed a decrease in delta for absolute powers. These results show good agreement with state-of-the-art research. The database allows to create large groups for many different medications. Additionally, it provides a collection of records labeled as "normal" after expert assessment, which is convenient for the creation of control groups.<br><br>CONCLUSIONS: The pipeline allows fast testing of different hypotheses regarding links between medications and EEG spectrum through ecological usage of readily available data. It can be utilized to make informed decisions about the design of new clinical studies.},
}
@article {pmid39045996,
year = {2024},
author = {Lima, AGCF and Ribeiro, CJN and Lima, SVMA and Barbosa, YM and Oliveira, IM and Araújo, KCGM},
title = {Space-time analysis of work-related musculoskeletal disorders in Brazil: an ecological study.},
journal = {Cadernos de saude publica},
volume = {40},
number = {7},
pages = {e00141823},
doi = {10.1590/0102-311XEN141823},
pmid = {39045996},
issn = {1678-4464},
mesh = {Humans ; Brazil/epidemiology ; *Musculoskeletal Diseases/epidemiology ; *Occupational Diseases/epidemiology ; *Spatio-Temporal Analysis ; Incidence ; Male ; Female ; Bayes Theorem ; Risk Factors ; Adult ; },
abstract = {This study aimed to analyze the incidence of work-related musculoskeletal disorders (WMSD) in Brazil from 2007 to 2019, examining the spatial, temporal, and spatiotemporal patterns of their occurrence. An ecological time series study was conducted using spatial analysis techniques. WMSD morbidity data from 2007 to 2019 were collected from the Brazilian Information System for Notificable Diseases of the Brazilian Health Informatics Department. Incidence rates were standardized and smoothed using the local empirical Bayes' theorem. Time trends were analyzed by segmented linear regression. Spatial analysis was performed using Moran's univariate global (I) and local (LISA) indexes. The spatiotemporal scan statistic was used to identify high-risk spatiotemporal clusters for WMSD. A total of 93,387 cases of WMSD were recorded in Brazil. Temporal trends showed an increase in all regions except the Northeast, which remained stable. The incidence of WMSD showed a spatial dependence, with spatial and space-time clusters identified, especially in the Southeast region, overlapping the largest economic-industrial center of the country. The spatiotemporal clustering observed in one region suggests the highest level of industrial and economic development. Our findings highlight the need to implement intersectoral surveillance policies, inspect working conditions, and invest in the prevention and promotion of workers' health.},
}
@article {pmid39045504,
year = {2024},
author = {Märtz, J and Tallian, A and Wikenros, C and Heeres, RW},
title = {"ClusterApp": A Shiny R application to guide cluster studies based on GPS data.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11695},
pmid = {39045504},
issn = {2045-7758},
abstract = {The rapid evolution of GPS devices, and therefore, collection of GPS data can be used to investigate a wide variety of topics in wildlife research. The combination of remotely collected GPS data with on-the-ground field investigations is a powerful tool for exploring behavioral ecology. "GPS cluster studies" are aimed at pinpointing and investigating identified clusters in the field. Activity clusters can be based on various parameters (e.g., distance between GPS locations and the number of locations needed to establish a cluster), which are closely related to the set research questions. Variation in methods across years within the same study may result in data collection biases. Therefore, a streamlined method to parametrize, generate interactive maps, and extract activity cluster data using a predefined approach will limit biases, and make field work and data management straightforward for field technicians. We developed the "ClusterApp" Shiny application in the R software to facilitate a step-by-step guide to execute cluster analyses and data management of cluster studies on any species using GPS data. We illustrate the use of the "ClusterApp" with two location datasets constructed by data collected on brown bears (Ursus arctos) and gray wolves (Canis lupus).},
}
@article {pmid38995977,
year = {2024},
author = {Rosenblatt, E and Cook, JD and DiRenzo, GV and Grant, EHC and Arce, F and Pepin, KM and Rudolph, FJ and Runge, MC and Shriner, S and Walsh, DP and Mosher, BA},
title = {Epidemiological modeling of SARS-CoV-2 in white-tailed deer (Odocoileus virginianus) reveals conditions for introduction and widespread transmission.},
journal = {PLoS computational biology},
volume = {20},
number = {7},
pages = {e1012263},
pmid = {38995977},
issn = {1553-7358},
mesh = {Animals ; *Deer/virology ; *COVID-19/transmission/epidemiology/veterinary/virology ; *SARS-CoV-2 ; Humans ; Epidemiological Models ; Animals, Wild/virology ; Computational Biology ; Disease Outbreaks/veterinary/statistics &amp; numerical data ; Zoonoses/transmission/epidemiology/virology ; },
abstract = {Emerging infectious diseases with zoonotic potential often have complex socioecological dynamics and limited ecological data, requiring integration of epidemiological modeling with surveillance. Although our understanding of SARS-CoV-2 has advanced considerably since its detection in late 2019, the factors influencing its introduction and transmission in wildlife hosts, particularly white-tailed deer (Odocoileus virginianus), remain poorly understood. We use a Susceptible-Infected-Recovered-Susceptible epidemiological model to investigate the spillover risk and transmission dynamics of SARS-CoV-2 in wild and captive white-tailed deer populations across various simulated scenarios. We found that captive scenarios pose a higher risk of SARS-CoV-2 introduction from humans into deer herds and subsequent transmission among deer, compared to wild herds. However, even in wild herds, the transmission risk is often substantial enough to sustain infections. Furthermore, we demonstrate that the strength of introduction from humans influences outbreak characteristics only to a certain extent. Transmission among deer was frequently sufficient for widespread outbreaks in deer populations, regardless of the initial level of introduction. We also explore the potential for fence line interactions between captive and wild deer to elevate outbreak metrics in wild herds that have the lowest risk of introduction and sustained transmission. Our results indicate that SARS-CoV-2 could be introduced and maintained in deer herds across a range of circumstances based on testing a range of introduction and transmission risks in various captive and wild scenarios. Our approach and findings will aid One Health strategies that mitigate persistent SARS-CoV-2 outbreaks in white-tailed deer populations and potential spillback to humans.},
}
@article {pmid38920364,
year = {2024},
author = {Mau, RL and Hayer, M and Purcell, AM and Geisen, S and Hungate, BA and Schwartz, E},
title = {Measurements of soil protist richness and community composition are influenced by primer pair, annealing temperature, and bioinformatics choices.},
journal = {Applied and environmental microbiology},
volume = {90},
number = {7},
pages = {e0080024},
pmid = {38920364},
issn = {1098-5336},
support = {DE-AC52-07NA27344//U.S. Department of Energy (DOE)/ ; DE-SC0020172//U.S. Department of Energy (DOE)/ ; DE-SC0023126//U.S. Department of Energy (DOE)/ ; },
mesh = {*RNA, Ribosomal, 18S/genetics ; *Computational Biology/methods ; *Eukaryota/genetics/classification ; *DNA Primers/genetics ; *Soil Microbiology ; Biodiversity ; Temperature ; Soil/parasitology/chemistry ; Polymerase Chain Reaction ; },
abstract = {Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding.IMPORTANCEEcosystem functioning is driven by the activity and interactions of the microbial community, in both aquatic and terrestrial environments. Protists are a group of highly diverse, mostly unicellular microbes whose identity and roles in terrestrial ecosystem ecology have been largely ignored until recently. This study highlights the importance of choices researchers make, such as primer pair, on the results and conclusions about protist diversity and community composition in soils. In order to better understand the roles protist taxa play in terrestrial ecosystems, biases in methodological and analytical choices should be understood and acknowledged.},
}
@article {pmid38108929,
year = {2024},
author = {Liu, M and Wang, L and Yu, Q and Song, J and Zhu, L and Jia, KH and Qin, X},
title = {The response of LncRNAs associated with photosynthesis-and pigment synthesis-related genes to green light in Chlamydomonas reinhardtii.},
journal = {Photosynthesis research},
volume = {161},
number = {1-2},
pages = {65-78},
pmid = {38108929},
issn = {1573-5079},
mesh = {*Chlamydomonas reinhardtii/genetics/metabolism/radiation effects ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Gene Ontology ; Gene Regulatory Networks ; *Green Light ; *Photosynthesis/genetics ; Pigments, Biological/metabolism ; *RNA, Long Noncoding/genetics/metabolism ; Transcriptome ; },
abstract = {The quality of light is an important abiotic factor that affects the growth and development of green plants. Ultraviolet, red, blue, and far-red light all have demonstrated roles in regulating green plant growth and development, as well as light morphogenesis. However, the mechanism underlying photosynthetic organism responses to green light throughout the life of them are not clear. In this study, we exposed the unicellular green alga Chlamydomonas reinhardtii to green light and analyzed the dynamics of transcriptome changes. Based on the whole transcriptome data from C. reinhardtii, a total of 9974 differentially expressed genes (DEGs) were identified under green light. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that these DEGs were mainly related to "carboxylic acid metabolic process," "enzyme activity," "carbon metabolism," and "photosynthesis and other processes." At the same time, 253 differentially expressed long non-coding RNAs (DELs) were characterized as green light responsive. We also made a detailed analysis of the responses of photosynthesis- and pigment synthesis-related genes in C. reinhardtii to green light and found that these genes exhibited obvious dynamic expression. Lastly, we constructed a co-expression regulatory network, comprising 49 long non-coding RNAs (lncRNAs) and 20 photosynthesis and pigment related genes, of which 9 mRNAs were also the predicted trans/cis-targets of 8 lncRNAs, these results suggested that lncRNAs may affect the expression of mRNAs related to photosynthesis and pigment synthesis. Our findings give a preliminary explanation of the response mechanism of C. reinhardtii to green light at the transcriptional level.},
}
@article {pmid35268740,
year = {2022},
author = {Maiti, P and Sharma, P and Nand, M and Bhatt, ID and Ramakrishnan, MA and Mathpal, S and Joshi, T and Pant, R and Mahmud, S and Simal-Gandara, J and Alshehri, S and Ghoneim, MM and Alruwaily, M and Awadh, AAA and Alshahrani, MM and Chandra, S},
title = {Integrated Machine Learning and Chemoinformatics-Based Screening of Mycotic Compounds against Kinesin Spindle ProteinEg5 for Lung Cancer Therapy.},
journal = {Molecules (Basel, Switzerland)},
volume = {27},
number = {5},
pages = {},
pmid = {35268740},
issn = {1420-3049},
mesh = {*Kinesins/metabolism/antagonists &amp; inhibitors ; Humans ; *Lung Neoplasms/drug therapy/metabolism/pathology ; *Machine Learning ; *Cheminformatics/methods ; *Molecular Docking Simulation ; Molecular Dynamics Simulation ; Antineoplastic Agents/pharmacology/chemistry ; },
abstract = {Among the various types of cancer, lung cancer is the second most-diagnosed cancer worldwide. The kinesin spindle protein, Eg5, is a vital protein behind bipolar mitotic spindle establishment and maintenance during mitosis. Eg5 has been reported to contribute to cancer cell migration and angiogenesis impairment and has no role in resting, non-dividing cells. Thus, it could be considered as a vital target against several cancers, such as renal cancer, lung cancer, urothelial carcinoma, prostate cancer, squamous cell carcinoma, etc. In recent years, fungal secondary metabolites from the Indian Himalayan Region (IHR) have been identified as an important lead source in the drug development pipeline. Therefore, the present study aims to identify potential mycotic secondary metabolites against the Eg5 protein by applying integrated machine learning, chemoinformatics based in silico-screening methods and molecular dynamic simulation targeting lung cancer. Initially, a library of 1830 mycotic secondary metabolites was screened by a predictive machine-learning model developed based on the random forest algorithm with high sensitivity (1) and an ROC area of 0.99. Further, 319 out of 1830 compounds screened with active potential by the model were evaluated for their drug-likeness properties by applying four filters simultaneously, viz., Lipinski's rule, CMC-50 like rule, Veber rule, and Ghose filter. A total of 13 compounds passed from all the above filters were considered for molecular docking, functional group analysis, and cell line cytotoxicity prediction. Finally, four hit mycotic secondary metabolites found in fungi from the IHR were screened viz., (-)-Cochlactone-A, Phelligridin C, Sterenin E, and Cyathusal A. All compounds have efficient binding potential with Eg5, containing functional groups like aromatic rings, rings, carboxylic acid esters, and carbonyl and with cell line cytotoxicity against lung cancer cell lines, namely, MCF-7, NCI-H226, NCI-H522, A549, and NCI H187. Further, the molecular dynamics simulation study confirms the docked complex rigidity and stability by exploring root mean square deviations, root mean square fluctuations, and radius of gyration analysis from 100 ns simulation trajectories. The screened compounds could be used further to develop effective drugs against lung and other types of cancer.},
}
@article {pmid38785034,
year = {2024},
author = {McEachran, MC and Harvey, JA and Mummah, RO and Bletz, MC and Teitelbaum, CS and Rosenblatt, E and Rudolph, FJ and Arce, F and Yin, S and Prosser, DJ and Mosher, BA and Mullinax, JM and DiRenzo, GV and Couret, J and Runge, MC and Grant, EHC and Cook, JD},
title = {Reframing wildlife disease management problems with decision analysis.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {38},
number = {4},
pages = {e14284},
doi = {10.1111/cobi.14284},
pmid = {38785034},
issn = {1523-1739},
support = {//National Science Foundation/ ; 2200310//PIPP Phase 1: International Center for Avian Influenza Pandemic Prediction and Prevention/ ; P.L. 116-136//Coronavirus Aid, Relief, and Economic Security Act/ ; },
mesh = {Animals ; *Animals, Wild ; *Decision Support Techniques ; *Conservation of Natural Resources/methods ; *Decision Making ; COVID-19/epidemiology ; SARS-CoV-2 ; Uncertainty ; },
abstract = {Contemporary wildlife disease management is complex because managers need to respond to a wide range of stakeholders, multiple uncertainties, and difficult trade-offs that characterize the interconnected challenges of today. Despite general acknowledgment of these complexities, managing wildlife disease tends to be framed as a scientific problem, in which the major challenge is lack of knowledge. The complex and multifactorial process of decision-making is collapsed into a scientific endeavor to reduce uncertainty. As a result, contemporary decision-making may be oversimplified, rely on simple heuristics, and fail to account for the broader legal, social, and economic context in which the decisions are made. Concurrently, scientific research on wildlife disease may be distant from this decision context, resulting in information that may not be directly relevant to the pertinent management questions. We propose reframing wildlife disease management challenges as decision problems and addressing them with decision analytical tools to divide the complex problems into more cognitively manageable elements. In particular, structured decision-making has the potential to improve the quality, rigor, and transparency of decisions about wildlife disease in a variety of systems. Examples of management of severe acute respiratory syndrome coronavirus 2, white-nose syndrome, avian influenza, and chytridiomycosis illustrate the most common impediments to decision-making, including competing objectives, risks, prediction uncertainty, and limited resources.},
}
@article {pmid38708866,
year = {2024},
author = {Villarreal-Rosas, J and Brown, CJ and Andradi-Brown, DA and Domínguez, R and Jacobo, P and Martínez, A and Mascote, C and Najera, E and Paiz, Y and Vázquez Moran, VH and Villarreal, J and Adame, MF},
title = {Integrating socioeconomic and ecological data into restoration practice.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {38},
number = {4},
pages = {e14286},
doi = {10.1111/cobi.14286},
pmid = {38708866},
issn = {1523-1739},
support = {//Advance Queensland Industry Research Fellowship/ ; //Jeremy and Hannelore Grantham Environmental Trust/ ; FT210100792//Australian Research Council/ ; },
mesh = {*Conservation of Natural Resources/methods/economics ; Mexico ; *Socioeconomic Factors ; Environmental Restoration and Remediation/economics ; Ecosystem ; Decision Support Techniques ; },
abstract = {Driven by the United Nations Decade on Restoration and international funding initiatives, such as the Mangrove Breakthrough, investment in mangrove restoration is expected to increase. Yet, mangrove restoration efforts frequently fail, usually because of ad hoc site-selection processes that do not consider mangrove ecology and the socioeconomic context. Using decision analysis, we developed an approach that accounts for socioeconomic and ecological data to identify sites with the highest likelihood of mangrove restoration success. We applied our approach in the Biosphere Reserve Marismas Nacionales Nayarit, Mexico, an area that recently received funding for implementing mangrove restoration actions. We identified 468 potential restoration sites, assessed their restorability potential based on socioeconomic and ecological metrics, and ranked sites for implementation with spatial optimization. The metrics we used included favorable conditions for propagules to establish and survive under sea-level rise, provision of ecosystem services, and community dynamics. Sites that were selected based on socioeconomic or ecological metrics alone had lower likelihood of mangrove restoration success than sites that were selected based on integrated socioeconomic and ecological metrics. For example, selecting sites based on only socioeconomic metrics captured 16% of the maximum attainable value of functioning mangroves able to provide propagules to potential restoration sites, whereas selecting sites based on ecological and socioeconomic metrics captured 46% of functioning mangroves. Our approach was developed as part of a collaboration between nongovernmental organizations, local government, and academics under rapid delivery time lines given preexisting mangrove restoration implementation commitments. The systematic decision process we used integrated socioeconomic and ecological considerations even under short delivery deadlines, and our approach can be adapted to help mangrove restoration site-selection decisions elsewhere.},
}
@article {pmid39032150,
year = {2024},
author = {Kim, J and Foo, JC and Murata, T and Togo, F},
title = {Reduced heart rate variability is related to fluctuations in psychological stress levels in daily life.},
journal = {Stress and health : journal of the International Society for the Investigation of Stress},
volume = {},
number = {},
pages = {e3447},
doi = {10.1002/smi.3447},
pmid = {39032150},
issn = {1532-2998},
support = {19K24283//Japan Society for the Promotion of Science/ ; 21K17681//Japan Society for the Promotion of Science/ ; 031L0190A//Bundesministerium f&#xfc;r Bildung und Forschung/ ; },
abstract = {Laboratory-based studies have shown that psychological stress caused by response to various stressors triggers acute changes in the cardiovascular system. A better understanding is needed of the emerging evidence on temporal associations between psychological stress and cardiovascular responses in natural settings. This study examined the association of psychological stress and heart rate variability (HRV) in daily life, at high resolution over 2 weeks, taking the effect of physical activity into account. Participants (n = 34) completed ecological momentary assessments (EMA) 6 times per day, reporting levels of perceived stress, low-arousal negative affect (LNA), and high-arousal negative affect. Chest-mounted heart-rate monitors were worn to assess HRV. Multilevel models were used to examine the association between psychological stress levels and preceding/subsequent HRV. Reduced time domain HRV measures (mean and standard deviation of R-wave to R-wave intervals) during the prior hour predicted higher levels of perceived stress. Frequency domain HRV measures higher low to high frequency (LF/HF) and lower HF to total power (HF nu) ratios during the preceding 10 min predicted higher perceived stress levels, suggesting the dominance of sympathetic nervous system activity. EMA reports of higher perceived stress levels were associated with reduced time domain HRV measures during the following 10 min. On the other hand, higher LNA were related to increased HRV measures, such as lower LF/HF and higher HF nu during the following hour. The dynamic associations observed may have therapeutic implications for 'just-in-time' interventions in the management of daily stress and cardiovascular health.},
}
@article {pmid39031697,
year = {2024},
author = {Zembere, K and Jones, CM and Mthawanji, R and Nkolokosa, C and Kamwezi, R and Kalonde, PK and Stanton, MC},
title = {Small dams drive Anopheles abundance during the dry season in a high malaria burden area of Malawi.},
journal = {Medical and veterinary entomology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mve.12733},
pmid = {39031697},
issn = {1365-2915},
support = {215184/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {This study explores the influence of small dams on the exposure to malaria vectors during the dry season in Kasungu district, Malawi, an area recently identified as high priority for malaria interventions by the National Malaria Control Programme. Small dam impoundments provide communities with a continuous supply of water for domestic and agricultural activities across sub-Saharan Africa and are considered vital to food security and climate change resilience. However, these permanent water bodies also create ideal breeding sites for mosquitoes in typically arid landscapes. The study focuses on a specific dam impoundment and its vicinity, aiming to assess its spatial and temporal influence on indoor vector densities. From May to August 2021, CDC light traps were used to measure indoor mosquito densities for two consecutive nights per month in three communities located at increasing distances from the dam (0, ~1 and ~2 km). Simultaneously, drone imagery was captured for each community, enabling the identification of additional standing water within approximately 400 m of selected households. Larval sampling was carried out within the impoundment periphery and in additional water bodies identified in the drone imagery. Generalised linear mixed models (GLMMs) were employed to analyse the indoor Anopheles abundance data, estimating the effects of household structure (open/closed eaves), month, temperature and water proximity on malaria vector exposure. Throughout 685 trapping nights, a total of 1256 mosquitoes were captured, with 33% (412) being female Anopheles. Among these, 91% were morphologically identified as Anopheles funestus s.l., and 5% as Anopheles gambiae s.l. Catches progressively decline in each consecutive trapping month as the environment became drier. This decline was much slower in Malangano, the community next to the dam, with abundance being notably higher in June and July. Further, the majority of An. gambiae s.l. were caught in May, with none identified in July and August. Anopheles larvae were found both in the impoundment and other smaller water bodies such as irrigation wells in each survey month; however, the presence of these smaller water bodies did not have a significant impact on adult female mosquito catches in the GLMM. The study concludes that proximity to the dam impoundment was the primary driver of differences between survey communities with the abundance in Chikhombwe (~1 km away) and Chiponde (~2 km away) being 0.35 (95% confidence interval [CI], 0.19-0.66) and 0.28 (95% CI, 0.16-0.47) lower than Malangano, respectively, after adjusting for other factors. These findings underscore the importance of targeted interventions, such as larval source management or housing improvements, near small dams to mitigate malaria transmission risks during the dry season. Further research is needed to develop cost-effective strategies for vector control within and around these impoundments.},
}
@article {pmid39027808,
year = {2024},
author = {Falk, S and Poole, O and , and , and , and , and , and , and , },
title = {The genome sequence of a hoverfly, Cheilosia impressa (Loew, 1840).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {74},
pmid = {39027808},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Cheilosia impressa (hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 395.0 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.87 kilobases in length.},
}
@article {pmid39026607,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Brindled Beauty, Lycia hirtaria (Clerck, 1759).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {303},
pmid = {39026607},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Lycia hirtaria (the Brindled Beauty; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 552.0 megabases in span. Most of the assembly is scaffolded into 14 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.58 kilobases in length.},
}
@article {pmid39026606,
year = {2023},
author = {Boyes, D and Crowley, LM and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Little Grey, Eudonia lacustrata (Panzer, 1804).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {302},
pmid = {39026606},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Eudonia lacustrata (the Little Grey; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 699.5 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.29 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,652 protein coding genes.},
}
@article {pmid39026203,
year = {2024},
author = {Piacenza, F and Di Rosa, M and Soraci, L and Montesanto, A and Corsonello, A and Cherubini, A and Fabbietti, P and Provinciali, M and Lisa, R and Bonfigli, AR and Filicetti, E and Greco, GI and Muglia, L and Lattanzio, F and Volpentesta, M and Biscetti, L},
title = {Interactions between patterns of multimorbidity and functional status among hospitalized older patients: a novel approach using cluster analysis and association rule mining.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {669},
pmid = {39026203},
issn = {1479-5876},
support = {RF-2013-02358848//Ministero della Salute/ ; },
mesh = {Humans ; Male ; Female ; *Multimorbidity ; Aged ; Cluster Analysis ; *Hospitalization ; Aged, 80 and over ; *Activities of Daily Living ; Functional Status ; Data Mining ; Retrospective Studies ; },
abstract = {BACKGROUND: Multimorbidity (MM) is generally defined as the presence of 2 or more chronic diseases in the same patient and seems to be frequently associated with frailty and poor quality of life. However, the complex interplay between MM and functional status in hospitalized older patients has not been fully elucidated so far. Here, we implemented a 2-step approach, combining cluster analysis and association rule mining to explore how patterns of MM and disease associations change as a function of disability.<br><br>METHODS: This retrospective cohort study included 3366 hospitalized older patients discharged from acute care units of Ancona and Cosenza sites of Italian National Institute on Aging (INRCA-IRCCS) between 2011 and 2017. Cluster analysis and association rule mining (ARM) were used to explore patterns of MM and disease associations in the whole population and after stratifying by dependency in activities of daily living (ADL) at discharge. Sensitivity analyses in men and women were conducted to test for robustness of study findings.<br><br>RESULTS: Out of 3366 included patients, 78% were multimorbid. According to functional status, 22.2% of patients had no disability in ADL (functionally independent group), 22.7% had 1 ADL dependency (mildly dependent group), and 57.4% 2 or more ADL impaired (moderately-severely dependent group). Two main MM clusters were identified in the whole general population and in single ADL groups. ARM revealed interesting within-cluster disease associations, characterized by high lift and confidence. Specifically, in the functionally independent group, the most significant ones involved atrial fibrillation (AF)-anemia and chronic kidney disease (CKD) (lift&#x2009;=&#x2009;2.32), followed by coronary artery disease (CAD)-AF and heart failure (HF) (lift&#x2009;=&#x2009;2.29); in patients with moderate-severe ADL disability, the most significant ARM involved CAD-HF and AF (lift&#x2009;=&#x2009;1.97), thyroid dysfunction and AF (lift&#x2009;=&#x2009;1.75), cerebrovascular disease (CVD)-CAD and AF (lift&#x2009;=&#x2009;1.55), and hypertension-anemia and CKD (lift&#x2009;=&#x2009;1.43).<br><br>CONCLUSIONS: Hospitalized older patients have high rates of MM and functional impairment. Combining cluster analysis to ARM may assist physicians in discovering unexpected disease associations in patients with different ADL status. This could be relevant in the view of individuating personalized diagnostic and therapeutic approaches, according to the modern principles of precision medicine.},
}
@article {pmid39024004,
year = {2024},
author = {Hernandez, R and Hoogendoorn, C and Gonzalez, JS and Pyatak, EA and Crespo-Ramos, G and Schneider, S},
title = {Reliability and Validity of Ecological Momentary Assessment Response Time-Based Measures of Emotional Clarity: Secondary Data Analysis.},
journal = {JMIR mental health},
volume = {11},
number = {},
pages = {e58352},
doi = {10.2196/58352},
pmid = {39024004},
issn = {2368-7959},
mesh = {Humans ; *Ecological Momentary Assessment ; Female ; Male ; Reproducibility of Results ; Adult ; *Emotions ; Middle Aged ; Diabetes Mellitus, Type 1/psychology ; Reaction Time/physiology ; Emotional Regulation/physiology ; Data Analysis ; Personal Satisfaction ; Surveys and Questionnaires ; Secondary Data Analysis ; },
abstract = {BACKGROUND: Emotional clarity has often been assessed with self-report measures, but efforts have also been made to measure it passively, which has advantages such as avoiding potential inaccuracy in responses stemming from social desirability bias or poor insight into emotional clarity. Response times (RTs) to emotion items administered in ecological momentary assessments (EMAs) may be an indirect indicator of emotional clarity. Another proposed indicator is the drift rate parameter, which assumes that, aside from how fast a person responds to emotion items, the measurement of emotional clarity also requires the consideration of how careful participants were in providing responses.<br><br>OBJECTIVE: This paper aims to examine the reliability and validity of RTs and drift rate parameters from EMA emotion items as indicators of individual differences in emotional clarity.<br><br>METHODS: Secondary data analysis was conducted on data from 196 adults with type 1 diabetes who completed a 2-week EMA study involving the completion of 5 to 6 surveys daily. If lower RTs and higher drift rates (from EMA emotion items) were indicators of emotional clarity, we hypothesized that greater levels (ie, higher clarity) should be associated with greater life satisfaction; lower levels of neuroticism, depression, anxiety, and diabetes distress; and fewer difficulties with emotion regulation. Because prior literature suggested emotional clarity could be valence specific, EMA items for negative affect (NA) and positive affect were examined separately.<br><br>RESULTS: Reliability of the proposed indicators of emotional clarity was acceptable with a small number of EMA prompts (ie, 4 to 7 prompts in total or 1 to 2 days of EMA surveys). Consistent with expectations, the average drift rate of NA items across multiple EMAs had expected associations with other measures, such as correlations of r=-0.27 (P<.001) with depression symptoms, r=-0.27 (P=.001) with anxiety symptoms, r=-0.15 (P=.03) with emotion regulation difficulties, and r=0.63 (P<.001) with RTs to NA items. People with a higher NA drift rate responded faster to NA emotion items, had greater subjective well-being (eg, fewer depression symptoms), and had fewer difficulties with overall emotion regulation, which are all aligned with the expectation for an emotional clarity measure. Contrary to expectations, the validities of average RTs to NA items, the drift rate of positive affect items, and RTs to positive affect items were not strongly supported by our results.<br><br>CONCLUSIONS: Study findings provided initial support for the validity of NA drift rate as an indicator of emotional clarity but not for that of other RT-based clarity measures. Evidence was preliminary because the sample size was not sufficient to detect small but potentially meaningful correlations, as the sample size of the diabetes EMA study was chosen for other more primary research questions. Further research on passive emotional clarity measures is needed.},
}
@article {pmid39023004,
year = {2024},
author = {Rillig, MC and Li, C and Rodríguez Del Río, &#xc1; and Zhu, YG and Jin, L},
title = {Elevated levels of antibiotic resistance genes as a factor of human-caused global environmental change.},
journal = {Global change biology},
volume = {30},
number = {7},
pages = {e17419},
doi = {10.1111/gcb.17419},
pmid = {39023004},
issn = {1365-2486},
support = {C5063-22G//Research Grants Council of Hong Kong/ ; 2021-DST-004//Ningbo S&amp;T/ ; P0044024//Hong Kong Polytechnic University/ ; P0040336//Hong Kong Polytechnic University/ ; //Alexander-von-Humboldt Foundation/ ; },
mesh = {Humans ; *Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Climate Change ; Ecosystem ; Human Activities ; },
abstract = {Antibiotic resistance genes (ARGs) have moved into focus as a critically important response variable in global change biology, given the increasing environmental and human health threat posed by these genes. However, we propose that elevated levels of ARGs should also be considered a factor of global change, not just a response. We provide evidence that elevated levels of ARGs are a global change factor, since this phenomenon is linked to human activity, occurs globally, and affects biota. We explain why ARGs could be considered the global change factor, rather than the organisms containing them; and we highlight the difference between ARGs and the presence of antibiotics, which are not necessarily linked since elevated levels of ARGs are caused by multiple factors. Importantly, shifting the perspective to elevated levels of ARGs as a factor of global change opens new avenues of research, where ARGs can be the experimental treatment. This includes asking questions about how elevated ARG levels interact with other global change factors, or how ARGs influence ecosystem processes, biodiversity or trophic relationships. Global change biology stands to profit from this new framing in terms of capturing more completely the real extent of human impacts on this planet.},
}
@article {pmid39018100,
year = {2024},
author = {Corponi, F and Li, BM and Anmella, G and Valenzuela-Pascual, C and Mas, A and Pacchiarotti, I and Valentí, M and Grande, I and Benabarre, A and Garriga, M and Vieta, E and Young, AH and Lawrie, SM and Whalley, HC and Hidalgo-Mazzei, D and Vergari, A},
title = {Wearable Data From Subjects Playing Super Mario, Taking University Exams, or Performing Physical Exercise Help Detect Acute Mood Disorder Episodes via Self-Supervised Learning: Prospective, Exploratory, Observational Study.},
journal = {JMIR mHealth and uHealth},
volume = {12},
number = {},
pages = {e55094},
doi = {10.2196/55094},
pmid = {39018100},
issn = {2291-5222},
mesh = {Humans ; *Supervised Machine Learning ; Prospective Studies ; *Wearable Electronic Devices/statistics &amp; numerical data/standards ; Male ; Female ; *Mood Disorders/diagnosis/psychology ; Adult ; Exercise/psychology/physiology ; Universities/statistics &amp; numerical data/organization &amp; administration ; },
abstract = {BACKGROUND: Personal sensing, leveraging data passively and near-continuously collected with wearables from patients in their ecological environment, is a promising paradigm to monitor mood disorders (MDs), a major determinant of the worldwide disease burden. However, collecting and annotating wearable data is resource intensive. Studies of this kind can thus typically afford to recruit only a few dozen patients. This constitutes one of the major obstacles to applying modern supervised machine learning techniques to MD detection.<br><br>OBJECTIVE: In this paper, we overcame this data bottleneck and advanced the detection of acute MD episodes from wearables' data on the back of recent advances in self-supervised learning (SSL). This approach leverages unlabeled data to learn representations during pretraining, subsequently exploited for a supervised task.<br><br>METHODS: We collected open access data sets recording with the Empatica E4 wristband spanning different, unrelated to MD monitoring, personal sensing tasks-from emotion recognition in Super Mario players to stress detection in undergraduates-and devised a preprocessing pipeline performing on-/off-body detection, sleep/wake detection, segmentation, and (optionally) feature extraction. With 161 E4-recorded subjects, we introduced E4SelfLearning, the largest-to-date open access collection, and its preprocessing pipeline. We developed a novel E4-tailored transformer (E4mer) architecture, serving as the blueprint for both SSL and fully supervised learning; we assessed whether and under which conditions self-supervised pretraining led to an improvement over fully supervised baselines (ie, the fully supervised E4mer and pre-deep learning algorithms) in detecting acute MD episodes from recording segments taken in 64 (n=32, 50%, acute, n=32, 50%, stable) patients.<br><br>RESULTS: SSL significantly outperformed fully supervised pipelines using either our novel E4mer or extreme gradient boosting (XGBoost): n=3353 (81.23%) against n=3110 (75.35%; E4mer) and n=2973 (72.02%; XGBoost) correctly classified recording segments from a total of 4128 segments. SSL performance was strongly associated with the specific surrogate task used for pretraining, as well as with unlabeled data availability.<br><br>CONCLUSIONS: We showed that SSL, a paradigm where a model is pretrained on unlabeled data with no need for human annotations before deployment on the supervised target task of interest, helps overcome the annotation bottleneck; the choice of the pretraining surrogate task and the size of unlabeled data for pretraining are key determinants of SSL success. We introduced E4mer, which can be used for SSL, and shared the E4SelfLearning collection, along with its preprocessing pipeline, which can foster and expedite future research into SSL for personal sensing.},
}
@article {pmid39015757,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Wainscot Smudge, Ypsolopha scabrella (Linnaeus, 1761).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {341},
pmid = {39015757},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Ypsolopha scabrella (the Wainscot Smudge; Arthropoda; Insecta; Lepidoptera; Ypsolophidae). The genome sequence is 853.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 20,594 protein coding genes.},
}
@article {pmid39015615,
year = {2024},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , and , },
title = {The genome sequence of the Mottled Pug, Eupithecia exiguata (Hübner, 1813).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {65},
pmid = {39015615},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Eupithecia exiguata (the Mottled Pug; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 372.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.39 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,194 protein coding genes.},
}
@article {pmid39015613,
year = {2024},
author = {Obbard, DJ and , and , and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Drosophila histrio (Meigen, 1830).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {56},
pmid = {39015613},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Drosophila histrio (the drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 189.2 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.02 kilobases in length.},
}
@article {pmid39015611,
year = {2024},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , and , },
title = {The genome sequence of the Dotted Grey Groundling, Athrips mouffetella (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {42},
pmid = {39015611},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Athrips mouffetella (the Dotted Grey Groundling; Arthropoda; Insecta; Lepidoptera; Gelechiidae). The genome sequence is 869.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.23 kilobases in length. Gene annotation of this assembly on Ensembl identified 22,889 protein coding genes.},
}
@article {pmid39014019,
year = {2024},
author = {Cavaliere, M and Yang, G and De Dreu, CKW and Gross, J},
title = {Cooperation and social organization depend on weighing private and public reputations.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16443},
pmid = {39014019},
issn = {2045-2322},
mesh = {Humans ; *Cooperative Behavior ; Social Networking ; Game Theory ; Interpersonal Relations ; },
abstract = {To avoid exploitation by defectors, people can use past experiences with others when deciding to cooperate or not ('private information'). Alternatively, people can derive others' reputation from 'public' information provided by individuals within the social network. However, public information may be aligned or misaligned with one's own private experiences and different individuals, such as 'friends' and 'enemies', may have different opinions about the reputation of others. Using evolutionary agent-based simulations, we examine how cooperation and social organization is shaped when agents (1) prioritize private or public information about others' reputation, and (2) integrate others' opinions using a friend-focused or a friend-and-enemy focused heuristic (relying on reputation information from only friends or also enemies, respectively). When agents prioritize public information and rely on friend-and-enemy heuristics, we observe polarization cycles marked by high cooperation, invasion by defectors, and subsequent population fragmentation. Prioritizing private information diminishes polarization and defector invasions, but also results in limited cooperation. Only when using friend-focused heuristics and following past experiences or the recommendation of friends create prosperous and stable populations based on cooperation. These results show how combining one's own experiences and the opinions of friends can lead to stable and large-scale cooperation and highlight the important role of following the advice of friends in the evolution of group cooperation.},
}
@article {pmid39008135,
year = {2024},
author = {Urbano, F and Viterbi, R and Pedrotti, L and Vettorazzo, E and Movalli, C and Corlatti, L},
title = {Correction to: Enhancing biodiversity conservation and monitoring in protected areas through efficient data management.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {8},
pages = {733},
doi = {10.1007/s10661-024-12886-7},
pmid = {39008135},
issn = {1573-2959},
}
@article {pmid39007251,
year = {2024},
author = {Pili, AN and Leroy, B and Measey, JG and Farquhar, JE and Toomes, A and Cassey, P and Chekunov, S and Grenié, M and van Winkel, D and Maria, L and Diesmos, MLL and Diesmos, AC and Zurell, D and Courchamp, F and Chapple, DG},
title = {Forecasting potential invaders to prevent future biological invasions worldwide.},
journal = {Global change biology},
volume = {30},
number = {7},
pages = {e17399},
doi = {10.1111/gcb.17399},
pmid = {39007251},
issn = {1365-2486},
support = {DP210103050//Australian Research Council/ ; FT200100108//Australian Research Council/ ; IL230100175//Australian Research Council/ ; //Monash University Faculty of Science's Dean's Postgraduate Research Scholarship and Dean's International Postgraduate Research Scholarship, and by Monash University Graduate Research Office's Graduate Research Completion Award and Post-Graduate Publication Award/ ; BIFA3_026//the Philippine Department of Environment and Natural Resources FORIS project and the Global Biodiversity Information Facility Biodiversity Fund for Asia Project/ ; },
mesh = {*Introduced Species ; Animals ; *Forecasting ; *Reptiles/physiology ; *Amphibians/physiology ; Risk Assessment/methods ; Models, Theoretical ; Models, Biological ; },
abstract = {The ever-increasing and expanding globalisation of trade and transport underpins the escalating global problem of biological invasions. Developing biosecurity infrastructures is crucial to anticipate and prevent the transport and introduction of invasive alien species. Still, robust and defensible forecasts of potential invaders are rare, especially for species without known invasion history. Here, we aim to support decision-making by developing a quantitative invasion risk assessment tool based on invasion syndromes (i.e., generalising typical attributes of invasive alien species). We implemented a workflow based on 'Multiple Imputation with Chain Equation' to estimate invasion syndromes from imputed datasets of species' life-history and ecological traits and macroecological patterns. Importantly, our models disentangle the factors explaining (i) transport and introduction and (ii) establishment. We showcase our tool by modelling the invasion syndromes of 466 amphibians and reptile species with invasion history. Then, we project these models to amphibians and reptiles worldwide (16,236 species [c.76% global coverage]) to identify species with a risk of being unintentionally transported and introduced, and risk of establishing alien populations. Our invasion syndrome models showed high predictive accuracy with a good balance between specificity and generality. Unintentionally transported and introduced species tend to be common and thrive well in human-disturbed habitats. In contrast, those with established alien populations tend to be large-sized, are habitat generalists, thrive well in human-disturbed habitats, and have large native geographic ranges. We forecast that 160 amphibians and reptiles without known invasion history could be unintentionally transported and introduced in the future. Among them, 57 species have a high risk of establishing alien populations. Our reliable, reproducible, transferable, statistically robust and scientifically defensible quantitative invasion risk assessment tool is a significant new addition to the suite of decision-support tools needed for developing a future-proof preventative biosecurity globally.},
}
@article {pmid39004875,
year = {2024},
author = {Taylor, A and Sigona, A and Kelly, M},
title = {Centering Amah Mutsun voices in the analysis of a culturally important, fire-managed coastal grassland.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {},
number = {},
pages = {e3014},
doi = {10.1002/eap.3014},
pmid = {39004875},
issn = {1051-0761},
support = {//Critical Mission Studies Grant program of the University of California/ ; //Joseph A. Myers Center for Research on Native American Issues, UC Berkeley/ ; //California Native Plant Society (both statewide and from the Santa Clara Valley chapter)/ ; //UC Berkeley Chapter of Sigma Xi/ ; //California Native Grasslands Association/ ; //Department of Environmental Science, Policy, and Management at UC Berkeley/ ; //University of California Graduate Division Fellowship/ ; //Phi Beta Kappa Fellowship, UC Berkeley/ ; //Inter-institutional Network for Food, Agriculture and Sustainability and Intertribal Agriculture Council Tribal Fellowship/ ; //UC Berkeley Graduate Fellowship in Climate Equity/ ; //Ford Foundation Predoctoral Fellowship Program/ ; //Wilderness Society Scholarship/ ; //UC Berkeley Chancellor's Fellowship/ ; },
abstract = {Indigenous communities throughout California, USA, are increasingly advocating for and practicing cultural fire stewardship, leading to a host of social, cultural, and ecological benefits. Simultaneously, state agencies are recognizing the importance of controlled burning and cultural fire as a means of reducing the risk of severe wildfire while benefiting fire-adapted ecosystems. However, much of the current research on the impacts of controlled burning ignores the cultural importance of these ecosystems, and risks further marginalizing Indigenous knowledge systems. Our work adds a critical Indigenous perspective to the study of controlled burning in California's unique coastal grasslands, one of the most biodiverse and endangered ecosystems in the country. In this study, we partnered with the Amah Mutsun Tribal Band to investigate how the abundance and occurrence of shrubs, cultural plants, and invasive plants differed among three adjacent coastal grasslands with varying fire histories. These three sites are emblematic of the state's diverging approaches to grassland management: fire suppression, fire suppression followed by wildfire, and an exceedingly rare example of a grassland that has been repeatedly burned approximately every 2 years for more than 30 years. We found that Danthonia californica was significantly more abundant on the burned sites, whereas all included shrub species (Baccharis pilularis, Frangula californica, and Rubus ursinus) were significantly more abundant on the site with no recorded fire, results that have important implications for future cultural revitalization efforts and the loss of coastal grasslands to shrub encroachment. In addition to conducting a culturally relevant vegetation survey, we used Sentinel-2 satellite imagery to compare the relative severities of the two most recent fire events within the study area. Critically, we used interviews with Amah Mutsun tribal members to contextualize the results of our vegetation survey and remote sensing analysis, and to investigate how cultural burning contrasts from typical Western fire management approaches in this region. Our study is a novel example of how interviews, field data, and satellite imagery can be combined to gain a deeper ecological and cultural understanding of fire in California's endangered coastal grasslands.},
}
@article {pmid39004058,
year = {2024},
author = {Guo, J and Jin, Y and Liu, S and Li, T and Ji, D and Hou, C and Tang, H},
title = {Investigation of the causes and mechanisms of hypoxia in the central Bohai Sea in the summer of 2022.},
journal = {Marine pollution bulletin},
volume = {206},
number = {},
pages = {116710},
doi = {10.1016/j.marpolbul.2024.116710},
pmid = {39004058},
issn = {1879-3363},
abstract = {The deep-water area in the central Bohai Sea (BS) serves as a spawning ground and nursery for fish, shrimp, and crabs. Frequent hypoxia will affect the ecological environment in the central BS. Data from an on-site investigation of the central BS in the spring and summer of 2022 were used to analyze the relevant factors generating the occurrence of hypoxia in the central BS through the eutrophication index E, apparent oxygen consumption (AOU), and Spearman correlation. The hypoxia area was largely distributed in the study area's deep water section, and stratification was the main cause of hypoxia at the bottom. Organic matter mineralization, degradation, and biological respiration further exacerbated the hypoxia. In the summer of 2022, temperature stratification was the dominant factor influencing hypoxia.},
}
@article {pmid39001963,
year = {2024},
author = {Lu, Y and Xiao, X and Liang, Y and Li, J and Guo, C and Xu, L and Liu, Q and Xiao, Y and Zhou, S},
title = {Distribution and transformation of potentially toxic elements in cracks under coal mining disturbance in farmland.},
journal = {Environmental geochemistry and health},
volume = {46},
number = {9},
pages = {312},
pmid = {39001963},
issn = {1573-2983},
support = {52130402//State Key Program of National Natural Science Foundation of China/ ; },
mesh = {*Soil Pollutants/analysis/toxicity ; *Coal Mining ; *Environmental Monitoring ; *Metals, Heavy/analysis/toxicity ; Soil/chemistry ; Farms ; Risk Assessment ; },
abstract = {The ground cracks resulting from coal mining activities induce alterations in the physical and chemical characteristics of soil. However, limited knowledge exists regarding the impact of subsidence caused by coal mining on the distribution of potentially toxic elements (PTEs) fractions in farmland soil. In this study, we collected 19 soil profiles at varying depths from the soil surface and at horizontal distances of 0, 1, 2, and 5 m from the vertical crack. Using BCR extraction fractionation, we determined the geochemical fractions and total concentrations of Chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), cadmium (Cd) and lead (Pb) to investigate their ecological risk, spatial fraction distribution, and main influencing factors. Results showed that the E r i values of Cd appearing in 68.7% of the samples were higher than 40 and less than 80, presented a moderate ecological risk. Chromium (Cr), nickel (Ni), copper (Cu), zinc (Zn), arsenic (As), and lead (Pb) were mainly bound to residual fractions (> 60%) with lower mobility and Cd was dominated by F1 (acid-soluble fractions, 50%) and F2 (reducible fractions, 29%) in surface soil (0-20 cm). The geochemical fractionation revealed that the mobile fractions (F1-acid-soluble and F2-reducible) of PTEs were primarily located near the crack, influenced by available potassium. In contrast, the less mobile fractions (F3-oxidizable and F4-residual) exhibited higher concentrations at distances of 2 and 5 m from the crack, except for arsenic, influenced by the presence of clay particles and available phosphorus.},
}
@article {pmid39001714,
year = {2024},
author = {Williams, TA and Davin, AA and Szánthó, LL and Stamatakis, A and Wahl, NA and Woodcroft, BJ and Soo, RM and Eme, L and Sheridan, PO and Gubry-Rangin, C and Spang, A and Hugenholtz, P and Szöllősi, GJ},
title = {Phylogenetic reconciliation: making the most of genomes to understand microbial ecology and evolution.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae129},
pmid = {39001714},
issn = {1751-7370},
abstract = {In recent years, phylogenetic reconciliation has emerged as a promising approach for studying microbial ecology and evolution. The core idea is to model how gene trees evolve along a species tree, and to explain differences between them via evolutionary events including gene duplications, transfers, and losses. Here, we describe how phylogenetic reconciliation provides a natural framework for studying genome evolution, and highlight recent applications including ancestral gene content inference, the rooting of species trees, and the insights into metabolic evolution and ecological transitions they yield. Reconciliation analyses have elucidated the evolution of diverse microbial lineages, from Chlamydiae to Asgard archaea, shedding light on ecological adaptation, host-microbe interactions, and symbiotic relationships. However, there are many opportunities for broader application of the approach in microbiology. Continuing improvements to make reconciliation models more realistic and scalable, and integration of ecological metadata such as habitat, pH, temperature and oxygen use, offer enormous potential for understanding the rich tapestry of microbial life.},
}
@article {pmid39000743,
year = {2024},
author = {Macchia, A and Marinelli, L and Barbaccia, FI and de Caro, T and Hansen, A and Schuberthan, LM and Izzo, FC and Pintus, V and Testa Chiari, K and La Russa, MF},
title = {Mattel's ©Barbie: Preventing Plasticizers Leakage in PVC Artworks and Design Objects through Film-Forming Solutions.},
journal = {Polymers},
volume = {16},
number = {13},
pages = {},
pmid = {39000743},
issn = {2073-4360},
abstract = {The main conservation problem of p-PVC artworks is phthalate-based plasticizer migration. Phthalate migration from the bulk to the surface of the materials leads to the formation of a glossy and oily film on the outer layers, ultimately reducing the flexibility of the material. This study aimed to develop a removable coating for the preservation of contemporary artworks and design objects made of plasticized polyvinyl chloride (p-PVC). Several coatings incorporating chitosan, collagen, and cellulose ethers were assessed as potential barriers to inhibiting plasticizer migration. Analytical techniques including optical microscopy (OM), ultraviolet/visible/near-infrared spectroscopy (UV/Vis/NIR), Fourier transform infrared spectroscopy with attenuated total reflection (FTIR-ATR), and scanning electron microscopy (SEM) were utilized to evaluate the optical and chemical stability of selected coating formulations applied to laboratory p-PVC sheet specimens. Subsequently, formulations were tested on a real tangible example of a design object, ©Barbie doll, characterized by the prevalent issue of plasticizer migration. Furthermore, the results obtained with the tested formulations were evaluated by a group of conservators using a tailored survey. Finally, a suitable coating formulation capable of safeguarding plastic substrates was suggested.},
}
@article {pmid39000053,
year = {2024},
author = {Wang, XY and Ren, CX and Fan, QW and Xu, YP and Wang, LW and Mao, ZL and Cai, XZ},
title = {Integrated Assays of Genome-Wide Association Study, Multi-Omics Co-Localization, and Machine Learning Associated Calcium Signaling Genes with Oilseed Rape Resistance to Sclerotinia sclerotiorum.},
journal = {International journal of molecular sciences},
volume = {25},
number = {13},
pages = {},
pmid = {39000053},
issn = {1422-0067},
support = {2021C02064//Zhejiang Science and Technology Major Program on Agricultural New Variety Breeding/ ; LZ18C140002//Zhejiang Provincial Natural Science Foundation of China/ ; 324CXTD430//Hainan Provincial Natural Science Foundation of China/ ; },
mesh = {*Ascomycota/pathogenicity ; *Machine Learning ; *Disease Resistance/genetics ; *Genome-Wide Association Study ; *Plant Diseases/microbiology/genetics ; *Brassica napus/genetics/microbiology/immunology ; *Calcium Signaling/genetics ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Genomics/methods ; Multiomics ; },
abstract = {Sclerotinia sclerotiorum (Ss) is one of the most devastating fungal pathogens, causing huge yield loss in multiple economically important crops including oilseed rape. Plant resistance to Ss pertains to quantitative disease resistance (QDR) controlled by multiple minor genes. Genome-wide identification of genes involved in QDR to Ss is yet to be conducted. In this study, we integrated several assays including genome-wide association study (GWAS), multi-omics co-localization, and machine learning prediction to identify, on a genome-wide scale, genes involved in the oilseed rape QDR to Ss. Employing GWAS and multi-omics co-localization, we identified seven resistance-associated loci (RALs) associated with oilseed rape resistance to Ss. Furthermore, we developed a machine learning algorithm and named it Integrative Multi-Omics Analysis and Machine Learning for Target Gene Prediction (iMAP), which integrates multi-omics data to rapidly predict disease resistance-related genes within a broad chromosomal region. Through iMAP based on the identified RALs, we revealed multiple calcium signaling genes related to the QDR to Ss. Population-level analysis of selective sweeps and haplotypes of variants confirmed the positive selection of the predicted calcium signaling genes during evolution. Overall, this study has developed an algorithm that integrates multi-omics data and machine learning methods, providing a powerful tool for predicting target genes associated with specific traits. Furthermore, it makes a basis for further understanding the role and mechanisms of calcium signaling genes in the QDR to Ss.},
}
@article {pmid38997687,
year = {2024},
author = {Prakofjewa, J and Sartori, M and Šarka, P and Kalle, R and Pieroni, A and Sõukand, R},
title = {Knowledge in motion: temporal dynamics of wild food plant use in the Polish-Lithuanian-Belarusian border region.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {20},
number = {1},
pages = {65},
pmid = {38997687},
issn = {1746-4269},
support = {grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; grant agreement No 714874//European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme/ ; },
mesh = {Lithuania ; Poland ; *Plants, Edible/classification ; Republic of Belarus ; Humans ; Knowledge ; Ethnobotany ; },
abstract = {BACKGROUND: Understanding how Local Ecological Knowledge (LEK) evolves over time is crucial for fostering social and environmental responsibility. This study aims to develop a conceptual model of plant knowledge circulation, providing insights into the temporal dynamics of LEK in the Polish-Lithuanian-Belarusian border region. It explores the key patterns and driving forces behind changes in the use of wild plants for food.<br><br>METHODS: Field research was conducted in 60 rural settlements across Podlasie Voivodeship (Poland), Vilnius Region (Lithuania), and Hrodna Region (Belarus). This included 200 semi-structured interviews and participant observation among two local communities, Lithuanians and Poles. To assess the temporal dynamics of wild food use, we performed a cross-ethnic, cross-border analysis over time, dividing the data into three major temporal dimensions: past, continuous, and recently acquired uses.<br><br>RESULTS: Of the 72 wild plant taxa reported by Poles or Lithuanians in the Polish-Lithuanian-Belarusian borderland, 47 were continuously used for food, 58 were utilised in the past, and 41 were recently acquired. Cross-country trends were similar, with Poland showing more past uses. Diachronic comparisons between Poles and Lithuanians in each studied country revealed no significant differences. Recently acquired taxa overlapped considerably with those used continuously and in the past. The most diversely utilised taxa showed the greatest overlaps. By observing the movement of specific plant taxa within various time dimensions, we distinguished overlapping flow variations: retention (3 taxa), decay (11), invention (8), stagnation (17), revitalisation (6), re-invention (3), and knowledge in motion (24). Shifts in the use of wild food plants were influenced by changes in environmental conditions, governmental policies, cultural practices, and economic factors.<br><br>CONCLUSION: The findings of this study have important implications for improving methods of tracking changes in LEK and enhancing our understanding of the relationship between people and nature. Our results underscore the importance of considering knowledge circulation over time in different directions. Recognising the various stages of knowledge circulation might help in pursuing sustainable solutions that balance the needs of human communities with environmental protection.},
}
@article {pmid38994633,
year = {2024},
author = {Gómez-García, A and Prinz, AK and Jiménez, DAA and Zamora, WJ and Barazorda-Ccahuana, HL and Chávez-Fumagalli, M&#xc1; and Valli, M and Andricopulo, AD and da S Bolzani, V and Olmedo, DA and Solís, PN and Núñez, MJ and Rodríguez Pérez, JR and Sánchez, HAV and Cortés Hernández, HF and Mosquera Martinez, OM and Koch, O and Medina-Franco, JL},
title = {Updating and profiling the natural product-likeness of Latin American compound libraries.},
journal = {Molecular informatics},
volume = {43},
number = {7},
pages = {e202400052},
doi = {10.1002/minf.202400052},
pmid = {38994633},
issn = {1868-1751},
mesh = {*Biological Products/chemistry/pharmacology ; Latin America ; Small Molecule Libraries/pharmacology/chemistry ; Drug Discovery ; Cheminformatics ; Databases, Chemical ; },
abstract = {Compound databases of natural products play a crucial role in drug discovery and development projects and have implications in other areas, such as food chemical research, ecology and metabolomics. Recently, we put together the first version of the Latin American Natural Product database (LANaPDB) as a collective effort of researchers from six countries to ensemble a public and representative library of natural products in a geographical region with a large biodiversity. The present work aims to conduct a comparative and extensive profiling of the natural product-likeness of an updated version of LANaPDB and the individual ten compound databases that form part of LANaPDB. The natural product-likeness profile of the Latin American compound databases is contrasted with the profile of other major natural product databases in the public domain and a set of small-molecule drugs approved for clinical use. As part of the extensive characterization, we employed several chemoinformatics metrics of natural product likeness. The results of this study will capture the attention of the global community engaged in natural product databases, not only in Latin America but across the world.},
}
@article {pmid38992177,
year = {2024},
author = {Alvarez-Mora, I and Arturi, K and Béen, F and Buchinger, S and El Mais, AER and Gallampois, C and Hahn, M and Hollender, J and Houtman, C and Johann, S and Krauss, M and Lamoree, M and Margalef, M and Massei, R and Brack, W and Muz, M},
title = {Progress, applications, and challenges in high-throughput effect-directed analysis for toxicity driver identification - is it time for HT-EDA?.},
journal = {Analytical and bioanalytical chemistry},
volume = {},
number = {},
pages = {},
pmid = {38992177},
issn = {1618-2650},
abstract = {The rapid increase in the production and global use of chemicals and their mixtures has raised concerns about their potential impact on human and environmental health. With advances in analytical techniques, in particular, high-resolution mass spectrometry (HRMS), thousands of compounds and transformation products with potential adverse effects can now be detected in environmental samples. However, identifying and prioritizing the toxicity drivers among these compounds remain a significant challenge. Effect-directed analysis (EDA) emerged as an important tool to address this challenge, combining biotesting, sample fractionation, and chemical analysis to unravel toxicity drivers in complex mixtures. Traditional EDA workflows are labor-intensive and time-consuming, hindering large-scale applications. The concept of high-throughput (HT) EDA has recently gained traction as a means of accelerating these workflows. Key features of HT-EDA include the combination of microfractionation and downscaled bioassays, automation of sample preparation and biotesting, and efficient data processing workflows supported by novel computational tools. In addition to microplate-based fractionation, high-performance thin-layer chromatography (HPTLC) offers an interesting alternative to HPLC in HT-EDA. This review provides an updated perspective on the state-of-the-art in HT-EDA, and novel methods/tools that can be incorporated into HT-EDA workflows. It also discusses recent studies on HT-EDA, HT bioassays, and computational prioritization tools, along with considerations regarding HPTLC. By identifying current gaps in HT-EDA and proposing new approaches to overcome them, this review aims to bring HT-EDA a step closer to monitoring applications.},
}
@article {pmid38989474,
year = {2024},
author = {Li, R and Li, J and Lemer, S and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The genome sequence of a heart cockle, Fragum fragum (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {129},
pmid = {38989474},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual specimen of Fragum fragum (a heart cockle; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,153.1 megabases in span. Most of the assembly is scaffolded into 19 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 22.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,262 protein coding genes.},
}
@article {pmid38986397,
year = {2024},
author = {Hung, CC and Hsieh, HH and Chou, WC and Liu, EC and Chow, CH and Chang, Y and Lee, TM and Santschi, PH and Ranatunga, RRMKP and Bacosa, HP and Shih, YY},
title = {Assessing CO2 sources and sinks in and around Taiwan: Implication for achieving regional carbon neutrality by 2050.},
journal = {Marine pollution bulletin},
volume = {206},
number = {},
pages = {116664},
doi = {10.1016/j.marpolbul.2024.116664},
pmid = {38986397},
issn = {1879-3363},
abstract = {Taiwan has pledged to achieve net-zero carbon emissions by 2050, but the current extent of carbon sinks in Taiwan remains unclear. Therefore, this study aims to first review the existing nature-based carbon sinks on land and in the oceans around Taiwan. Subsequently, we suggest potential strategies to reduce CO2 emissions and propose carbon dioxide removal methods (CDRs). The natural carbon sinks by forests, sediments, and oceans in and around Taiwan are approximately 21.5, 42.1, and 96.8 Mt-CO2 y[-1], respectively, which is significantly less than Taiwan's CO2 emissions (280 Mt-CO2 y[-1]). Taiwan must consider decarbonization strategies like using electric vehicles, renewable energy, and hydrogen energy by formulating enabling policies. Besides more precisely assessing both terrestrial and marine carbon sinks, Taiwan should develop novel CDRs such as bioenergy with carbon capture and storage, afforestation, reforestation, biochar, seaweed cultivation, and ocean alkalinity enhancement, to reach carbon neutrality by 2050.},
}
@article {pmid38985613,
year = {2024},
author = {Filice, M and Crocco, MC and Agostino, RG and Barberi, RC and Amelio, D and Imbrogno, S and Formoso, V and Cerra, MC},
title = {An X-ray computed μ-tomography analysis for the characterization of 3D-heart shape in a model of cardiac plasticity.},
journal = {Vascular pharmacology},
volume = {155},
number = {},
pages = {107310},
doi = {10.1016/j.vph.2024.107310},
pmid = {38985613},
issn = {1879-3649},
mesh = {Animals ; *Imaging, Three-Dimensional ; *X-Ray Microtomography ; Heart/diagnostic imaging ; Radiographic Image Interpretation, Computer-Assisted ; },
}
@article {pmid38982382,
year = {2024},
author = {Blazanin, M},
title = {gcplyr: an R package for microbial growth curve data analysis.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {232},
pmid = {38982382},
issn = {1471-2105},
mesh = {*Software ; Computational Biology/methods ; Data Analysis ; },
abstract = {BACKGROUND: Characterization of microbial growth is of both fundamental and applied interest. Modern platforms can automate collection of high-throughput microbial growth curves, necessitating the development of computational tools to handle and analyze these data to produce insights.<br><br>RESULTS: To address this need, here I present a newly-developed R package: gcplyr. gcplyr can flexibly import growth curve data in common tabular formats, and reshapes it under a tidy framework that is flexible and extendable, enabling users to design custom analyses or plot data with popular visualization packages. gcplyr can also incorporate metadata and generate or import experimental designs to merge with data. Finally, gcplyr carries out model-free (non-parametric) analyses. These analyses do not require mathematical assumptions about microbial growth dynamics, and gcplyr is able to extract a broad range of important traits, including growth rate, doubling time, lag time, maximum density and carrying capacity, diauxie, area under the curve, extinction time, and more.<br><br>CONCLUSIONS: gcplyr makes scripted analyses of growth curve data in R straightforward, streamlines common data wrangling and analysis steps, and easily integrates with common visualization and statistical analyses.},
}
@article {pmid38979368,
year = {2024},
author = {Xiao, Y and Elmasry, M and Bai, JDK and Chen, A and Chen, Y and Jackson, B and Johnson, JO and Gillies, RJ and Prasanna, P and Chen, C and Damaghi, M},
title = {Eco-evolutionary Guided Pathomic Analysis to Predict DCIS Upstaging.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38979368},
issn = {2692-8205},
support = {P30 CA076292/CA/NCI NIH HHS/United States ; R01 CA249016/CA/NCI NIH HHS/United States ; R01 CA272601/CA/NCI NIH HHS/United States ; U01 CA261841/CA/NCI NIH HHS/United States ; },
abstract = {Cancers evolve in a dynamic ecosystem. Thus, characterizing cancer's ecological dynamics is crucial to understanding cancer evolution and can lead to discovering novel biomarkers to predict disease progression. Ductal carcinoma in situ (DCIS) is an early-stage breast cancer characterized by abnormal epithelial cell growth confined within the milk ducts. Although there has been extensive research on genetic and epigenetic causes of breast carcinogenesis, none of these studies have successfully identified a biomarker for the progression and/or upstaging of DCIS. In this study, we show that ecological habitat analysis of hypoxia and acidosis biomarkers can significantly improve prediction of DCIS upstaging. First, we developed a novel eco-evolutionary designed approach to define habitats in the tumor intra-ductal microenvironment based on oxygen diffusion distance in our DCIS cohort of 84 patients. Then, we identify cancer cells with metabolic phenotypes attributed to their habitat conditions, such as the expression of CA9 indicating hypoxia responding phenotype, and LAMP2b indicating a hypoxia-induced acid adaptation. Traditionally these markers have shown limited predictive capabilities for DCIS upstaging, if any. However, when analyzed from an ecological perspective, their power to differentiate between indolent and upstaged DCIS increased significantly. Second, using eco-evolutionary guided computational and digital pathology techniques, we discovered distinct spatial patterns of these biomarkers and used the distribution of such patterns to predict patient upstaging. The patterns were characterized by both cellular features and spatial features. With a 5-fold validation on the biopsy cohort, we trained a random forest classifier to achieve the area under curve(AUC) of 0.74. Our results affirm the importance of using eco-evolutionary-designed approaches in biomarkers discovery studies in the era of digital pathology by demonstrating the role of eco-evolution dynamics in predicting cancer progression.},
}
@article {pmid38976642,
year = {2024},
author = {Pisarenco, VA and Vizueta, J and Rozas, J},
title = {GALEON: a comprehensive bioinformatic tool to analyse and visualize gene clusters in complete genomes.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {7},
pages = {},
pmid = {38976642},
issn = {1367-4811},
support = {MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovaci&#xf3;n of Spain/ ; },
mesh = {*Multigene Family ; *Software ; *Computational Biology/methods ; Genome ; Genomics/methods ; Evolution, Molecular ; Humans ; },
abstract = {MOTIVATION: Gene clusters, defined as a set of genes encoding functionally related proteins, are abundant in eukaryotic genomes. Despite the increasing availability of chromosome-level genomes, the comprehensive analysis of gene family evolution remains largely unexplored, particularly for large and highly dynamic gene families or those including very recent family members. These challenges stem from limitations in genome assembly contiguity, particularly in repetitive regions such as large gene clusters. Recent advancements in sequencing technology, such as long reads and chromatin contact mapping, hold promise in addressing these challenges.<br><br>RESULTS: To facilitate the identification, analysis, and visualization of physically clustered gene family members within chromosome-level genomes, we introduce GALEON, a user-friendly bioinformatic tool. GALEON identifies gene clusters by studying the spatial distribution of pairwise physical distances among gene family members along with the genome-wide gene density. The pipeline also enables the simultaneous analysis and comparison of two gene families and allows the exploration of the relationship between physical and evolutionary distances. This tool offers a novel approach for studying the origin and evolution of gene families.<br><br>GALEON is freely available from https://www.ub.edu/softevol/galeon and https://github.com/molevol-ub/galeon.},
}
@article {pmid38974014,
year = {2024},
author = {Cassee, FR and Bleeker, EAJ and Durand, C and Exner, T and Falk, A and Friedrichs, S and Heunisch, E and Himly, M and Hofer, S and Hofstätter, N and Hristozov, D and Nymark, P and Pohl, A and Soeteman-Hernández, LG and Suarez-Merino, B and Valsami-Jones, E and Groenewold, M},
title = {Roadmap towards safe and sustainable advanced and innovative materials. (Outlook for 2024-2030).},
journal = {Computational and structural biotechnology journal},
volume = {25},
number = {},
pages = {105-126},
pmid = {38974014},
issn = {2001-0370},
abstract = {The adoption of innovative advanced materials holds vast potential, contingent upon addressing safety and sustainability concerns. The European Commission advocates the integration of Safe and Sustainable by Design (SSbD) principles early in the innovation process to streamline market introduction and mitigate costs. Within this framework, encompassing ecological, social, and economic factors is paramount. The NanoSafety Cluster (NSC) delineates key safety and sustainability areas, pinpointing unresolved issues and research gaps to steer the development of safe(r) materials. Leveraging FAIR data management and integration, alongside the alignment of regulatory aspects, fosters informed decision-making and innovation. Integrating circularity and sustainability mandates clear guidance, ensuring responsible innovation at every stage. Collaboration among stakeholders, anticipation of regulatory demands, and a commitment to sustainability are pivotal for translating SSbD into tangible advancements. Harmonizing standards and test guidelines, along with regulatory preparedness through an exchange platform, is imperative for governance and market readiness. By adhering to these principles, the effective and sustainable deployment of innovative materials can be realized, propelling positive transformation and societal acceptance.},
}
@article {pmid38973368,
year = {2024},
author = {Martínez, L and Zattara, EE and Arbetman, MP and Morales, CL and Masonbrink, RE and Severin, AJ and Aizen, MA and Toth, AL},
title = {Chromosome-Level Assembly and Annotation of the Genome of the Endangered Giant Patagonian Bumble Bee Bombus dahlbomii.},
journal = {Genome biology and evolution},
volume = {16},
number = {7},
pages = {},
doi = {10.1093/gbe/evae146},
pmid = {38973368},
issn = {1759-6653},
support = {//Fulbright Science and Technology Award, Argentina Commission/ ; //Iowa State University Faculty Professional Development Leave/ ; NGS-57001R-19//National Geographic Society/ ; },
mesh = {Animals ; Bees/genetics ; *Endangered Species ; *Molecular Sequence Annotation ; *Genome, Insect ; Male ; Chromosomes, Insect/genetics ; },
abstract = {This article describes a genome assembly and annotation for Bombus dahlbomii, the giant Patagonian bumble bee. DNA from a single, haploid male collected in Argentina was used for PacBio (HiFi) sequencing, and Hi-C technology was then used to map chromatin contacts. Using Juicer and manual curation, the genome was scaffolded into 18 main pseudomolecules, representing a high-quality, near chromosome-level assembly. The sequenced genome size is estimated at 265 Mb. The genome was annotated based on RNA sequencing data of another male from Argentina, and BRAKER3 produced 15,767 annotated genes. The genome and annotation show high completeness, with >95% BUSCO scores for both the genome and annotated genes (based on conserved genes from Hymenoptera). This genome provides a valuable resource for studying the biology of this iconic and endangered species, as well as for understanding the impacts of its decline and designing strategies for its preservation.},
}
@article {pmid38972117,
year = {2024},
author = {Hyman, S and Zhang, J and Lim, YH and Jovanovic Andersen, Z and Cole-Hunter, T and Li, Y and Møller, P and Daras, K and Williams, R and Thomas, ML and Labib, SM and Topping, D},
title = {Residential greenspace and COVID-19 Severity: A cohort study of 313,657 individuals in Greater Manchester, United Kingdom.},
journal = {Environment international},
volume = {190},
number = {},
pages = {108843},
doi = {10.1016/j.envint.2024.108843},
pmid = {38972117},
issn = {1873-6750},
abstract = {BACKGROUND: Greenspaces contribute positively to mental and physical well-being, promote social cohesion, and alleviate environmental stressors, such as air pollution. Ecological studies suggest that greenspace may affect incidence and severity of Coronavirus Disease 2019 (COVID-19).<br><br>OBJECTIVE: This study examines the association between residential greenspace and COVID-19 related hospitalization and death.<br><br>METHOD: In this retrospective cohort based on patient records from the Greater Manchester Care Records, all first COVID-19 cases diagnosed between March 1, 2020, and May 31, 2022 were followed until COVID-19 related hospitalization or death within 28&#xa0;days. Residential greenspace availability was assessed using the Normalized Difference Vegetation Index per lower super output area in Greater Manchester. The association of greenspace with COVID-19 hospitalization and mortality were estimated using multivariate logistic regression models after adjusting for potential individual, temporal, and spatial confounders. We explored potential effect modifications of the associations with greenspace and COVID-19 severity by age, sex, body mass index, smoking, deprivation, and certain comorbidities. Combined effects of greenspace and air pollution (NO2 and PM2.5) were investigated by mutually adjusting pairs with correlation coefficients&#xa0;&#x2264;&#xa0;0&#xb7;7.<br><br>RESULTS: Significant negative associations were observed between greenspace availability and COVID-19 hospitalization and mortality with odds ratios [OR] (95&#xa0;% Confidence Intervals [CI]) of 0&#xb7;96 (0&#xb7;94-0&#xb7;97) and 0&#xb7;84 (0&#xb7;80-0&#xb7;88) (per interquartile range [IQR]), respectively. These were significantly modified by deprivation (P-value for interaction&#xa0;<&#xa0;0.05), showing that those most deprived obtained largest benefits from greenspace. Inclusion of NO2 and PM2.5 diminished associations to null for COVID-19 hospitalization, but only reduced them slightly for mortality, where inverse associations remained.<br><br>CONCLUSION: In the Greater Manchester area, residential greenspace is associated with reduced risk of hospitalization or death in individuals with COVID-19, with deprived groups obtaining the greatest benefits. Associations were strongest for COVID-19 mortality, which were robust to inclusion of air pollutants in the models.},
}
@article {pmid38968897,
year = {2024},
author = {Zhu, Y and Chen, F and Jiang, F and Hua, Z and Luo, Z and Ma, J},
title = {Enhanced remediation of PFAS-metal co-contaminated soil by ceramsite supported Fe3O4-MoS2 heterojunction as a high-performance piezocatalyst.},
journal = {Journal of environmental management},
volume = {365},
number = {},
pages = {121716},
doi = {10.1016/j.jenvman.2024.121716},
pmid = {38968897},
issn = {1095-8630},
mesh = {*Soil Pollutants/chemistry/metabolism ; *Soil/chemistry ; *Metals, Heavy/chemistry ; Environmental Restoration and Remediation/methods ; Biodegradation, Environmental ; },
abstract = {In this study, a novel piezoremediation system was developed to remediate an actual soil co-polluted by high contents of per- and polyfluoroalkyl substances (PFAS, 5725 μg/kg soil) and heavy metals (6455 mg/kg soil). Two piezocatalysts, MoS2/ceramsite (MC) and Fe3O4-MoS2/ceramsite (FMC), were synthesized using a facile hydrothermal-coprecipitation method. These two materials were employed to treat the co-contaminated soil in soil slurry environment under sonication. FMC exhibited significantly higher piezoremediation performance than MC, wherein 91.6% of PFAS, 97.8% of Cr[6+] ions and 81% of total metals (Cr, Cu, Zn and Ni) were removed from the soil after 50 min of the FMC piezoremediation process. FMC also exhibited the advantages of easy separation from the slurry phase and excellent reusability. In comparison with MC, the Fe3O4-MoS2 heterojunction in FMC can stabilize MoS2 particles on the surface of ceramsite granules, promote the separation of electron/hole pairs, accelerate charge transfer, therefore enhancing piezocatalytic performance. The electron spin resonance analysis and free radical quenching tests show that [•]OH was the dominant oxidative radical responsible for PFAS degradation. The count of bacteria and the bacterial community structure in the treated soil can be basically restored to the initial states after 30 days of incubation under nutrient stimulation. Overall, this study not only provides a deep insight on soil remediation process, but also offers an efficient and reliable technique for simultaneous decontamination of organic and metal pollutants in soil.},
}
@article {pmid38968305,
year = {2024},
author = {Fu, X and Withers, J and Miyamae, JA and Moore, TY},
title = {ArborSim: Articulated, branching, OpenSim routing for constructing models of multi-jointed appendages with complex muscle-tendon architecture.},
journal = {PLoS computational biology},
volume = {20},
number = {7},
pages = {e1012243},
pmid = {38968305},
issn = {1553-7358},
mesh = {*Tendons/physiology/anatomy &amp; histology ; Humans ; Biomechanical Phenomena ; *Software ; *Joints/physiology/anatomy &amp; histology ; *Muscle, Skeletal/physiology/anatomy &amp; histology ; Models, Biological ; Computational Biology ; Computer Simulation ; Animals ; },
abstract = {Computational models of musculoskeletal systems are essential tools for understanding how muscles, tendons, bones, and actuation signals generate motion. In particular, the OpenSim family of models has facilitated a wide range of studies on diverse human motions, clinical studies of gait, and even non-human locomotion. However, biological structures with many joints, such as fingers, necks, tails, and spines, have been a longstanding challenge to the OpenSim modeling community, especially because these structures comprise numerous bones and are frequently actuated by extrinsic muscles that span multiple joints-often more than three-and act through a complex network of branching tendons. Existing model building software, typically optimized for limb structures, makes it difficult to build OpenSim models that accurately reflect these intricacies. Here, we introduce ArborSim, customized software that efficiently creates musculoskeletal models of highly jointed structures and can build branched muscle-tendon architectures. We used ArborSim to construct toy models of articulated structures to determine which morphological features make a structure most sensitive to branching. By comparing the joint kinematics of models constructed with branched and parallel muscle-tendon units, we found that among various parameters-the number of tendon branches, the number of joints between branches, and the ratio of muscle fiber length to muscle tendon unit length-the number of tendon branches and the number of joints between branches are most sensitive to branching modeling method. Notably, the differences between these models showed no predictable pattern with increased complexity. As the proportion of muscle increased, the kinematic differences between branched and parallel models units also increased. Our findings suggest that stress and strain interactions between distal tendon branches and proximal tendon and muscle greatly affect the overall kinematics of a musculoskeletal system. By incorporating complex muscle-tendon branching into OpenSim models using ArborSim, we can gain deeper insight into the interactions between the axial and appendicular skeleton, model the evolution and function of diverse animal tails, and understand the mechanics of more complex motions and tasks.},
}
@article {pmid38968199,
year = {2024},
author = {Stratton, CA and Thompson, Y and Zio, K and Morrison, WR and Murrell, EG},
title = {uafR: An R package that automates mass spectrometry data processing.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0306202},
pmid = {38968199},
issn = {1932-6203},
mesh = {*Gas Chromatography-Mass Spectrometry/methods ; *Algorithms ; *Software ; Cheminformatics/methods ; },
abstract = {Chemical information has become increasingly ubiquitous and has outstripped the pace of analysis and interpretation. We have developed an R package, uafR, that automates a grueling retrieval process for gas -chromatography coupled mass spectrometry (GC -MS) data and allows anyone interested in chemical comparisons to quickly perform advanced structural similarity matches. Our streamlined cheminformatics workflows allow anyone with basic experience in R to pull out component areas for tentative compound identifications using the best published understanding of molecules across samples (pubchem.gov). Interpretations can now be done at a fraction of the time, cost, and effort it would typically take using a standard chemical ecology data analysis pipeline. The package was tested in two experimental contexts: (1) A dataset of purified internal standards, which showed our algorithms correctly identified the known compounds with R2 values ranging from 0.827-0.999 along concentrations ranging from 1 × 10-5 to 1 × 103 ng/μl, (2) A large, previously published dataset, where the number and types of compounds identified were comparable (or identical) to those identified with the traditional manual peak annotation process, and NMDS analysis of the compounds produced the same pattern of significance as in the original study. Both the speed and accuracy of GC -MS data processing are drastically improved with uafR because it allows users to fluidly interact with their experiment following tentative library identifications [i.e. after the m/z spectra have been matched against an installed chemical fragmentation database (e.g. NIST)]. Use of uafR will allow larger datasets to be collected and systematically interpreted quickly. Furthermore, the functions of uafR could allow backlogs of previously collected and annotated data to be processed by new personnel or students as they are being trained. This is critical as we enter the era of exposomics, metabolomics, volatilomes, and landscape level, high-throughput chemotyping. This package was developed to advance collective understanding of chemical data and is applicable to any research that benefits from GC -MS analysis. It can be downloaded for free along with sample datasets from Github at github.org/castratton/uafR or installed directly from R or RStudio using the developer tools: 'devtools::install_github("castratton/uafR")'.},
}
@article {pmid38967613,
year = {2024},
author = {Hanners, A and Melnyk, B and Bedell, T and Conroy, S and Volek, J and Brock, G and Kelley, M},
title = {A pilot study of Keto Prescribed+: A healthy thinking and eating educational program for African American women.},
journal = {Journal of the American Association of Nurse Practitioners},
volume = {36},
number = {7},
pages = {377-384},
pmid = {38967613},
issn = {2327-6924},
support = {L30 HL159699/HL/NHLBI NIH HHS/United States ; UL1TR002733//Center for Clinical and Translational Science, Ohio State University/ ; TL1TR002735//Center for Clinical and Translational Science, Ohio State University/ ; },
mesh = {Humans ; Female ; Pilot Projects ; *Black or African American/psychology/statistics &amp; numerical data ; Adult ; Middle Aged ; Obesity/therapy/psychology ; },
abstract = {African American (AA) women have the highest prevalence of obesity in addition to health disparities in preventable diet-related diseases (i.e., diabetes, hypertension), which places them at increased risk for cardiovascular disease. The purpose of this pilot study was to assess the feasibility, acceptability, and preliminary effectiveness of the Keto Prescribed+ (KetoRx+) program on associated physical and psychosocial outcomes among this population. The KetoRx+ program is a healthy eating and thinking educational intervention. The program combined online and in-person community group sessions over 8 weeks. The Keto Prescribed+ was found to be feasible and acceptable with comments on ways to increase acceptability from participants completing program (n = 10). Physical outcomes changed showed an average decrease in weight of 10lbs (SD = 5), baseline average 226lbs. Waist-to-hip ratio and systolic blood pressure also trended down. Psychosocial outcomes showed improvement trends. The KetoRx+ program is feasible and acceptable for overweight or obese AA women. Preliminary efficacy was established for most physical and psychosocial outcomes. However, more research is needed to identify specific program components contributing to healthy lifestyle behavior change and to establish program efficacy and effectiveness. Culturally adapted community-based biopsychosocial interventions using ketogenic nutrition therapy may help improve cardiovascular health of adult AA women.},
}
@article {pmid38966305,
year = {2024},
author = {Crowley, LM and Roy, HE and Brown, PMJ and , and , and , and , and , and , and , },
title = {The genome sequence of the ten-spot ladybird, Adalia decempunctata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {106},
pmid = {38966305},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Adalia decempunctata (the ten-spot ladybird; Arthropoda; Insecta; Coleoptera; Coccinellidae). The genome sequence is 489.4 megabases in span. Most of the assembly is scaffolded into 12 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.68 kilobases in length.},
}
@article {pmid38964062,
year = {2024},
author = {Jeon, Y and Kwon, YS and Noh, YJ and Lee, SM and Song, JW and Kim, JH and Seo, JS},
title = {Unraveling the mechanisms of benzo[a]pyrene degradation by Pigmentiphaga kullae strain KIT-003 using a multi-omics approach.},
journal = {Ecotoxicology and environmental safety},
volume = {281},
number = {},
pages = {116665},
doi = {10.1016/j.ecoenv.2024.116665},
pmid = {38964062},
issn = {1090-2414},
mesh = {*Benzo(a)pyrene/metabolism/toxicity ; *Biodegradation, Environmental ; Republic of Korea ; Proteomics ; Water Pollutants, Chemical/metabolism/toxicity ; Gas Chromatography-Mass Spectrometry ; Catechols/metabolism ; Rivers/chemistry/microbiology ; Multiomics ; },
abstract = {Polycyclic aromatic hydrocarbons (PAHs), notably benzo[a]pyrene (BaP), are environmental contaminants with multiple adverse ecological implications. Numerous studies have suggested the use of BaP biodegradation using various bacterial strains to remove BaP from the environment. This study investigates the BaP biodegradation capability of Pigmentiphaga kullae strain KIT-003, isolated from the Nak-dong River (South Korea) under specific environmental conditions. The optimum conditions of biodegradation were found to be pH 7.0, 35°C, and a salinity of 0 %. GC-MS analysis suggested alternative pathways by which KIT-003 produced catechol from BaP through several intermediate metabolites, including 4-formylchrysene-5-carboxylic acid, 5,6-dihydro-5,6-dihydroxychrysene-5-carboxylic acid (isomer: 3,4-dihydro-3,4-dihydroxychrysene-4-carboxylic acid), naphthalene-1,2-dicarboxylic acid, and 2-hydroxy-1-naphthoic acid. Proteomic profiles indicated upregulation of enzymes associated with aromatic compound degradation, such as nahAc and nahB, and of those integral to the tricarboxylic acid cycle, reflecting the strain's adaptability to and degradation of BaP. Lipidomic analysis of KIT-003 demonstrated that BaP exposure induced an accumulation of glycerolipids such as diacylglycerol and triacylglycerol, indicating their crucial role in bacterial adaptation mechanisms under BaP stress. This study provides significant scientific knowledge regarding the intricate mechanisms involved in BaP degradation by microorganisms.},
}
@article {pmid38960861,
year = {2024},
author = {Dolenz, S and van der Valk, T and Jin, C and Oppenheimer, J and Sharif, MB and Orlando, L and Shapiro, B and Dalén, L and Heintzman, PD},
title = {Unravelling reference bias in ancient DNA datasets.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {7},
pages = {},
pmid = {38960861},
issn = {1367-4811},
support = {2021.0048//Knut and Alice Wallenberg Foundation/ ; },
mesh = {*DNA, Ancient/analysis ; Humans ; *Sequence Analysis, DNA/methods ; Software ; Animals ; Sequence Alignment/methods ; Computational Biology/methods ; Algorithms ; },
abstract = {MOTIVATION: The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths.<br><br>RESULTS: For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings.<br><br>AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts).},
}
@article {pmid38956468,
year = {2024},
author = {Li, X and Cao, T and Liu, H and Fu, L and Wang, Q},
title = {Identification and expression analysis of Sox family genes in echinoderms.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {655},
pmid = {38956468},
issn = {1471-2164},
support = {ZR2021QD158//Natural Science Foundation of Shandong Province, China/ ; ZR2021MC151//Natural Science Foundation of Shandong Province, China/ ; 2023XBZD003//Scientific Research Project of Yantai Vocational College/ ; },
mesh = {Animals ; *SOX Transcription Factors/genetics/metabolism ; *Phylogeny ; *Echinodermata/genetics ; *Multigene Family ; Gene Expression Profiling ; Evolution, Molecular ; Gene Expression Regulation, Developmental ; Computational Biology/methods ; },
abstract = {The Sox gene family, a collection of transcription factors widely distributed throughout the animal kingdom, plays a crucial role in numerous developmental processes. Echinoderms occupy a pivotal position in many research fields, such as neuroscience, sex determination and differentiation, and embryonic development. However, to date, no comprehensive study has been conducted to characterize and analyze Sox genes in echinoderms. In the present study, the evolution and expression of Sox family genes across 11 echinoderms were analyzed using bioinformatics methods. The results revealed a total of 70 Sox genes, with counts ranging from 5 to 8 across different echinoderms. Phylogenetic analysis revealed that the identified Sox genes could be categorized into seven distinct classes: the SoxB1 class, SoxB2 class, SoxC class, SoxD class, SoxE class, SoxF class and SoxH class. Notably, the SoxB1, SoxB2, and SoxF genes were ubiquitously present in all the echinoderms studied, which suggests that these genes may be conserved in echinoderms. The spatiotemporal expression patterns observed for Sox genes in the three echinoderms indicated that various Sox members perform distinct functional roles. Notably, SoxB1 is likely involved in echinoderm ovary development, while SoxH may play a crucial role in testis development in starfish and sea cucumber. In general, the present investigation provides a molecular foundation for exploring the Sox gene in echinoderms, providing a valuable resource for future phylogenetic and genomic studies.},
}
@article {pmid38955825,
year = {2024},
author = {Pan, H and Wattiez, R and Gillan, D},
title = {Soil Metaproteomics for Microbial Community Profiling: Methodologies and Challenges.},
journal = {Current microbiology},
volume = {81},
number = {8},
pages = {257},
pmid = {38955825},
issn = {1432-0991},
support = {No.2023-BSBA-024//Joint Funds of the Natural Science Foundation of Liaoning Province of China/ ; },
mesh = {*Soil Microbiology ; *Proteomics/methods ; *Metagenomics/methods ; *Bacteria/genetics/classification/metabolism/isolation &amp; purification ; *Microbiota ; Fungi/classification/genetics/metabolism/isolation &amp; purification ; Soil/chemistry ; Computational Biology/methods ; },
abstract = {Soil represents a complex and dynamic ecosystem, hosting a myriad of microorganisms that coexist and play vital roles in nutrient cycling and organic matter transformation. Among these microorganisms, bacteria and fungi are key members of the microbial community, profoundly influencing the fate of nitrogen, sulfur, and carbon in terrestrial environments. Understanding the intricacies of soil ecosystems and the biological processes orchestrated by microbial communities necessitates a deep dive into their composition and metabolic activities. The advent of next-generation sequencing and 'omics' techniques, such as metagenomics and metaproteomics, has revolutionized our understanding of microbial ecology and the functional dynamics of soil microbial communities. Metagenomics enables the identification of microbial community composition in soil, while metaproteomics sheds light on the current biological functions performed by these communities. However, metaproteomics presents several challenges, both technical and computational. Factors such as the presence of humic acids and variations in extraction methods can influence protein yield, while the absence of high-resolution mass spectrometry and comprehensive protein databases limits the depth of protein identification. Notwithstanding these limitations, metaproteomics remains a potent tool for unraveling the intricate biological processes and functions of soil microbial communities. In this review, we delve into the methodologies and challenges of metaproteomics in soil research, covering aspects such as protein extraction, identification, and bioinformatics analysis. Furthermore, we explore the applications of metaproteomics in soil bioremediation, highlighting its potential in addressing environmental challenges.},
}
@article {pmid38954338,
year = {2024},
author = {Yao, Z and Zhou, X and Jin, T and Wang, L and Liu, N and Wu, L},
title = {Remediation of phenanthrene contaminated soil by persulphate coupled with Pseudomonas aeruginosa GZ7 based on oxidation prediction model.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {31},
pages = {44415-44430},
pmid = {38954338},
issn = {1614-7499},
support = {52270171//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 51974314//Innovative Research Group Project of the National Natural Science Foundation of China/ ; },
mesh = {*Phenanthrenes/metabolism ; *Pseudomonas aeruginosa ; *Soil Pollutants ; *Oxidation-Reduction ; *Soil/chemistry ; Soil Microbiology ; Environmental Restoration and Remediation/methods ; Biodegradation, Environmental ; Polycyclic Aromatic Hydrocarbons ; Sulfates/chemistry ; },
abstract = {Chemical oxidation coupled with microbial remediation has attracted widespread attention for the removal of polycyclic aromatic hydrocarbons (PAHs). Among them, the precise evaluation of the feasible oxidant concentration of PAH-contaminated soil is the key to achieving the goal of soil functional ecological remediation. In this study, phenanthrene (PHE) was used as the target pollutant, and Fe[2+]-activated persulphate (PS) was used to remediate four types of soils. Linear regression analysis identified the following important factors influencing remediation: PS dosage and soil PHE content for PHE degradation, Fe[2+] dosage, hydrolysable nitrogen (HN), and available phosphorus for PS decomposition. A comprehensive model of "soil characteristics-oxidation conditions-remediation effect" with a high predictive accuracy was constructed. Based on model identification, Pseudomonas aeruginosa GZ7, which had high PAHs degrading ability after domestication, was further applied to coupling repair remediation. The results showed that the optimal PS dose was 0.75% (w/w). The response relationship between soil physical, chemical, and biological indicators at the intermediate interface and oxidation conditions was analysed. Coupled remediation effects were clarified using microbial diversity sequencing. The introduction of Pseudomonas aeruginosa GZ7 stimulated the relative abundance of Cohnella, Enterobacter, Paenibacillus, and Bacillus, which can promote material metabolism and energy transformation during remediation.},
}
@article {pmid38954067,
year = {2024},
author = {Bazkiaee, PA and Kamkar, B and Amiri, E and Kazemi, H and Rezaei, M and Araji, HA},
title = {Multi-criteria GIS-based land suitability analysis for rice cultivation: a case study in Guilan Province, Iran.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {7},
pages = {680},
pmid = {38954067},
issn = {1573-2959},
mesh = {*Oryza/growth &amp; development ; Iran ; *Geographic Information Systems ; *Environmental Monitoring/methods ; *Agriculture/methods ; *Soil/chemistry ; Conservation of Natural Resources ; Climate ; },
abstract = {Ensuring food security and sustainable resource management has become a paramount global concern, prompting significant attention to land suitability analysis for enhancing agricultural production. In this study, an AHP-weighted overlay method was employed to delineate rice cultivation suitability in Guilan province, Iran, a central hub for rice production. Sixteen climatic, topographic, and soil variables were integrated, and individual maps were reclassified to align with the specific requisites for rice production. The results revealed three suitability classes: including 'very suitable,' 'suitable,' and 'moderately suitable', covering 91%, 6%, and 3% of the land, respectively. Soil attributes, particularly organic matter, significantly influenced suitability (weight value of 0.745), with topographic and soil factors outweighing climate in assessment. While salinity is generally absent, organic matter deficiency affects 44% of the land. Phosphorus imbalances are prevalent, with potassium toxicity observed in 10%. Microelement deficiencies, especially in iron and zinc, are noted. Additionally, the results indicated that topographic and soil attributes played a more significant role than climate-related factors in assessing land suitability for rice cultivation within the study area. This research provides a comprehensive spatial analysis of all variables in the study region, shedding light on the complexities of land suitability for rice cultivation. These findings contribute to the understanding of agricultural sustainability and resource management strategies in the context of food security.},
}
@article {pmid38951915,
year = {2024},
author = {Koci, O and Russell, RK and Shaikh, MG and Edwards, C and Gerasimidis, K and Ijaz, UZ},
title = {CViewer: a Java-based statistical framework for integration of shotgun metagenomics with other omics datasets.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {117},
pmid = {38951915},
issn = {2049-2618},
support = {NE/L011956/1//NERC Environmental Bioinformatics Centre/ ; BB/T010657/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
mesh = {*Metagenomics/methods ; Humans ; *Software ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Computational Biology/methods ; Metagenome ; Crohn Disease/microbiology/genetics ; },
abstract = {BACKGROUND: Shotgun metagenomics for microbial community survey recovers enormous amount of information for microbial genomes that include their abundances, taxonomic, and phylogenetic information, as well as their genomic makeup, the latter of which then helps retrieve their function based on annotated gene products, mRNA, protein, and metabolites. Within the context of a specific hypothesis, additional modalities are often included, to give host-microbiome interaction. For example, in human-associated microbiome projects, it has become increasingly common to include host immunology through flow cytometry. Whilst there are plenty of software approaches available, some that utilize marker-based and assembly-based approaches, for downstream statistical analyses, there is still a dearth of statistical tools that help consolidate all such information in a single platform. By virtue of stringent computational requirements, the statistical workflow is often passive with limited visual exploration.<br><br>RESULTS: In this study, we have developed a Java-based statistical framework (https://github.com/KociOrges/cviewer) to explore shotgun metagenomics data, which integrates seamlessly with conventional pipelines and offers exploratory as well as hypothesis-driven analyses. The end product is a highly interactive toolkit with a multiple document interface, which makes it easier for a person without specialized knowledge to perform analysis of multiomics datasets and unravel biologically relevant patterns. We have designed algorithms based on frequently used numerical ecology and machine learning principles, with value-driven from integrated omics tools which not only find correlations amongst different datasets but also provide discrimination based on case-control relationships.<br><br>CONCLUSIONS: CViewer was used to analyse two distinct metagenomic datasets with varying complexities. These include a dietary intervention study to understand Crohn's disease changes during a dietary treatment to include remission, as well as a gut microbiome profile for an obesity dataset comparing subjects who suffer from obesity of different aetiologies and against controls who were lean. Complete analyses of both studies in CViewer then provide very powerful mechanistic insights that corroborate with the published literature and demonstrate its full potential. Video Abstract.},
}
@article {pmid38947430,
year = {2024},
author = {Li, S and Mao, Y and Yang, J and Li, Y and Dong, J and Wang, Z and Jiang, L and He, S},
title = {Efficient integration of covalent triazine frameworks (CTFs) for augmented photocatalytic efficacy: A review of synthesis, strategies, and applications.},
journal = {Heliyon},
volume = {10},
number = {11},
pages = {e32202},
pmid = {38947430},
issn = {2405-8440},
abstract = {Heterogeneous photocatalysis emerges as an exceptionally appealing technological avenue for the direct capture, conversion, and storage of renewable solar energy, facilitating the generation of sustainable and ecologically benign solar fuels and a spectrum of other pertinent applications. Heterogeneous nanocomposites, incorporating Covalent Triazine Frameworks (CTFs), exhibit a wide-ranging spectrum of light absorption, well-suited electronic band structures, rapid charge carrier mobility, ample resource availability, commendable chemical robustness, and straightforward synthetic routes. These attributes collectively position them as highly promising photocatalysts with applicability in diverse fields, including but not limited to the production of photocatalytic solar fuels and the decomposition of environmental contaminants. As the field of photocatalysis through the hybridization of CTFs undergoes rapid expansion, there is a pressing and substantive need for a systematic retrospective analysis and forward-looking evaluation to elucidate pathways for enhancing performance. This comprehensive review commences by directing attention to diverse synthetic methodologies for the creation of composite materials. And then it delves into a thorough exploration of strategies geared towards augmenting performance, encompassing the introduction of electron donor-acceptor (D-A) units, heteroatom doping, defect Engineering, architecture of Heterojunction and optimization of morphology. Following this, it systematically elucidates applications primarily centered around the efficient generation of photocatalytic hydrogen, reduction of carbon dioxide through photocatalysis, and the degradation of organic pollutants. Ultimately, the discourse turns towards unresolved challenges and the prospects for further advancement, offering valuable guidance for the potent harnessing of CTFs in high-efficiency photocatalytic processes.},
}
@article {pmid38945180,
year = {2024},
author = {Pearl, RL and Donze, LF and Rosas, LG and Agurs-Collins, T and Baskin, ML and Breland, JY and Shanks, CB and Stowers, KC and Johnson, S and Lee, BY and Martin, MY and Mujuru, P and Odoms-Young, A and Panza, E and Pronk, NP and Calicutt, K and Nadglowski, J and Nece, PM and Tedder, M and Chow, LS and Krishnamurti, H and Jay, M and Xi, D and Jastreboff, AM and Stanford, FC},
title = {Ending Weight Stigma to Advance Health Equity.},
journal = {American journal of preventive medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.amepre.2024.06.021},
pmid = {38945180},
issn = {1873-2607},
}
@article {pmid38941024,
year = {2024},
author = {Holstein, T and Muth, T},
title = {Bioinformatic Workflows for Metaproteomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2820},
number = {},
pages = {187-213},
pmid = {38941024},
issn = {1940-6029},
mesh = {*Proteomics/methods ; *Computational Biology/methods ; *Workflow ; *Software ; *Microbiota/genetics ; Humans ; Databases, Protein ; Metagenomics/methods ; },
abstract = {The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the investigation of the composition and function of microbial community samples have been developed. Metaproteomics, the comprehensive analysis of the proteins from microbial communities, allows for the investigation of not only the taxonomy but also the functional and quantitative composition of microbiome samples. Due to the complexity of the investigated communities, methods developed for single organism proteomics cannot be readily applied to metaproteomic samples. For this purpose, methods specifically tailored to metaproteomics are required. In this work, a detailed overview of current bioinformatic solutions and protocols in metaproteomics is given. After an introduction to the proteomic database search, the metaproteomic post-processing steps are explained in detail. Ten specific bioinformatic software solutions are focused on, covering various steps including database-driven identification and quantification as well as taxonomic and functional assignment.},
}
@article {pmid38938637,
year = {2024},
author = {Yang, J and Deng, H and Zhang, Y and Zhou, Y and Miao, T},
title = {Application of amodal segmentation for shape reconstruction and occlusion recovery in occluded tomatoes.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1376138},
pmid = {38938637},
issn = {1664-462X},
abstract = {Common object detection and image segmentation methods are unable to accurately estimate the shape of the occluded fruit. Monitoring the growth status of shaded crops in a specific environment is challenging, and certain studies related to crop harvesting and pest detection are constrained by the natural shadow conditions. Amodal segmentation can focus on the occluded part of the fruit and complete the overall shape of the fruit. We proposed a Transformer-based amodal segmentation algorithm to infer the amodal shape of occluded tomatoes. Considering the high cost of amodal annotation, we only needed modal dataset to train the model. The dataset was taken from two greenhouses on the farm and contains rich occlusion information. We introduced boundary estimation in the hourglass structured network to provide a priori information about the completion of the amodal shapes, and reconstructed the occluded objects using a GAN network (with discriminator) and GAN loss. The model in this study showed accuracy, with average pairwise accuracy of 96.07%, mean intersection-over-union (mIoU) of 94.13% and invisible mIoU of 57.79%. We also examined the quality of pseudo-amodal annotations generated by our proposed model using Mask R-CNN. Its average precision (AP) and average precision with intersection over union (IoU) 0.5 (AP50) reached 63.91%,86.91% respectively. This method accurately and rationally achieves the shape of occluded tomatoes, saving the cost of manual annotation, and is able to deal with the boundary information of occlusion while decoupling the relationship of occluded objects from each other. Future work considers how to complete the amodal segmentation task without overly relying on the occlusion order and the quality of the modal mask, thus promising applications to provide technical support for the advancement of ecological monitoring techniques and ecological cultivation.},
}
@article {pmid38937989,
year = {2024},
author = {Wu, H and Mu, C and Li, X and Fan, W and Shen, L and Zhu, W},
title = {Breed-Driven Microbiome Heterogeneity Regulates Intestinal Stem Cell Proliferation via Lactobacillus-Lactate-GPR81 Signaling.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2400058},
doi = {10.1002/advs.202400058},
pmid = {38937989},
issn = {2198-3844},
support = {32030104//National Natural Science Foundation of China/ ; 2022YFD1300402//National Key Research and Development Program of China/ ; },
abstract = {Genetically lean and obese individuals have distinct intestinal microbiota and function. However, the underlying mechanisms of the microbiome heterogeneity and its regulation on epithelial function such as intestinal stem cell (ISC) fate remain unclear. Employing pigs of genetically distinct breeds (obese Meishan and lean Yorkshire), this study reveals transcriptome-wide variations in microbial ecology of the jejunum, characterized by enrichment of active Lactobacillus species, notably the predominant Lactobacillus amylovorus (L. amylovorus), and lactate metabolism network in obese breeds. The L. amylovorus-dominant heterogeneity is paralleled with epithelial functionality difference as reflected by highly expressed GPR81, more proliferative ISCs and activated Wnt/β-catenin signaling. Experiments using in-house developed porcine jejunal organoids prove that live L. amylovorus and its metabolite lactate promote intestinal organoid growth. Mechanistically, L. amylovorus and lactate activate Wnt/β-catenin signaling in a GPR81-dependent manner to promote ISC-mediated epithelial proliferation. However, heat-killed L. amylovorus fail to cause these changes. These findings uncover a previously underrepresented role of L. amylovorus in regulating jejunal stem cells via Lactobacillus-lactate-GPR81 axis, a key mechanism bridging breed-driven intestinal microbiome heterogeneity with ISC fate. Thus, results from this study provide new insights into the role of gut microbiome and stem cell interactions in maintaining intestinal homeostasis.},
}
@article {pmid38936731,
year = {2024},
author = {Li, Y and Hou, K and Chang, Y and Yuan, B and Li, X},
title = {A methodological study on the identification of ecological security change processes and zoning control strategies -- Based on the perspective of sustainable development.},
journal = {The Science of the total environment},
volume = {946},
number = {},
pages = {174190},
doi = {10.1016/j.scitotenv.2024.174190},
pmid = {38936731},
issn = {1879-1026},
abstract = {Ecological security (ES) is a crucial indicator for assessing the sustainable development of a region. Currently, most studies on ES primarily focus on process analysis, and the integration of environmental variability into the development of tailored control strategies for regions with varying ecological quality is overlooked. Therefore, in this study, we identified regional ES change processes, employed an optimized system to calculate the ecological security index (ESI), and identified ecological corridors (ECs) through the Minimum Constrained Resource (MCR) model to determine zoning strategies for typical arid regions, using the Ningxia region in the Yellow River Basin of China as an example. The findings showed that (1) from 2006 to 2020, the ESI values of most regions were between 0.2 and 0.4, with small but consistent increases in the ESI values over the years. (2) The proportion of regions with high ES ratings increased by 9.08 % across all districts and counties, and the center of gravity of ES shifted in a north-south and east-west direction. (3) The ESI exhibited a strong positive spatial correlation, characterized by spatial diffusion and spillover effects in most regions. (4) The ECs were predominantly distributed in a north-south direction, involving a total of 20 districts and counties. Based on the principles of sustainable development, we developed a model for the dynamic identification and zoning control of regional ES, aiming to provide a practical framework for effective ecological restoration and protection measures. Additionally, the strategies and methodologies presented in this study serve as important references for similar regions worldwide to facilitate the zoning control of ES, highlighting the broader significance and applicability of the study.},
}
@article {pmid38935782,
year = {2024},
author = {Louvet, A and Mantoux, C and Machon, N},
title = {Assessing the extinction risk of the spontaneous flora in urban tree bases.},
journal = {PLoS computational biology},
volume = {20},
number = {6},
pages = {e1012191},
pmid = {38935782},
issn = {1553-7358},
mesh = {*Extinction, Biological ; *Trees ; *Bayes Theorem ; *Cities ; *Ecosystem ; Computational Biology ; Markov Chains ; Models, Biological ; Paris ; },
abstract = {As the spatial arrangement of trees planted along streets in cities makes their bases potential ecological corridors for the flora, urban tree bases may be a key contributor to the overall connectivity of the urban ecosystem. However, these tree bases are also a highly fragmented environment in which extinctions are frequent. The goal of this study was to assess the plant species' ability to survive and spread through urban tree bases. To do so, we developed a Bayesian framework to assess the extinction risk of a plant metapopulation using presence/absence data, assuming that the occupancy dynamics was described by a Hidden Markov Model. The novelty of our approach is to take into account the combined effect of low-distance dispersal and the potential presence of a seed bank on the extinction risk. We introduced a metric of the extinction risk and examined its performance over a wide range of metapopulation parameters. We applied our framework to yearly floristic inventories carried out in 1324 tree bases in Paris, France. While local extinction risks were generally high, extinction risks at the street scale varied greatly from one species to another. We identified 10 plant species that could survive and spread through urban tree bases, and three plant traits correlated with the extinction risk at the metapopulation scale: the maximal height, and the beginning and end of the flowering period. Our results suggest that some plant species can use urban tree bases as ecological corridors despite high local extinction risks by forming a seed bank. We also identified other plant traits correlated with the ability to survive in tree bases, related to the action of gardeners. Moreover, our findings demonstrate that our Bayesian estimation framework based on percolation theory has the potential to be extended to more general metapopulations.},
}
@article {pmid38932245,
year = {2024},
author = {Conradie, T and Caparros-Martin, JA and Egan, S and Kicic, A and Koks, S and Stick, SM and Agudelo-Romero, P},
title = {Exploring the Complexity of the Human Respiratory Virome through an In Silico Analysis of Shotgun Metagenomic Data Retrieved from Public Repositories.},
journal = {Viruses},
volume = {16},
number = {6},
pages = {},
pmid = {38932245},
issn = {1999-4915},
support = {NHMRC115648//National Health and Medical Research Council/ ; Synergy grant APP118364//National Health and Medical Research Council/ ; Theme Collaboration Award 2023//Telethon Kids Institute/ ; N/A//Google cloud education program/ ; Investigator grant 2021/GR000216//National Health and Medical Research Council/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Virome ; *Genome, Viral ; *Respiratory System/virology ; *Viruses/genetics/classification/isolation &amp; purification ; Metagenome ; Computer Simulation ; Phylogeny ; Computational Biology/methods ; Microbiota ; Bacteriophages/genetics/classification/isolation &amp; purification ; },
abstract = {BACKGROUND: Respiratory viruses significantly impact global morbidity and mortality, causing more disease in humans than any other infectious agent. Beyond pathogens, various viruses and bacteria colonize the respiratory tract without causing disease, potentially influencing respiratory diseases' pathogenesis. Nevertheless, our understanding of respiratory microbiota is limited by technical constraints, predominantly focusing on bacteria and neglecting crucial populations like viruses. Despite recent efforts to improve our understanding of viral diversity in the human body, our knowledge of viral diversity associated with the human respiratory tract remains limited.<br><br>METHODS: Following a comprehensive search in bibliographic and sequencing data repositories using keyword terms, we retrieved shotgun metagenomic data from public repositories (n = 85). After manual curation, sequencing data files from 43 studies were analyzed using EVEREST (pipEline for Viral assEmbly and chaRactEriSaTion). Complete and high-quality contigs were further assessed for genomic and taxonomic characterization.<br><br>RESULTS: Viral contigs were obtained from 194 out of the 868 FASTQ files processed through EVEREST. Of the 1842 contigs that were quality assessed, 8% (n = 146) were classified as complete/high-quality genomes. Most of the identified viral contigs were taxonomically classified as bacteriophages, with taxonomic resolution ranging from the superkingdom level down to the species level. Captured contigs were spread across 25 putative families and varied between RNA and DNA viruses, including previously uncharacterized viral genomes. Of note, airway samples also contained virus(es) characteristic of the human gastrointestinal tract, which have not been previously described as part of the lung virome. Additionally, by performing a meta-analysis of the integrated datasets, ecological trends within viral populations linked to human disease states and their biogeographical distribution along the respiratory tract were observed.<br><br>CONCLUSION: By leveraging publicly available repositories of shotgun metagenomic data, the present study provides new insights into viral genomes associated with specimens from the human respiratory tract across different disease spectra. Further studies are required to validate our findings and evaluate the potential impact of these viral communities on respiratory tract physiology.},
}
@article {pmid38924481,
year = {2024},
author = {Ramos, SR and Reynolds, H and Johnson, C and Melkus, G and Kershaw, T and Thayer, J and Vorderstrasse, A},
title = {Perceptions on HIV-related Comorbidities and Usability of a Virtual Environment as CVD Prevention Education in Sexual Minority Men with HIV: Formative Phases of a Pilot RCT.},
journal = {Journal of medical Internet research},
volume = {},
number = {},
pages = {},
doi = {10.2196/57351},
pmid = {38924481},
issn = {1438-8871},
abstract = {BACKGROUND: Sexual minority men with HIV are at increased risk of cardiovascular disease (CVD) and have been underrepresented in behavioral research and in clinical trials.<br><br>OBJECTIVE: To explore perceptions about HIV-related comorbidities and assess the interest and usability of a virtual environment as CVD prevention education in Black and Latinx sexual minority men with HIV.<br><br>METHODS: This is a 3-phase pilot randomized control behavioral trial. We report on formative phases 1 and 2 that informed virtual environment content and features using qualitative interviews, usability testing, and beta testing with 25 individuals. In Phase 1, 15 participants completed interviews exploring HIV-related illnesses of concern that would be used to tailor the virtual environment. In Phase 2, usability and beta testing were conducted with 10 participants to assess interest, features, and content.<br><br>RESULTS: In Phase 1, we found CVD risk factors included high blood pressure, heart attack, stroke, and diabetes. Cancer (prostate, colon, and others) was a common concern and so were the development of mental health conditions. In Phase 2, all participants completed the 12-item usability checklist with favorable feedback within 30 to 60 minutes. Beta-testing interviews suggested: 1) Mixed perceptions about health and HIV, 2) High risk for comorbid conditions, 3) Virtual environment features were promising, and 4) need for diverse avatar representations.<br><br>CONCLUSIONS: We identified several comorbid conditions of concern and findings carry significant implications for mitigating barriers to preventative health screenings given the shared risk factors between HIV and related comorbidities. Highly rated aspects of the virtual environment were anonymity, meeting others who identify as gay or bisexual with HIV, validating LGBTQ+ images and content, and accessibility to CVD prevention education. Critical end-user feedback from beta-testing suggested more options for avatar customization in skin, hair, body representation. Our next phase will test the virtual environment as a new approach to advancing cardiovascular health equity in ethnic and racial sexual minority men with HIV.<br><br>CLINICALTRIAL: clinicaltrials.gov (NCT04061915).<br><br>RR2-10.2196/38348.},
}
@article {pmid38917233,
year = {2024},
author = {Costa, IB and Pimenta, IDSF and Aiquoc, KM and Oliveira, &#xc2;GRDC},
title = {Congenital syphilis, syphilis in pregnancy and prenatal care in Brazil: An ecological study.},
journal = {PloS one},
volume = {19},
number = {6},
pages = {e0306120},
pmid = {38917233},
issn = {1932-6203},
mesh = {Humans ; Pregnancy ; Female ; Brazil/epidemiology ; *Syphilis, Congenital/epidemiology ; *Prenatal Care ; *Pregnancy Complications, Infectious/epidemiology ; Incidence ; Adult ; Socioeconomic Factors ; Syphilis/epidemiology/diagnosis ; Adolescent ; Young Adult ; },
abstract = {The aim of this research was to evaluate the incidence of congenital syphilis and the ratio between congenital syphilis and syphilis in pregnant women in Brazil according to socioeconomic indicators (inadequate water supply and sanitation; illiteracy at 15 years of age or older; household income per capita; proportion of poor people; Gini index; human development index; and average health expenditure per inhabitant by the health system) and prenatal quality-of-care indicators. We conducted an ecological study using a sample composed of 257 municipalities, each with ≥ 100,000 inhabitants. Data was collected from four public databases: the Brazilian Institute of Geography and Statistics, comprising socioeconomical data from the 2010 census; and the data of 2019 available in the databases of the Department of Informatics of the Brazilian Health System, Information and Management of Primary Care, and the Electronic Citizen Information System. Descriptive analysis of dependent and independent variables and bivariate analysis by Negative Binomial regression were carried out. The mean incidence of congenital syphilis was 38% higher in municipalities with a Human Development Index up to 0.785 (ratio of means [RM] = 1.38; p = 0.049) and 57% higher among populations where less than 50% of primary healthcare services provided a rapid test for syphilis (RM = 1.57; p < 0.001). The ratio between congenital syphilis and syphilis in pregnant women was 29% higher in municipalities with a low household income per capita (RM = 1.29; p < 0.001) and 28% higher in locations where less than 50% of the primary healthcare services provided a rapid test for syphilis (RM = 1.28; p < 0.001). There was no statistical significance of the quality of prenatal care compared to the outcomes. This result underscores the challenges in detecting syphilis infections among pregnant women during prenatal care, consequently increasing the risk of vertical transmission of the disease to the fetus. Traits of inequality in the occurrence of congenital syphilis also draw attention to strategies to reduce health inequities and improve prenatal care.},
}
@article {pmid38916705,
year = {2024},
author = {Yu, J and Chen, S},
title = {The Use of Big Data Analysis in Digital Empowerment of Sustainable Technological Innovation Management of Ecological Enterprises.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {31},
pages = {43956-43966},
pmid = {38916705},
issn = {1614-7499},
mesh = {*Big Data ; China ; Inventions ; Ecology ; Empowerment ; Environmental Monitoring/methods ; Conservation of Natural Resources ; },
abstract = {With the social economy's rapid progress and the popularization of environmental awareness, ecological enterprises have gradually become a crucial trend in the development of modern enterprises. This work intends to promote the development of ecological enterprises to a higher level. This work first analyzes the management mode of ecological enterprises in the context of big data in China. Then, it establishes various indicators to analyze the role of sustainable technological innovation in enterprise development and the impact of digital empowerment on enterprise development. Finally, this work takes China's manufacturing industry and ecological enterprises in Hubei Province as examples to summarize the digital empowerment of sustainable technological innovation management of ecological enterprises under the background of big data. The final result indicates that sustainable technological innovation significantly reduces ecological enterprises' resource consumption and waste emissions. Additionally, it has a significant positive effect on improving enterprise output value and economic benefits. The digital empowerment of enterprises has a significant driving effect on sustainable technological innovation, with a digital driving coefficient of 26. This work provides a feasible scheme for the specific application of big data analysis in the technology innovation management of ecological enterprises, including market demand analysis, environmental monitoring and governance, technology assessment and risk management. This work expounds the role of big data analysis technology in improving decision-making efficiency, optimizing resource allocation and enhancing the competitiveness of enterprises in the digital empowerment of ecological enterprises.},
}
@article {pmid38915508,
year = {2024},
author = {Shukla, HG and Chakraborty, M and Emerson, JJ},
title = {Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38915508},
issn = {2692-8205},
support = {S10 OD021718/OD/NIH HHS/United States ; R35 GM153327/GM/NIGMS NIH HHS/United States ; P30 AR075047/AR/NIAMS NIH HHS/United States ; R01 GM123303/GM/NIGMS NIH HHS/United States ; S10 OD010794/OD/NIH HHS/United States ; P30 CA062203/CA/NCI NIH HHS/United States ; R00 GM129411/GM/NIGMS NIH HHS/United States ; },
abstract = {Many essential functions of organisms are encoded in highly repetitive genomic regions, including histones involved in DNA packaging, centromeres that are core components of chromosome segregation, ribosomal RNA comprising the protein translation machinery, telomeres that ensure chromosome integrity, piRNA clusters encoding host defenses against selfish elements, and virtually the entire Y chromosome. These regions, formed by highly similar tandem arrays, pose significant challenges for experimental and informatic study, impeding sequence-level descriptions essential for understanding genetic variation. Here, we report the assembly and variation analysis of such repetitive regions in Drosophila melanogaster, offering significant improvements to the existing community reference assembly. Our work successfully recovers previously elusive segments, including complete reconstructions of the histone locus and the pericentric heterochromatin of the X chromosome, spanning the Stellate locus to the distal flank of the rDNA cluster. To infer structural changes in these regions where alignments are often not practicable, we introduce landmark anchors based on unique variants that are putatively orthologous. These regions display considerable structural variation between different D. melanogaster strains, exhibiting differences in copy number and organization of homologous repeat units between haplotypes. In the histone cluster, although we observe minimal genetic exchange indicative of crossing over, the variation patterns suggest mechanisms such as unequal sister chromatid exchange. We also examine the prevalence and scale of concerted evolution in the histone and Stellate clusters and discuss the mechanisms underlying these observed patterns.},
}
@article {pmid38915006,
year = {2024},
author = {Reininghaus, U and Schwannauer, M and Barne, I and Beames, JR and Bonnier, RA and Brenner, M and Breznoščáková, D and Dančík, D and De Allegri, M and Di Folco, S and Durstewitz, D and Gugel, J and Hajdúk, M and Heretik, A and Izáková, &#x13d; and Katreniakova, Z and Kiekens, G and Koppe, G and Kurilla, A and Marelli, L and Nagyova, I and Nguyen, H and Pečeňák, J and Schulte-Strathaus, JCC and Sotomayor-Enriquez, K and Uyttebroek, L and Weermeijer, J and Wolters, M and Wensing, M and Boehnke, JR and Myin-Germeys, I and Schick, A},
title = {Strategies, processes, outcomes, and costs of implementing experience sampling-based monitoring in routine mental health care in four European countries: study protocol for the IMMERSE effectiveness-implementation study.},
journal = {BMC psychiatry},
volume = {24},
number = {1},
pages = {465},
pmid = {38915006},
issn = {1471-244X},
support = {945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 945263//Horizon 2020/ ; 389624707//DFG/ ; 101063326//Marie Sk&#x142;odowska-Curie fellowship/ ; 1204924N//Research Foundation Flanders/ ; APVV-22-0587//Agent&#xfa;ra na Podporu V&#xfd;skumu a V&#xfd;voja/ ; },
mesh = {Humans ; *Mental Health Services/economics ; Germany ; Belgium ; Slovakia ; Mental Disorders/therapy/economics ; Ecological Momentary Assessment ; Europe ; Cost-Benefit Analysis/methods ; },
abstract = {BACKGROUND: Recent years have seen a growing interest in the use of digital tools for delivering person-centred mental health care. Experience Sampling Methodology (ESM), a structured diary technique for capturing moment-to-moment variation in experience and behaviour in service users' daily life, reflects a particularly promising avenue for implementing a person-centred approach. While there is evidence on the effectiveness of ESM-based monitoring, uptake in routine mental health care remains limited. The overarching aim of this hybrid effectiveness-implementation study is to investigate, in detail, reach, effectiveness, adoption, implementation, and maintenance as well as contextual factors, processes, and costs of implementing ESM-based monitoring, reporting, and feedback into routine mental health care in four European countries (i.e., Belgium, Germany, Scotland, Slovakia).<br><br>METHODS: In this hybrid effectiveness-implementation study, a parallel-group, assessor-blind, multi-centre cluster randomized controlled trial (cRCT) will be conducted, combined with a process and economic evaluation. In the cRCT, 24 clinical units (as the cluster and unit of randomization) at eight sites in four European countries will be randomly allocated using an unbalanced 2:1 ratio to one of two conditions: (a) the experimental condition, in which participants receive a Digital Mobile Mental Health intervention (DMMH) and other implementation strategies in addition to treatment as usual (TAU) or (b) the control condition, in which service users are provided with TAU. Outcome data in service users and clinicians will be collected at four time points: at baseline (t0), 2-month post-baseline (t1), 6-month post-baseline (t2), and 12-month post-baseline (t3). The primary outcome will be patient-reported service engagement assessed with the service attachment questionnaire at 2-month post-baseline. The process and economic evaluation will provide in-depth insights into in-vivo context-mechanism-outcome configurations and economic costs of the DMMH and other implementation strategies in routine care, respectively.<br><br>DISCUSSION: If this trial provides evidence on reach, effectiveness, adoption, implementation and maintenance of implementing ESM-based monitoring, reporting, and feedback, it will form the basis for establishing its public health impact and has significant potential to bridge the research-to-practice gap and contribute to swifter ecological translation of digital innovations to real-world delivery in routine mental health care.<br><br>TRIAL REGISTRATION: ISRCTN15109760 (ISRCTN registry, date: 03/08/2022).},
}
@article {pmid38914930,
year = {2024},
author = {Jiang, G and Zheng, JY and Ren, SN and Yin, W and Xia, X and Li, Y and Wang, HL},
title = {A comprehensive workflow for optimizing RNA-seq data analysis.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {631},
pmid = {38914930},
issn = {1471-2164},
mesh = {*Workflow ; *RNA-Seq/methods ; *Software ; Fungi/genetics ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; Alternative Splicing ; },
abstract = {BACKGROUND: Current RNA-seq analysis software for RNA-seq data tends to use similar parameters across different species without considering species-specific differences. However, the suitability and accuracy of these tools may vary when analyzing data from different species, such as humans, animals, plants, fungi, and bacteria. For most laboratory researchers lacking a background in information science, determining how to construct an analysis workflow that meets their specific needs from the array of complex analytical tools available poses a significant challenge.<br><br>RESULTS: By utilizing RNA-seq data from plants, animals, and fungi, it was observed that different analytical tools demonstrate some variations in performance when applied to different species. A comprehensive experiment was conducted specifically for analyzing plant pathogenic fungal data, focusing on differential gene analysis as the ultimate goal. In this study, 288 pipelines using different tools were applied to analyze five fungal RNA-seq datasets, and the performance of their results was evaluated based on simulation. This led to the establishment of a relatively universal and superior fungal RNA-seq analysis pipeline that can serve as a reference, and certain standards for selecting analysis tools were derived for reference. Additionally, we compared various tools for alternative splicing analysis. The results based on simulated data indicated that rMATS remained the optimal choice, although consideration could be given to supplementing with tools such as SpliceWiz.<br><br>CONCLUSION: The experimental results demonstrate that, in comparison to the default software parameter configurations, the analysis combination results after tuning can provide more accurate biological insights. It is beneficial to carefully select suitable analysis software based on the data, rather than indiscriminately choosing tools, in order to achieve high-quality analysis results more efficiently.},
}
@article {pmid38911902,
year = {2024},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the White-point, Mythimna albipuncta (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {62},
pmid = {38911902},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Mythimna albipuncta (the White-point; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 698.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 13,679 protein coding genes.},
}
@article {pmid38908558,
year = {2024},
author = {Yang, Y and Li, Z and Wen, J},
title = {Long term impact of Wenchuan earthquake on population mental and behavioral disorders in heavily-stricken areas: An ecological study based on big data.},
journal = {Journal of affective disorders},
volume = {361},
number = {},
pages = {589-595},
doi = {10.1016/j.jad.2024.06.070},
pmid = {38908558},
issn = {1573-2517},
mesh = {Humans ; *Earthquakes ; China/epidemiology ; Male ; Female ; Middle Aged ; Adult ; *Mental Disorders/epidemiology ; *Disasters/statistics &amp; numerical data ; *Survivors/psychology/statistics &amp; numerical data ; Prevalence ; Adolescent ; Aged ; *Big Data ; Young Adult ; Risk Factors ; Child ; Urbanization ; },
abstract = {BACKGROUND: This study aimed to explore and evaluate the development trends and differential changes in the prevalence of mental and behavioral disorders among the earthquake survivors in exposure groups (highly hard-hit areas) and control groups (general disaster areas) from 2015 to 2019, as well as to investigate the potential influencing factors.<br><br>METHODS: Data was obtained from the Sichuan Health Information System and the Sichuan Health Yearbook, the prevalence of the exposure group and the control group were calculated, the difference between the two groups was evaluated using the prevalence rate ratio, and a fixed effect model was developed to investigate the potential influencing factors of the prevalence.<br><br>RESULTS: The prevalence by gender and age in the exposure group was always greater than those in the control group (RR>1), although the disparity between the two proceeded to diminish with time. The urbanization rate (&#x3b2;&#xa0;=&#xa0;0.0448, P&#xa0;<&#xa0;0.05) and disaster area levels (&#x3b2;&#xa0;=&#xa0;0.0104, P&#xa0;<&#xa0;0.05) were risk factors for the prevalence of mental and behavioral disorders.<br><br>LIMITATIONS: The study only collected data at the group level following the Wenchuan earthquake. Consequently, the findings are only applicable at the group level. Furthermore, diagnostic criteria for various types of mental and behavioral disorders diseases were not provided.<br><br>CONCLUSIONS: The earthquake has a significant long-term impact on mental health. It is necessary to continuously monitor the mental health of Wenchuan earthquake survivors and take appropriate post-disaster intervention measures.},
}
@article {pmid38907904,
year = {2024},
author = {Roved, J},
title = {MHCtools 1.5: Analysis of MHC Sequencing Data in R.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2809},
number = {},
pages = {275-295},
pmid = {38907904},
issn = {1940-6029},
mesh = {*Major Histocompatibility Complex/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Software ; Animals ; *Haplotypes/genetics ; Computational Biology/methods ; Sequence Analysis, DNA/methods ; Genetic Variation ; Genotyping Techniques/methods ; Genotype ; },
abstract = {The genes of the major histocompatibility complex (MHC) play a vital role in the vertebrate immune system and have attracted considerable interest in evolutionary biology. While the MHC has been characterized in detail in humans (human leukocyte antigen, HLA) and in model organisms such as the mouse, studies in non-model organisms often lack prior knowledge about structure, genetic variability, and evolutionary properties of this locus. MHC genotyping in non-model species commonly relies on PCR-based amplicon sequencing, and while several published protocols facilitate generation of MHC sequence data, there is a lack of transparent and standardized tools for downstream data analysis.Here, I present the R package MHCtools version 1.5, which contains 15 tools that (i) assist accurate MHC genotyping from high-throughput amplicon sequencing data, and provide standardized methods to analyze (ii) MHC diversity, (iii) MHC supertypes, and (iv) MHC haplotypes.I hope that MHCtools will be helpful in future studies of the MHC in non-model species and that it may help to advance our understanding of the important roles of the MHC in ecology and evolution.},
}
@article {pmid38904377,
year = {2024},
author = {Berasategui, A and Salem, H and Moller, AG and Christopher, Y and Vidaurre Montoya, Q and Conn, C and Read, TD and Rodrigues, A and Ziemert, N and Gerardo, N},
title = {Genomic insights into the evolution of secondary metabolism of Escovopsis and its allies, specialized fungal symbionts of fungus-farming ants.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0057624},
doi = {10.1128/msystems.00576-24},
pmid = {38904377},
issn = {2379-5077},
abstract = {The metabolic intimacy of symbiosis often demands the work of specialists. Natural products and defensive secondary metabolites can drive specificity by ensuring infection and propagation across host generations. But in contrast to bacteria, little is known about the diversity and distribution of natural product biosynthetic pathways among fungi and how they evolve to facilitate symbiosis and adaptation to their host environment. In this study, we define the secondary metabolism of Escovopsis and closely related genera, symbionts in the gardens of fungus-farming ants. We ask how the gain and loss of various biosynthetic pathways correspond to divergent lifestyles. Long-read sequencing allowed us to define the chromosomal features of representative Escovopsis strains, revealing highly reduced genomes composed of seven to eight chromosomes. The genomes are highly syntenic with macrosynteny decreasing with increasing phylogenetic distance, while maintaining a high degree of mesosynteny. An ancestral state reconstruction analysis of biosynthetic pathways revealed that, while many secondary metabolites are shared with non-ant-associated Sordariomycetes, 56 pathways are unique to the symbiotic genera. Reflecting adaptation to diverging ant agricultural systems, we observe that the stepwise acquisition of these pathways mirrors the ecological radiations of attine ants and the dynamic recruitment and replacement of their fungal cultivars. As different clades encode characteristic combinations of biosynthetic gene clusters, these delineating profiles provide important insights into the possible mechanisms underlying specificity between these symbionts and their fungal hosts. Collectively, our findings shed light on the evolutionary dynamic nature of secondary metabolism in Escovopsis and its allies, reflecting adaptation of the symbionts to an ancient agricultural system.IMPORTANCEMicrobial symbionts interact with their hosts and competitors through a remarkable array of secondary metabolites and natural products. Here, we highlight the highly streamlined genomic features of attine-associated fungal symbionts. The genomes of Escovopsis species, as well as species from other symbiont genera, many of which are common with the gardens of fungus-growing ants, are defined by seven chromosomes. Despite a high degree of metabolic conservation, we observe some variation in the symbionts' potential to produce secondary metabolites. As the phylogenetic distribution of the encoding biosynthetic gene clusters coincides with attine transitions in agricultural systems, we highlight the likely role of these metabolites in mediating adaptation by a group of highly specialized symbionts.},
}
@article {pmid38902323,
year = {2024},
author = {Horváth, G and Sos, T and Bóné, G and Lőrincz, CE and Pap, PL and Herczeg, G},
title = {Integrating behavioural thermoregulatory strategy into the animal personality framework using the common lizard, Zootoca vivipara as a model.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {14200},
pmid = {38902323},
issn = {2045-2322},
support = {PD 132041//Nemzeti Kutat&#xe1;si, Fejleszt&#xe9;si &#xe9;s Innovaci&#xf3;s Alap/ ; },
mesh = {Animals ; *Lizards/physiology ; *Body Temperature Regulation/physiology ; *Behavior, Animal/physiology ; Personality/physiology ; Male ; Female ; },
abstract = {The study of consistent between-individual behavioural variation in single (animal personality) and across two or more behavioural traits (behavioural syndrome) is a central topic of behavioural ecology. Besides behavioural type (individual mean behaviour), behavioural predictability (environment-independent within-individual behavioural variation) is now also seen as an important component of individual behavioural strategy. Research focus is still on the 'Big Five' traits (activity, exploration, risk-taking, sociability and aggression), but another prime candidate to integrate to the personality framework is behavioural thermoregulation in small-bodied poikilotherms. Here, we found animal personality in thermoregulatory strategy (selected body temperature, voluntary thermal maximum, setpoint range) and 'classic' behavioural traits (activity, sheltering, risk-taking) in common lizards (Zootoca vivipara). Individual state did not explain the between-individual variation. There was a positive behavioural type-behavioural predictability correlation in selected body temperature. Besides an activity-risk-taking syndrome, we also found a risk-taking-selected body temperature syndrome. Our results suggest that animal personality and behavioural syndrome are present in common lizards, both including thermoregulatory and 'classic' behavioural traits, and selecting high body temperature with high predictability is part of the risk-prone behavioural strategy. We propose that thermoregulatory behaviour should be considered with equal weight to the 'classic' traits in animal personality studies of poikilotherms employing active behavioural thermoregulation.},
}
@article {pmid38899724,
year = {2024},
author = {Parra, J and Jarmusch, SA and Duncan, KR},
title = {Multi-omics analysis of antagonistic interactions among free-living Pseudonocardia from diverse ecosystems.},
journal = {Environmental microbiology},
volume = {26},
number = {6},
pages = {e16635},
doi = {10.1111/1462-2920.16635},
pmid = {38899724},
issn = {1462-2920},
support = {2-1-4-17-1-037//Ministerio de Ciencia Tecnolog&#xed;a y Telecomunicaciones, Costa Rica/ ; NNF19OC0055625//Novo Nordisk Fonden/ ; DNRF137//Danmarks Grundforskningsfond/ ; },
mesh = {Antibiosis ; *Ecosystem ; Genomics ; Geologic Sediments/microbiology ; *Metabolomics ; Multigene Family ; Multiomics ; *Phylogeny ; *Pseudonocardia/genetics ; },
abstract = {Actinomycetes are a phylogenetically diverse bacterial group which are widely distributed across terrestrial and aquatic ecosystems. Within this order, the genus Pseudonocardia and their specialised metabolites have been the focus of previous ecological studies due to their antagonistic interactions with other microorganisms and their mutualistic interactions with insects. However, the chemical ecology of free-living Pseudonocardia remains understudied. This study applies a multi-omics approach to investigate the chemical ecology of free-living actinomycetes from the genus Pseudonocardia. In a comparative genomics analysis, it was observed that the biosynthetic gene cluster family distribution was influenced mainly by phylogenetic distance rather than the geographic or ecological origin of strains. This finding was also observed in the mass spectrometry-based metabolomic profiles of nine Pseudonocardia species isolated from marine sediments and two terrestrial species. Antagonist interactions between these 11 species were examined, and matrix-assisted laser desorption/ionisation-mass spectrometry imaging was used to examine in situ chemical interactions between the Southern Ocean strains and their phylogenetically close relatives. Overall, it was demonstrated that phylogeny was the main predictor of antagonistic interactions among free-living Pseudonocardia. Moreover, two features at m/z 441.15 and m/z 332.20 were identified as metabolites related to these interspecies interactions.},
}
@article {pmid38897481,
year = {2024},
author = {Kepp, KP and Aavitsland, P and Ballin, M and Balloux, F and Baral, S and Bardosh, K and Bauchner, H and Bendavid, E and Bhopal, R and Blumstein, DT and Boffetta, P and Bourgeois, F and Brufsky, A and Collignon, PJ and Cripps, S and Cristea, IA and Curtis, N and Djulbegovic, B and Faude, O and Flacco, ME and Guyatt, GH and Hajishengallis, G and Hemkens, LG and Hoffmann, T and Joffe, AR and Klassen, TP and Koletsi, D and Kontoyiannis, DP and Kuhl, E and La Vecchia, C and Lallukka, T and Lambris, J and Levitt, M and Makridakis, S and Maltezou, HC and Manzoli, L and Marusic, A and Mavragani, C and Moher, D and Mol, BW and Muka, T and Naudet, F and Noble, PW and Nordström, A and Nordström, P and Pandis, N and Papatheodorou, S and Patel, CJ and Petersen, I and Pilz, S and Plesnila, N and Ponsonby, AL and Rivas, MA and Saltelli, A and Schabus, M and Schippers, MC and Schünemann, H and Solmi, M and Stang, A and Streeck, H and Sturmberg, JP and Thabane, L and Thombs, BD and Tsakris, A and Wood, SN and Ioannidis, JPA},
title = {Panel stacking is a threat to consensus statement validity.},
journal = {Journal of clinical epidemiology},
volume = {173},
number = {},
pages = {111428},
doi = {10.1016/j.jclinepi.2024.111428},
pmid = {38897481},
issn = {1878-5921},
abstract = {Consensus statements can be very influential in medicine and public health. Some of these statements use systematic evidence synthesis but others fail on this front. Many consensus statements use panels of experts to deduce perceived consensus through Delphi processes. We argue that stacking of panel members toward one particular position or narrative is a major threat, especially in absence of systematic evidence review. Stacking may involve financial conflicts of interest, but nonfinancial conflicts of strong advocacy can also cause major bias. Given their emerging importance, we describe here how such consensus statements may be misleading, by analyzing in depth a recent high-impact Delphi consensus statement on COVID-19 recommendations as a case example. We demonstrate that many of the selected panel members and at least 35% of the core panel members had advocated toward COVID-19 elimination (Zero-COVID) during the pandemic and were leading members of aggressive advocacy groups. These advocacy conflicts were not declared in the Delphi consensus publication, with rare exceptions. Therefore, we propose that consensus statements should always require rigorous evidence synthesis and maximal transparency on potential biases toward advocacy or lobbyist groups to be valid. While advocacy can have many important functions, its biased impact on consensus panels should be carefully avoided.},
}
@article {pmid38896539,
year = {2024},
author = {Sänger, M and De Mecquenem, N and Lewińska, KE and Bountris, V and Lehmann, F and Leser, U and Kosch, T},
title = {A qualitative assessment of using ChatGPT as large language model for scientific workflow development.},
journal = {GigaScience},
volume = {13},
number = {},
pages = {},
pmid = {38896539},
issn = {2047-217X},
support = {//German Research Foundation/ ; },
mesh = {*Workflow ; Programming Languages ; Software ; Computational Biology/methods ; Humans ; },
abstract = {BACKGROUND: Scientific workflow systems are increasingly popular for expressing and executing complex data analysis pipelines over large datasets, as they offer reproducibility, dependability, and scalability of analyses by automatic parallelization on large compute clusters. However, implementing workflows is difficult due to the involvement of many black-box tools and the deep infrastructure stack necessary for their execution. Simultaneously, user-supporting tools are rare, and the number of available examples is much lower than in classical programming languages.<br><br>RESULTS: To address these challenges, we investigate the efficiency of large language models (LLMs), specifically ChatGPT, to support users when dealing with scientific workflows. We performed 3 user studies in 2 scientific domains to evaluate ChatGPT for comprehending, adapting, and extending workflows. Our results indicate that LLMs efficiently interpret workflows but achieve lower performance for exchanging components or purposeful workflow extensions. We characterize their limitations in these challenging scenarios and suggest future research directions.<br><br>CONCLUSIONS: Our results show a high accuracy for comprehending and explaining scientific workflows while achieving a reduced performance for modifying and extending workflow descriptions. These findings clearly illustrate the need for further research in this area.},
}
@article {pmid38892087,
year = {2024},
author = {Suárez, I and Collado, IG and Garrido, C},
title = {Revealing Hidden Genes in Botrytis cinerea: New Insights into Genes Involved in the Biosynthesis of Secondary Metabolites.},
journal = {International journal of molecular sciences},
volume = {25},
number = {11},
pages = {},
pmid = {38892087},
issn = {1422-0067},
support = {PID-2021-1228990-B-C21 and PID-2021-1228990-B-C22//MCIN/AEI/ 10.13039/501100011033 and ERDF A way of making Europe/ ; },
mesh = {*Botrytis/genetics/pathogenicity ; *Secondary Metabolism/genetics ; *Peptide Synthases/genetics/metabolism ; *Polyketide Synthases/genetics/metabolism ; Fungal Proteins/genetics/metabolism ; Computational Biology/methods ; Multigene Family ; Genes, Fungal ; },
abstract = {Utilizing bioinformatics tools, this study expands our understanding of secondary metabolism in Botrytis cinerea, identifying novel genes within polyketide synthase (PKS), non-ribosomal peptide synthetase (NRPS), sesquiterpene cyclase (STC), diterpene cyclase (DTC), and dimethylallyltryptophan synthase (DMATS) families. These findings enrich the genetic framework associated with B. cinerea's pathogenicity and ecological adaptation, offering insights into uncharted metabolic pathways. Significantly, the discovery of previously unannotated genes provides new molecular targets for developing targeted antifungal strategies, promising to enhance crop protection and advance our understanding of fungal biochemistry. This research not only broadens the scope of known secondary metabolites but also opens avenues for future exploration into B. cinerea's biosynthetic capabilities, potentially leading to novel antifungal compounds. Our work underscores the importance of integrating bioinformatics and genomics for fungal research, paving the way for sustainable agricultural practices by pinpointing precise molecular interventions against B. cinerea. This study sets a foundation for further investigations into the fungus's secondary metabolism, with implications for biotechnology and crop disease management.},
}
@article {pmid38888768,
year = {2024},
author = {Sanderson, H and White, AP},
title = {Methods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2813},
number = {},
pages = {19-37},
pmid = {38888768},
issn = {1940-6029},
mesh = {*Salmonella/genetics ; Humans ; *Genomics/methods ; *Salmonella Infections/microbiology/epidemiology ; *Phylogeny ; *Genome, Bacterial ; *Molecular Epidemiology/methods ; Virulence Factors/genetics ; Disease Outbreaks ; Drug Resistance, Bacterial/genetics ; Interspersed Repetitive Sequences/genetics ; },
abstract = {Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.},
}
@article {pmid38882711,
year = {2023},
author = {Waterhouse, RM and Adam-Blondon, AF and Balech, B and Barta, E and Ying Shi Chua, P and Di Cola, V and Heil, KF and Hughes, GM and Jermiin, LS and Kalaš, M and Lanfear, J and Pafilis, E and Palagi, PM and Papageorgiou, AC and Paupério, J and Psomopoulos, F and Raes, N and Burgin, J and Gabaldón, T},
title = {The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {},
pmid = {38882711},
issn = {2046-1402},
mesh = {Humans ; *Biodiversity ; Conservation of Natural Resources ; },
abstract = {Biodiversity loss is now recognised as one of the major challenges for humankind to address over the next few decades. Unless major actions are taken, the sixth mass extinction will lead to catastrophic effects on the Earth's biosphere and human health and well-being. ELIXIR can help address the technical challenges of biodiversity science, through leveraging its suite of services and expertise to enable data management and analysis activities that enhance our understanding of life on Earth and facilitate biodiversity preservation and restoration. This white paper, prepared by the ELIXIR Biodiversity Community, summarises the current status and responses, and presents a set of plans, both technical and community-oriented, that should both enhance how ELIXIR Services are applied in the biodiversity field and how ELIXIR builds connections across the many other infrastructures active in this area. We discuss the areas of highest priority, how they can be implemented in cooperation with the ELIXIR Platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for a Biodiversity Community in ELIXIR and is an appeal to identify and involve new stakeholders.},
}
@article {pmid38882082,
year = {2024},
author = {Fei, J and Jiang, X and Yang, H and Fan, K and Che, Y and Sun, B and Guo, T},
title = {Research and Development of a Big Data Application Platform for Intelligent Blast Furnace Intensive Management and Control.},
journal = {ACS omega},
volume = {9},
number = {23},
pages = {24674-24684},
pmid = {38882082},
issn = {2470-1343},
abstract = {The blast furnaces of Anshan Iron and Steel have completed large-scale modernization, and a large amount of information technology has been popularized and applied to the process of blast furnaces. This paper takes the Anshan Iron and Steel blast furnace group as the research background. Based on big data and industrial Internet technology, combining the smelting process mechanism of blast furnace production and using artificial intelligence, cloud analysis, and other technologies, the data management platform was used to effectively integrate the data of each process of the blast furnace and design the data asset catalogue. The big data application platform for the intensive control of the blast furnace was established. The data were in multidimensional in-depth mining, and the intelligent application model of the blast furnace was established. The visual intelligent monitoring of the safe production and operation of the blast furnace was realized, and the production operation of the blast furnace was guided. The overall information and intelligent level of production operation and management of the blast furnace have been improved.},
}
@article {pmid38880940,
year = {2024},
author = {Medo, A and Ohte, N and Doi, H and Kamdee, K and Koba, K and Arai, N and Mitsunaga, Y and Kume, M and Kojima, D and Nose, T and Yokoyama, A and Viputhanumas, T and Mitamura, H},
title = {Trophic niche partitioning and intraspecific variation in food resource use in the genus Pangasianodon in a reservoir revealed by stable isotope analysis of multiple tissues.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.15842},
pmid = {38880940},
issn = {1095-8649},
support = {16H05792//Japan Society for the Promotion of Science/ ; 22J13642//Japan Society for the Promotion of Science/ ; 202180216//Japan Society for the Promotion of Science/ ; //Shikata Memorial Trust for Nature Conservation/ ; 25610919060008//Thailand Institute of Nuclear Technology/ ; },
abstract = {Understanding the mechanism by which non-native fish species integrate into native communities is crucial for evaluating the possibility of their establishment success. The genus Pangasianodon, comprising Pangasianodon gigas and Pangasianodon hypophthalmus, has been introduced into reservoirs, which are non-native habitats, for fishery stock enhancement. P. gigas and P. hypophthalmus often successfully establish and co-occur in several Thai reservoirs, but there is little information on differences in food resource use between the two species. To investigate the trophic niche width of P. gigas and P. hypophthalmus in a Thai reservoir, we conducted stable carbon and nitrogen ratio (δ[13]C and δ[15]N) analyses. We examined the degree of individual specialization in both species using the δ[13]C and δ[15]N values of muscle and liver tissues, which provides long- and short-term diet information. The isotopic niches did not overlap between P. gigas and P. hypophthalmus. The δ[15]N value of P. gigas was significantly higher than that of P. hypophthalmus, whereas the δ[13]C value did not significantly differ between the two species. The isotopic niche sizes were larger in P. hypophthalmus than in P. gigas. Individual specialization was observed in P. hypophthalmus but not in P. gigas, indicating that intraspecific variation in food resource use was larger in P. hypophthalmus compared to P. gigas. These findings suggest that trophic niche partitioning was one of the factors facilitating the establishment success of P. gigas and P. hypophthalmus in a reservoir, but the establishment process may differ between the two species.},
}
@article {pmid38873190,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Notch-wing Button, Acleris emargana (Fabricius, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {376},
pmid = {38873190},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Acleris emargana (the Notch-wing Button; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 691.4 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,886 protein coding genes.},
}
@article {pmid38870844,
year = {2024},
author = {Rocha, LP and Machado, &#xcd;E and Fogal, AS and Malta, DC and Velasquez-Melendez, G and Felisbino-Mendes, MS},
title = {Burden of disease and direct costs to the health system attributable to high body mass index in Brazil.},
journal = {Public health},
volume = {233},
number = {},
pages = {121-129},
doi = {10.1016/j.puhe.2024.05.013},
pmid = {38870844},
issn = {1476-5616},
mesh = {Humans ; Brazil/epidemiology ; *Body Mass Index ; Cross-Sectional Studies ; Male ; *Cost of Illness ; Female ; Middle Aged ; Adult ; *Health Care Costs/statistics &amp; numerical data ; Hospitalization/statistics &amp; numerical data/economics ; National Health Programs/economics/statistics &amp; numerical data ; Obesity/epidemiology/economics ; Aged ; Disability-Adjusted Life Years ; },
abstract = {OBJECTIVES: Excess weight, measured by a high body mass index (BMI), is associated with the onset of many diseases, which can, in turn, lead to disability and premature death, subsequently placing a significant burden on healthcare services. This study analysed the burden of disease and the direct costs to the Brazilian Unified Health System (Sistema Único de Saúde [SUS]) attributable to high BMI in the Brazilian population.<br><br>STUDY DESIGN: Ecological study.<br><br>METHODS: This ecological study had two components: (1) a time-series assessment to analyse the burden of diseases attributable to high BMI from 1990 to 2019 in Brazil; and (2) a cross-sectional design to estimate the direct costs of SUS hospitalisations and outpatient procedures attributable to high BMI in 2019. Estimates from the Global Burden of Disease study and the costs of hospital admissions and outpatient procedures from the Department of Informatics of the Brazilian Unified Health System were used. Deaths, years of life lost to premature death (YLLs), years lived with disability (YLDs), and years of life lost adjusted for disability (DALYs) were analysed. The direct health cost was obtained in Brazilian Real (R$) and converted in international Dollars (INT$).<br><br>RESULTS: The current study found a reduction in the number of DALYs, YLLs, and deaths per 100,000 population of cardiovascular disease (CVD) attributable to high BMI and an increase in YLD due to diabetes and cardiovascular disease attributable to high BMI from 1990 to 2019. In 2019, high BMI resulted in 2404 DALYs, 658 YLDs, 1746 YLLs, and 76 deaths per 100,000 inhabitants. In the same year, INT$377.30 million was spent on hospitalisations and high- and medium-complexity procedures to control non-communicable diseases attributable to high BMI. The states in the South and Southeast regions of Brazil presented the highest total cost per 10,000 inhabitants. CVDs and chronic kidney disease showed the highest costs per hospital admission, whereas neoplasms and CVDs presented the highest costs for outpatient procedures.<br><br>CONCLUSIONS: High BMI causes significant disease burden and financial costs. The highest expenses observed were not in locations with the highest burden of disease attributable to high BMI. These findings highlight the need to improve current public policies and apply cost-effective intervention packages, focussing on equity and the promotion of healthier lifestyles to reduce overweight/obesity, especially in localities with low socioeconomic status.},
}
@article {pmid38870774,
year = {2024},
author = {Bucci, S and Berry, N and Ainsworth, J and Berry, K and Edge, D and Eisner, E and Emsley, R and Forbes, G and Hassan, L and Lewis, S and Machin, M and Haddock, G},
title = {Effects of Actissist, a digital health intervention for early psychosis: A randomized clinical trial.},
journal = {Psychiatry research},
volume = {339},
number = {},
pages = {116025},
doi = {10.1016/j.psychres.2024.116025},
pmid = {38870774},
issn = {1872-7123},
abstract = {Schizophrenia affects 24 million people worldwide. Digital health interventions drawing on psychological principles have been developed, but their effectiveness remains unclear. This parallel, assessor-blinded, randomized clinical trial aimed to investigate whether a cognitive behaviour therapy-informed digital health intervention (Actissist app) confers added benefit on psychotic symptoms over and above remote symptom monitoring (ClinTouch app). Participants recruited from UK community health services were randomized 1:1 to receive either Actissist plus treatment as usual (TAU) or ClinTouch plus TAU. Eligible participants were adults with schizophrenia-spectrum psychosis within five years of first episode onset meeting a criterion level of positive symptoms severity. The primary outcome was Positive and Negative Syndrome Scale (PANSS) symptoms total score at 12 weeks post-randomization. Intention-to-treat analysis included 172 participants, with 149 participants (86.6 %) providing primary outcome data. Actissist plus TAU was not associated with greater reduction than an active control remote symptom monitoring app (ClinTouch) in PANSS total score at post-randomization. There were no significant effects between groups across secondary measures. There were no serious adverse reactions. Both groups improved on the primary psychotic symptoms measure at primary end-point and on secondary measures over time. The Actissist app is safe but not superior to digital symptom monitoring.},
}
@article {pmid38868628,
year = {2023},
author = {Obbard, DJ and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Hirtodrosophila cameraria (Haliday, 1833).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {361},
pmid = {38868628},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Hirtodrosophila cameraria (a drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 214.5 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.94 kilobases in length.},
}
@article {pmid38867756,
year = {2024},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , and , },
title = {The genome sequence of the Marbled White Spot, Protodeltote pygarga (Hufnagel, 1766).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {7},
pmid = {38867756},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Protodeltote pygarga (the Marbled White Spot; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 421.1 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.48 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,784 protein coding genes.},
}
@article {pmid38867206,
year = {2024},
author = {Anjos, C and Duarte, D and Fatsini, E and Matias, D and Cabrita, E},
title = {Comparative transcriptome analysis reveals molecular damage associated with cryopreservation in Crassostrea angulata D-larvae rather than to cryoprotectant exposure.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {591},
pmid = {38867206},
issn = {1471-2164},
support = {SFRH/BD/130910/2017//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; CCMAR/Multi/04326/2022//Funda&#xe7;&#xe3;o para a Ci&#xea;ncia e a Tecnologia/ ; 0139_VENUS_5_E//Interreg POCTEP/ ; JRA2-H2020-INFRAIA-2016-2017//European Commission/ ; EBB-EAPA_501/2016//Interreg Atlantic Area/ ; },
mesh = {Animals ; *Cryopreservation ; *Crassostrea/genetics/growth &amp; development ; *Cryoprotective Agents/pharmacology/toxicity ; *Larva/genetics/drug effects/growth &amp; development ; *Gene Expression Profiling ; Transcriptome ; Gene Ontology ; },
abstract = {BACKGROUND: The Portuguese oyster Crassostrea angulata, a bivalve of significant economic and ecological importance, has faced a decline in both production and natural populations due to pathologies, climate change, and anthropogenic factors. To safeguard its genetic diversity and improve reproductive management, cryopreservation emerges as a valuable strategy. However, the cryopreservation methodologies lead to some damage in structures and functions of the cells and tissues that can affect post-thaw quality. Transcriptomics may help to understand the molecular consequences related to cryopreservation steps and therefore to identify different freezability biomarkers. This study investigates the molecular damage induced by cryopreservation in C. angulata D-larvae, focusing on two critical steps: exposure to cryoprotectant solution and the freezing/thawing process.<br><br>RESULTS: Expression analysis revealed 3 differentially expressed genes between larvae exposed to cryoprotectant solution and fresh larvae and 611 differentially expressed genes in cryopreserved larvae against fresh larvae. The most significantly enriched gene ontology terms were "carbohydrate metabolic process", "integral component of membrane" and "chitin binding" for biological processes, cellular components and molecular functions, respectively. Kyoto Encyclopedia of Genes and Genomes enrichment analysis identified the "neuroactive ligand receptor interaction", "endocytosis" and "spliceosome" as the most enriched pathways. RNA sequencing results were validate by quantitative RT-PCR, once both techniques presented the same gene expression tendency and a group of 11 genes were considered important molecular biomarkers to be used in further studies for the evaluation of cryodamage.<br><br>CONCLUSIONS: The current work provided valuable insights into the molecular repercussions of cryopreservation on D-larvae of Crassostrea angulata, revealing that the freezing process had a more pronounced impact on larval quality compared to any potential cryoprotectant-induced toxicity. Additionally, was identify 11 genes serving as biomarkers of freezability for D-larvae quality assessment. This research contributes to the development of more effective cryopreservation protocols and detection methods for cryodamage in this species.},
}
@article {pmid38865434,
year = {2024},
author = {Iverson, AR and Humple, DL and Cormier, RL and Hahn, TP and Block, TA and Shizuka, D and Lyon, BE and Chaine, AS and Hudson, EJ and Hull, EM},
title = {Winter GPS tagging reveals home ranges during the breeding season for a boreal-nesting migrant songbird, the Golden-crowned Sparrow.},
journal = {PloS one},
volume = {19},
number = {6},
pages = {e0305369},
pmid = {38865434},
issn = {1932-6203},
mesh = {Animals ; *Seasons ; *Geographic Information Systems ; *Animal Migration/physiology ; *Sparrows/physiology ; *Homing Behavior/physiology ; Breeding ; Ecosystem ; British Columbia ; Alaska ; Nesting Behavior/physiology ; },
abstract = {Determining space use for species is fundamental to understanding their ecology, and tracking animals can reveal insights into their spatial ecology on home ranges and territories. Recent technological advances have led to GPS-tracking devices light enough for birds as small as ~30 g, creating novel opportunities to remotely monitor fine-scale movements and space use for these smaller species. We tested whether miniaturized GPS tags can allow us to understand space use of migratory birds away from their capture sites and sought to understand both pre-breeding space use as well as territory and habitat use on the breeding grounds. We used GPS tags to characterize home ranges on the breeding grounds for a migratory songbird with limited available breeding information, the Golden-crowned Sparrow (Zonotrichia atricapilla). Using GPS points from 23 individuals across 26 tags (three birds tagged twice), we found home ranges in Alaska and British Columbia were on average 44.1 ha (95% kernel density estimate). In addition, estimates of territory sizes based on field observations (mean 2.1 ha, 95% minimum convex polygon [MCP]) were three times smaller than 95% MCPs created using GPS tags (mean 6.5 ha). Home ranges included a variety of land cover classes, with shrubland particularly dominant (64-100% of home range cover for all but one bird). Three birds tracked twice returned to the same breeding area each year, supporting high breeding site fidelity for this species. We found reverse spring migration for five birds that flew up to 154 km past breeding destinations before returning. GPS-tracking technology allowed for critical ecological insights into this migratory species that breeds in very remote locations.},
}
@article {pmid38865431,
year = {2024},
author = {Tedersoo, L and Hosseyni Moghaddam, MS and Mikryukov, V and Hakimzadeh, A and Bahram, M and Nilsson, RH and Yatsiuk, I and Geisen, S and Schwelm, A and Piwosz, K and Prous, M and Sildever, S and Chmolowska, D and Rueckert, S and Skaloud, P and Laas, P and Tines, M and Jung, JH and Choi, JH and Alkahtani, S and Anslan, S},
title = {EUKARYOME: the rRNA gene reference database for identification of all eukaryotes.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
pmid = {38865431},
issn = {1758-0463},
support = {Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; Distinguished Scientist Fellowship Programme//King Saud University/ ; MOBERC66 MOBTP198//European Regional Development Fund/ ; //LOEWE Zentrum AdRIA/ ; },
mesh = {*Eukaryota/genetics ; RNA, Ribosomal, 18S/genetics ; Databases, Genetic ; Databases, Nucleic Acid ; Animals ; Genes, rRNA/genetics ; Phylogeny ; },
abstract = {Molecular identification of micro- and macroorganisms based on nuclear markers has revolutionized our understanding of their taxonomy, phylogeny and ecology. Today, research on the diversity of eukaryotes in global ecosystems heavily relies on nuclear ribosomal RNA (rRNA) markers. Here, we present the research community-curated reference database EUKARYOME for nuclear ribosomal 18S rRNA, internal transcribed spacer (ITS) and 28S rRNA markers for all eukaryotes, including metazoans (animals), protists, fungi and plants. It is particularly useful for the identification of arbuscular mycorrhizal fungi as it bridges the four commonly used molecular markers-ITS1, ITS2, 18S V4-V5 and 28S D1-D2 subregions. The key benefits of this database over other annotated reference sequence databases are that it is not restricted to certain taxonomic groups and it includes all rRNA markers. EUKARYOME also offers a number of reference long-read sequences that are derived from (meta)genomic and (meta)barcoding-a unique feature that can be used for taxonomic identification and chimera control of third-generation, long-read, high-throughput sequencing data. Taxonomic assignments of rRNA genes in the database are verified based on phylogenetic approaches. The reference datasets are available in multiple formats from the project homepage, http://www.eukaryome.org.},
}
@article {pmid38863181,
year = {2024},
author = {Wong, RE and Berner, LT and Sullivan, PF and Potter, CS and Dial, RJ},
title = {Pixel walking along the boreal forest-Arctic tundra ecotone: Large scale ground-truthing of satellite-derived greenness (NDVI).},
journal = {Global change biology},
volume = {30},
number = {6},
pages = {e17374},
doi = {10.1111/gcb.17374},
pmid = {38863181},
issn = {1365-2486},
support = {80NSSC22K1247/NASA/NASA/United States ; 80NSSC20M0070//Alaska Space Grant Program/ ; DEB-2133494//National Science Foundation/ ; OPP-1748773//National Science Foundation/ ; OPP-1748849//National Science Foundation/ ; 80NSSC19M0062//Alaska NASA EPSCoR/ ; },
mesh = {Alaska ; Arctic Regions ; *Satellite Imagery ; *Tundra ; Remote Sensing Technology/methods ; Taiga ; Environmental Monitoring/methods ; },
abstract = {In this Technical Advance, we describe a novel method to improve ecological interpretation of remotely sensed vegetation greenness measurements that involved sampling 24,395 Landsat pixels (30 m) across 639 km of Alaska's central Brooks Range. The method goes well beyond the spatial scale of traditional plot-based sampling and thereby more thoroughly relates ground-based observations to satellite measurements. Our example dataset illustrates that, along the boreal-Arctic boundary, vegetation with the greatest Landsat Normalized Difference Vegetation Index (NDVI) is taller than 1 m, woody, and deciduous; whereas vegetation with lower NDVI tends to be shorter, evergreen, or non-woody. The field methods and associated analyses advance efforts to inform satellite data with ground-based vegetation observations using field samples collected at spatial scales that closely match the resolution of remotely sensed imagery.},
}
@article {pmid38862613,
year = {2024},
author = {Venu, V and Roth, C and Adikari, SH and Small, EM and Starkenburg, SR and Sanbonmatsu, KY and Steadman, CR},
title = {Multi-omics analysis reveals the dynamic interplay between Vero host chromatin structure and function during vaccinia virus infection.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {721},
pmid = {38862613},
issn = {2399-3642},
support = {20210134ER//DOE | LDRD | Los Alamos National Laboratory (Los Alamos Lab)/ ; },
mesh = {*Chromatin/metabolism/genetics ; Animals ; *Vaccinia virus/genetics/physiology ; Chlorocebus aethiops ; Vero Cells ; Vaccinia/virology/immunology ; Host-Pathogen Interactions/genetics ; Multiomics ; },
abstract = {The genome folds into complex configurations and structures thought to profoundly impact its function. The intricacies of this dynamic structure-function relationship are not well understood particularly in the context of viral infection. To unravel this interplay, here we provide a comprehensive investigation of simultaneous host chromatin structural (via Hi-C and ATAC-seq) and functional changes (via RNA-seq) in response to vaccinia virus infection. Over time, infection significantly impacts global and local chromatin structure by increasing long-range intra-chromosomal interactions and B compartmentalization and by decreasing chromatin accessibility and inter-chromosomal interactions. Local accessibility changes are independent of broad-scale chromatin compartment exchange (~12% of the genome), underscoring potential independent mechanisms for global and local chromatin reorganization. While infection structurally condenses the host genome, there is nearly equal bidirectional differential gene expression. Despite global weakening of intra-TAD interactions, functional changes including downregulated immunity genes are associated with alterations in local accessibility and loop domain restructuring. Therefore, chromatin accessibility and local structure profiling provide impactful predictions for host responses and may improve development of efficacious anti-viral counter measures including the optimization of vaccine design.},
}
@article {pmid38862357,
year = {2024},
author = {Knight, E and Rhinehart, T and de Zwaan, DR and Weldy, MJ and Cartwright, M and Hawley, SH and Larkin, JL and Lesmeister, D and Bayne, E and Kitzes, J},
title = {Individual identification in acoustic recordings.},
journal = {Trends in ecology &amp; evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2024.05.007},
pmid = {38862357},
issn = {1872-8383},
abstract = {Recent advances in bioacoustics combined with acoustic individual identification (AIID) could open frontiers for ecological and evolutionary research because traditional methods of identifying individuals are invasive, expensive, labor-intensive, and potentially biased. Despite overwhelming evidence that most taxa have individual acoustic signatures, the application of AIID remains challenging and uncommon. Furthermore, the methods most commonly used for AIID are not compatible with many potential AIID applications. Deep learning in adjacent disciplines suggests opportunities to advance AIID, but such progress is limited by training data. We suggest that broadscale implementation of AIID is achievable, but researchers should prioritize methods that maximize the potential applications of AIID, and develop case studies with easy taxa at smaller spatiotemporal scales before progressing to more difficult scenarios.},
}
@article {pmid38860489,
year = {2024},
author = {Toga, K and Sakamoto, T and Kanda, M and Tamura, K and Okuhara, K and Tabunoki, H and Bono, H},
title = {Long-read genome assembly of the Japanese parasitic wasp Copidosoma floridanum (Hymenoptera: Encyrtidae).},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae127},
pmid = {38860489},
issn = {2160-1836},
abstract = {Copidosoma floridanum is a cosmopolitan species and an egg-larval parasitoid of the Plusiine moth. C. floridanum has a unique development mode called polyembryony, in which over two thousands of genetically identical embryos are produced from a single egg. Some embryos develop into sterile soldier larvae precociously, and their emergence period and aggressive behavior are differed between the US and Japanese C. floridanum strains. Genome sequencing expects to contribute our understanding of the molecular bases underlying progression of polyembryony. However, only the genome sequence of the US strain from generating by short-read assembly has been reported. In the present study, we determined the genome sequence of the Japanese strain using Pacific Biosciences high-fidelity reads and generating a highly contiguous assembly (552.7 Mb, N50: 17.9 Mb). Gene prediction and annotation identified 13,886 transcripts derived from 10,786 gene models. We searched the genomic differences between US and Japanese strains. Among gene models predicted in this study, 100 gene loci in the Japanese strain had extremely different gene structure from those in the US strain. This was accomplished through the functional annotation (GGSEARCH) and long-read sequencing. Genomic differences between strains were also reflected to amino acid sequences of vasa that plays a central role in caste determination in this species. The genome assemblies constructed in this study will facilitate the genomic comparisons between Japanese and US strains, leading to our understanding of detail genomic regions responsible for the ecological and physiological characters of C. floridanum.},
}
@article {pmid38856681,
year = {2024},
author = {Dasgupta, S},
title = {Thinking Beyond Disease Silos: Dysregulated Genes Common in Tuberculosis and Lung Cancer as Identified by Systems Biology and Machine Learning.},
journal = {Omics : a journal of integrative biology},
volume = {28},
number = {7},
pages = {347-356},
doi = {10.1089/omi.2024.0116},
pmid = {38856681},
issn = {1557-8100},
mesh = {Humans ; *Machine Learning ; *Lung Neoplasms/genetics ; *Tuberculosis/genetics ; *Systems Biology/methods ; Computational Biology/methods ; Gene Expression Profiling/methods ; Gene Regulatory Networks ; },
abstract = {The traditional way of thinking about human diseases across clinical and narrow phenomics silos often masks the underlying shared molecular substrates across human diseases. One Health and planetary health fields particularly address such complexities and invite us to think across the conventional disease nosologies. For example, tuberculosis (TB) and lung cancer (LC) are major pulmonary diseases with significant planetary health implications. Despite distinct etiologies, they can coexist in a given community or patient. This is both a challenge and an opportunity for preventive medicine, diagnostics, and therapeutics innovation. This study reports a bioinformatics analysis of publicly available gene expression data, identifying overlapping dysregulated genes, downstream regulators, and pathways in TB and LC. Analysis of NCBI-GEO datasets (GSE83456 and GSE103888) unveiled differential expression of CEACAM6, MUC1, ADM, DYSF, PLOD2, and GAS6 genes in both diseases, with pathway analysis indicating association with lysine degradation pathway. Random forest, a machine-learning-based classification, achieved accuracies of 84% for distinguishing TB from controls and 83% for discriminating LC from controls using these specific genes. Additionally, potential drug targets were identified, with molecular docking confirming the binding affinity of warfarin to GAS6. Taken together, the present study speaks of the pressing need to rethink clinical diagnostic categories of human diseases and that TB and LC might potentially share molecular substrates. Going forward, planetary health and One Health scholarship are poised to cultivate new ways of thinking about diseases not only across medicine and ecology but also across traditional diagnostic conventions.},
}
@article {pmid38855721,
year = {2023},
author = {Boyes, D and Broad, GR and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Cloaked Minor, Mesoligia furuncula (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {251},
pmid = {38855721},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Mesoligia furuncula (the Cloaked Minor; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 889.6 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,903 protein coding genes.},
}
@article {pmid38854694,
year = {2024},
author = {Christenhusz, MJM and Pannell, JR and Twyford, AD and , and , and , and , and , and , and , },
title = {The genome sequence of the Annual Mercury, Mercurialis annua L., 1753 (Euphorbiaceae).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {102},
pmid = {38854694},
issn = {2398-502X},
abstract = {We present a genome assembly from a diploid female Mercurialis annua (the Annual Mercury; Tracheophyta; Magnoliopsida; Malpighiales; Euphorbiaceae). The genome sequence is 453.2 megabases in span. Most of the assembly is scaffolded into 8 chromosomal pseudomolecules, including the X chromosome. The organelle genomes have also been assembled, and the mitochondrial genome is 435.28 kilobases in length, while the plastid genome is 169.65 kilobases in length.},
}
@article {pmid38853065,
year = {2024},
author = {O'Connor, JB and Mottlowitz, M and Wagner, BD and Harris, JK and Laguna, TA},
title = {Metabolomics analysis of bronchoalveolar lavage fluid predicts unique features of the lower airway in pediatric cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2024.04.017},
pmid = {38853065},
issn = {1873-5010},
abstract = {BACKGROUND: Progressive, obstructive lung disease resulting from chronic infection and inflammation is the leading cause of morbidity and mortality in persons with cystic fibrosis (PWCF). Metabolomics and next -generation sequencing (NGS) of airway secretions can allow for better understanding of cystic fibrosis (CF) pathophysiology. In this study, global metabolomic profiling on bronchoalveolar lavage fluid (BALF) obtained from pediatric PWCF and disease controls (DCs) was performed and compared to lower airway microbiota, inflammation, and lung function.<br><br>METHODS: BALF was collected from children undergoing flexible bronchoscopies for clinical indications. Metabolomic profiling was performed using a platform developed by Metabolon Inc. Total bacterial load (TBL) was measured using quantitative polymerase chain reaction (qPCR), and bacterial communities were characterized using 16S ribosomal RNA (rRNA) sequencing. Random Forest Analysis (RFA), principal component analysis (PCA), and hierarchical clustering analysis (HCA) were performed.<br><br>RESULTS: One hundred ninety-five BALF samples were analyzed, 142 (73 %) from PWCF. Most metabolites (425/665) and summed categories (7/9) were significantly increased in PWCF. PCA of the metabolomic data revealed CF BALF exhibited more dispersed clustering compared to DC BALF. Higher metabolite concentrations correlated with increased inflammation, increased abundance of Staphylococcus, and decreased lung function.<br><br>CONCLUSIONS: The lower airway metabolome of PWCF was defined by a complex expansion of metabolomic activity. These findings could be attributed to heightened inflammation in PWCF and aspects of the CF airway polymicrobial ecology. CF-specific metabolomic features are associated with the unique underlying biology of the CF airway.},
}
@article {pmid38852834,
year = {2024},
author = {Goodus, MT and Alfredo, AN and Carson, KE and Dey, P and Pukos, N and Schwab, JM and Popovich, PG and Gao, J and Mo, X and Bruno, RS and McTigue, DM},
title = {Spinal cord injury-induced metabolic impairment and steatohepatitis develops in non-obese rats and is exacerbated by premorbid obesity.},
journal = {Experimental neurology},
volume = {379},
number = {},
pages = {114847},
doi = {10.1016/j.expneurol.2024.114847},
pmid = {38852834},
issn = {1090-2430},
abstract = {Impaired sensorimotor functions are prominent complications of spinal cord injury (SCI). A clinically important but less obvious consequence is development of metabolic syndrome (MetS), including increased adiposity, hyperglycemia/insulin resistance, and hyperlipidemia. MetS predisposes SCI individuals to earlier and more severe diabetes and cardiovascular disease compared to the general population, which trigger life-threatening complications (e.g., stroke, myocardial infarcts). Although each comorbidity is known to be a risk factor for diabetes and other health problems in obese individuals, their relative contribution or perceived importance in propagating systemic pathology after SCI has received less attention. This could be explained by an incomplete understanding of MetS promoted by SCI compared with that from the canonical trigger diet-induced obesity (DIO). Thus, here we compared metabolic-related outcomes after SCI in lean rats to those of uninjured rats with DIO. Surprisingly, SCI-induced MetS features were equal to or greater than those in obese uninjured rats, including insulin resistance, endotoxemia, hyperlipidemia, liver inflammation and steatosis. Considering the endemic nature of obesity, we also evaluated the effect of premorbid obesity in rats receiving SCI; the combination of DIO + SCI exacerbated MetS and liver pathology compared to either alone, suggesting that obese individuals that sustain a SCI are especially vulnerable to metabolic dysfunction. Notably, premorbid obesity also exacerbated intraspinal lesion pathology and worsened locomotor recovery after SCI. Overall, these results highlight that normal metabolic function requires intact spinal circuitry and that SCI is not just a sensory-motor disorder, but also has significant metabolic consequences.},
}
@article {pmid38845010,
year = {2024},
author = {Wang, S and Lee, HC and Lee, S},
title = {Predicting herb-disease associations using network-based measures in human protein interactome.},
journal = {BMC complementary medicine and therapies},
volume = {24},
number = {Suppl 2},
pages = {218},
pmid = {38845010},
issn = {2662-7671},
support = {GIST Research Institute IIBR//Gwangju Institute of Science and Technology/ ; GIST Research Institute (GRI) GIST-MIT research Collaboration//Gwangju Institute of Science and Technology/ ; 2021M3A9G8022959//Ministry of Science and ICT, South Korea/ ; 2021R1C1C1006336//Ministry of Science and ICT, South Korea/ ; HR22C141105//Ministry of Health and Welfare/ ; },
mesh = {Humans ; *Protein Interaction Maps ; Computer Simulation ; Computational Biology/methods ; },
abstract = {BACKGROUND: Natural herbs are frequently used to treat diseases or to relieve symptoms in many countries. Moreover, as their safety has been proven for a long time, they are considered as main sources of new drug development. However, in many cases, the herbs are still prescribed relying on ancient records and/or traditional practices without scientific evidences. More importantly, the medicinal efficacy of the herbs has to be evaluated in the perspective of MCMT (multi-compound multi-target) effects, but most efforts focus on identifying and analyzing a single compound experimentally. To overcome these hurdles, computational approaches which are based on the scientific evidences and are able to handle the MCMT effects are needed to predict the herb-disease associations.<br><br>RESULTS: In this study, we proposed a network-based in silico method to predict the herb-disease associations. To this end, we devised a new network-based measure, WACP (weighted average closest path length), which not only quantifies proximity between herb-related genes and disease-related genes but also considers compound compositions of each herb. As a result, we confirmed that our method successfully predicts the herb-disease associations in the human protein interactome (AUROC&#x2009;=&#x2009;0.777). In addition, we observed that our method is superior than the other simple network-based proximity measures (e.g. average shortest and closest path length). Additionally, we analyzed the associations between Brassica oleracea var. italica and its known associated diseases more specifically as case studies. Finally, based on the prediction results of the WACP, we suggested novel herb-disease pairs which are expected to have potential relations and their literature evidences.<br><br>CONCLUSIONS: This method could be a promising solution to modernize the use of the natural herbs by providing the scientific evidences about the molecular associations between the herb-related genes targeted by multiple compounds and the disease-related genes in the human protein interactome.},
}
@article {pmid38844398,
year = {2024},
author = {Xiao, Z and Robertson, S and Long, E and Flaig, R and Kirby, L and Romaniuk, L and Murray, A and Whalley, H},
title = {Loneliness in the Digital World: protocol for a co-produced ecological momentary assessment study in adolescents.},
journal = {BMJ open},
volume = {14},
number = {6},
pages = {e087374},
pmid = {38844398},
issn = {2044-6055},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Loneliness/psychology ; Adolescent ; *Ecological Momentary Assessment ; *Mental Health ; Female ; Child ; Male ; Social Interaction ; Surveys and Questionnaires ; Research Design ; Depression ; Scotland ; Anxiety ; },
abstract = {INTRODUCTION: Loneliness has been identified as an important public health issue, peaking during adolescence. Previous research has suggested that social interaction is a key factor in loneliness, and positive social interaction can act as a protective factor against loneliness. However, it is unclear whether there are differing impacts of in-person and online social interaction on adolescents' loneliness and mental health. Ecological Momentary Assessment (EMA) designs are ideally suited for better understanding these associations.<br><br>METHOD AND ANALYSIS: In the 'Loneliness in the Digital World' study, we will use a co-developed EMA design to capture daily social interactions, loneliness and mental health such as positive and negative emotions, depression and anxiety in approximately 200 adolescents aged 12-15 years. We will combine this with comprehensive information gathered from online surveys. Analysing the data using techniques such as dynamic structural equation modelling, we will examine, among other research questions, the associations between online and in-person social interaction and feelings of loneliness. The results can help inform interventions to support adolescents with high levels of loneliness and poor mental health.<br><br>ETHICS AND DISSEMINATION: We received the ethics approval for the data collection from The Academic and Clinical Central Office for Research and Development, followed by the College of Medicine and Veterinary Medicine Ethics panel at University of Edinburgh, and finally reviewed by East of Scotland Research Ethics Service. The results will be disseminated through journal publications, conferences and seminar presentations and to relevant stakeholders such as teachers.},
}
@article {pmid38841890,
year = {2024},
author = {Pedersen, MB and Beedholm, K and Hubancheva, A and Koseva, K and Uebel, AS and Hochradel, K and Madsen, PT and Stidsholt, L},
title = {Clutter resilience via auditory stream segregation in echolocating greater mouse-eared bats.},
journal = {The Journal of experimental biology},
volume = {227},
number = {12},
pages = {},
doi = {10.1242/jeb.246889},
pmid = {38841890},
issn = {1477-9145},
support = {//Frands Christian Frantsen Foundation/ ; FP2 0135-00343B//Natur og Univers, Det Frie Forskningsr&#xe5;d/ ; AU337272//Fonden Frands Christian Frantsens Legat/ ; 41386//Villum Fonden/ ; CF16-0405//Carlsbergfondet/ ; },
mesh = {Animals ; *Chiroptera/physiology ; *Echolocation/physiology ; Male ; Female ; Vocalization, Animal/physiology ; },
abstract = {Bats use echolocation to navigate and hunt in darkness, and must in that process segregate target echoes from unwanted clutter echoes. Bats may do this by approaching a target at steep angles relative to the plane of the background, utilizing their directional transmission and receiving systems to minimize clutter from background objects, but it remains unknown how bats negotiate clutter that cannot be spatially avoided. Here, we tested the hypothesis that when movement no longer offers spatial release, echolocating bats mitigate clutter by calling at lower source levels and longer call intervals to ease auditory streaming. We trained five greater mouse-eared bats (Myotis myotis) to land on a spherical loudspeaker with two microphones attached. We used a phantom-echo setup, where the loudspeaker/target transmitted phantom clutter echoes by playing back the bats' own calls at time delays of 1, 3 and 5 ms with a virtual target strength 7 dB higher than the physical target. We show that the bats successfully landed on the target, irrespective of the clutter echo delays. Rather than decreasing their source levels, the bats used similar source level distributions in clutter and control trials. Similarly, the bats did not increase their call intervals, but instead used the same distribution of call intervals across control and clutter trials. These observations reject our hypothesis, leading us to conclude that bats display great resilience to clutter via short auditory integration times and acute auditory stream segregation rather than via biosonar adjustments.},
}
@article {pmid38840517,
year = {2024},
author = {Walker, XJ and Hart, S and Hansen, WD and Jean, M and Brown, CD and Stuart Chapin, F and Hewitt, R and Hollingsworth, TN and Mack, MC and Johnstone, JF},
title = {Factors limiting the potential range expansion of lodgepole pine in Interior Alaska.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {34},
number = {5},
pages = {e2983},
doi = {10.1002/eap.2983},
pmid = {38840517},
issn = {1051-0761},
support = {05-1-2-06//Joint Fire Science Program/ ; //Natural Sciences and Engineering Research Council of Canada/ ; PNW01-JV11261952-23//U.S. Fish and Wildlife Service/ ; RC-2109//Strategic Environmental Research and Development Program/ ; RC-2754//Strategic Environmental Research and Development Program/ ; DEB-0620579//National Science Foundation/ ; DEB-1636476//National Science Foundation/ ; DEB-2224776//National Science Foundation/ ; USFS-PNW01-JV11261952-23//National Science Foundation/ ; RJVA-PNW-20-JV-11261932-018//National Science Foundation/ ; OPP-2116862//National Science Foundation/ ; NNX15AT71A/NASA/NASA/United States ; },
mesh = {*Pinus/physiology ; Alaska ; Climate Change ; Models, Biological ; Seedlings ; Demography ; Animals ; Ecosystem ; },
abstract = {Understanding the factors influencing species range limits is increasingly crucial in anticipating migrations due to human-caused climate change. In the boreal biome, ongoing climate change and the associated increases in the rate, size, and severity of disturbances may alter the distributions of boreal tree species. Notably, Interior Alaska lacks native pine, a biogeographical anomaly that carries implications for ecosystem structure and function. The current range of lodgepole pine (Pinus contorta var. latifolia) in the adjacent Yukon Territory may expand into Interior Alaska, particularly with human assistance. Evaluating the potential for pine expansion in Alaska requires testing constraints on range limits such as dispersal limitations, environmental tolerance limits, and positive or negative biotic interactions. In this study, we used field experiments with pine seeds and transplanted seedlings, complemented by model simulations, to assess the abiotic and biotic factors influencing lodgepole pine seedling establishment and growth after fire in Interior Alaska. We found that pine could successfully recruit, survive, grow, and reproduce across our broadly distributed network of experimental sites. Our results show that both mammalian herbivory and competition from native tree species are unlikely to constrain pine growth and that environmental conditions commonly found in Interior Alaska fall well within the tolerance limits for pine. If dispersal constraints are released, lodgepole pine could have a geographically expansive range in Alaska, and once established, its growth is sufficient to support pine-dominated stands. Given the impacts of lodgepole pine on ecosystem processes such as increases in timber production, carbon sequestration, landscape flammability, and reduced forage quality, natural or human-assisted migration of this species is likely to substantially alter responses of Alaskan forest ecosystems to climate change.},
}
@article {pmid38839953,
year = {2024},
author = {Senior, RA and Bagwyn, R and Leng, D and Killion, AK and Jetz, W and Wilcove, DS},
title = {Global shortfalls in documented actions to conserve biodiversity.},
journal = {Nature},
volume = {630},
number = {8016},
pages = {387-391},
pmid = {38839953},
issn = {1476-4687},
mesh = {Animals ; *Biodiversity ; *Conservation of Natural Resources/methods/statistics &amp; numerical data ; Databases, Factual ; *Endangered Species/statistics &amp; numerical data ; Extinction, Biological ; *Internationality ; Introduced Species/statistics &amp; numerical data ; },
abstract = {Threatened species are by definition species that are in need of assistance. In the absence of suitable conservation interventions, they are likely to disappear soon[1]. There is limited understanding of how and where conservation interventions are applied globally, or how well they work[2,3]. Here, using information from the International Union for Conservation of Nature Red List and other global databases, we find that for species at risk from three of the biggest drivers of biodiversity loss-habitat loss, overexploitation for international trade and invasive species[4]-many appear to lack the appropriate types of conservation interventions. Indeed, although there has been substantial recent expansion of the protected area network, we still find that 91% of threatened species have insufficient representation of their habitats within protected areas. Conservation interventions are not implemented uniformly across different taxa and regions and, even when present, have infrequently led to substantial improvements in the status of species. For 58% of the world's threatened terrestrial species, we find conservation interventions to be notably insufficient or absent. We cannot determine whether such species are truly neglected, or whether efforts to recover them are not included in major conservation databases. If they are indeed neglected, the outlook for many of the world's threatened species is grim without more and better targeted action.},
}
@article {pmid38838462,
year = {2024},
author = {Runge, MC and Shea, K and Howerton, E and Yan, K and Hochheiser, H and Rosenstrom, E and Probert, WJM and Borchering, R and Marathe, MV and Lewis, B and Venkatramanan, S and Truelove, S and Lessler, J and Viboud, C},
title = {Scenario design for infectious disease projections: Integrating concepts from decision analysis and experimental design.},
journal = {Epidemics},
volume = {47},
number = {},
pages = {100775},
doi = {10.1016/j.epidem.2024.100775},
pmid = {38838462},
issn = {1878-0067},
support = {U24 GM132013/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *COVID-19/epidemiology/prevention &amp; control/transmission ; *Decision Support Techniques ; Forecasting ; SARS-CoV-2 ; Communicable Diseases/epidemiology ; Pandemics/prevention &amp; control ; Decision Making ; Research Design ; },
abstract = {Across many fields, scenario modeling has become an important tool for exploring long-term projections and how they might depend on potential interventions and critical uncertainties, with relevance to both decision makers and scientists. In the past decade, and especially during the COVID-19 pandemic, the field of epidemiology has seen substantial growth in the use of scenario projections. Multiple scenarios are often projected at the same time, allowing important comparisons that can guide the choice of intervention, the prioritization of research topics, or public communication. The design of the scenarios is central to their ability to inform important questions. In this paper, we draw on the fields of decision analysis and statistical design of experiments to propose a framework for scenario design in epidemiology, with relevance also to other fields. We identify six different fundamental purposes for scenario designs (decision making, sensitivity analysis, situational awareness, horizon scanning, forecasting, and value of information) and discuss how those purposes guide the structure of scenarios. We discuss other aspects of the content and process of scenario design, broadly for all settings and specifically for multi-model ensemble projections. As an illustrative case study, we examine the first 17 rounds of scenarios from the U.S. COVID-19 Scenario Modeling Hub, then reflect on future advancements that could improve the design of scenarios in epidemiological settings.},
}
@article {pmid38837409,
year = {2024},
author = {Rico-Jiménez, M and Udaondo, Z and Krell, T and Matilla, MA},
title = {Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0016524},
doi = {10.1128/msystems.00165-24},
pmid = {38837409},
issn = {2379-5077},
abstract = {UNLABELLED: The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria.<br><br>IMPORTANCE: Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.},
}
@article {pmid38831386,
year = {2024},
author = {Duo, H and Li, Y and Lan, Y and Tao, J and Yang, Q and Xiao, Y and Sun, J and Li, L and Nie, X and Zhang, X and Liang, G and Liu, M and Hao, Y and Li, B},
title = {Systematic evaluation with practical guidelines for single-cell and spatially resolved transcriptomics data simulation under multiple scenarios.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {145},
pmid = {38831386},
issn = {1474-760X},
support = {KJQN202100538//Science and Technology Research Program of Chongqing Municipal Education Commission/ ; 62101087//National Natural Science Foundation of China/ ; 2021MD703942//China Postdoctoral Science Foundation/ ; YKC23027//Graduate Research Innovation Project of Chongqing Normal University/ ; YNPRAEC-2023004//Open Fund of Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology/ ; },
mesh = {*Single-Cell Analysis/methods ; *Gene Expression Profiling/methods ; Humans ; Software ; Computer Simulation ; Transcriptome ; Computational Biology/methods ; Sequence Analysis, RNA/methods ; RNA-Seq/methods/standards ; },
abstract = {BACKGROUND: Single-cell RNA sequencing (scRNA-seq) and spatially resolved transcriptomics (SRT) have led to groundbreaking advancements in life sciences. To develop bioinformatics tools for scRNA-seq and SRT data and perform unbiased benchmarks, data simulation has been widely adopted by providing explicit ground truth and generating customized datasets. However, the performance of simulation methods under multiple scenarios has not been comprehensively assessed, making it challenging to choose suitable methods without practical guidelines.<br><br>RESULTS: We systematically evaluated 49 simulation methods developed for scRNA-seq and/or SRT data in terms of accuracy, functionality, scalability, and usability using 152 reference datasets derived from 24 platforms. SRTsim, scDesign3, ZINB-WaVE, and scDesign2 have the best accuracy performance across various platforms. Unexpectedly, some methods tailored to scRNA-seq data have potential compatibility for simulating SRT data. Lun, SPARSim, and scDesign3-tree outperform other methods under corresponding simulation scenarios. Phenopath, Lun, Simple, and MFA yield high scalability scores but they cannot generate realistic simulated data. Users should consider the trade-offs between method accuracy and scalability (or functionality) when making decisions. Additionally, execution errors are mainly caused by failed parameter estimations and appearance of missing or infinite values in calculations. We provide practical guidelines for method selection, a standard pipeline Simpipe (https://github.com/duohongrui/simpipe ; https://doi.org/10.5281/zenodo.11178409), and an online tool Simsite (https://www.ciblab.net/software/simshiny/) for data simulation.<br><br>CONCLUSIONS: No method performs best on all criteria, thus a good-yet-not-the-best method is recommended if it solves problems effectively and reasonably. Our comprehensive work provides crucial insights for developers on modeling gene expression data and fosters the simulation process for users.},
}
@article {pmid38826163,
year = {2024},
author = {Onyango, B and Copeland, R and Mbogholi, J and Wamalwa, M and Kibet, C and Tonnang, HEZ and Senagi, K},
title = {WiPFIM: A digital platform for interlinking biocollections of wild plants, fruits, associated insects, and their molecular barcodes.},
journal = {Ecology and evolution},
volume = {14},
number = {6},
pages = {e11457},
pmid = {38826163},
issn = {2045-7758},
abstract = {The current knowledge on insects feeding on fruits is limited, and some of the scarce existing data on the fruit-associated insects are secluded within the host institutions. Consequently, their value is not fully realized. Moreover, in countries like Kenya, the integration of biocollections data within a digital framework has not been fully exploited. To address these gaps, this article presents a description of the development of a web-based platform for data sharing and integrating biodiversity historical data of wild plants, fruits, associated insects, and their molecular barcodes (WiPFIM) while leveraging data science technologies. The barcodes corresponding to the biocollections data were retrieved from BOLD database. The platform is an online resource about fruit-insect interactions that can be of interest to a worldwide community of users and can be useful in building innovative tools. The platform is accessible online at https://test-dmmg.icipe.org/wpfhi.},
}
@article {pmid38825206,
year = {2024},
author = {Wei, Q and Xue, L and Liao, S and Liu, Y},
title = {Ecohydrological indicators and environmental flow assessment in the middle and lower reaches of the Huai River, China.},
journal = {The Science of the total environment},
volume = {940},
number = {},
pages = {173639},
doi = {10.1016/j.scitotenv.2024.173639},
pmid = {38825206},
issn = {1879-1026},
abstract = {The vitality of river ecosystems is vital for the sustainable development of river basins, with the assessment of environmental flow (EF) playing a pivotal role in eco-informatics. This study delves into the middle and lower reaches (MLR) of the Huai River basin (HRB) in China, utilizing hydrological data spanning from 1950 to 2020. Its principal objective lies in the selection of ecohydrological indicators to refine the estimation of EF in the HRB. Employing principal component analysis (PCA), ecologically relevant hydrological indicators (ERHIs) were discerned and scrutinized for their hydrological characteristics. The analysis extended to evaluating hydrological shifts at different stations using ERHIs, determining suitable EF in the MLR, and delineating the trajectories of appropriate intra-annual flows in different hydrological years through HEC-RPT. Based on a variety of mutation test methods, the change point of runoff sequence was determined in 1991. The PCA analysis identified eight ERHIs, reflecting hydrological changes of 49.79 % and 56.26 % at Bengbu and Sanhezha, respectively, which indicate a moderate alteration. Based on ERHIs, the other stations in the HRB exhibited hydrological alterations ranging from 33 % to 47 %, notably highlighting substantial changes in maximal 30d flow and flow fall rate. The optimal flood pulse discharge in the middle reaches is 4150 m[3]/s, 3140 m[3]/s and 2150 m[3]/s in wet, dry and dry years, respectively. Downstream, flood pulse flow in wet, normal and dry years should exceed 4070 m[3]/s, 3110 m[3]/s and 1980 m[3]/s, respectively. The research contributes significantly to the management of rivers and the sustainable conservation of the ecological milieu.},
}
@article {pmid38824636,
year = {2024},
author = {Xie, PZ and Fan, YX and Chapman, C and Ma, C and Wu, CF and Hu, P and Hu, LL and Fan, PF},
title = {Determinants of macaques' space use: A test for the ecological constraints model using GPS collars.},
journal = {American journal of primatology},
volume = {86},
number = {8},
pages = {e23636},
doi = {10.1002/ajp.23636},
pmid = {38824636},
issn = {1098-2345},
support = {33000-42090019//Forestry Administration of Guangdong Province/ ; Basic Research 20180285//Shenzhen Science and Technology Innovation Committee/ ; 23lgzy002//Fundamental Research Funds for the Central Universities, Sun Yat-sun University/ ; },
mesh = {Animals ; *Macaca mulatta/physiology ; *Geographic Information Systems ; *Homing Behavior ; China ; Male ; Female ; Ecosystem ; Temperature ; Seasons ; Islands ; },
abstract = {As a central topic in Behavioral Ecology, animal space use involves dynamic responses to social and ecological factors. We collared 22 rhesus macaques (Macaca mulatta) from six groups on Neilingding Island, China, and collected 80,625 hourly fixes over a year. Using this high-resolution location data set, we quantified the macaques' space use at the individual level and tested the ecological constraints model while considering various environmental and human interfering factors. As predicted by the ecological constraints model, macaques in larger groups had longer daily path lengths (DPLs) and larger home ranges. We found an inverted U-shape relationship between mean daily temperatures and DPLs, indicating that macaques traveled farther on mild temperature days, while they decreased DPLs when temperatures were too high or too low. Anthropogenic food subsidies were positively correlated to DPLs, while the effect of rainfall was negative. Macaques decreased their DPLs and core areas when more flowers and less leaves were available, suggesting that macaques shifted their space use patterns to adapt to the seasonal differences in food resources. By applying GPS collars on a large number of individuals living on a small island, we gained valuable insights into within-group exploitation competition in wild rhesus macaques.},
}
@article {pmid38823656,
year = {2024},
author = {Sundar Panja, A},
title = {The systematic codon usage bias has an important effect on genetic adaption in native species.},
journal = {Gene},
volume = {926},
number = {},
pages = {148627},
doi = {10.1016/j.gene.2024.148627},
pmid = {38823656},
issn = {1879-0038},
mesh = {*Codon Usage ; *Selection, Genetic ; *Evolution, Molecular ; Endangered Species ; Mutation ; Animals ; Codon/genetics ; Adaptation, Physiological/genetics ; Extremophiles/genetics ; },
abstract = {Random mutations increase genetic variety and natural selection enhances adaption over generations. Codon usage biases (CUB) provide clues about the genome adaptation mechanisms of native species and extremophile species. Significant numbers of gene (CDS) of nine classes of endangered, native species, including extremophiles and mesophiles were utilised to compute CUB. Codon usage patterns differ among the lineages of endangered and extremophiles with native species. Polymorphic usage of nucleotides with codon burial suggests parallelism of native species within relatively confined taxonomic groups. Utilizing the deviation pattern of CUB of endangered and native species, I present a calculation parameter to estimate the extinction risk of endangered species. Species diversity and extinction risk are both positively associated with the propensity of random mutation in CDS (Coding DNA sequence). Codon bias tenet profoundly selected and it governs to adaptive evolution of native species.},
}
@article {pmid38823290,
year = {2024},
author = {Lopez-Labrador, FX and Huber, M and Sidorov, IA and Brown, JR and Cuypers, L and Laenen, L and Vanmechelen, B and Maes, P and Fischer, N and Pichler, I and Storey, N and Atkinson, L and Schmutz, S and Kufner, V and van Boheemen, S and Mulders, CE and Grundhoff, A and Blümke, P and Robitaille, A and Cinek, O and Hubáčková, K and Mourik, K and Boers, SA and Stauber, L and Salmona, M and Cappy, P and Ramette, A and Franze', A and LeGoff, J and Claas, ECJ and Rodriguez, C and de Vries, JJC and , },
title = {Multicenter benchmarking of short and long read wet lab protocols for clinical viral metagenomics.},
journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology},
volume = {173},
number = {},
pages = {105695},
doi = {10.1016/j.jcv.2024.105695},
pmid = {38823290},
issn = {1873-5967},
mesh = {*Metagenomics/methods/standards ; Humans ; *Benchmarking ; *Viruses/genetics/classification/isolation &amp; purification ; *Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing/methods/standards ; Virus Diseases/diagnosis/virology ; Computational Biology/methods ; },
abstract = {Metagenomics is gradually being implemented for diagnosing infectious diseases. However, in-depth protocol comparisons for viral detection have been limited to individual sets of experimental workflows and laboratories. In this study, we present a benchmark of metagenomics protocols used in clinical diagnostic laboratories initiated by the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS). A mock viral reference panel was designed to mimic low biomass clinical specimens. The panel was used to assess the performance of twelve metagenomic wet lab protocols currently in use in the diagnostic laboratories of participating ENNGS member institutions. Both Illumina and Nanopore, shotgun and targeted capture probe protocols were included. Performance metrics sensitivity, specificity, and quantitative potential were assessed using a central bioinformatics pipeline. Overall, viral pathogens with loads down to 10[4] copies/ml (corresponding to CT values of 31 in our PCR assays) were detected by all the evaluated metagenomic wet lab protocols. In contrast, lower abundant mixed viruses of CT values of 35 and higher were detected only by a minority of the protocols. Considering the reference panel as the gold standard, optimal thresholds to define a positive result were determined per protocol, based on the horizontal genome coverage. Implementing these thresholds, sensitivity and specificity of the protocols ranged from 67 to 100 % and 87 to 100 %, respectively. A variety of metagenomic protocols are currently in use in clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implying the need for standardization of metagenomic analysis for use in clinical settings.},
}
@article {pmid38822995,
year = {2024},
author = {Meier, TA and Refahi, MS and Hearne, G and Restifo, DS and Munoz-Acuna, R and Rosen, GL and Woloszynek, S},
title = {The Role and Applications of Artificial Intelligence in the Treatment of Chronic Pain.},
journal = {Current pain and headache reports},
volume = {},
number = {},
pages = {},
pmid = {38822995},
issn = {1534-3081},
abstract = {PURPOSE OF REVIEW: This review aims to explore the interface between artificial intelligence (AI) and chronic pain, seeking to identify areas of focus for enhancing current treatments and yielding novel therapies.<br><br>RECENT FINDINGS: In the United States, the prevalence of chronic pain is estimated to be upwards of 40%. Its impact extends to increased healthcare costs, reduced economic productivity, and strain on healthcare resources. Addressing this condition is particularly challenging due to its complexity and the significant variability in how patients respond to treatment. Current options often struggle to provide long-term relief, with their benefits rarely outweighing the risks, such as dependency or other side effects. Currently, AI has impacted four key areas of chronic pain treatment and research: (1) predicting outcomes based on clinical information; (2) extracting features from text, specifically clinical notes; (3) modeling 'omic data to identify meaningful patient subgroups with potential for personalized treatments and improved understanding of disease processes; and (4) disentangling complex neuronal signals responsible for pain, which current therapies attempt to modulate. As AI advances, leveraging state-of-the-art architectures will be essential for improving chronic pain treatment. Current efforts aim to extract meaningful representations from complex data, paving the way for personalized medicine. The identification of unique patient subgroups should reveal targets for tailored chronic pain treatments. Moreover, enhancing current treatment approaches is achievable by gaining a more profound understanding of patient physiology and responses. This can be realized by leveraging AI on the increasing volume of data linked to chronic pain.},
}
@article {pmid38822898,
year = {2024},
author = {Asefa, A and Reuber, VM and Miehe, G and Wraase, L and Wube, T and Farwig, N and Schabo, DG},
title = {Giant root-rat engineering and livestock grazing activities regulate plant functional trait diversity of an Afroalpine vegetation community in the Bale Mountains, Ethiopia.},
journal = {Oecologia},
volume = {},
number = {},
pages = {},
pmid = {38822898},
issn = {1432-1939},
support = {NA 783/12-2, FA-925/14-1 und SCHA-2085/3-1, MI271/33-2]//German Research Council (DFG) within the Research Unit 2358 ("The Mountain Exile Hypothesis")/ ; },
abstract = {Disturbances from rodent engineering and human activities profoundly impact ecosystem structure and functioning. Whilst we know that disturbances modulate plant communities, comprehending the mechanisms through which rodent and human disturbances influence the functional trait diversity and trait composition of plant communities is important to allow projecting future changes and to enable informed decisions in response to changing intensity of the disturbances. Here, we evaluated the changes in functional trait diversity and composition of Afroalpine plant communities in the Bale Mountains of Ethiopia along gradients of engineering disturbances of a subterranean endemic rodent, the giant root-rat (Tachyoryctes macrocephalus Rüppell 1842) and human activities (settlement establishment and livestock grazing). We conducted RLQ (co-inertia analysis) and fourth-corner analyses to test for trait-disturbance (rodent engineering/human activities) covariation. Overall, our results show an increase in plant functional trait diversity with increasing root-rat engineering and increasing human activities. We found disturbance specific association with traits. Specifically, we found strong positive association of larger seed mass with increasing root-rat fresh burrow density, rhizomatous vegetative propagation negatively associated with increasing root-rat old burrow, and stolonifereous vegetative propagation positively associated with presence of root-rat mima mound. Moreover, both leaf size and leaf nitrogen content were positively associated with livestock dung abundance but negatively with distance from settlement. Overall, our results suggest that disturbances by rodents filter plant traits related to survival and reproduction strategies, whereas human activities such as livestock grazing act as filters for traits related to leaf economics spectrum along acquisitive resource-use strategy.},
}
@article {pmid38820292,
year = {2023},
author = {Damian-Serrano, A and Sutherland, KR},
title = {A Developmental Ontology for the Colonial Architecture of Salps.},
journal = {The Biological bulletin},
volume = {245},
number = {1},
pages = {9-18},
doi = {10.1086/730459},
pmid = {38820292},
issn = {1939-8697},
mesh = {Animals ; *Urochordata/growth &amp; development/physiology/anatomy &amp; histology ; Life Cycle Stages/physiology ; Biological Ontologies ; },
abstract = {AbstractColonial animals are composed of clonal individuals that remain physically connected and physiologically integrated. Salps are tunicates with a dual life cycle, including an asexual solitary stage that buds sexual colonies composed of jet-propelling zooids that efficiently swim together as a single unit by multijet propulsion. Colonies from different species develop distinct architectures characterized by their zooid arrangement patterns, but this diversity has received little attention. Thus, these architectures have never been formally defined using a framework of variables and axes that would allow comparative analyses. We set out to define an ontology of the salp colony architecture morphospace and describe the developmental pathways that build the different architectures. To inform these definitions, we collected and photographed live specimens of adult and developing colonies through offshore scuba diving. Since all salp colonies begin their development as a transversal double chain, we characterized each adult colonial architecture as a series of developmental transitions, such as rotations and translations of zooids, relative to their orientation at this early shared stage. We hypothesize that all adult architectures are either final or intermediate stages within three developmental pathways toward bipinnate, cluster, or helical forms. This framework will enable comparative studies on the biomechanical implications, ecological functions, evolutionary history, and engineering applications of the diversity of salp colony architectures.},
}
@article {pmid38819559,
year = {2024},
author = {Sanchez, FB and Sato Guima, SE and Setubal, JC},
title = {How to Obtain and Compare Metagenome-Assembled Genomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2802},
number = {},
pages = {135-163},
pmid = {38819559},
issn = {1940-6029},
mesh = {*Metagenome/genetics ; *Metagenomics/methods ; Software ; Computational Biology/methods ; Databases, Genetic ; Sequence Analysis, DNA/methods ; Genome, Bacterial ; },
abstract = {Metagenome-assembled genomes, or MAGs, are genomes retrieved from metagenome datasets. In the vast majority of cases, MAGs are genomes from prokaryotic species that have not been isolated or cultivated in the lab. They, therefore, provide us with information on these species that are impossible to obtain otherwise, at least until new cultivation methods are devised. Thanks to improvements and cost reductions of DNA sequencing technologies and growing interest in microbial ecology, the rise in number of MAGs in genome repositories has been exponential. This chapter covers the basics of MAG retrieval and processing and provides a practical step-by-step guide using a real dataset and state-of-the-art tools for MAG analysis and comparison.},
}
@article {pmid38816346,
year = {2024},
author = {Locke, MA and Witthaus, LM and Lizotte, RE and Heintzman, LJ and Moore, MT and O'Reilly, A and Wells, RR and Langendoen, EJ and Bingner, RL and Gholson, DM and Taylor, JM and Johnson, FE},
title = {The LTAR cropland common experiment in the Lower Mississippi River Basin.},
journal = {Journal of environmental quality},
volume = {},
number = {},
pages = {},
doi = {10.1002/jeq2.20577},
pmid = {38816346},
issn = {1537-2537},
abstract = {The Lower Mississippi River Basin-Long-Term Agroecosystem Research Site (LMRB-LTAR) encompasses six states from Missouri to the Gulf of Mexico and is coordinated by the USDA-ARS National Sedimentation Laboratory, Oxford, MS. The overarching goal of LTAR is to assess regionally diverse and geographically scalable farming practices for enhanced sustainability of agroecosystem goods and services under changing environment and resource-use conditions. The LMRB-LTAR overall goal is to assess sustainable row crop agricultural production systems that integrate regional environmental and socioeconomic needs. Primary row crops in the region include soybeans, corn, cotton, rice, and sugarcane with crop rotations influenced by commodity crop price and other factors. The field-scale common experiment (CE) includes four row crop farms (26-101 ha) established in 2021 and 2023. Three fields are managed with alternative practices, including reduced tillage, cover crops, and automated prescription irrigation, and three fields are managed with prevailing farming practices, consisting of conventional tillage, no cover crop, and nonprescription irrigation. Treatment effects on crop productivity, soil quality, water use efficiency, water quality, and carbon storage are assessed. Research from the LMRB CE will deliver outcomes linked to overarching LTAR network goals, including innovative agricultural systems, strengthened partnerships, data management technologies, and precision environmental tools.},
}
@article {pmid38814981,
year = {2024},
author = {Mullon, C and Peña, J and Lehmann, L},
title = {The evolution of environmentally mediated social interactions and posthumous spite under isolation by distance.},
journal = {PLoS computational biology},
volume = {20},
number = {5},
pages = {e1012071},
pmid = {38814981},
issn = {1553-7358},
mesh = {*Biological Evolution ; *Social Interaction ; Computational Biology ; Phenotype ; Animals ; Environment ; Humans ; },
abstract = {Many social interactions happen indirectly via modifications of the environment, e.g. through the secretion of functional compounds or the depletion of renewable resources. Here, we derive the selection gradient on a quantitative trait affecting dynamical environmental variables that feed back on reproduction and survival in a finite patch-structured population subject to isolation by distance. Our analysis shows that the selection gradient depends on how a focal individual influences the fitness of all future individuals in the population through modifications of the environmental variables they experience, weighted by the neutral relatedness between recipients and the focal. The evolutionarily relevant trait-driven environmental modifications are formalized as the extended phenotypic effects of an individual, quantifying how a trait change in an individual in the present affects the environmental variables in all patches at all future times. When the trait affects reproduction and survival through a payoff function, the selection gradient can be expressed in terms of extended phenotypic effects weighted by scaled relatedness. We show how to compute extended phenotypic effects, relatedness, and scaled relatedness using Fourier analysis, which allow us to investigate a broad class of environmentally mediated social interactions in a tractable way. We use our approach to study the evolution of a trait controlling the costly production of some lasting commons (e.g. a common-pool resource or a toxic compound) that can diffuse in space and persist in time. We show that indiscriminate posthumous spite readily evolves in this scenario. More generally, whether selection favours environmentally mediated altruism or spite is determined by the spatial correlation between an individual's lineage and the commons originating from its patch. The sign of this correlation depends on interactions between dispersal patterns and the commons' renewal dynamics. More broadly, we suggest that selection can favour a wide range of social behaviours when these have carry-over effects in space and time.},
}
@article {pmid38814957,
year = {2024},
author = {Schoenecker, KA and King, SRB and Hennig, JD and Cole, MJ and Scasta, JD and Beck, JL},
title = {Effects of telemetry collars on two free-roaming feral equid species.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0303312},
pmid = {38814957},
issn = {1932-6203},
mesh = {Animals ; *Telemetry ; *Equidae/physiology ; *Geographic Information Systems ; Horses ; Female ; Male ; },
abstract = {There are two species of free-roaming feral equids in North America: horses (Equus caballus) and donkeys or "burros" (E. asinus). Both species were introduced as domestic animals to North America in the early 1500s and currently inhabit rangelands across the western United States, Canada, and all continents except Antarctica. Despite their global distribution, little is known about their fine scale spatial ecology. Contemporary research tools to assess space use include global positioning system (GPS) tracking collars, but older models were problematic due to stiff collar belting causing poor fit. We tested modern designs of GPS collars on n = 105 horses and n = 60 burros for 4 years in five populations (3 horse, 2 burro) across the western United States, to assess whether collars posed welfare risks to horses or burros. We found no difference in survival of collared versus uncollared mares and jennies, and no difference in survival of their foals. In 4036 of 4307 observations for horses (93.7%) and 2115 of 2258 observations for burros (93.6%), collars were observed symmetrical, maintaining proper fit on the neck. Fur effects from collars (sweaty neck, indented fur, broken fur) were seen in 3% of horse observations and 25% of burro observations. Superficial effects (chafes and marks on skin surface) were seen in 2% of horse observations and 11% of burro observations; no severe effects from collars were seen. Body condition was not affected by collars; mean body condition of collared horses was 4.70 ± 0.54 (mean ± s.d) and 4.71 ± 0.65 for collared burros. Behavior results indicated minimal effects; collared horses stood slightly more than uncollared, and collared burros stood and foraged more in one population, but not in the other. For 6.3% of observations of horses and 6.4% of observations of burros, we found an effect of time wearing a collar on the cumulative sum of fur effects which increased over time (burros: rs = 0.87, P = <0.0001; horses: rs = 0.31, P = 0.002). Burros also showed an increase over time in the number of superficial effects, but horses did not. Collars occasionally moved into the wrong position, shifting forward over the ears; we observed this on 19 horses and 1 burro. Of those, most collars went over the ears in summer (n = 12). All collars were equipped with a remote release mechanism as well as a timed-release mechanism for redundancy, thus removed when observed in wrong position to avoid rubbing or discomfort. Our finding of no consequential physical effects in 98% of horse observations, and 89% of burro observations suggests the consequences of collars on free-roaming equid welfare and survival is biologically insignificant, although collars should be monitored regularly and continue to be equipped with a remote release mechanism to remove a collar if needed. With frequent welfare-driven, visual monitoring, collaring of free-roaming equids can be a safe and useful tool to increase our understanding of their spatial ecology, demography, habitat use, behavior, and interactions with other wildlife.},
}
@article {pmid38813661,
year = {2024},
author = {Cong, Y and Endo, T},
title = {A Quadruple Revolution: Deciphering Biological Complexity with Artificial Intelligence, Multiomics, Precision Medicine, and Planetary Health.},
journal = {Omics : a journal of integrative biology},
volume = {28},
number = {6},
pages = {257-260},
doi = {10.1089/omi.2024.0110},
pmid = {38813661},
issn = {1557-8100},
mesh = {*Precision Medicine/methods/trends ; *Artificial Intelligence ; Humans ; Systems Biology/methods ; Genomics/methods ; Machine Learning ; Multiomics ; },
abstract = {A quiet quadruple revolution has been in the making in systems science with convergence of (1) artificial intelligence, machine learning, and other digital technologies; (2) multiomics big data integration; (3) growing interest in the "variability science" of precision/personalized medicine that aims to account for patient-to-patient and between-population differences in disease susceptibilities and responses to health interventions such as drugs, nutrition, vaccines, and radiation; and (4) planetary health scholarship that both scales up and integrates biological, clinical, and ecological contexts of health and disease. Against this overarching background, this article presents and highlights some of the salient challenges and prospects of multiomics research, emphasizing the attendant pivotal role of systems medicine and systems biology. In addition, we emphasize the rapidly growing importance of planetary health research for systems medicine, particularly amid climate emergency, ecological degradation, and loss of planetary biodiversity. Looking ahead, we anticipate that the integration and utilization of multiomics big data and artificial intelligence will drive further progress in systems medicine and systems biology, heralding a promising future for both human and planetary health.},
}
@article {pmid38813550,
year = {2023},
author = {Boyes, D and , and , and , and , and , and , },
title = {The genome sequence of the Six-belted Clearwing, Bembecia ichneumoniformis (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {515},
pmid = {38813550},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Bembecia ichneumoniformis (the Six-belted Clearwing; Arthropoda; Insecta; Lepidoptera; Sesiidae). The genome sequence is 511.4 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.32 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,114 protein coding genes.},
}
@article {pmid38813548,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the July Highflyer, Hydriomena furcata (Thunberg, 1784).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {496},
pmid = {38813548},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Hydriomena furcata (the July Highflyer; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 423.3 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.89 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,324 protein coding genes.},
}
@article {pmid38813465,
year = {2024},
author = {Falk, S and Poole, O and , and , and , and , and , and , and , },
title = {The genome sequence of the parsley Cheilosia, Cheilosia pagana (Meigen, 1822).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {54},
pmid = {38813465},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Cheilosia pagana (the parsley Cheilosia; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 354.1 megabases in span. Most of the assembly is scaffolded into 6 chromosomal pseudomolecules, including the X sex chromosome. The mitochondrial genome has also been assembled and is 16.76 kilobases in length.},
}
@article {pmid38808804,
year = {2024},
author = {Freitas, GA and Marcon, GEB and Welch, JR and Silva, CMFPD},
title = {Analysis of the completeness and consistency of records of violence against indigenous women in the health macro-region of Dourados, Mato Grosso do Sul state, Brazil, 2009-2020.},
journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil},
volume = {33},
number = {},
pages = {e20231075},
pmid = {38808804},
issn = {2237-9622},
mesh = {Humans ; Brazil ; Female ; *Violence/statistics &amp; numerical data ; Time Factors ; Indians, South American/statistics &amp; numerical data ; Gender-Based Violence/statistics &amp; numerical data ; Indigenous Peoples/statistics &amp; numerical data ; Educational Status ; Adult ; Information Systems ; },
abstract = {OBJECTIVE: To analyze the temporal trend of completeness and consistency of data on notifications of violence against indigenous women in the health macro-region of Dourados, state of Mato Grosso do Sul, Brazil, between 2009 and 2020.<br><br>METHODS: An ecological time series study was conducted using data from the Notifiable Health Conditions Information System; Prais-Winsten regression was used to analyze the trend of data completeness and consistency, as well as the proportion of completed and coherent fields.<br><br>RESULTS: A total of 2,630 cases were reported; completeness was found to be very poor in the variable "occupation" (48.9%) and poor in the variables "schooling" (68.3%) and "time of occurrence" (67.9%); in the analysis of temporal trends, only the variable "occupation" showed a decreasing trend (p = 0.045).<br><br>CONCLUSION: The data analyzed demonstrated the need for improvement in the completeness of the variables "schooling", "occupation" and "time of occurrence" of the violent act.<br><br>MAIN RESULTS: There was a progressive increase in notifications over the years. Most of the variables showed regular or excellent completeness and consistency. In the analysis of temporal trend, only the "occupation" variable showed a decreasing trend.<br><br>IMPLICATIONS FOR SERVICES: Care for victims of violence is part of the daily routine of health services, and it is essential for health professionals to provide adequate compulsory notification for a comprehensive understanding of the victims' profile, thus assisting in addressing this issue.<br><br>PERSPECTIVES: Further studies are needed to understand the factors associated with violence against indigenous women, which could help the development of health promotion actions and violence prevention strategies targeting these women.},
}
@article {pmid38808214,
year = {2024},
author = {Kyalo, H and Tonnang, HEZ and Egonyu, JP and Olukuru, J and Tanga, CM and Senagi, K},
title = {A convolutional neural network with image and numerical data to improve farming of edible crickets as a source of food-A decision support system.},
journal = {Frontiers in artificial intelligence},
volume = {7},
number = {},
pages = {1403593},
pmid = {38808214},
issn = {2624-8212},
abstract = {Crickets (Gryllus bimaculatus) produce sounds as a natural means to communicate and convey various behaviors and activities, including mating, feeding, aggression, distress, and more. These vocalizations are intricately linked to prevailing environmental conditions such as temperature and humidity. By accurately monitoring, identifying, and appropriately addressing these behaviors and activities, the farming and production of crickets can be enhanced. This research implemented a decision support system that leverages machine learning (ML) algorithms to decode and classify cricket songs, along with their associated key weather variables (temperature and humidity). Videos capturing cricket behavior and weather variables were recorded. From these videos, sound signals were extracted and classified such as calling, aggression, and courtship. Numerical and image features were extracted from the sound signals and combined with the weather variables. The extracted numerical features, i.e., Mel-Frequency Cepstral Coefficients (MFCC), Linear Frequency Cepstral Coefficients, and chroma, were used to train shallow (support vector machine, k-nearest neighbors, and random forest (RF)) ML algorithms. While image features, i.e., spectrograms, were used to train different state-of-the-art deep ML models, i,e., convolutional neural network architectures (ResNet152V2, VGG16, and EfficientNetB4). In the deep ML category, ResNet152V2 had the best accuracy of 99.42%. The RF algorithm had the best accuracy of 95.63% in the shallow ML category when trained with a combination of MFCC+chroma and after feature selection. In descending order of importance, the top 6 ranked features in the RF algorithm were, namely humidity, temperature, C#, mfcc11, mfcc10, and D. From the selected features, it is notable that temperature and humidity are necessary for growth and metabolic activities in insects. Moreover, the songs produced by certain cricket species naturally align to musical tones such as C# and D as ranked by the algorithm. Using this knowledge, a decision support system was built to guide farmers about the optimal temperature and humidity ranges and interpret the songs (calling, aggression, and courtship) in relation to weather variables. With this information, farmers can put in place suitable measures such as temperature regulation, humidity control, addressing aggressors, and other relevant interventions to minimize or eliminate losses and enhance cricket production.},
}
@article {pmid38807051,
year = {2024},
author = {Xie, J and Lan, Y and Zou, C and He, J and Huang, Q and Zeng, J and Pan, M and Mei, Y and Luo, J and Zou, D},
title = {Single-nucleus analysis reveals microenvironment-specific neuron and glial cell enrichment in Alzheimer's disease.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {526},
pmid = {38807051},
issn = {1471-2164},
support = {YCSW2023244//the Innovation Project of Guangxi Graduate Education/ ; 2024GXNSFBA010054//the Joint Project on Regional High-Incidence Diseases Research of Guangxi Natural Science Foundation/ ; 2024GXNSFDA010001//the Joint Project on Regional High-Incidence Diseases Research of Guangxi Natural Science Foundation/ ; },
mesh = {*Alzheimer Disease/genetics/pathology/metabolism ; Humans ; *Neuroglia/metabolism/pathology ; *Neurons/metabolism ; *Single-Cell Analysis ; Cellular Microenvironment/genetics ; Computational Biology/methods ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) is a complicated neurodegenerative disease. Neuron-glial cell interactions are an important but not fully understood process in the progression of AD. We used bioinformatic methods to analyze single-nucleus RNA sequencing (snRNA-seq) data to investigate the cellular and molecular biological processes of AD.<br><br>METHOD: snRNA-seq data were downloaded from Gene Expression Omnibus (GEO) datasets and reprocessed to identify 240,804 single nuclei from healthy controls and patients with AD. The cellular composition of AD was further explored using Uniform Manifold Approximation and Projection (UMAP). Enrichment analysis for the functions of the DEGs was conducted and cell development trajectory analyses were used to reveal underlying cell fate decisions. iTALK was performed to identify ligand-receptor pairs among various cell types in the pathological ecological microenvironment of AD.<br><br>RESULTS: Six cell types and multiple subclusters were identified based on the snRNA-seq data. A subcluster of neuron and glial cells co-expressing lncRNA-SNHG14, myocardin-related transcription factor A (MRTFA), and MRTFB was found to be more abundant in the AD group. This subcluster was enriched in mitogen-activated protein kinase (MAPK)-, immune-, and apoptosis-related pathways. Through molecular docking, we found that lncRNA-SNHG14 may bind MRTFA and MRTFB, resulting in an interaction between neurons and glial cells.<br><br>CONCLUSIONS: The findings of this study describe a regulatory relationship between lncRNA-SNHG14, MRTFA, and MRTFB in the six main cell types of AD. This relationship may contribute to microenvironment remodeling in AD and provide a theoretical basis for a more in-depth analysis of AD.},
}
@article {pmid38805961,
year = {2024},
author = {Edwin, IE and Chukwuka, O and Ochege, FU and Ling, Q and Chen, B and Nzabarinda, V and Ajaero, C and Hamdi, R and Luo, G},
title = {Quantifying land change dynamics, resilience and feedback: A comparative analysis of the lake Chad basin in Africa and Aral Sea basin in Central Asia.},
journal = {Journal of environmental management},
volume = {361},
number = {},
pages = {121218},
doi = {10.1016/j.jenvman.2024.121218},
pmid = {38805961},
issn = {1095-8630},
mesh = {*Lakes ; *Climate Change ; Africa ; Geographic Information Systems ; Conservation of Natural Resources ; Asia ; },
abstract = {The intricate interaction of natural and anthropogenic factors drives changes in land and water in response to societal demands and climate change. However, there has been insufficient information on the feedback effects in dryland hotspots altered by land change dynamics. This research compared two transboundary inland lakes, the Lake Chad basin (LCB) in Africa and the Aral Sea basin (ASB) in Central Asia, using remote sensing and geographic information system techniques to analyze and quantify present and future land cover dynamics, resilience, and their feedback effects. The study integrated Cellular Automata, Markov Chain, and Multilayer Perceptron models to predict LULC changes up to 2030. Descriptive statistics, ordinary least squares regression, hotspot Gi-Bin, trend analysis, and advanced geostatistical methods were utilized to identify relationships, patterns, magnitudes, and directions of observed changes in the feedback effects. From 2000 to 2030, the analysis unveils intriguing trends, including an increase in cropland from 48% to 51% and a decrease in shrubland from 18% to 15% in the LCB. The grassland increased from 21% to 22%, and the settlement expanded from 0.10 to 0.60% in the ASB. Water bodies remained stable at 1.60 % in LCB, while in ASB, it declined from 3% to 2%. These changes were significantly influenced by population, elevation, and temperature in both basins, with irrigation also playing a significant role in the ASB and slope in LCB. The study further revealed discernible shifts in normalized difference vegetation index, temperature, and precipitation linked to specific land cover conversions, suggesting alterations in surface properties and vegetation health. This study underscores the complex interplay between land cover dynamics, resilience, climate variability, and feedback mechanisms in LCB and ASB.},
}
@article {pmid38805695,
year = {2024},
author = {McElroy, KE and Masonbrink, R and Chudalayandi, S and Severin, AJ and Serb, JM},
title = {A chromosome-level genome assembly of the disco clam, Ctenoides ales.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae115},
pmid = {38805695},
issn = {2160-1836},
abstract = {The bivalve subclass Pteriomorphia, which includes the economically important scallops, oysters, mussels, and ark clams, exhibits extreme ecological, morphological, and behavioral diversity. Among this diversity are five morphologically distinct eye types, making Pteriomorphia an excellent setting to explore the molecular basis for the evolution of novel traits. Of pteriomorphian bivalves, Limida is the only order lacking genomic resources, greatly limiting the potential phylogenomic analyses related to eyes and phototransduction. Here, we present a limid genome assembly, the disco clam, Ctenoides ales, which is characterized by invaginated eyes, exceptionally long tentacles, and a flashing light display. This genome assembly was constructed with PacBio long reads and Dovetail Omni-CTM proximity-ligation sequencing. The final assembly is ∼2.3Gb and over 99% of the total length is contained in 18 pseudomolecule scaffolds. We annotated 41,064 protein coding genes and report a BUSCO completeness of 91.9% for metazoa_obd10. Additionally, we report a complete and annotated mitochondrial genome, which also had been lacking from Limida. The ∼20Kb mitogenome has 12 protein coding genes, 22 tRNAs, 2 rRNA genes, and a 1,589 bp duplicated sequence containing the origin of replication. The C. ales nuclear genome size is substantially larger than other pteriomorphian genomes, mainly accounted for by transposable element sequences. We inventoried the genome for opsins, the signaling proteins that initiate phototransduction, and found that, unlike its closest eyed-relatives, the scallops, C. ales lacks duplication of the rhabdomeric Gq-protein coupled opsin that is typically used for invertebrate vision. In fact, C. ales has uncharacteristically few opsins relative to the other pteriomorphian families, all of which have unique expansions of xenopsins, a recently discovered opsin subfamily. This chromosome-level assembly, along with the mitogenome, will be valuable resources for comparative genomics and phylogenetics in bivalves and particularly for the understudied but charismatic limids.},
}
@article {pmid38805543,
year = {2024},
author = {Lansch-Justen, L and El Karoui, M and Alexander, HK},
title = {Estimating mutation rates under heterogeneous stress responses.},
journal = {PLoS computational biology},
volume = {20},
number = {5},
pages = {e1012146},
pmid = {38805543},
issn = {1553-7358},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*Mutation Rate ; *Escherichia coli/genetics ; *Stress, Physiological/genetics ; *Models, Genetic ; SOS Response, Genetics/genetics ; Computer Simulation ; Computational Biology/methods ; Mutation ; },
abstract = {Exposure to environmental stressors, including certain antibiotics, induces stress responses in bacteria. Some of these responses increase mutagenesis and thus potentially accelerate resistance evolution. Many studies report increased mutation rates under stress, often using the standard experimental approach of fluctuation assays. However, single-cell studies have revealed that many stress responses are heterogeneously expressed in bacterial populations, which existing estimation methods have not yet addressed. We develop a population dynamic model that considers heterogeneous stress responses (subpopulations of cells with the response off or on) that impact both mutation rate and cell division rate, inspired by the DNA-damage response in Escherichia coli (SOS response). We derive the mutant count distribution arising in fluctuation assays under this model and then implement maximum likelihood estimation of the mutation-rate increase specifically associated with the expression of the stress response. Using simulated mutant count data, we show that our inference method allows for accurate and precise estimation of the mutation-rate increase, provided that this increase is sufficiently large and the induction of the response also reduces the division rate. Moreover, we find that in many cases, either heterogeneity in stress responses or mutant fitness costs could explain similar patterns in fluctuation assay data, suggesting that separate experiments would be required to identify the true underlying process. In cases where stress responses and mutation rates are heterogeneous, current methods still correctly infer the effective increase in population mean mutation rate, but we provide a novel method to infer distinct stress-induced mutation rates, which could be important for parameterising evolutionary models.},
}
@article {pmid38805169,
year = {2024},
author = {Peng, X and Yang, Y and Zhong, R and Yang, Y and Yan, F and Liang, N and Yuan, S},
title = {Zinc and Inflammatory Bowel Disease: From Clinical Study to Animal Experiment.},
journal = {Biological trace element research},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12011-024-04193-6},
pmid = {38805169},
issn = {1559-0720},
support = {2081921001//Chengdu University/ ; CDUCX2024759//Training Program for Innovation and Entrepreneurship of Chengdu University/ ; 32370557//National Natural Science Foundation of China/ ; NCKL202201//Nanchong Key Laboratory of Wildlife Nutrition Ecology and Disease Control/ ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gastrointestinal tract (GI) with a high incidence rate globally, and IBD patients are often accompanied by zinc deficiency. This review aims to summarize the potential therapeutic value of zinc supplementation in IBD clinical patients and animal models. Zinc supplementation can relieve the severity of IBD especially in patients with zinc deficiency. The clinical severity of IBD were mainly evaluated through some scoring methods involving clinical performance, endoscopic observation, blood biochemistry, and pathologic biopsy. Through conducting animal experiments, it has been found that zinc plays an important role in alleviating clinical symptoms and improving pathological lesions. In both clinical observation and animal experiment of IBD, the therapeutic mechanisms of zinc interventions have been found to be related to immunomodulation, intestinal epithelial repair, and gut microbiota's balance. Furthermore, the antioxidant activity of zinc was clarified in animal experiment. Appropriate zinc supplementation is beneficial for IBD therapy, and the present evidence highlights that alleviating zinc-deficient status can effectively improve the severity of clinical symptoms in IBD patients and animal models.},
}
@article {pmid38803273,
year = {2024},
author = {Wang, Y and Yang, Y and Liu, Y and Liu, C and Xu, M and Fang, M and Mu, X},
title = {CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish.},
journal = {Database : the journal of biological databases and curation},
volume = {2024},
number = {},
pages = {},
pmid = {38803273},
issn = {1758-0463},
support = {2022SBH00001//Guangdong Rural Revitalization Strategy Special Provincial Organization/ ; 2023KJ134 2023KJ150//Modern Agriculture Industry Technology Innovation Team/ ; CAMC-2018F//China-ASEAN Maritime Cooperation Fund/ ; FGRC18537//National Freshwater Genetic Resource Center/ ; 2022SBH00001//Guangdong Rural Revitalization Strategy Special Provincial Organization/ ; 2023KJ134 2023KJ150//Modern Agriculture Industry Technology Innovation Team/ ; CAMC-2018F//China-ASEAN Maritime Cooperation Fund/ ; FGRC18537//National Freshwater Genetic Resource Center/ ; },
mesh = {Animals ; *Fishes/genetics/classification ; *RNA, Ribosomal, 18S/genetics ; *Electron Transport Complex IV/genetics ; *DNA Barcoding, Taxonomic/methods ; Databases, Genetic ; Phylogeny ; Databases, Nucleic Acid ; },
abstract = {Fish, being a crucial component of aquatic ecosystems, holds significant importance from both economic and ecological perspectives. However, the identification of fish at the species level remains challenging, and there is a lack of a taxonomically complete and comprehensive reference sequence database for fish. Therefore, we developed CoSFISH, an online fish database. Currently, the database contains 21 535 cytochrome oxidase I sequences and 1074 18S rRNA sequences of 21 589 species, belonging to 8 classes and 90 orders. We additionally incorporate online analysis tools to aid users in comparing, aligning and analyzing sequences, as well as designing primers. Users can upload their own data for analysis, in addition to using the data stored in the database directly. CoSFISH offers an extensive fish database and incorporates online analysis tools, making it a valuable resource for the study of fish diversity, phylogenetics and biological evolution. Database URL: http://210.22.121.250:8888/CoSFISH/home/indexPage.},
}
@article {pmid38803140,
year = {2024},
author = {Jacobson, OT and Barrett, BJ and Perry, SE and Finerty, GE and Tiedeman, KM and Crofoot, MC},
title = {A new approach to geostatistical synthesis of historical records reveals capuchin spatial responses to climate and demographic change.},
journal = {Ecology letters},
volume = {27},
number = {5},
pages = {e14443},
doi = {10.1111/ele.14443},
pmid = {38803140},
issn = {1461-0248},
support = {//Wenner-Gren Foundation/ ; //American Society of Primatologists/ ; //Alexander von Humboldt-Stiftung/ ; //Max-Planck-Gesellschaft/ ; //Department of Anthropology, University of California, Los Angeles/ ; 20113909//National Geographic Society/ ; 45176R-18//National Geographic Society/ ; 7968-06//National Geographic Society/ ; 8671-09//National Geographic Society/ ; 9795-15//National Geographic Society/ ; 9633991//National Science Foundation/ ; BCS-0613226//National Science Foundation/ ; BCS-1638428//National Science Foundation/ ; BCS-848360//National Science Foundation/ ; DDIG 1232371//National Science Foundation/ ; SE9870429//National Science Foundation/ ; //Achievement Rewards for College Scientists Foundation/ ; //Leakey Foundation/ ; 1650042//National Science Foundation Graduate Research Fellowship Program/ ; Grant 0208/TWCF/TWCF/United States ; },
mesh = {Animals ; Costa Rica ; *Climate Change ; *Cebus/physiology ; Homing Behavior ; Geographic Information Systems ; Population Dynamics ; Demography ; },
abstract = {Recent proliferation of GPS technology has transformed animal movement research. Yet, time-series data from this recent technology rarely span beyond a decade, constraining longitudinal research. Long-term field sites hold valuable historic animal location records, including hand-drawn maps and semantic descriptions. Here, we introduce a generalised workflow for converting such records into reliable location data to estimate home ranges, using 30 years of sleep-site data from 11 white-faced capuchin (Cebus imitator) groups in Costa Rica. Our findings illustrate that historic sleep locations can reliably recover home range size and geometry. We showcase the opportunity our approach presents to resolve open questions that can only be addressed with very long-term data, examining how home ranges are affected by climate cycles and demographic change. We urge researchers to translate historical records into usable movement data before this knowledge is lost; it is essential to understanding how animals are responding to our changing world.},
}
@article {pmid38802965,
year = {2024},
author = {Hosseinzadeh-Shanjani, Z and Khodayari-Zarnaq, R and Khosravi, MF and Arab-Zozani, M and Alizadeh, G},
title = {Factors affecting major depression in Iran: a mixed-method study.},
journal = {Journal of health, population, and nutrition},
volume = {43},
number = {1},
pages = {73},
pmid = {38802965},
issn = {2072-1315},
mesh = {Humans ; Iran/epidemiology ; *Depressive Disorder, Major/epidemiology ; Risk Factors ; Health Policy ; Socioeconomic Factors ; Economic Recession ; Politics ; Female ; Male ; },
abstract = {Depression is a major cause of disability and, if left untreated, can increase the risk of suicide. Evidence on the determinants of depression is incomplete, making it challenging to interpret results across studies. This study aims to identify the social, economic, environmental, political, and technological factors influencing the great recession in Iran. The study was conducted in two parts. The first step involved a literature review to identify the factors, using PubMed, Scopus, and Web of Science for the search. The reference lists of all identified articles were reviewed to find relevant studies, and the extracted information was summarized and reported descriptively. The second steps involved compiling and consulting 14 experts from different fields, using a framework analysis method. Twenty-four articles were used as primary sources of information, and a total of 28 factors were found to exist. After removing duplicates and related factors, 19 of these were subsequently declared as factors, resulting in a total of 36 determinants being identified. Most of these factors belong to the social category. The health policies implemented have a significant impact on disease risk factors and ultimately their occurrence. Political decisions and policy-making processes play a crucial role in all areas, particularly in addressing disease risk factors. Severe depression can disrupt all aspects of the healthcare system, underscoring the importance of access to care. Policies concerning physical education, transportation, nutrition, employment, green spaces, recreational facilities, and tobacco are vital in this context. The influence of health policies on disease risk factors and disease occurrence is profound. Severe depression can have far-reaching effects on the healthcare system, emphasizing the critical need for access to care. The formulation of policies to combat depression must be thoroughly evaluated in terms of economic, political, social, technological, and environmental factors. The findings suggest that addressing social inequalities and emphasizing the role of political action, as highlighted by the social determinants of health, should be top priorities in addressing depression. Efforts to prevent depression should incorporate ecological approaches that consider the impact of the socioeconomic environment on depressive symptoms.},
}
@article {pmid38802223,
year = {2024},
author = {Lv, H and Lu, Z and Fu, G and Lv, S and Jiang, J and Xie, Y and Luo, X and Zeng, J and Xue, S},
title = {Pollution characteristics and quantitative source apportionment of heavy metals within a zinc smelting site by GIS-based PMF and APCS-MLR models.},
journal = {Journal of environmental sciences (China)},
volume = {144},
number = {},
pages = {100-112},
doi = {10.1016/j.jes.2023.09.033},
pmid = {38802223},
issn = {1001-0742},
mesh = {*Metals, Heavy/analysis ; *Zinc/analysis ; *Environmental Monitoring/methods ; *Soil Pollutants/analysis ; *Metallurgy ; Geographic Information Systems ; Models, Chemical ; },
abstract = {The abandoned smelters present a substantial pollution threat to the nearby soil and groundwater. In this study, 63 surface soil samples were collected from a zinc smelter to quantitatively describe the pollution characteristics, ecological risks, and source apportionment of heavy metal(loid)s (HMs). The results revealed that the average contents of Zn, Cd, Pb, As, and Hg were 0.4, 12.2, 3.3, 5.3, and 12.7 times higher than the risk screening values of the construction sites, respectively. Notably, the smelter was accumulated heavily with Cd and Hg, and the contribution of Cd (0.38) and Hg (0.53) to ecological risk was 91.58%. ZZ3 and ZZ7 were the most polluted workshops, accounting for 25.7% and 35.0% of the pollution load and ecological risk, respectively. The influence of soil parent materials on pollution was minor compared to various workshops within the smelter. Combined with PMF, APCS-MLR and GIS analysis, four sources of HMs were identified: P1(25.5%) and A3(18.4%) were atmospheric deposition from the electric defogging workshop and surface runoff from the smelter; P2(32.7%) and A2(20.9%) were surface runoff of As-Pb foul acid; P3(14.5%) and A4(49.8%) were atmospheric deposition from the leach slag drying workshop; P4(27.3%) and A1(10.8%) were the smelting process of zinc products. This paper described the distribution characteristics and specific sources of HMs in different process workshops, providing a new perspective for the precise remediation of the smelter by determining the priority control factors.},
}
@article {pmid38800997,
year = {2024},
author = {Madrigal, G and Minhas, BF and Catchen, J},
title = {Klumpy: A tool to evaluate the integrity of long-read genome assemblies and illusive sequence motifs.},
journal = {Molecular ecology resources},
volume = {},
number = {},
pages = {e13982},
doi = {10.1111/1755-0998.13982},
pmid = {38800997},
issn = {1755-0998},
support = {1645087//Division of Antarctic Sciences/ ; },
abstract = {The improvement and decreasing costs of third-generation sequencing technologies has widened the scope of biological questions researchers can address with de novo genome assemblies. With the increasing number of reference genomes, validating their integrity with minimal overhead is vital for establishing confident results in their applications. Here, we present Klumpy, a tool for detecting and visualizing both misassembled regions in a genome assembly and genetic elements (e.g. genes) of interest in a set of sequences. By leveraging the initial raw reads in combination with their respective genome assembly, we illustrate Klumpy's utility by investigating antifreeze glycoprotein (afgp) loci across two icefishes, by searching for a reported absent gene in the northern snakehead fish, and by scanning the reference genomes of a mudskipper and bumblebee for misassembled regions. In the two former cases, we were able to provide support for the noncanonical placement of an afgp locus in the icefishes and locate the missing snakehead gene. Furthermore, our genome scans were able identify an unmappable locus in the mudskipper reference genome and identify a putative repetitive element shared among several species of bees.},
}
@article {pmid38800521,
year = {2024},
author = {Obbard, DJ and , and , and , and , and , and , },
title = {The genome sequence of the drosophilid fruit fly, Drosophila phalerata (Meigen, 1830).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {63},
pmid = {38800521},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Drosophila phalerata (drosophilid fruit fly, Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 223.9 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.14 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,973 protein coding genes.},
}
@article {pmid38800516,
year = {2024},
author = {Li, R and Li, J and Lopez, JV and Oatley, G and Clayton-Lucey, IA and Sinclair, E and Aunin, E and Gettle, N and Santos, C and Paulini, M and Niu, H and McKenna, V and O'Brien, R and , and , and , and , and , },
title = {The genome sequence of the giant clam, Tridacna gigas (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {145},
pmid = {38800516},
issn = {2398-502X},
abstract = {We present a chromosomal-level genome assembly from an individual Tridacna gigas (the giant clam; Mollusca; Bivalvia; Veneroida; Cardiidae). The genome sequence is 1,175.9 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 25.34 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,177 protein coding genes.},
}
@article {pmid38798998,
year = {2023},
author = {Obbard, DJ and , and , and , and , },
title = {The genome sequence of a drosophilid fruit fly, Drosophila funebris (Fabricius, 1789).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {437},
pmid = {38798998},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Drosophila funebris (drosophilid fruit fly; Arthropoda; Insecta; Diptera; Drosophilidae). The genome sequence is 181.1 megabases in span. Most of the assembly is scaffolded into 7 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.15 kilobases in length.},
}
@article {pmid38798994,
year = {2023},
author = {Hawkes, WLS and Wotton, KR and , and , and , and , and , and , },
title = {The genome sequence of the Common Spotted Hoverfly, Eupeodes luniger (Meigen, 1822).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {472},
pmid = {38798994},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Eupeodes luniger (the Common Spotted Hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 616.9 megabases in span. Most of the assembly is scaffolded into 4 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 17.45 kilobases in length.},
}
@article {pmid38798992,
year = {2023},
author = {Hawkes, WLS and Wotton, KR and , and , and , and , and , and , },
title = {The genome sequence of the slender grass hoverfly, Melanostoma scalare (Fabricius, 1794).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {489},
pmid = {38798992},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Melanostoma scalare (the slender grass hoverfly; Arthropoda; Insecta; Diptera; Syrphidae). The genome sequence is 738.2 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 16.08 kilobases in length.},
}
@article {pmid38796535,
year = {2024},
author = {Wenk, EH and Sauquet, H and Gallagher, RV and Brownlee, R and Boettiger, C and Coleman, D and Yang, S and Auld, T and Barrett, R and Brodribb, T and Choat, B and Dun, L and Ellsworth, D and Gosper, C and Guja, L and Jordan, GJ and Le Breton, T and Leigh, A and Lu-Irving, P and Medlyn, B and Nolan, R and Ooi, M and Sommerville, KD and Vesk, P and White, M and Wright, IJ and Falster, DS},
title = {The AusTraits plant dictionary.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {537},
pmid = {38796535},
issn = {2052-4463},
mesh = {*Plants ; Databases, Factual ; Dictionaries as Topic ; },
abstract = {Traits with intuitive names, a clear scope and explicit description are essential for all trait databases. The lack of unified, comprehensive, and machine-readable plant trait definitions limits the utility of trait databases, including reanalysis of data from a single database, or analyses that integrate data across multiple databases. Both can only occur if researchers are confident the trait concepts are consistent within and across sources. Here we describe the AusTraits Plant Dictionary (APD), a new data source of terms that extends the trait definitions included in a recent trait database, AusTraits. The development process of the APD included three steps: review and formalisation of the scope of each trait and the accompanying trait description; addition of trait metadata; and publication in both human and machine-readable forms. Trait definitions include keywords, references, and links to related trait concepts in other databases, enabling integration of AusTraits with other sources. The APD will both improve the usability of AusTraits and foster the integration of trait data across global and regional plant trait databases.},
}
@article {pmid38796014,
year = {2024},
author = {Graham, CC},
title = {The role of Geographic Information Systems in mitigating plastics pollution in the Global South-A spatial analysis of recycling facilities in Costa Rica.},
journal = {The Science of the total environment},
volume = {937},
number = {},
pages = {173396},
doi = {10.1016/j.scitotenv.2024.173396},
pmid = {38796014},
issn = {1879-1026},
mesh = {Costa Rica ; *Plastics/analysis ; *Geographic Information Systems ; *Recycling ; *Environmental Pollution/statistics &amp; numerical data ; Spatial Analysis ; Conservation of Natural Resources/methods ; Environmental Monitoring ; },
abstract = {Costa Rica is at the forefront of environmental conservation in Central America, with its focus on sustainability and green practices. Building on this foundation, the country joins a cohort of middle-income developing countries that have set forth ambitious goals to eliminate plastic pollution and become plastics-free. Recycling remains one of the most effective ways of removing plastic waste from the environment. Although GIS has been utilized in environmental research, its use is still expanding in developing countries of the Global South. These countries are experiencing unprecedented adverse climate and ecological impacts while also pursuing fundamental socioeconomic growth. The application of more cost-effective and strategic technological solutions, as well as data-driven decision-making, could fast-track the achievement of their urgent environmental goals. Using Geographic Information Systems (GIS) analysis, this study applies hot spot, location-allocation, and time-distance measures to examine Costa Rica's capacity to recycle plastic waste. Focusing specifically on availability and the public's access to recycling facilities, this article offers insights into the resource constraints and evolution of plastics governance in developing countries with environmentally-focused priorities. The findings of this study suggest that while Costa Rica is implementing progressive plastics regulatory policies, the ability to achieve plastics-free status is hampered by shortfalls in the number and distribution of recycling facilities and the public's access to recycling services. Expanding recycling infrastructure, including transportation, and adopting a less canton-centric waste administration system could contribute to resolving these challenges. This study contributes to discourses on global plastics governance and environmental change management in the Global South.},
}
@article {pmid38795997,
year = {2024},
author = {Lu, J and Peng, Q and Song, Y and Lyu, L and Chen, D and Huang, P and Peng, F and Liu, Y},
title = {Characteristics and effects of global sloping land urbanization from 2000 to 2020.},
journal = {The Science of the total environment},
volume = {937},
number = {},
pages = {173348},
doi = {10.1016/j.scitotenv.2024.173348},
pmid = {38795997},
issn = {1879-1026},
abstract = {Cities usually expand on flat land. However, in recent decades, the increasing scarcity of available flat land has compelled many cities to expand to sloping land (sloping land urbanization, SLU), and the understanding for global SLU is still unclear. This study, based on the currently available high-precision global Digital Elevation Model (FABDEM) and global land cover dataset (GlobeLand30), investigated the characteristics and impacts of SLU in 26,402 urban residential areas worldwide from 2000 to 2020. Results show that the total area of SLU globally is 16,383 km[2], accounting for 9.54 % of the overall urban expansion. This phenomenon is widespread globally and relatively concentrated in a few countries, with 42.78 %, 24.35 %, and 21.83 % of the area coming from cultivated land, forest, and grassland respectively. Global SLU has accommodated 34.78 million urban population, and indirectly protected 8922 km[2] of flat cultivated land, while causing a net loss of 4373 km[2] of green ecological land. Deliberately balancing the dual effects of SLU is crucial for advancing sustainable global urbanization.},
}
@article {pmid38791265,
year = {2024},
author = {Bartas, M and Brázda, V and Pečinka, P},
title = {Special Issue "Bioinformatics of Unusual DNA and RNA Structures".},
journal = {International journal of molecular sciences},
volume = {25},
number = {10},
pages = {},
pmid = {38791265},
issn = {1422-0067},
support = {CZ.10.03.01/00/22_003/0000003//Operational Programme Just Transition, European Union/ ; },
mesh = {*RNA/chemistry/metabolism ; *DNA/chemistry/metabolism ; *Computational Biology/methods ; *Nucleic Acid Conformation ; Humans ; },
abstract = {Nucleic acids are not only static carriers of genetic information but also play vital roles in controlling cellular lifecycles through their fascinating structural diversity [...].},
}
@article {pmid38789640,
year = {2024},
author = {Leigh, DM and Vandergast, AG and Hunter, ME and Crandall, ED and Funk, WC and Garroway, CJ and Hoban, S and Oyler-McCance, SJ and Rellstab, C and Segelbacher, G and Schmidt, C and Vázquez-Domínguez, E and Paz-Vinas, I},
title = {Best practices for genetic and genomic data archiving.},
journal = {Nature ecology &amp; evolution},
volume = {8},
number = {7},
pages = {1224-1232},
pmid = {38789640},
issn = {2397-334X},
support = {31BD30_193900//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; },
mesh = {*Genomics ; Databases, Genetic ; Data Management ; Metadata ; },
abstract = {Genetic and genomic data are collected for a vast array of scientific and applied purposes. Despite mandates for public archiving, data are typically used only by the generating authors. The reuse of genetic and genomic datasets remains uncommon because it is difficult, if not impossible, due to non-standard archiving practices and lack of contextual metadata. But as the new field of macrogenetics is demonstrating, if genetic data and their metadata were more accessible and FAIR (findable, accessible, interoperable and reusable) compliant, they could be reused for many additional purposes. We discuss the main challenges with existing genetic and genomic data archives, and suggest best practices for archiving genetic and genomic data. Recognizing that this is a longstanding issue due to little formal data management training within the fields of ecology and evolution, we highlight steps that research institutions and publishers could take to improve data archiving.},
}
@article {pmid38787862,
year = {2024},
author = {Wang, L and Cui, H},
title = {Identification and classification of urban employment centers based on big data: A case study of Beijing.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0299726},
pmid = {38787862},
issn = {1932-6203},
mesh = {Beijing ; Humans ; *Employment/statistics &amp; numerical data ; *Transportation/statistics &amp; numerical data ; Big Data ; Workplace ; Urban Population ; },
abstract = {The layout, scale and spatial form of urban employment centers are important guidelines for the rational layout of public service facilities such as urban transportation, medical care, and education. In this paper, we use Internet cell phone positioning data to identify the workplace and residence of users in the Beijing city area and obtain commuting data of the employed to measure the employment center system in Beijing. Firstly, the employment density distribution is generated using the data of the working places of the employed persons, and the employment centers are identified based on the employment density of Beijing. Then, we use the business registration data of employment centers to measure the industrial diversity within the employment centers by using the ecological Shannon Wiener Diversity Index, and combine the commuting links between employment centers and places of residence to measure the energy level of each employment center, analyze the hinterland and sphere of influence of each center, and finally using the industrial diversity index of employment centers and the average commuting time of employed persons, combined with the K-Means clustering algorithm, to classify the employment centers in Beijing. The employment center identification and classification method based on big data constructed in this study can help solve the limitations of the previous employment center system research in terms of center identification and commuting linkage measurement due to large spatial units and lack of commuting data to a certain extent. The study can provide reference for the regular understanding and technical analysis of employment centers and provide help for the employment multi-center system in Beijing in terms of quantifying the employment spatial structure, guiding the construction of multi-center system, and adjusting the land use rules.},
}
@article {pmid38784435,
year = {2024},
author = {Boyes, D and Crowley, LM and Holland, PWH and , and , and , and , and , and , and , },
title = {The genome sequence of the Summer Chafer, Amphimallon solstitiale (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {138},
pmid = {38784435},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Amphimallon solstitiale (the Summer Chafer; Arthropoda; Insecta; Coleoptera; Scarabaeidae). The genome sequence is 1,584.1 megabases in span. Most of the assembly is scaffolded into 11 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 19.29 kilobases in length.},
}
@article {pmid38781445,
year = {2024},
author = {Vuruputoor, VS and Starovoitov, A and Cai, Y and Liu, Y and Rahmatpour, N and Hedderson, TA and Wilding, N and Wegrzyn, JL and Goffinet, B},
title = {Crossroads of assembling a moss genome: navigating contaminants and horizontal gene transfer in the moss Physcomitrellopsis africana.},
journal = {G3 (Bethesda, Md.)},
volume = {14},
number = {7},
pages = {},
pmid = {38781445},
issn = {2160-1836},
support = {DEB-0919284//US National Science Foundation/ ; },
mesh = {*Gene Transfer, Horizontal ; *Bryopsida/genetics ; *Genome, Plant ; *Phylogeny ; Genomics/methods ; Molecular Sequence Annotation ; },
abstract = {The first chromosome-scale reference genome of the rare narrow-endemic African moss Physcomitrellopsis africana (P. africana) is presented here. Assembled from 73 × Oxford Nanopore Technologies (ONT) long reads and 163 × Beijing Genomics Institute (BGI)-seq short reads, the 414 Mb reference comprises 26 chromosomes and 22,925 protein-coding genes [Benchmarking Universal Single-Copy Ortholog (BUSCO) scores: C:94.8% (D:13.9%)]. This genome holds 2 genes that withstood rigorous filtration of microbial contaminants, have no homolog in other land plants, and are thus interpreted as resulting from 2 unique horizontal gene transfers (HGTs) from microbes. Further, P. africana shares 176 of the 273 published HGT candidates identified in Physcomitrium patens (P. patens), but lacks 98 of these, highlighting that perhaps as many as 91 genes were acquired in P. patens in the last 40 million years following its divergence from its common ancestor with P. africana. These observations suggest rather continuous gene gains via HGT followed by potential losses during the diversification of the Funariaceae. Our findings showcase both dynamic flux in plant HGTs over evolutionarily "short" timescales, alongside enduring impacts of successful integrations, like those still functionally maintained in extant P. africana. Furthermore, this study describes the informatic processes employed to distinguish contaminants from candidate HGT events.},
}
@article {pmid38781323,
year = {2024},
author = {Edwards, SV and Cloutier, A and Cockburn, G and Driver, R and Grayson, P and Katoh, K and Baldwin, MW and Sackton, TB and Baker, AJ},
title = {A nuclear genome assembly of an extinct flightless bird, the little bush moa.},
journal = {Science advances},
volume = {10},
number = {21},
pages = {eadj6823},
doi = {10.1126/sciadv.adj6823},
pmid = {38781323},
issn = {2375-2548},
mesh = {Animals ; *Birds/genetics ; *Genome ; *Extinction, Biological ; Cell Nucleus/genetics ; Phylogeny ; Fossils ; Genome, Mitochondrial ; Flight, Animal ; New Zealand ; Male ; DNA Transposable Elements/genetics ; Genomics/methods ; },
abstract = {We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.},
}
@article {pmid38779566,
year = {2024},
author = {Scanu, M and Toto, F and Petito, V and Masi, L and Fidaleo, M and Puca, P and Baldelli, V and Reddel, S and Vernocchi, P and Pani, G and Putignani, L and Scaldaferri, F and Del Chierico, F},
title = {An integrative multi-omic analysis defines gut microbiota, mycobiota, and metabolic fingerprints in ulcerative colitis patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1366192},
pmid = {38779566},
issn = {2235-2988},
mesh = {Humans ; *Colitis, Ulcerative/microbiology/metabolism ; *Gastrointestinal Microbiome ; Male ; Adult ; Female ; *Bacteria/classification/isolation &amp; purification/metabolism/genetics ; Middle Aged ; *Metabolomics/methods ; *RNA, Ribosomal, 16S/genetics ; *Gas Chromatography-Mass Spectrometry ; *Feces/microbiology ; *Fungi/classification/isolation &amp; purification/metabolism ; Dysbiosis/microbiology ; Metabolome ; Aged ; Young Adult ; Solid Phase Microextraction ; Mycobiome ; Multiomics ; },
abstract = {BACKGROUND: Ulcerative colitis (UC) is a multifactorial chronic inflammatory bowel disease (IBD) that affects the large intestine with superficial mucosal inflammation. A dysbiotic gut microbial profile has been associated with UC. Our study aimed to characterize the UC gut bacterial, fungal, and metabolic fingerprints by omic approaches.<br><br>METHODS: The 16S rRNA- and ITS2-based metataxonomics and gas chromatography-mass spectrometry/solid phase microextraction (GC-MS/SPME) metabolomic analysis were performed on stool samples of 53 UC patients and 37 healthy subjects (CTRL). Univariate and multivariate approaches were applied to separated and integrated omic data, to define microbiota, mycobiota, and metabolic signatures in UC. The interaction between gut bacteria and fungi was investigated by network analysis.<br><br>RESULTS: In the UC cohort, we reported the increase of Streptococcus, Bifidobacterium, Enterobacteriaceae, TM7-3, Granulicatella, Peptostreptococcus, Lactobacillus, Veillonella, Enterococcus, Peptoniphilus, Gemellaceae, and phenylethyl alcohol; and we also reported the decrease of Akkermansia; Ruminococcaceae; Ruminococcus; Gemmiger; Methanobrevibacter; Oscillospira; Coprococus; Christensenellaceae; Clavispora; Vishniacozyma; Quambalaria; hexadecane; cyclopentadecane; 5-hepten-2-ol, 6 methyl; 3-carene; caryophyllene; p-Cresol; 2-butenal; indole, 3-methyl-; 6-methyl-3,5-heptadiene-2-one; 5-octadecene; and 5-hepten-2-one, 6 methyl. The integration of the multi-omic data confirmed the presence of a distinctive bacterial, fungal, and metabolic fingerprint in UC gut microbiota. Moreover, the network analysis highlighted bacterial and fungal synergistic and/or divergent interkingdom interactions.<br><br>CONCLUSION: In this study, we identified intestinal bacterial, fungal, and metabolic UC-associated biomarkers. Furthermore, evidence on the relationships between bacterial and fungal ecosystems provides a comprehensive perspective on intestinal dysbiosis and ecological interactions between microorganisms in the framework of UC.},
}
@article {pmid38779149,
year = {2024},
author = {Boyes, D and Mulhair, PO and , and , and , and , and , and , and , },
title = {The genome sequence of the Water Veneer, Acentria ephemerella (Denis &amp; Schiffermüller, 1775).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {134},
pmid = {38779149},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Acentria ephemerella (the Water Veneer; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 340.8 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.35 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,748 protein coding genes.},
}
@article {pmid38779060,
year = {2023},
author = {Boyes, D and Mulhair, PO and , and , and , and , and , and , },
title = {The genome sequence of the Scarce Umber, Agriopis aurantiaria (Hübner, 1799).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {463},
pmid = {38779060},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Agriopis aurantiaria (the Scarce Umber; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 485.4 megabases in span. The whole assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,963 protein coding genes.},
}
@article {pmid38779056,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Pinion-streaked Snout, Schrankia costaestrigalis (Stephens, 1834).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {203},
pmid = {38779056},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Schrankia costaestrigalis (the Pinion-streaked Snout; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 572.0 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.1 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,453 protein coding genes.},
}
@article {pmid38779055,
year = {2023},
author = {Boyes, D and , and , and , and , and , and , },
title = {The genome sequence of the Diamondback Moth, Plutella xylostella (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {404},
pmid = {38779055},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Plutella xylostella (the Diamondback Moth; Arthropoda; Insecta; Lepidoptera; Plutellidae). The genome sequence is 323.3 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 35.12 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,190 protein coding genes.},
}
@article {pmid38779054,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Coxcomb Prominent, Ptilodon capucinus (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {242},
pmid = {38779054},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Ptilodon capucinus (the Coxcomb Prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 348.7 megabases in span. The assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.38 kilobases in length. Gene annotation of this assembly on Ensembl identified 16,968 protein coding genes.},
}
@article {pmid38779050,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Grey Poplar Bell, Epinotia nisella (Clerck, 1759).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {281},
pmid = {38779050},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Epinotia nisella (the Grey Poplar Bell; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 585.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.44 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,952 protein coding genes.},
}
@article {pmid38779048,
year = {2023},
author = {Boyes, D and Mulley, JF and , and , and , and , and , and , },
title = {The genome sequence of the Six-striped Rustic, Xestia sexstrigata (Haworth, 1809).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {399},
pmid = {38779048},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Xestia sexstrigata (the Six-striped Rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 638.3 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.36 kilobases in length. Gene annotation of this assembly on Ensembl identified 15,104 protein coding genes.},
}
@article {pmid38779046,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Red-green Carpet, Chloroclysta siterata (Hufnagel, 1767).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {206},
pmid = {38779046},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Chloroclysta siterata (the Red-green Carpet; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 437.9 megabases in span. Most of the assembly is scaffolded into 21 chromosomal pseudomolecules including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.7 kilobases in length. Gene annotation of this assembly on Ensembl identified 11,814 protein coding genes.},
}
@article {pmid38778011,
year = {2024},
author = {Mercuri, AM and Clò, E and Zappa, J and Bosi, G and Furia, E and Ricucci, C and Di Lena, M and Camerini, F and Florenzano, A},
title = {BRAIN - Holocene archaeo-data for assessing plant-cultural diversity in Italy and other Mediterranean regions.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {520},
pmid = {38778011},
issn = {2052-4463},
mesh = {*Archaeology ; Botany/history ; Italy ; Mediterranean Region ; *Plants ; *Pollen ; Databases as Topic ; },
abstract = {In the field of botany applied to archaeological and palaeoecological studies, the multi- and inter-disciplinary nature of this research produces a lack of data sharing and scattered articles in the specialty literature or in national and international journals. The vast production of archaeobotany and palynology data makes it necessary to develop a tool for the availability, accessibility, and dissemination of existing research. Many databases exist on palaeoecology, archaeobotany or pollen data. There are no collections focused on archaeological sites and human-induced environments and centred on Southern Europe and the Mediterranean. BRAIN - Botanical Records of Archaeobotany Italian Network is the first database listing sites from which all types of plant records are available in Italy and nearby Mediterranean regions. BRAIN represents the largest integrated collection of archaeo/palaeo-botanical data and a range of descriptive information that makes data recovery FAIR ready. This unique network hosts data on the availability of anthropogenic pollen, palynomorphs and plant macroremains in the same database, and experts of different research fields may contribute to it.},
}
@article {pmid38777192,
year = {2024},
author = {Aggarwal, R and Peters, G},
title = {Freshwater ecotoxicity characterization factors for PMT/vPvM substances.},
journal = {Chemosphere},
volume = {360},
number = {},
pages = {142391},
doi = {10.1016/j.chemosphere.2024.142391},
pmid = {38777192},
issn = {1879-1298},
mesh = {*Water Pollutants, Chemical/toxicity ; *Ecotoxicology ; *Fresh Water/chemistry ; Environmental Monitoring/methods ; Risk Assessment ; Germany ; Databases, Factual ; },
abstract = {This study addresses the gap in freshwater ecotoxicological characterization factors (CFs) for Persistent, Mobile, and Toxic (PMT) and Very Persistent and Very Mobile (vPvM) substances. These CFs are vital for integrating the ecotoxicity impacts of these chemicals into life cycle assessments. Our goals are twofold: first, to calculate experimental freshwater CFs for PMT/vPvM substances listed by the German Environment Agency (UBA); second, to compare these CFs with those from the USEtox database. The expanded UBA list includes 343 PMT/vPvM substances, each representing a unique chemical structure, and linked to 474 REACH-registered substances. This study successfully computed CFs for 244 substances, with 107 overlapping the USEtox database and 137 being new. However, ecotoxicity data limitations prevented CF determination for 97 substances. This research enhances our understanding of freshwater CFs for PMT/vPvM substances, covering 72% of UBA's 343 PMT/vPvM substances. Data scarcity remains a significant challenge, which invariably impedes CF calculations. Notably, the disparities observed between CF values in the USEtox database and those derived in this research largely stem from variations in ecotoxicity data. Consequently, this research underscores the dynamic nature of CFs for substances, emphasizing the need for regular updates to ensure their accuracy and relevance.},
}
@article {pmid38776304,
year = {2024},
author = {Karlgren, K and Andersson Franko, M and Kilström, D},
title = {'Experiencing one thing and saying another'-Ecological Momentary Assessment (EMA) of nursing students' competence and challenge during clinical placements compared with retrospective interviews.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0302866},
pmid = {38776304},
issn = {1932-6203},
mesh = {Humans ; *Students, Nursing/psychology ; Female ; Retrospective Studies ; *Clinical Competence ; Male ; *Ecological Momentary Assessment ; Adult ; Young Adult ; Interviews as Topic ; Smartphone ; },
abstract = {UNLABELLED: Clinical placements are essential to nursing education and understanding students' challenges in the clinical context is important for educators. Nevertheless, few studies have investigated students' experiences in the clinical context itself but rely on methods which ask participants to generalize their clinical experiences retrospectively.<br><br>OBJECTIVES: This study aimed to explore nursing students' experiences of clinical activities during and after clinical placements with a focus on feelings of competence and challenge. A particular interest was on comparing momentary assessments in the clinical context with retrospective interview data.<br><br>METHODS: Smartphones were used for ecological momentary assessment of students' experiences of clinical activities during five-week placements at 21 nursing homes. Both quantitative and qualitative data were collected. Interviews were conducted after the placements.<br><br>RESULTS: 575 responses were obtained showing final-year nursing students rated their competence significantly higher and challenge significantly lower than first-year students. An analysis of the quantitative data using the four-channel flow model showed that first-year students' activities were to a significantly higher extent associated with flow and anxiety, compared to those of final-year students. Conversely, the final-year students' activities were to a significantly higher extent associated with boredom than those of first-year students. The analysis of the students' reflections resulted in five themes: Specific activities are challenging, Lack of challenge, Learning and developing, Reflects critically on competence, and Arrangement of the clinical placement.<br><br>DISCUSSION: Final-year nursing students were significantly less challenged during the placements compared to first-year students. There was overlap in how students described their clinical experiences during and after placements, but there were also striking differences. The first-year students were overwhelmed by the challenges during the placements but viewed these experiences as valuable learning experiences afterwards. The final-year students also described several challenging clinical activities during the placements but none of these challenges were brought up afterwards in the interviews and instead a lack of challenge was emphasized. Momentary assessment thus enabled capturing data about clinical activities which may be overlooked by retrospective methods.},
}
@article {pmid38776282,
year = {2024},
author = {MacPhail, VJ and Hatfield, R and Colla, SR},
title = {Bumble Bee Watch community science program increases scientific understanding of an important pollinator group across Canada and the USA.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0303335},
pmid = {38776282},
issn = {1932-6203},
mesh = {Animals ; Bees/physiology ; United States ; *Pollination ; Canada ; Databases, Factual ; },
abstract = {In a time of increasing threats to bumble bees (Hymenoptera: Apidae: Bombus), it is important to understand their ecology and distribution. As experts are limited in resources to conduct field surveys, there is potential for community scientists to help. The Bumble Bee Watch (BBW) community science program involves volunteers taking photos of bumble bees in Canada and the USA and submitting them, along with geographic and optional plant information, to a website or through an app. Taxon experts then verify the bee species identification. The Bumble Bees of North America database (BBNA) stores data (no photographs) collected and identified by more traditional scientific methods over the same range. Here we compared BBW data to BBNA data over all years and just 2010-2020 to understand the scientific contribution of community scientists to the state of the knowledge about native bumble bees. We found that BBW had similar geographic and species coverage as BBNA. It had records from all 63 provinces, states, and territories where bumble bees occur (including four more than BBNA in 2010-2020), and represented 41 of the 48 species in BBNA (with ten more species than BBNA in 2010-2020). While BBW contributed only 8.50% of records overall, it contributed 25.06% of all records over 2010-2020. BBW confirmed the persistence of species and identified new locations of species, both inside and outside of the previously known extent of occurrences. BBW also contributed a wealth of ecological information, such as unique plant genera and species data for almost all the bee species. Thus, while BBW had fewer bee records than the BBNA database overall, it helped to fill in data gaps and provided novel information, complementing the traditional methods. This community science program is valuable in helping to inform conservation management for bumble bee species.},
}
@article {pmid38774958,
year = {2024},
author = {Huson, D and Xavier, JC and Steel, M},
title = {Self-generating autocatalytic networks: structural results, algorithms and their relevance to early biochemistry.},
journal = {Journal of the Royal Society, Interface},
volume = {21},
number = {214},
pages = {20230732},
doi = {10.1098/rsif.2023.0732},
pmid = {38774958},
issn = {1742-5662},
mesh = {*Algorithms ; Catalysis ; Models, Biological ; Biochemistry ; Origin of Life ; },
abstract = {The concept of an autocatalytic network of reactions that can form and persist, starting from just an available food source, has been formalized by the notion of a reflexively autocatalytic and food-generated (RAF) set. The theory and algorithmic results concerning RAFs have been applied to a range of settings, from metabolic questions arising at the origin of life, to ecological networks, and cognitive models in cultural evolution. In this article, we present new structural and algorithmic results concerning RAF sets, by studying more complex modes of catalysis that allow certain reactions to require multiple catalysts (or to not require catalysis at all), and discuss the differing ways catalysis has been viewed in the literature. We also focus on the structure and analysis of minimal RAFs and derive structural results and polynomial-time algorithms. We then apply these new methods to a large metabolic network to gain insights into possible biochemical scenarios near the origin of life.},
}
@article {pmid38772433,
year = {2024},
author = {Chagas, &#xc9;CDS and Ferreira, FADS and Mwangi, VI and Terrazas, WCM and Becker, JN and Simões, RC and Pacífico, EMSS and Silva, ASD and Marques, CDS and Chagas, ECDS and Machado, MB and Figueira, EAG and Castro, DB and Ramos, TCA and Oliveira, JH},
title = {Spatio-temporal analysis of American Tegumentary Leishmaniasis incidences in the Brazilian state of Amazonas: 2011 to 2022.},
journal = {Acta tropica},
volume = {256},
number = {},
pages = {107266},
doi = {10.1016/j.actatropica.2024.107266},
pmid = {38772433},
issn = {1873-6254},
mesh = {Brazil/epidemiology ; Humans ; Incidence ; *Leishmaniasis, Cutaneous/epidemiology ; *Spatio-Temporal Analysis ; *Seasons ; Climate ; Female ; Male ; Adult ; Adolescent ; Young Adult ; Child ; },
abstract = {This study aimed to conduct a spatio-temporal analysis of tegumentary leishmaniasis occurrences in the Amazonas state, Brazil. An ecological study encompassing time series and spatial analysis was performed, exploring the geographic distribution and temporal trends of American Tegumentary Leishmaniasis (ATL) in Amazonas between 2011 and 2022. Secondary data extracted from the Department of Informatics of the Unified Health System (DATASUS) were utilized for this analysis. The study evaluated the relationship between disease cases and environmental/climatic variables (deforestation, temperature, precipitation, and relative humidity). Over the study period, 19,730 cases of tegumentary leishmaniasis were recorded, averaging an incidence of 41.4/100,000 inhabitants across the 62 municipalities of Amazonas state. Disease intensity varied with seasons. Generally, Amazonas state displayed a declining trend in ATL cases. However, certain municipalities, notably Rio Preto da Eva and Presidente Figueiredo, exhibited high incidence rates, while Canutama, Envira, Eirunepé, and Pauini municipalities demand closer attention due to their demonstrated increasing temporal trend of ATL cases. The analysis indicated a correlation between the number of ATL cases reported and relative humidity as well as precipitation. These findings underscore the significance of tegumentary leishmaniasis as a public health issue in the region and emphasize the necessity for public initiatives aimed at preventing this endemic illness.},
}
@article {pmid38771704,
year = {2024},
author = {Warren, WC and Rice, ES and X, M and Roback, E and Keene, A and Martin, F and Ogeh, D and Haggerty, L and Carroll, RA and McGaugh, S and Rohner, N},
title = {Astyanax mexicanus surface and cavefish chromosome-scale assemblies for trait variation discovery.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkae103},
pmid = {38771704},
issn = {2160-1836},
abstract = {The ability of organisms to adapt to sudden extreme environmental changes produces some of the most drastic examples of rapid phenotypic evolution. The Mexican Tetra, Astyanax mexicanus, is abundant in the surface waters of northeastern Mexico, but repeated colonizations of cave environments have resulted in the independent evolution of troglomorphic phenotypes in several populations. Here, we present three chromosome-scale assemblies of this species, for one surface and two cave populations, enabling the first whole-genome comparisons between independently evolved cave populations to evaluate the genetic basis for the evolution of adaptation to the cave environment. Our assemblies represent the highest quality of sequence completeness with predicted protein-coding and non-coding gene metrics far surpassing prior resources and, to our knowledge, all long-read assembled teleost genomes, including zebrafish. Whole genome synteny alignments show highly conserved gene order among cave forms in contrast to a higher number of chromosomal rearrangements when compared to other phylogenetically close or distant teleost species. By phylogenetically assessing gene orthology across distant branches of amniotes, we discover gene orthogroups unique to A. mexicanus. When compared to a representative surface fish genome, we find a rich amount of structural sequence diversity, defined here as the number and size of insertions and deletions as well as expanding and contracting repeats across cave forms. These new more complete genomic resources ensure higher trait resolution for comparative, functional, developmental, and genetic studies of drastic trait differences within a species.},
}
@article {pmid38770718,
year = {2024},
author = {Schwarzerova, J and Hurta, M and Barton, V and Lexa, M and Walther, D and Provaznik, V and Weckwerth, W},
title = {A perspective on genetic and polygenic risk scores-advances and limitations and overview of associated tools.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {3},
pages = {},
pmid = {38770718},
issn = {1477-4054},
support = {FEKT/FIT-J-23-8274//Brno University of Technology intra-university junior project/ ; },
mesh = {Humans ; *Multifactorial Inheritance ; *Genetic Predisposition to Disease ; *Software ; Computational Biology/methods ; Genome-Wide Association Study/methods ; Risk Factors ; Risk Assessment/methods ; Genetic Risk Score ; },
abstract = {Polygenetic Risk Scores are used to evaluate an individual's vulnerability to developing specific diseases or conditions based on their genetic composition, by taking into account numerous genetic variations. This article provides an overview of the concept of Polygenic Risk Scores (PRS). We elucidate the historical advancements of PRS, their advantages and shortcomings in comparison with other predictive methods, and discuss their conceptual limitations in light of the complexity of biological systems. Furthermore, we provide a survey of published tools for computing PRS and associated resources. The various tools and software packages are categorized based on their technical utility for users or prospective developers. Understanding the array of available tools and their limitations is crucial for accurately assessing and predicting disease risks, facilitating early interventions, and guiding personalized healthcare decisions. Additionally, we also identify potential new avenues for future bioinformatic analyzes and advancements related to PRS.},
}
@article {pmid38767676,
year = {2024},
author = {Geng, A and Zhang, C and Wang, J and Zhang, X and Qiu, W and Wang, L and Xi, J and Yang, B},
title = {Current advances of chlorinated organics degradation by bioelectrochemical systems: a review.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {7},
pages = {208},
pmid = {38767676},
issn = {1573-0972},
support = {2022YFC3702000//National Key Research and Development Program of China/ ; BE2020773//Social Development Project/ ; 23KJA610008//the Natural Science Foundation of Jiangsu Higher Education Institutions of China/ ; },
mesh = {*Biodegradation, Environmental ; *Electrochemical Techniques ; Wastewater/chemistry ; Hydrocarbons, Chlorinated/metabolism ; Water Pollutants, Chemical/metabolism ; Groundwater/chemistry ; Organic Chemicals/metabolism ; },
abstract = {Chlorinated organic compounds (COCs) are typical refractory organic compounds, having high biological toxicity. These compounds are a type of pervasive pollutants that can be present in polluted soil, air, and various types of waterways, such as groundwater, rivers, and lakes, posing a significant threat to the ecological environment and human health. Bioelectrochemical systems (BESs) are an effective strategy for the degradation of bio-refractory compounds. BESs improve the waste treatment efficiency through the application of weak electrical stimulation. This review discusses the processes of BESs configurations and degradation performances in different environmental media including wastewater, soil, waste gas and groundwater. In addition, the degradation mechanisms and performance-enhancing additives are summarized. The future challenges and perspectives on the development of BES for COCs removal are briefly discussed.},
}
@article {pmid38767452,
year = {2024},
author = {Rashidi, A and Ebadi, M and Rehman, TU and Elhusseini, H and Kazadi, D and Halaweish, H and Khan, MH and Hoeschen, A and Cao, Q and Luo, X and Kabage, AJ and Lopez, S and Ramamoorthy, S and Holtan, SG and Weisdorf, DJ and Khoruts, A and Staley, C},
title = {Multi-omics Analysis of a Fecal Microbiota Transplantation Trial Identifies Novel Aspects of Acute GVHD Pathogenesis.},
journal = {Cancer research communications},
volume = {4},
number = {6},
pages = {1454-1466},
pmid = {38767452},
issn = {2767-9764},
support = {KL2 TR002492/TR/NCATS NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; KL2TR002492//Foundation for the National Institutes of Health (FNIH)/ ; UL1TR002494//Foundation for the National Institutes of Health (FNIH)/ ; P30CA07759//HHS | NIH | National Cancer Institute (NCI)/ ; Chainbreaker grant//UMN | Clinical and Translational Science Institute, University of Minnesota (CTSI)/ ; n/a//Achieving Cures Together/ ; },
mesh = {Humans ; *Graft vs Host Disease/microbiology/immunology ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Hematopoietic Stem Cell Transplantation/methods/adverse effects ; Adult ; Leukemia, Myeloid, Acute/therapy/microbiology/immunology ; Transplantation, Homologous/methods/adverse effects ; Faecalibacterium ; Aged ; Acute Disease ; Feces/microbiology ; Metabolome ; Multiomics ; },
abstract = {UNLABELLED: Acute GVHD (aGVHD) is a major complication of allogeneic hematopoietic cell transplantation (alloHCT) associated with gut microbiota disruptions. However, whether therapeutic microbiota modulation prevents aGVHD is unknown. We conducted a randomized, placebo-controlled trial of third-party fecal microbiota transplantation (FMT) administered at the peak of microbiota injury in 100 patients with acute myeloid leukemia receiving induction chemotherapy and alloHCT recipients. Despite improvements in microbiome diversity, expansion of commensals, and shrinkage of potential pathogens, aGVHD occurred more frequently after FMT than placebo. Although this unexpected finding could be explained by clinical differences between the two arms, we asked whether a microbiota explanation might be also present. To this end, we performed multi-omics analysis of preintervention and postintervention gut microbiome and serum metabolome. We found that postintervention expansion of Faecalibacterium, a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, predicted a higher risk for aGVHD. Faecalibacterium expansion occurred predominantly after FMT and was due to engraftment of unique donor taxa, suggesting that donor Faecalibacterium-derived antigens might have stimulated allogeneic immune cells. Faecalibacterium and ursodeoxycholic acid (an anti-inflammatory secondary bile acid) were negatively correlated, offering an alternative mechanistic explanation. In conclusion, we demonstrate context dependence of microbiota effects where a normally beneficial bacteria may become detrimental in disease. While FMT is a broad, community-level intervention, it may need precision engineering in ecologically complex settings where multiple perturbations (e.g., antibiotics, intestinal damage, alloimmunity) are concurrently in effect.<br><br>SIGNIFICANCE: Post-FMT expansion of Faecalibacterium, associated with donor microbiota engraftment, predicted a higher risk for aGVHD in alloHCT recipients. Although Faecalibacterium is a commensal genus with gut-protective and anti-inflammatory properties under homeostatic conditions, our findings suggest that it may become pathogenic in the setting of FMT after alloHCT. Our results support a future trial with precision engineering of the FMT product used as GVHD prophylaxis after alloHCT.},
}
@article {pmid38764972,
year = {2023},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the Common Emerald, Hemithea aestivaria (Hübner, 1789).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {243},
pmid = {38764972},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Hemithea aestivaria (the Common Emerald; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 501.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.05 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,477 protein coding genes.},
}
@article {pmid38764970,
year = {2023},
author = {Boyes, D and Lewis, OT and , and , and , and , and , and , },
title = {The genome sequence of the Pebble Hook-tip, Drepana falcataria (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {207},
pmid = {38764970},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Drepana falcataria (the Pebble Hook-tip; Arthropoda; Insecta; Lepidoptera; Drepanidae). The genome sequence is 326.7 megabases in span. The whole assembly is scaffolded into 31 chromosomal pseudomolecules, including the assembled Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.},
}
@article {pmid38764134,
year = {2024},
author = {Wang, J and Li, Y and Rahman, MM and Li, B and Yan, Z and Song, G and Zhao, Y and Wu, J and Chu, C},
title = {Unraveling the drivers and impacts of leaf phenological diversity in a subtropical forest: A fine-scale analysis using PlanetScope CubeSats.},
journal = {The New phytologist},
volume = {243},
number = {2},
pages = {607-619},
doi = {10.1111/nph.19850},
pmid = {38764134},
issn = {1469-8137},
support = {20220816162849005//Shenzhen Science and Technology Program/ ; 32301350//National Natural Science Foundation of China/ ; 31925027//National Natural Science Foundation of China/ ; 31922090//National Natural Science Foundation of China/ ; 32271595//National Natural Science Foundation of China/ ; 17305321//Hong Kong Research Grant Council General Research Fund/ ; //HKU Seed Funding for Strategic Interdisciplinary Research Scheme, the Hung Ying Physical Science Research Fund 2021-22/ ; //Innovation and Technology Fund (funding support to State Key Laboratories in Hong Kong of Agrobiotechnology) of the HKSAR, China/ ; LVEC-2023rc01//Key Talent Project of the State Key Laboratory of Vegetation and Environmental Change/ ; },
mesh = {*Plant Leaves/physiology ; *Forests ; *Biodiversity ; *Tropical Climate ; Biomass ; Soil ; China ; },
abstract = {Leaf phenology variations within plant communities shape community assemblages and influence ecosystem properties and services. However, questions remain regarding quantification, drivers, and productivity impacts of intra-site leaf phenological diversity. With a 50-ha subtropical forest plot in China's Heishiding Provincial Nature Reserve (part of the global ForestGEO network) as a testbed, we gathered a unique dataset combining ground-derived abiotic (topography, soil) and biotic (taxonomic diversity, functional diversity, functional traits) factors. We investigated drivers underlying leaf phenological diversity extracted from high-resolution PlanetScope data, and its influence on aboveground biomass (AGB) using structural equation modeling (SEM). Our results reveal considerable fine-scale leaf phenological diversity across the subtropical forest landscape. This diversity is directly and indirectly influenced by abiotic and biotic factors (e.g. slope, soil, traits, taxonomic diversity; r[2] = 0.43). While a notable bivariate relationship between AGB and leaf phenological diversity was identified (r = -0.24, P < 0.05), this relationship did not hold in SEM analysis after considering interactions with other biotic and abiotic factors (P > 0.05). These findings unveil the underlying mechanism regulating intra-site leaf phenological diversity. While leaf phenology is known to be associated with ecosystem properties, our findings confirm that AGB is primarily influenced by functional trait composition and taxonomic diversity rather than leaf phenological diversity.},
}
@article {pmid38764024,
year = {2024},
author = {Trujillano, F and Jimenez, G and Manrique, E and Kahamba, NF and Okumu, F and Apollinaire, N and Carrasco-Escobar, G and Barrett, B and Fornace, K},
title = {Using image segmentation models to analyse high-resolution earth observation data: new tools to monitor disease risks in changing environments.},
journal = {International journal of health geographics},
volume = {23},
number = {1},
pages = {13},
pmid = {38764024},
issn = {1476-072X},
support = {/WT_/Wellcome Trust/United Kingdom ; 221963/Z/20/Z//Wellcome Trust and Royal Society/ ; BB/X511110/1//BBSRC and EPSRC Impact Accelerator Accounts/ ; },
mesh = {Humans ; Animals ; *Climate Change ; Malaria/epidemiology ; Mosquito Vectors ; Remote Sensing Technology/methods ; Geographic Information Systems ; Image Processing, Computer-Assisted/methods ; },
abstract = {BACKGROUND: In the near future, the incidence of mosquito-borne diseases may expand to new sites due to changes in temperature and rainfall patterns caused by climate change. Therefore, there is a need to use recent technological advances to improve vector surveillance methodologies. Unoccupied Aerial Vehicles (UAVs), often called drones, have been used to collect high-resolution imagery to map detailed information on mosquito habitats and direct control measures to specific areas. Supervised classification approaches have been largely used to automatically detect vector habitats. However, manual data labelling for model training limits their use for rapid responses. Open-source foundation models such as the Meta AI Segment Anything Model (SAM) can facilitate the manual digitalization of high-resolution images. This pre-trained model can assist in extracting features of interest in a diverse range of images. Here, we evaluated the performance of SAM through the Samgeo package, a Python-based wrapper for geospatial data, as it has not been applied to analyse remote sensing images for epidemiological studies.<br><br>RESULTS: We tested the identification of two land cover classes of interest: water bodies and human settlements, using different UAV acquired imagery across five malaria-endemic areas in Africa, South America, and Southeast Asia. We employed manually placed point prompts and text prompts associated with specific classes of interest to guide the image segmentation and assessed the performance in the different geographic contexts. An average Dice coefficient value of 0.67 was obtained for buildings segmentation and 0.73 for water bodies using point prompts. Regarding the use of text prompts, the highest Dice coefficient value reached 0.72 for buildings and 0.70 for water bodies. Nevertheless, the performance was closely dependent on each object, landscape characteristics and selected words, resulting in varying performance.<br><br>CONCLUSIONS: Recent models such as SAM can potentially assist manual digitalization of imagery by vector control programs, quickly identifying key features when surveying an area of interest. However, accurate segmentation still requires user-provided manual prompts and corrections to obtain precise segmentation. Further evaluations are necessary, especially for applications in rural areas.},
}
@article {pmid38762947,
year = {2024},
author = {Liu, D and Zhou, M and Tan, H and Xiong, G and Wang, L and Shi, L and Li, C and Wu, W and Qiao, Y},
title = {Metabolomics, volatolomics, and bioinformatics analyses of the effects of ultra-high pressure pretreatment on taste and flavour parameters of cured Culter alburnus.},
journal = {Food chemistry},
volume = {453},
number = {},
pages = {139649},
doi = {10.1016/j.foodchem.2024.139649},
pmid = {38762947},
issn = {1873-7072},
mesh = {Animals ; *Taste ; *Flavoring Agents/chemistry/metabolism ; *Metabolomics ; *Computational Biology ; Fish Products/analysis/microbiology ; Pressure ; Cyprinidae/metabolism/microbiology ; Volatile Organic Compounds/chemistry/metabolism/analysis ; Bacteria/metabolism/genetics/classification/isolation &amp; purification ; Humans ; Food Handling ; Amino Acids/metabolism/analysis ; },
abstract = {The effects of ultra-high pressure (UHP) pretreatment (50-250 MPa) on the fish curing were studied. UHP increased the overall volatile compound concentration of cured fish. Among 50-250 MPa five treatment groups, 150 MPa UHP group exhibited the highest total free amino acid content (294.34 mg/100 g) with that of the control group being 92.39 mg/100 g. The activity of cathepsin L was increased under 50-200 MPa UHP treatment (62.28-58.15 U/L), compared with that in the control group (53.80 U/L). UHP treatment resulted in a significant increase in small molecule compounds, especially the amino acid dipeptides and ATP metabolic products. Under UHP treatments, the bacterial phyla Actinobacteriota (1.04-5.25 %), Bacteroidota (0.20-4.47 %), and Deinococcota (0.00-0.05 %) exhibited an increased abundance, and they promoted taste and flavor formation. Our results indicated that UHP is a promising pretreatment method to improve taste and flavour in cured fish by affecting the microorganisms, cathepsin, and proteins.},
}
@article {pmid38760814,
year = {2024},
author = {Sakai, K and Igarashi, Y and Tounai, S and Shirai, C and Tsurugi, Y and Kakuno, F and Komasa, Y and Fujimura, M and Uruha, M and Mori, K and Tateishi, S},
title = {Key issues in Japan's public health centers to prepare for future pandemics: a text mining study using a topic model.},
journal = {BMC health services research},
volume = {24},
number = {1},
pages = {636},
pmid = {38760814},
issn = {1472-6963},
mesh = {Humans ; Japan ; *COVID-19/epidemiology ; Cross-Sectional Studies ; *Pandemics ; Surveys and Questionnaires ; Data Mining/methods ; Public Health ; SARS-CoV-2 ; Male ; },
abstract = {BACKGROUND: In Japan, over 450 public health centers played a central role in the operation of the local public health system in response to the COVID-19 pandemic. This study aimed to identify key issues for improving the system for public health centers for future pandemics.<br><br>METHODS: We conducted a cross-sectional study using an online questionnaire. The respondents were first line workers in public health centers or local governments during the pandemic. We solicited open-ended responses concerning improvements needed for future pandemics. Issues were identified from these descriptions using morphological analysis and a topic model with KHcoder3.0. The number of topics was estimated using Perplexity as a measure, and Latent Dirichlet Allocation for meaning identification.<br><br>RESULTS: We received open-ended responses from 784 (48.6%) of the 1,612 survey respondents, which included 111 physicians, 330 nurses, and 172 administrative staff. Morphological analysis processed these descriptions into 36,632 words. The topic model summarized them into eight issues: 1) establishment of a crisis management system, 2) division of functions among public health centers, prefectures, and medical institutions, 3) clear role distribution in public health center staff, 4) training of specialists, 5) information sharing system (information about infectious diseases and government policies), 6) response to excessive workload (support from other local governments, cooperation within public health centers, and outsourcing), 7) streamlining operations, and 8) balance with regular duties.<br><br>CONCLUSIONS: This study identified key issues that need to be addressed to prepare Japan's public health centers for future pandemics. These findings are vital for discussions aimed at strengthening the public health system based on experiences from the COVID-19 pandemic.},
}
@article {pmid38758962,
year = {2024},
author = {Massey, A and Boennec, C and Restrepo-Ortiz, CX and Blanchet, C and Alizon, S and Sofonea, MT},
title = {Real-time forecasting of COVID-19-related hospital strain in France using a non-Markovian mechanistic model.},
journal = {PLoS computational biology},
volume = {20},
number = {5},
pages = {e1012124},
pmid = {38758962},
issn = {1553-7358},
mesh = {*COVID-19/epidemiology ; Humans ; France/epidemiology ; *Forecasting/methods ; *SARS-CoV-2 ; Computational Biology/methods ; Retrospective Studies ; Models, Statistical ; Pandemics/statistics &amp; numerical data ; Hospitals/statistics &amp; numerical data ; Hospitalization/statistics &amp; numerical data ; Bed Occupancy/statistics &amp; numerical data ; },
abstract = {Projects such as the European Covid-19 Forecast Hub publish forecasts on the national level for new deaths, new cases, and hospital admissions, but not direct measurements of hospital strain like critical care bed occupancy at the sub-national level, which is of particular interest to health professionals for planning purposes. We present a sub-national French framework for forecasting hospital strain based on a non-Markovian compartmental model, its associated online visualisation tool and a retrospective evaluation of the real-time forecasts it provided from January to December 2021 by comparing to three baselines derived from standard statistical forecasting methods (a naive model, auto-regression, and an ensemble of exponential smoothing and ARIMA). In terms of median absolute error for forecasting critical care unit occupancy at the two-week horizon, our model only outperformed the naive baseline for 4 out of 14 geographical units and underperformed compared to the ensemble baseline for 5 of them at the 90% confidence level (n = 38). However, for the same level at the 4 week horizon, our model was never statistically outperformed for any unit despite outperforming the baselines 10 times spanning 7 out of 14 geographical units. This implies modest forecasting utility for longer horizons which may justify the application of non-Markovian compartmental models in the context of hospital-strain surveillance for future pandemics.},
}
@article {pmid38752675,
year = {2024},
author = {Schaupp, CM and Byrne, G and Chan, M and Haggard, DE and Hazemi, M and Jankowski, MD and LaLone, CA and LaTier, A and Mattingly, KZ and Olker, JH and Renner, J and Sharma, B and Villeneuve, DL},
title = {An automated computational data pipeline to rapidly acquire, score, and rank toxicological data for ecological hazard assessment.},
journal = {Integrated environmental assessment and management},
volume = {},
number = {},
pages = {},
doi = {10.1002/ieam.4945},
pmid = {38752675},
issn = {1551-3793},
support = {//USEPA Office of Research and Development, Chemical Safety for Sustainability National Research Program/ ; },
abstract = {Biological Evaluations support Endangered Species Act (ESA) consultation with the US Fish and Wildlife Service and National Marine Fisheries Service by federal action agencies, such as the USEPA, regarding impacts of federal activities on threatened or endangered species. However, they are often time-consuming and challenging to conduct. The identification of pollutant benchmarks or guidance to protect taxa for states and tribes when USEPA has not yet developed criteria recommendations is also of importance to ensure a streamlined approach to Clean Water Act program implementation. Due to substantial workloads, tight regulatory timelines, and the often-protracted length of ESA consultations, there is a need to streamline the development of biological evaluation toxicity assessments for determining the impact of chemical pollutants on ESA-listed species. Moreover, there is limited availability of species-specific toxicity data for many contaminants, further complicating the consultation process. New approach methodologies are being increasingly used in toxicology and chemical safety assessment to rapidly and cost-effectively provide data that can fill gaps in hazard and/or exposure characterization. Here, we present the development of an automated computational pipeline-RASRTox (Rapidly Acquire, Score, and Rank Toxicological data)-to rapidly extract and categorize ecological toxicity benchmark values from curated data sources (ECOTOX, ToxCast) and well-established quantitative structure-activity relationships (TEST, ECOSAR). As a proof of concept, points-of-departure (PODs) generated in RASRTox for 13 chemicals were compared against benchmark values derived using traditional methods-toxicity reference values (TRVs) and water quality criteria (WQC). The RASRTox PODs were generally within an order of magnitude of corresponding TRVs, though less concordant compared with WQC. The greatest utility of RASRTox, however, lies in its ability to quickly and systematically identify critical studies that may serve as a basis for screening value derivation by toxicologists as part of an ecological hazard assessment. As such, the strategy described in this case study can potentially be adapted for other risk assessment contexts and stakeholder needs. Integr Environ Assess Manag 2024;00:1-15. © 2024 Society of Environmental Toxicology &amp; Chemistry (SETAC). This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.},
}
@article {pmid38746391,
year = {2024},
author = {Acheampong, DA and Jenjaroenpun, P and Wongsurawat, T and Krulilung, A and Pomyen, Y and Kandel, S and Kunadirek, P and Chuaypen, N and Kusonmano, K and Nookaew, I},
title = {CAIM: Coverage-based Analysis for Identification of Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38746391},
issn = {2692-8205},
support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R01 CA143130/CA/NCI NIH HHS/United States ; },
abstract = {Accurate taxonomic profiling of microbial taxa in a metagenomic sample is vital to gain insights into microbial ecology. Recent advancements in sequencing technologies have contributed tremendously toward understanding these microbes at species resolution through a whole shotgun metagenomic (WMS) approach. In this study, we developed a new bioinformatics tool, CAIM, for accurate taxonomic classification and quantification within both long- and short-read metagenomic samples using an alignment-based method. CAIM depends on two different containment techniques to identify species in metagenomic samples using their genome coverage information to filter out false positives rather than the traditional approach of relative abundance. In addition, we propose a nucleotide-count based abundance estimation, which yield lesser root mean square error than the traditional read-count approach. We evaluated the performance of CAIM on 28 metagenomic mock communities and 2 synthetic datasets by comparing it with other top-performing tools. CAIM maintained a consitently good performance across datasets in identifying microbial taxa and in estimating relative abundances than other tools. CAIM was then applied to a real dataset sequenced on both Nanopore (with and without amplification) and Illumina sequencing platforms and found high similality of taxonomic profiles between the sequencing platforms. Lastly, CAIM was applied to fecal shotgun metagenomic datasets of 232 colorectal cancer patients and 229 controls obtained from 4 different countries and primary 44 liver cancer patients and 76 controls. The predictive performance of models using the genome-coverage cutoff was better than those using the relative-abundance cutoffs in discriminating colorectal cancer and primary liver cancer patients from healthy controls with a highly confident species markers.},
}
@article {pmid38741754,
year = {2024},
author = {Klatt, S and Otte, FW and Beavan, A and Schumacher, T and Millar, SK},
title = {How did you perform? Investigating football players' perception of self-regulated passing performances under auditory noise environments.},
journal = {Frontiers in psychology},
volume = {15},
number = {},
pages = {1390487},
pmid = {38741754},
issn = {1664-1078},
abstract = {INTRODUCTION: This paper deals with the question on how sport performances may be influenced by internal, emotional processes, which stem from outside feedback.<br><br>METHODS: In terms of methods, players' subjective performance ratings for four experimental auditory cue conditions were examined; these included both 'positive' and 'negative' stadium noise, 'no (auditory) conditions,' and a control/'baseline' condition. This resulted in a qualitative-analytic data set that was obtained succeeding each auditory cue condition using a unique football training machine (i.e., known as 'Footbonaut'). Without having received any coaching/performance feedback, players were asked to rate and individually comment on their perceived performance ratings for each experimental auditory condition.<br><br>RESULTS: Findings indicate stronger and more significant correlations between auditory conditions and subjective ratings compared to the non-auditory condition and its subjective rating. Furthermore, data provides initial insight into players' emotional experiences during each of the practice conditions.<br><br>DISCUSSION: These noteworthy findings on players' abilities to accurately judge their performances based on selfmonitoring and intrinsic feedback are discussed from an Ecological Dynamics perspective, linked to a Nonlinear Pedagogy for coaching. Here, representative and affective learning designs for skill learning and performance preparation are presented. Finally, a hypothetical catalyst effect of auditory stadium noise on subjective performance rating is proposed.},
}
@article {pmid38741150,
year = {2024},
author = {Sõukand, R},
title = {Dark local knowledge: the yet-to-be scientifically discovered and locally acknowledged aspects of local knowledge systems.},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {20},
number = {1},
pages = {50},
pmid = {38741150},
issn = {1746-4269},
mesh = {*Knowledge ; Humans ; Science ; },
abstract = {This essay brings forward the idea that there is more than meets the eye in local knowledge systems than what science can show us now. To comprehend this, we need to make a conceptual jump and look for the "dark matter" (the notion borrowed from astronomy that refers to a hypothetical form of matter that does not interact with light or electromagnetic fields) that can potentially sustain local knowledge. Considering that it is a complex of knowledge, practices, and beliefs contained in TEK, knowledge in LEK does not correspond to the notion of knowledge in science. Therefore, in order to map LEK-science interactions, we will refer to the concept of peoples' knowledge of LEK as acknowledgement and the scientific recognition and awareness of information, facts, and principles as knowledge. Applying this to a Johari Window, we can observe four categories of LEK in a known-unknown/acknowledged-unacknowledged matrix. We can refer to unknown and unacknowledged as dark local knowledge. Indeed, local knowledge systems contain many aspects that modern science cannot yet explain, as a major part of its components are not even considered in scholarly research. Dark local knowledge can potentially provide us with the invaluable touch of experience of countless generations, opening different ways of seeing reality.},
}
@article {pmid38739654,
year = {2024},
author = {Bloxham, B and Lee, H and Gore, J},
title = {Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches.},
journal = {PLoS computational biology},
volume = {20},
number = {5},
pages = {e1012049},
pmid = {38739654},
issn = {1553-7358},
mesh = {*Biodiversity ; *Models, Biological ; *Ecosystem ; Computational Biology ; Animals ; },
abstract = {How natural communities maintain their remarkable biodiversity and which species survive in complex communities are central questions in ecology. Resource competition models successfully explain many phenomena but typically predict only as many species as resources can coexist. Here, we demonstrate that sequential resource utilization, or diauxie, with periodic growth cycles can support many more species than resources. We explore how communities modify their own environments by sequentially depleting resources to form sequences of temporal niches, or intermediately depleted environments. Biodiversity is enhanced when community-driven or environmental fluctuations modulate the resource depletion order and produce different temporal niches on each growth cycle. Community-driven fluctuations under constant environmental conditions are rare, but exploring them illuminates the temporal niche structure that emerges from sequential resource utilization. With environmental fluctuations, we find most communities have more stably coexisting species than resources with survivors accurately predicted by the same temporal niche structure and each following a distinct optimal strategy. Our results thus present a new niche-based approach to understanding highly diverse fluctuating communities.},
}
@article {pmid38729378,
year = {2024},
author = {Yu, H and Yin, D and Yang, B and Yang, Y and Chen, F},
title = {Challenges for sustainable development goal of land degradation neutrality in drylands: Evidence from the Northern Slope of the Tianshan Mountains, China.},
journal = {The Science of the total environment},
volume = {932},
number = {},
pages = {173094},
doi = {10.1016/j.scitotenv.2024.173094},
pmid = {38729378},
issn = {1879-1026},
abstract = {The SDG 15.3.1 target of Land Degradation Neutrality (LDN) only has 15 years from conception (in 2015) to realization (in 2030). Therefore, investigating the effectiveness and challenges of LDN has become a priority, especially in drylands, where fragile ecosystems intersect with multiple disturbances. In this study, solutions are proposed and validated based on the challenges of LDN. We chose the Northern Slope of the Tianshan Mountains as a case study and set baselines in 2005 and 2010. The region and degree of land change (including degraded, stable, and improved) were depicted at the pixel scale (100 × 100 m), and LDN realization was assessed at the regional scale (including administrative districts and 5000 × 5000 m grids). The results showed a significant disparity between the two baselines. The number of areas that realized the LDN target was rare, regardless of the scale of the administrative districts or grids. Chord plots, Spearman's correlation, and curve estimation were employed to reveal the relationship between LDN and seven natural or socioeconomic factors. We found that substantial degradation was closely related to the expansion of unused, urban, and mining land and reduction in water, glaciers, and forests. Further evidence suggests that agricultural development both positively and negatively affects LDN, whereas urbanization and mining activities are undesirable for LDN. Notably, the adverse effects of glacier melting require additional attention. Therefore, we consider the easy-to-achieve and hard-to-achieve baselines as the mandatory and desirable targets of LDN, respectively, and focus further efforts in three aspects: preventing agricultural exploitation from occupying ecological resources, defining reasonable zones for urbanization and mining, and reducing greenhouse gas emissions to mitigate warming. Overall, this study is expected to be a beneficial addition to existing LDN theoretical systems and serve as a case validation of the challenges of LDN in drylands.},
}
@article {pmid38724591,
year = {2024},
author = {Bhandari, N and Bald, L and Wraase, L and Zeuss, D},
title = {Multispectral analysis-ready satellite data for three East African mountain ecosystems.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {473},
pmid = {38724591},
issn = {2052-4463},
support = {5064//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 2358//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Climate Change ; *Ecosystem ; Environmental Monitoring/methods ; Ethiopia ; Remote Sensing Technology ; *Satellite Imagery ; Tanzania ; },
abstract = {The East African mountain ecosystems are facing increasing threats due to global change, putting their unique socio-ecological systems at risk. To monitor and understand these changes, researchers and stakeholders require accessible analysis-ready remote sensing data. Although satellite data is available for many applications, it often lacks accurate geometric orientation and has extensive cloud cover. This can generate misleading results and make it unreliable for time-series analysis. Therefore, it needs comprehensive processing before usage, which encompasses multi-step operations, requiring large computational and storage capacities, as well as expert knowledge. Here, we provide high-quality, atmospherically corrected, and cloud-free analysis-ready Sentinel-2 imagery for the Bale Mountains (Ethiopia), Mounts Kilimanjaro and Meru (Tanzania) ecosystems in East Africa. Our dataset ranges from 2017 to 2021 and is provided as monthly and annual aggregated products together with 24 spectral indices. Our dataset enables researchers and stakeholders to conduct immediate and impactful analyses. These applications can include vegetation mapping, wildlife habitat assessment, land cover change detection, ecosystem monitoring, and climate change research.},
}
@article {pmid38724027,
year = {2024},
author = {Dar, FA and Hamid, M and Malik, RA and Wani, SA and Singh, CP and Shah, MA and Khuroo, AA},
title = {ToTE: A global database on trees of the treeline ecotone.},
journal = {Ecology},
volume = {105},
number = {6},
pages = {e4309},
doi = {10.1002/ecy.4309},
pmid = {38724027},
issn = {1939-9170},
support = {923/CSIR-UGC NET JUNE 2019//University Grants Commission/ ; SR/FST/LS-II/2017/103(C)//Department of Science &amp; Technology, Govt. of India, New Delhi/ ; SAC/EPSA/ALPINE/SHRESTI/10/2019//Space Applications Centre (SAC) ISRO, Ahmedabad/ ; },
mesh = {*Trees ; *Databases, Factual ; Biodiversity ; Forests ; Ecosystem ; },
abstract = {Globally, treelines form a transition zone between tree-dominated forest downslope and treeless alpine vegetation upslope. Treelines represent the highest boundary of "tree" life form in high-elevation mountains and at high latitudes. Recently, treelines have been shifting upslope in response to climate warming, so it has become important to understand global tree diversity and treeline distributions. However, to the best of our knowledge, no global database on tree flora of treelines exists, which limits our capacity to undertake macroecological analyses. Here, for the first time, we present a global data set on the trees of the treeline ecotone, supported by an online ToTE database. We synthesized the database from 1202 studies published over the last 60 years (1962 to 2022) following the Preferred Reporting Items in Systematic Reviews and Meta-Analysis (PRISMA) protocol. We classified the tree species in the database into three categories: treeline tree (TL) species, near to treeline (NTL) tree species, and tree species with an upper montane range limit (TUMR). The ToTE Version-1 presents a total of 208 tree taxa, including 189 species, five subspecies, and 14 varieties, belonging to 54 genera and 26 families distributed across 34 mountain regions worldwide that either grow exactly at the treeline or have a range limit below the treeline. Of the total taxa, 155, 14, and 39 belong to TL, NTL, and TUMR, respectively. Genera such as Abies, Picea, Pinus, Larix, and Juniperus are more represented in the treeline tree category. On the other hand, Acer, Prunus, Populus, and Quercus have more representatives in the near to treeline category, whereas Erica, Nothofagus, and Polylepis contribute more tree species with an upper montane range limit. Furthermore, families such as Rosaceae and Pinaceae include trees that occur both at the treeline and with an upper montane range limit, whereas Sapindaceae includes trees that occur exclusively near to treeline. Our database also includes information on the global distribution patterns of treeline tree species richness across mountains and biomes. The mountains with the highest number of tree species are the Andes (39) followed by the Himalaya (37). Close to 67% of tree species show restricted distributions in different mountains, with the highest endemism in the Andes and the Himalaya. In terms of tree species distribution, Pinus sylvestris was widespread, with a distribution across nine mountain regions, followed by Picea glauca and Fagus sylvatica, both distributed across five mountain regions. In terms of species' distribution across biomes, the temperate biome harbors the highest treeline tree species richness (152 species), which may reflect the fact that the majority of studies are available from the temperate regions of the world. The remaining 56 species are distributed within five other biomes, with the least in dry tropical and subarctic (four species each). Furthermore, currently 40 treeline tree species fall under different International Union for Conservation of Nature threat categories. We anticipate that our database will help advance research on macroecological, biogeographic, evolutionary, climate-change, and conservation aspects of the treeline on a global scale. The data are released under a Creative Commons Attribution 4.0 international license. Please cite this data paper when the data are reused.},
}
@article {pmid38723067,
year = {2024},
author = {Holstad, A and Voje, KL and Opedal, &#xd8;H and Bolstad, GH and Bourg, S and Hansen, TF and Pélabon, C},
title = {Evolvability predicts macroevolution under fluctuating selection.},
journal = {Science (New York, N.Y.)},
volume = {384},
number = {6696},
pages = {688-693},
doi = {10.1126/science.adi8722},
pmid = {38723067},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; *Fossils ; Genetic Variation ; *Selection, Genetic ; Datasets as Topic ; },
abstract = {Heritable variation is a prerequisite for evolutionary change, but the relevance of genetic constraints on macroevolutionary timescales is debated. By using two datasets on fossil and contemporary taxa, we show that evolutionary divergence among populations, and to a lesser extent among species, increases with microevolutionary evolvability. We evaluate and reject several hypotheses to explain this relationship and propose that an effect of evolvability on population and species divergence can be explained by the influence of genetic constraints on the ability of populations to track rapid, stationary environmental fluctuations.},
}
@article {pmid38721834,
year = {2024},
author = {Freedman, AH and Sackton, TB},
title = {Rethinking eco-evo studies of gene expression for non-model organisms in the genomic era.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17378},
doi = {10.1111/mec.17378},
pmid = {38721834},
issn = {1365-294X},
abstract = {Recent advances in genomic technology, including the rapid development of long-read sequencing technology and single-cell RNA-sequencing methods, are poised to significantly expand the kinds of studies that are feasible in ecological genomics. In this perspective, we review these new technologies and discuss their potential impact on gene expression studies in non-model organisms. Although traditional RNA-sequencing methods have been an extraordinarily powerful tool to apply functional genomics in an ecological context, bulk RNA-seq approaches often rely on de novo transcriptome assembly, and cannot capture expression changes in rare cell populations or distinguish shifts in cell type abundance. Advancements in genome assembly technology, particularly long-read sequencing, and improvements in the scalability of single-cell RNA-sequencing (scRNA-seq) offer unprecedented resolution in understanding cellular heterogeneity and gene regulation. We discuss the potential of these technologies to enable disentangling differential gene regulation from cell type composition differences and uncovering subtle expression patterns masked by bulk RNA-seq. The integration of these approaches provides a more nuanced understanding of the ecological and evolutionary dynamics of gene expression, paving the way for refined models and deeper insights into the generation of biodiversity.},
}
@article {pmid38721398,
year = {2024},
author = {Ross, KE and Bastian, FB and Buys, M and Cook, CE and D'Eustachio, P and Harrison, M and Hermjakob, H and Li, D and Lord, P and Natale, DA and Peters, B and Sternberg, PW and Su, AI and Thakur, M and Thomas, PD and Bateman, A and , },
title = {Perspectives on tracking data reuse across biodata resources.},
journal = {Bioinformatics advances},
volume = {4},
number = {1},
pages = {vbae057},
pmid = {38721398},
issn = {2635-0041},
support = {R35 GM141873/GM/NIGMS NIH HHS/United States ; },
abstract = {MOTIVATION: Data reuse is a common and vital practice in molecular biology and enables the knowledge gathered over recent decades to drive discovery and innovation in the life sciences. Much of this knowledge has been collated into molecular biology databases, such as UniProtKB, and these resources derive enormous value from sharing data among themselves. However, quantifying and documenting this kind of data reuse remains a challenge.<br><br>RESULTS: The article reports on a one-day virtual workshop hosted by the UniProt Consortium in March 2023, attended by representatives from biodata resources, experts in data management, and NIH program managers. Workshop discussions focused on strategies for tracking data reuse, best practices for reusing data, and the challenges associated with data reuse and tracking. Surveys and discussions showed that data reuse is widespread, but critical information for reproducibility is sometimes lacking. Challenges include costs of tracking data reuse, tensions between tracking data and open sharing, restrictive licenses, and difficulties in tracking commercial data use.&#xa0;Recommendations that emerged from the discussion include: development of standardized formats for documenting data reuse, education about the obstacles posed by restrictive licenses, and continued recognition by funding agencies that data management is a critical activity that requires dedicated resources.<br><br>Summaries of survey results are available at: https://docs.google.com/forms/d/1j-VU2ifEKb9C-sW6l3ATB79dgHdRk5v_lESv2hawnso/viewanalytics (survey of data providers) and https://docs.google.com/forms/d/18WbJFutUd7qiZoEzbOytFYXSfWFT61hVce0vjvIwIjk/viewanalytics (survey of users).},
}
@article {pmid38720068,
year = {2024},
author = {Mahon, MB and Sack, A and Aleuy, OA and Barbera, C and Brown, E and Buelow, H and Civitello, DJ and Cohen, JM and de Wit, LA and Forstchen, M and Halliday, FW and Heffernan, P and Knutie, SA and Korotasz, A and Larson, JG and Rumschlag, SL and Selland, E and Shepack, A and Vincent, N and Rohr, JR},
title = {A meta-analysis on global change drivers and the risk of infectious disease.},
journal = {Nature},
volume = {629},
number = {8013},
pages = {830-836},
pmid = {38720068},
issn = {1476-4687},
mesh = {Animals ; Humans ; Anthropogenic Effects ; *Biodiversity ; *Climate Change/statistics &amp; numerical data ; *Communicable Diseases/epidemiology/etiology ; Conservation of Natural Resources/trends ; Datasets as Topic ; *Environmental Pollution/adverse effects ; Forestry ; Forests ; *Introduced Species/statistics &amp; numerical data ; Plant Diseases/etiology ; Risk Assessment ; Urbanization ; },
abstract = {Anthropogenic change is contributing to the rise in emerging infectious diseases, which are significantly correlated with socioeconomic, environmental and ecological factors[1]. Studies have shown that infectious disease risk is modified by changes to biodiversity[2-6], climate change[7-11], chemical pollution[12-14], landscape transformations[15-20] and species introductions[21]. However, it remains unclear which global change drivers most increase disease and under what contexts. Here we amassed a dataset from the literature that contains 2,938 observations of infectious disease responses to global change drivers across 1,497 host-parasite combinations, including plant, animal and human hosts. We found that biodiversity loss, chemical pollution, climate change and introduced species are associated with increases in disease-related end points or harm, whereas urbanization is associated with decreases in disease end points. Natural biodiversity gradients, deforestation and forest fragmentation are comparatively unimportant or idiosyncratic as drivers of disease. Overall, these results are consistent across human and non-human diseases. Nevertheless, context-dependent effects of the global change drivers on disease were found to be common. The findings uncovered by this meta-analysis should help target disease management and surveillance efforts towards global change drivers that increase disease. Specifically, reducing greenhouse gas emissions, managing ecosystem health, and preventing biological invasions and biodiversity loss could help to reduce the burden of plant, animal and human diseases, especially when coupled with improvements to social and economic determinants of health.},
}
@article {pmid38718196,
year = {2024},
author = {Leroux, A and Crainiceanu, C and Zeger, S and Taub, M and Ansari, B and Wager, TD and Bayman, E and Coffey, C and Langefeld, C and McCarthy, R and Tsodikov, A and Brummet, C and Clauw, DJ and Edwards, RR and Lindquist, MA and , },
title = {Statistical modeling of acute and chronic pain patient-reported outcomes obtained from ecological momentary assessment.},
journal = {Pain},
volume = {},
number = {},
pages = {},
doi = {10.1097/j.pain.0000000000003214},
pmid = {38718196},
issn = {1872-6623},
support = {U54 DA049113/DA/NIDA NIH HHS/United States ; },
abstract = {Ecological momentary assessment (EMA) allows for the collection of participant-reported outcomes (PROs), including pain, in the normal environment at high resolution and with reduced recall bias. Ecological momentary assessment is an important component in studies of pain, providing detailed information about the frequency, intensity, and degree of interference of individuals' pain. However, there is no universally agreed on standard for summarizing pain measures from repeated PRO assessment using EMA into a single, clinically meaningful measure of pain. Here, we quantify the accuracy of summaries (eg, mean and median) of pain outcomes obtained from EMA and the effect of thresholding these summaries to obtain binary clinical end points of chronic pain status (yes/no). Data applications and simulations indicate that binarizing empirical estimators (eg, sample mean, random intercept linear mixed model) can perform well. However, linear mixed-effect modeling estimators that account for the nonlinear relationship between average and variability of pain scores perform better for quantifying the true average pain and reduce estimation error by up to 50%, with larger improvements for individuals with more variable pain scores. We also show that binarizing pain scores (eg, <3 and ≥3) can lead to a substantial loss of statistical power (40%-50%). Thus, when examining pain outcomes using EMA, the use of linear mixed models using the entire scale (0-10) is superior to splitting the outcomes into 2 groups (<3 and ≥3) providing greater statistical power and sensitivity.},
}
@article {pmid38717702,
year = {2024},
author = {Zhou, Q and Song, Y and Zhang, Y and Ping, Z and Zheng, Y and Chen, H and Liu, P and Hong, P and Zheng, Z},
title = {Land use transition and its effect on ecosystem service value with introducing "three wastes" factor in the industrial county, China.},
journal = {Environmental science and pollution research international},
volume = {31},
number = {24},
pages = {34962-34980},
pmid = {38717702},
issn = {1614-7499},
support = {ZR2023MD033//Natural Science Foundation of Shandong Province/ ; LJNY202103//Key Technology Research and Development Program of Shandong Province/ ; },
mesh = {China ; *Ecosystem ; Conservation of Natural Resources ; Urbanization ; Forests ; Environmental Monitoring ; },
abstract = {Land use transition and its impact on ecosystem service value (ESV) are the foundation for optimizing the layout of territorial space and ecological civilization construction. With the acceleration of industrialization and urbanization, the area of construction land expands in China. To accurately estimate the ESV in industrial counties, the impact of construction land on the ecological environment should be fully considered. This paper took Gangcheng District, Jinan City, a steel base in the Shandong Province of China as an example, then the value coefficients of "three wastes" factors (waste gas, wastewater, and waste) were introduced, and an improved calculation method of ESV was put forward for industrial counties in combination with remote sensing and land use data. Finally, the land use transition and its ESV effect in typical industrial counties were analyzed using geo-informatic Tupu and grid method. The results showed that the most important land use transitions were from grassland and forestland to cultivated land, from cultivated land and forestland to construction land in 1990-2010, and from cultivated land transformed to forestland in 2010-2021. The types of land use transition were mainly repetitive and continuous. The ESV first decreased and then increased, with a slight overall decline for more than 30 years, showing a spatial distribution characteristic of "low in the south-central and high around." Land use transition had the impact on ESV with the negative contribution rate of 68.28% in 1990-2000 and 73.16% in 2000-2010, mainly caused by the transition from forestland and grassland to cultivated land and construction land, and the positive contribution rate of 81.72% in 2010-2021, mainly caused by the transition from cultivated land to forestland. Compared with the ESV calculation method without introducing the "three wastes" factor and Xie Gaodi's method, the improved method in this paper considered the inevitable impact of construction land on ESV in industrial counties and made the ESV calculated more accurate according to the regional nature. This paper cannot only enrich the theories and technical methods of land use transition and its effects, and provide a case reference for similar industrial counties, but also provide data and decision-making support for the spatial layout and ecological protection in the study area.},
}
@article {pmid38716048,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Ruddy Flat-body, Agonopterix subpropinquella (Stainton, 1849).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {487},
pmid = {38716048},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Agonopterix subpropinquella (the Ruddy Flat-body; Arthropoda; Insecta; Lepidoptera; Depressariidae). The genome sequence is 667.9 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 16.5 kilobases in length. Gene annotation of this assembly on Ensembl identified 18,796 protein coding genes.},
}
@article {pmid38714914,
year = {2024},
author = {Zhang, L and Zhang, Y and Liu, Y and Miao, W and Ai, J and Li, J and Peng, S and Li, S and Ye, L and Zeng, R and Shi, X and Ma, J and Lin, Y and Kuang, W and Cui, R},
title = {Multi-omics analysis revealed that the protein kinase MoKin1 affected the cellular response to endoplasmic reticulum stress in the rice blast fungus, Magnaporthe oryzae.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {449},
pmid = {38714914},
issn = {1471-2164},
mesh = {*Endoplasmic Reticulum Stress ; *Oryza/microbiology/genetics ; *Fungal Proteins/metabolism/genetics ; *Proteomics ; Plant Diseases/microbiology ; Gene Expression Regulation, Fungal ; Protein Kinases/metabolism/genetics ; Mutation ; Multiomics ; Ascomycota ; },
abstract = {BACKGROUND: Previous studies have shown that protein kinase MoKin1 played an important role in the growth, conidiation, germination and pathogenicity in rice blast fungus, Magnaporthe oryzae. ΔMokin1 mutant showed significant phenotypic defects and significantly reduced pathogenicity. However, the internal mechanism of how MoKin1 affected the development of physiology and biochemistry remained unclear in M. oryzae.<br><br>RESULT: This study adopted a multi-omics approach to comprehensively analyze MoKin1 function, and the results showed that MoKin1 affected the cellular response to endoplasmic reticulum stress (ER stress). Proteomic analysis revealed that the downregulated proteins in &#x394;Mokin1 mutant were enriched mainly in the response to ER stress triggered by the unfolded protein. Loss of MoKin1 prevented the ER stress signal from reaching the nucleus. Therefore, the phosphorylation of various proteins regulating the transcription of ER stress-related genes and mRNA translation was significantly downregulated. The insensitivity to ER stress led to metabolic disorders, resulting in a significant shortage of carbohydrates and a low energy supply, which also resulted in severe phenotypic defects in &#x394;Mokin1 mutant. Analysis of MoKin1-interacting proteins indicated that MoKin1 really took participate in the response to ER stress.<br><br>CONCLUSION: Our results showed the important role of protein kinase MoKin1 in regulating cellular response to ER stress, providing a new research direction to reveal the mechanism of MoKin1 affecting pathogenic formation, and to provide theoretical support for the new biological target sites searching and bio-pesticides developing.},
}
@article {pmid38714759,
year = {2024},
author = {Lee, KS and Landry, Z and Athar, A and Alcolombri, U and Pramoj Na Ayutthaya, P and Berry, D and de Bettignies, P and Cheng, JX and Csucs, G and Cui, L and Deckert, V and Dieing, T and Dionne, J and Doskocil, O and D'Souza, G and García-Timermans, C and Gierlinger, N and Goda, K and Hatzenpichler, R and Henshaw, RJ and Huang, WE and Iermak, I and Ivleva, NP and Kneipp, J and Kubryk, P and Küsel, K and Lee, TK and Lee, SS and Ma, B and Martínez-Pérez, C and Matousek, P and Meckenstock, RU and Min, W and Mojzeš, P and Müller, O and Kumar, N and Nielsen, PH and Notingher, I and Palatinszky, M and Pereira, FC and Pezzotti, G and Pilat, Z and Plesinger, F and Popp, J and Probst, AJ and Riva, A and Saleh, AAE and Samek, O and Sapers, HM and Schubert, OT and Stubbusch, AKM and Tadesse, LF and Taylor, GT and Wagner, M and Wang, J and Yin, H and Yue, Y and Zenobi, R and Zini, J and Sarkans, U and Stocker, R},
title = {MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data.},
journal = {Nature microbiology},
volume = {9},
number = {5},
pages = {1152-1156},
pmid = {38714759},
issn = {2058-5276},
support = {GBMF9197//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 542395//Simons Foundation/ ; },
mesh = {*Spectrum Analysis, Raman/methods ; *Internet ; Humans ; Databases, Factual ; },
}
@article {pmid38714055,
year = {2024},
author = {Li, Z and Wang, J and Yue, H and Rehman, A and Yousaf, M and Du, M and Zhang, X},
title = {Applying metabolic modeling and multi-omics to elucidate the biotransformation mechanisms of marine algal toxin domoic acid (DA) in sediments.},
journal = {Journal of hazardous materials},
volume = {472},
number = {},
pages = {134541},
doi = {10.1016/j.jhazmat.2024.134541},
pmid = {38714055},
issn = {1873-3336},
mesh = {*Kainic Acid/analogs &amp; derivatives/metabolism ; *Geologic Sediments/microbiology ; *Biotransformation ; *Marine Toxins/metabolism ; Microbiota ; Metabolome ; Biodegradation, Environmental ; Metagenome ; Water Pollutants, Chemical/metabolism ; Multiomics ; },
abstract = {Domoic acid (DA)-producing algal blooms are a global marine environmental issue. However, there has been no previous research addressing the question regarding the fate of DA in marine benthic environments. In this work, we investigated the DA fate in the water-sediment microcosm via the integrative analysis of a top-down metabolic model, metagenome, and metabolome. Results demonstrated that biodegradation is the leading mechanism for the nonconservative attenuation of DA. Specifically, DA degradation was prominently completed by the sediment aerobic community, with a degradation rate of 0.0681 ± 0.00954 d[-1]. The DA degradation pathway included hydration, dehydrogenation, hydrolysis, decarboxylation, automatic ring opening of hydration, and β oxidation reactions. Moreover, the reverse ecological analysis demonstrated that the microbial community transitioned from nutrient competition to metabolic cross-feeding during DA degradation, further enhancing the cooperation between DA degraders and other taxa. Finally, we reconstructed the metabolic process of microbial communities during DA degradation and confirmed that the metabolism of amino acid and organic acid drove the degradation of DA. Overall, our work not only elucidated the fate of DA in marine environments but also provided crucial insights for applying metabolic models and multi-omics to investigate the biotransformation of other contaminants.},
}
@article {pmid38713735,
year = {2024},
author = {Oszoli, I and Zachar, I},
title = {Group-selection via aggregative propagule-formation enables cooperative multicellularity in an individual based, spatial model.},
journal = {PLoS computational biology},
volume = {20},
number = {5},
pages = {e1012107},
pmid = {38713735},
issn = {1553-7358},
mesh = {*Models, Biological ; *Biological Evolution ; Computational Biology ; Ecosystem ; Animals ; Predatory Behavior/physiology ; Selection, Genetic ; Computer Simulation ; },
abstract = {The emergence of multicellularity is one of the major transitions in evolution that happened multiple times independently. During aggregative multicellularity, genetically potentially unrelated lineages cooperate to form transient multicellular groups. Unlike clonal multicellularity, aggregative multicellular organisms do not rely on kin selection instead other mechanisms maintain cooperation against cheater phenotypes that benefit from cooperators but do not contribute to groups. Spatiality with limited diffusion can facilitate group selection, as interactions among individuals are restricted to local neighbourhoods only. Selection for larger size (e.g. avoiding predation) may facilitate the emergence of aggregation, though it is unknown, whether and how much role such selection played during the evolution of aggregative multicellularity. We have investigated the effect of spatiality and the necessity of predation on the stability of aggregative multicellularity via individual-based modelling on the ecological timescale. We have examined whether aggregation facilitates the survival of cooperators in a temporally heterogeneous environment against cheaters, where only a subset of the population is allowed to periodically colonize a new, resource-rich habitat. Cooperators constitutively produce adhesive molecules to promote aggregation and propagule-formation while cheaters spare this expense to grow faster but cannot aggregate on their own, hence depending on cooperators for long-term survival. We have compared different population-level reproduction modes with and without individual selection (predation) to evaluate the different hypotheses. In a temporally homogeneous environment without propagule-based colonization, cheaters always win. Predation can benefit cooperators, but it is not enough to maintain the necessary cooperator amount in successive dispersals, either randomly or by fragmentation. Aggregation-based propagation however can ensure the adequate ratio of cooperators-to-cheaters in the propagule and is sufficient to do so even without predation. Spatiality combined with temporal heterogeneity helps cooperators via group selection, thus facilitating aggregative multicellularity. External stress selecting for larger size (e.g. predation) may facilitate aggregation, however, according to our results, it is neither necessary nor sufficient for aggregative multicellularity to be maintained when there is effective group-selection.},
}
@article {pmid38711355,
year = {2024},
author = {Tsutsui, K and Tanaka, R and Takeda, K and Fujii, K},
title = {Collaborative hunting in artificial agents with deep reinforcement learning.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {38711355},
issn = {2050-084X},
support = {20H04075//Japan Society for the Promotion of Science/ ; 21H04892//Japan Society for the Promotion of Science/ ; 21H05300//Japan Society for the Promotion of Science/ ; 22K17673//Japan Society for the Promotion of Science/ ; JPMJPR20CA//Japan Science and Technology Agency/ ; },
mesh = {Animals ; *Deep Learning ; *Predatory Behavior ; *Reinforcement, Psychology ; Cooperative Behavior ; Humans ; Computer Simulation ; Decision Making ; },
abstract = {Collaborative hunting, in which predators play different and complementary roles to capture prey, has been traditionally believed to be an advanced hunting strategy requiring large brains that involve high-level cognition. However, recent findings that collaborative hunting has also been documented in smaller-brained vertebrates have placed this previous belief under strain. Here, using computational multi-agent simulations based on deep reinforcement learning, we demonstrate that decisions underlying collaborative hunts do not necessarily rely on sophisticated cognitive processes. We found that apparently elaborate coordination can be achieved through a relatively simple decision process of mapping between states and actions related to distance-dependent internal representations formed by prior experience. Furthermore, we confirmed that this decision rule of predators is robust against unknown prey controlled by humans. Our computational ecological results emphasize that collaborative hunting can emerge in various intra- and inter-specific interactions in nature, and provide insights into the evolution of sociality.},
}
@article {pmid38709778,
year = {2024},
author = {Xu, N and Zeng, P and Guo, Y and Siddique, MA and Li, J and Ren, X and Tang, F and Zhang, R},
title = {The spatiotemporal evolution of rural landscape patterns in Chinese metropolises under rapid urbanization.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0301754},
pmid = {38709778},
issn = {1932-6203},
mesh = {China ; Cities ; Conservation of Natural Resources ; Ecosystem ; Geographic Information Systems ; Rural Population ; Spatio-Temporal Analysis ; *Urbanization ; },
abstract = {Understanding the evolution of rural landscapes in metropolises during rapid urbanization is crucial for formulating policies to protect the rural ecological environment. In this study, remote sensing and geographical information system data, as well as applied landscape index analysis, are used to examine the spatiotemporal evolution of rural landscape patterns in the Beijing-Tianjin region of China, which has experienced rapid urbanization. The relationships between land use/land cover changes and changes in rural landscape patterns are explored. The results revealed significant spatial differences in the rural landscapes in the Beijing-Tianjin region; farmland and forestland were the main types of landscapes, creating a "mountain-field-sea" natural landscape pattern. The conversion of rural landscapes in the Beijing-Tianjin region involved mainly the conversion of farmland to urban areas, with few exchanges between other landscape types. The urban areas in the Beijing-Tianjin region increased by 3% per decade; farmland decreased at the same rate. Additionally, the rural landscape patterns in the Beijing-Tianjin region were dominated by fragmentation, dispersion, and heterogeneity and moved from complex to regular. Water bodies displayed the most fragmented natural landscape; their number of patches increased by 36%, though their network characteristics were maintained. Forestland was the most concentrated natural landscape. In this study, theoretical support and a scientific reference for the optimization of rural landscape patterns and the improvement in rural living environments in rapidly urbanizing areas are provided.},
}
@article {pmid38707490,
year = {2023},
author = {Boyes, D and Phillips, D and , and , and , and , and , and , },
title = {The genome sequence of the Early Thorn, Selenia dentaria (Fabricius, 1775).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {485},
pmid = {38707490},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Selenia dentaria (the Early Thorn; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 1,030.8 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.41 kilobases in length. Gene annotation of this assembly on Ensembl identified 21,390 protein coding genes.},
}
@article {pmid38705187,
year = {2024},
author = {Meier, R and Hartop, E and Pylatiuk, C and Srivathsan, A},
title = {Towards holistic insect monitoring: species discovery, description, identification and traits for all insects.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1904},
pages = {20230120},
pmid = {38705187},
issn = {1471-2970},
mesh = {*Insecta/physiology/classification/genetics ; Animals ; *DNA Barcoding, Taxonomic/methods ; Biodiversity ; },
abstract = {Holistic insect monitoring needs scalable techniques to overcome taxon biases, determine species abundances, and gather functional traits for all species. This requires that we address taxonomic impediments and the paucity of data on abundance, biomass and functional traits. We here outline how these data deficiencies could be addressed at scale. The workflow starts with large-scale barcoding (megabarcoding) of all specimens from mass samples obtained at biomonitoring sites. The barcodes are then used to group the specimens into molecular operational taxonomic units that are subsequently tested/validated as species with a second data source (e.g. morphology). New species are described using barcodes, images and short diagnoses, and abundance data are collected for both new and described species. The specimen images used for species discovery then become the raw material for training artificial intelligence identification algorithms and collecting trait data such as body size, biomass and feeding modes. Additional trait data can be obtained from vouchers by using genomic tools developed by molecular ecologists. Applying this pipeline to a few samples per site will lead to greatly improved insect monitoring regardless of whether the species composition of a sample is determined with images, metabarcoding or megabarcoding. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.},
}
@article {pmid38704010,
year = {2024},
author = {Song, X and Li, C and Qiu, Z and Wang, C and Zeng, Q},
title = {Ecotoxicological effects of polyethylene microplastics and lead (Pb) on the biomass, activity, and community diversity of soil microbes.},
journal = {Environmental research},
volume = {252},
number = {Pt 3},
pages = {119012},
doi = {10.1016/j.envres.2024.119012},
pmid = {38704010},
issn = {1096-0953},
mesh = {*Soil Microbiology ; *Lead/toxicity ; *Soil Pollutants/toxicity ; *Microplastics/toxicity ; *Biomass ; *Polyethylene/toxicity ; Soil/chemistry ; Ecotoxicology ; },
abstract = {Microplastics and heavy metals are ubiquitous and persistent contaminants that are widely distributed worldwide, yet little is known about the effects of their interaction on soil ecosystems. A soil incubation experiment was conducted to investigate the individual and combined effects of polyethylene microplastics (PE-MPs) and lead (Pb) on soil enzymatic activities, microbial biomass, respiration rate, and community diversity. The results indicate that the presence of PE-MPs notably reduced soil pH and elevated soil Pb bioavailability, potentially exacerbated the combined toxicity on the biogeochemical cycles of soil nutrients, microbial biomass carbon and nitrogen, and the activities of soil urease, sucrase, and alkaline phosphatase. Soil CO2 emissions increased by 7.9% with PE-MPs alone, decreased by 46.3% with single Pb, and reduced by 69.4% with PE-MPs and Pb co-exposure, compared to uncontaminated soils. Specifically, the presence of PE-MPs and Pb, individually and in combination, facilitated the soil metabolic quotient, leading to reduced microbial metabolic efficiency. Moreover, the addition of Pb and PE-MPs modified the composition of the microbial community, leading to the enrichment of specific taxa. Tax4Fun analysis showed the effects of Pb, PE-MPs and their combination on the biogeochemical processes and ecological functions of microbes were mainly by altering amino acid metabolism, carbohydrate metabolism, membrane transport, and signal transduction. These findings offer valuable insights into the ecotoxicological effects of combined PE-MPs and Pb on soil microbial dynamics, reveals key assembly mechanisms and environmental drivers, and highlights the potential threat of MPs and heavy metals to the multifunctionality of soil ecosystems.},
}
@article {pmid38703986,
year = {2024},
author = {Li, JY and Yao, S and Mo, Z and Miao, Y and Chen, Y and He, W and Jin, L and Tang, W},
title = {Submerged plant-biochar composite system exhibits effective control over residual organic pollutants in the benthic organisms of aquaculture ponds.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {351},
number = {},
pages = {124078},
doi = {10.1016/j.envpol.2024.124078},
pmid = {38703986},
issn = {1873-6424},
mesh = {*Aquaculture ; *Water Pollutants, Chemical/analysis/metabolism ; *Charcoal/chemistry ; *Ponds/chemistry ; *Geologic Sediments/chemistry ; Corbicula ; Biodegradation, Environmental ; Hydrocharitaceae/metabolism ; Animals ; },
abstract = {As of now, submerged plants and biochar have demonstrated significant benefits in aquaculture pond sediment remediation. However, there is limited research on the synergistic effects of biochar and submerged plants in mitigating hydrophobic organic contaminant (HOC) accumulation in aquaculture benthic organisms and in controlling the nutrient (nitrogen and phosphorus) levels in aquaculture water. This study assesses a submerged plant-biochar system's efficacy in removing HOCs from simulated freshwater aquaculture ponds. Vallisneria natans was planted in sediment with varying levels of wheat straw biochar, while Corbicula fluminea served as the targeted benthic organism. The bioaccumulation experiment identified the optimal biochar ratio for the Vallisneria natans-biochar system in controlling HOCs in aquaculture products. Analyses included final accumulation concentrations in benthic organisms, changes in freely-dissolved concentrations in aquaculture sediment, and a mass balance calculation to explore key factors in their removal from the system. Results indicated that the Vallisneria natans-1.5% biochar composite system achieved optimal control of HOCs in sediment and aquaculture products. Biochar addition to the sediment in the composite system demonstrated a "promotion with low addition, inhibition with high addition" effect on Vallisneria natans growth. Notably, the addition of 1.5% biochar (VN1.5 group) significantly promoted the growth of Vallisneria natans leaves and roots. Comparing the final pollutant proportions in different environmental media, concentrations in water (0.20%-1.8%), clam accumulation (0.032%-0.11%), and plant absorption (0.10%-0.44%) constituted a minimal portion of the overall pollutant load in the system. The majority of pollutants (24%-65%) were degraded in the aquaculture environment, with microbial degradation likely playing a predominant role. Bacterial phyla, particularly Proteobacteria and Firmicutes, were identified as potential direct contributors to pollutant degradation in the Vallisneria natans-biochar system.},
}
@article {pmid38696025,
year = {2024},
author = {Xiao, Y and Luan, H and Lu, S and Xing, M and Guo, C and Qian, R and Xiao, X},
title = {Correction: Toxic effects of atmospheric deposition in mining areas on wheat seedlings.},
journal = {Environmental geochemistry and health},
volume = {46},
number = {6},
pages = {199},
doi = {10.1007/s10653-024-01986-5},
pmid = {38696025},
issn = {1573-2983},
}
@article {pmid38689759,
year = {2024},
author = {Falk, S and Poole, O and , and , and , and , and , and , and , },
title = {The genome sequence of a conopid fly, Myopa testacea (Linnaeus, 1767).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {99},
pmid = {38689759},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual male Myopa testacea (conopid fly; Arthropoda; Insecta; Diptera; Conopidae). The genome sequence is 243.3 megabases in span. Most of the assembly is scaffolded into 5 chromosomal pseudomolecules, including the X and Y sex chromosomes. The mitochondrial genome has also been assembled and is 17.61 kilobases in length. Gene annotation of this assembly on Ensembl identified 25,472 protein coding genes.},
}
@article {pmid38688387,
year = {2024},
author = {Hu, YL and Liu, Y and Fu, W and Yang, H},
title = {Efficiency and mechanism of enhanced norfloxacin removal using amorphous TiO2-modified biochar.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {351},
number = {},
pages = {124027},
doi = {10.1016/j.envpol.2024.124027},
pmid = {38688387},
issn = {1873-6424},
mesh = {*Charcoal/chemistry ; *Titanium/chemistry ; *Norfloxacin/chemistry ; Adsorption ; *Water Pollutants, Chemical/chemistry ; Anti-Bacterial Agents/chemistry ; Wastewater/chemistry ; Waste Disposal, Fluid/methods ; },
abstract = {Inadequate treatment of antibiotic-contaminated wastewater, including compounds such as norfloxacin (NOR), poses a substantial treat to both ecological safety and human well-being. An innovative approach was devised to address NOR pollution using amorphous TiO2 modified biochar (A-TiO2/BC) prepared via sol-gel impregnation. The resultant had a commendably specific surface area of 131.8 m[2]/g[-1], which was 1.91 times more than the original surface area of unmodified BC. A-TiO2/BC also exhibited abundant hydroxyl and oxygen-containing functional groups, thereby provided adequately active sites for NOR adsorption. R[2] values obtained from NOR isotherm adsorption models descended in order of Freundlich < Temkin < Sips < Langmuir, which indicated that the NOR removal by A-TiO2/BC mainly complied with monolayer adsorption accompanied by heterogeneous surface adsorption. Under weakly acidic conditions, NOR adsorption benefits from the synergistic physicochemical interactions of A-TiO2 and BC. Notably, A-TiO2/BC demonstrated an impressive NOR adsorption capacity of up to 78.14 mg g[-1], with a dosage of 20 mg L[-1] at 25 °C under pH 6. Such A-TiO2 modified biochar thus presents a promising alternative for NOR removal.},
}
@article {pmid38688113,
year = {2024},
author = {Ghani, MI and Yi, B and Rehmani, MS and Wei, X and Siddiqui, JA and Fan, R and Liu, Y and El-Sheikh, MA and Chen, X and Ahmad, P},
title = {Potential of melatonin and Trichoderma harzianum inoculation in ameliorating salt toxicity in watermelon: Insights into antioxidant system, leaf ultrastructure, and gene regulation.},
journal = {Plant physiology and biochemistry : PPB},
volume = {211},
number = {},
pages = {108639},
doi = {10.1016/j.plaphy.2024.108639},
pmid = {38688113},
issn = {1873-2690},
mesh = {*Citrullus/microbiology/drug effects/metabolism ; *Melatonin/pharmacology ; *Antioxidants/metabolism ; *Plant Leaves/drug effects/metabolism ; *Gene Expression Regulation, Plant/drug effects ; Salt Stress ; Hypocreales ; Photosynthesis/drug effects ; Oxidative Stress/drug effects ; },
abstract = {Melatonin (MT) is an extensively studied biomolecule with dual functions, serving as an antioxidant and a signaling molecule. Trichoderma Harzianum (TH) is widely recognized for its effectiveness as a biocontrol agent against many plant pathogens. However, the interplay between seed priming and MT (150 μm) in response to NaCl (100 mM) and its interaction with TH have rarely been investigated. This study aimed to evaluate the potential of MT and TH, alone and in combination, to mitigate salt stress (SS) in watermelon plants. The findings of this study revealed a significant decline in the morphological, physiological, and biochemical indices of watermelon seedlings exposed to SS. However, MT and TH treatments reduced the negative impact of salt stress. The combined application of MT and TH exerted a remarkable positive effect by increasing the growth, photosynthetic and gas exchange parameters, chlorophyll fluorescence indices, and ion balance (decreasing Na[+] and enhancing K[+]). MT and TH effectively alleviated oxidative injury by inhibiting hydrogen peroxide formation in saline and non-saline environments, as established by reduced lipid peroxidation and electrolyte leakage. Moreover, oxidative injury induced by SS on the cells was significantly mitigated by regulation of the antioxidant system, AsA-GSH-related enzymes, the glyoxalase system, augmentation of osmolytes, and activation of several genes involved in the defense system. Additionally, the reduction in oxidative damage was examined by chloroplast integrity via transmission electron microscopy (TEM). Overall, the results of this study provide a promising contribution of MT and TH in safeguarding the watermelon crop from oxidative damage induced by salt stress.},
}
@article {pmid38686023,
year = {2024},
author = {Boyes, D and Blaxter, ML and , and , and , and , and , and , },
title = {The genome sequence of the Tipped Oak Case-bearer, Coleophora flavipennella (Duponchel 1843).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {3},
pmid = {38686023},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Coleophora flavipennella (the Tipped Oak Case-bearer; Arthropoda; Insecta; Lepidoptera; Coleophoridae). The genome sequence is 989.3 megabases in span. Most of the assembly is scaffolded into 57 chromosomal pseudomolecules, including the W and Z sex chromosomes. The mitochondrial genome has also been assembled and is 15.77 kilobases in length.},
}
@article {pmid38684755,
year = {2024},
author = {Yang, P and Huang, G and Li, Y and Yu, L and Yin, Z and Li, Q},
title = {Identification of PANoptosis-related biomarkers and analysis of prognostic values in head and neck squamous cell carcinoma.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9824},
pmid = {38684755},
issn = {2045-2322},
mesh = {Humans ; *Squamous Cell Carcinoma of Head and Neck/genetics/pathology/metabolism/mortality ; *Biomarkers, Tumor/metabolism/genetics ; Prognosis ; *Head and Neck Neoplasms/genetics/pathology/metabolism ; *Gene Expression Regulation, Neoplastic ; Female ; Male ; Computational Biology/methods ; Gene Expression Profiling ; Fas-Associated Death Domain Protein/metabolism/genetics ; Lymphatic Metastasis ; },
abstract = {PANoptosis plays a crucial role in cancer initiation and progression. However, the roles of PANoptosis-related genes (PARGs) in the prognosis and immune landscape of head and neck squamous cell carcinoma (HNSCC) remain unclear. Integrated bioinformatics analyses based on the data of HNSCC patients in the TCGA database were conducted. We extracted 48 PARGs expression profile and then conducted differentially expressed analysis, following building a Cox model to predict the survival of HNSCC patients. Subsequently, the relationships between the risk score, immune landscape, chemo-, and immune-therapy responses were analyzed, respectively. Moreover, we investigated the prognostic value, and further predicted the pathways influenced by PARGs. Finally, we identified the biological function of crucial PARGs. A total of 18 differentially expressed PARGs were identified in HNSCC, and a Cox model including CASP8, FADD, NLRP1, TNF, and ZBP1 was constructed, which showed that the risk score was associated with the prognosis as well as immune infiltration of HNSCC patients, and the risk score could be regarded as an independent biomarker. Additionally, patients with high-risk score might be an indicator of lymph node metastasis and advanced clinical stage. High-risk scores also contributed to the chemotherapy resistance and immune escape of HNSCC patients. In addition, FADD and ZBP1 played a crucial role in various cancer-related pathways, such as the MAPK, WNT, and MTOR signaling pathways. On the other hand, we suggested that FADD facilitated the progression and 5-fluorouracil (5-FU) resistance of HNSCC cells. A signature based on PANoptosis showed great predictive power for lymph node metastasis and advanced stage, suggesting that the risk score might be an independent prognostic biomarker for HNSCC. Meanwhile, FADD, identified as a prognostic biomarker, may represent an effective therapeutic target for HNSCC.},
}
@article {pmid38684726,
year = {2024},
author = {Poquérusse, J and Brown, CL and Gaillard, C and Doughty, C and Dalén, L and Gallagher, AJ and Wooller, M and Zimov, N and Church, GM and Lamm, B and Hysolli, E},
title = {Assessing contemporary Arctic habitat availability for a woolly mammoth proxy.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9804},
pmid = {38684726},
issn = {2045-2322},
mesh = {Arctic Regions ; *Ecosystem ; Animals ; *Mammoths ; *Biomass ; Alaska ; Carbon/analysis/metabolism ; },
abstract = {Interest continues to grow in Arctic megafaunal ecological engineering, but, since the mass extinction of megafauna ~ 12-15 ka, key physiographic variables and available forage continue to change. Here we sought to assess the extent to which contemporary Arctic ecosystems are conducive to the rewilding of megaherbivores, using a woolly mammoth (M. primigenius) proxy as a model species. We first perform a literature review on woolly mammoth dietary habits. We then leverage Oak Ridge National Laboratories Distributive Active Archive Center Global Aboveground and Belowground Biomass Carbon Density Maps to generate aboveground biomass carbon density estimates in plant functional types consumed by the woolly mammoth at 300 m resolution on Alaska's North Slope. We supplement these analyses with a NASA Arctic Boreal Vulnerability Experiment dataset to downgrade overall biomass estimates to digestible levels. We further downgrade available forage by using a conversion factor representing the relationship between total biomass and net primary productivity (NPP) for arctic vegetation types. Integrating these estimates with the forage needs of woolly mammoths, we conservatively estimate Alaska's North Slope could support densities of 0.0-0.38 woolly mammoth km[-2] (mean 0.13) across a variety of habitats. These results may inform innovative rewilding strategies.},
}
@article {pmid38683839,
year = {2024},
author = {Ma, R and Li, C and Gao, A and Jiang, N and Li, J and Hu, W and Feng, X},
title = {Tick species diversity and potential distribution alternation of dominant ticks under different climate scenarios in Xinjiang, China.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {4},
pages = {e0012108},
pmid = {38683839},
issn = {1935-2735},
mesh = {*Ticks/classification ; *Tick-Borne Diseases/epidemiology/parasitology ; China/epidemiology ; *Datasets as Topic ; Biodiversity ; Animal Distribution ; Humans ; Animals ; Climate Change ; },
abstract = {Ticks are a hematophagous parasite and a vector of pathogens for numerous human and animal diseases of significant importance. The expansion of tick distribution and the increased risk of tick-borne diseases due to global climate change necessitates further study of the spatial distribution trend of ticks and their potential influencing factors. This study constructed a dataset of tick species distribution in Xinjiang for 60 years based on literature database retrieval and historical data collection (January 1963-January 2023). The distribution data were extracted, corrected, and deduplicated. The dominant tick species were selected for analysis using the MaxEnt model to assess their potential distribution in different periods under the current and BCC-CSM2.MR mode scenarios. The results indicated that there are eight genera and 48 species of ticks in 108 cities and counties of Xinjiang, with Hyalomma asiaticum, Rhipicephalus turanicus, Dermacentor marginatus, and Haemaphysalis punctatus being the top four dominant species. The MaxEnt model analysis revealed that the suitability areas of the four dominant ticks were mainly distributed in the north of Xinjiang, in areas such as Altay and Tacheng Prefecture. Over the next four periods, the medium and high suitable areas within the potential distribution range of the four tick species will expand towards the northwest. Additionally, new suitability areas will emerge in Altay, Changji Hui Autonomous Prefecture, and other local areas. The 60-year tick dataset in this study provides a map of preliminary tick distribution in Xinjiang, with a diverse array of tick species and distribution patterns throughout the area. In addition, the MaxEnt model revealed the spatial change characteristics and future distribution trend of ticks in Xinjiang, which can provide an instrumental data reference for tick monitoring and tick-borne disease risk prediction not only in the region but also in other countries participating in the Belt and Road Initiative.},
}
@article {pmid38683244,
year = {2024},
author = {Bai, Y and Song, K and Gao, M and Ma, J and Zhou, Y and Liu, H and Zeng, H and Wang, J and Zheng, X},
title = {Using multi-omics to explore the effect of Bacillus velezensis SAAS-63 on resisting nutrient stress in lettuce.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {313},
pmid = {38683244},
issn = {1432-0614},
mesh = {*Bacillus/metabolism/genetics ; *Lactuca/microbiology/growth &amp; development ; *Rhizosphere ; *Soil Microbiology ; *Nutrients/metabolism ; *Stress, Physiological ; Plant Roots/microbiology ; Microbiota ; Multiomics ; },
abstract = {To avoid the unreasonable use of chemical fertilizer, an environmentally friendly means of improving soil fertility is required. This study explored the role of the plant growth-promoting rhizosphere bacteria (PGPR) strain Bacillus velezensis SAAS-63 in improving nutrient stress in lettuce. Compared with no inoculation, B. velezensis SAAS-63 inoculants exhibited significantly increased fresh weight, root length, and shoot height under nutrient deficiency, as well as improved antioxidant activities and proline contents. The exogenous addition of B. velezensis SAAS-63 also significantly increased the accumulation of macroelements and micronutrients in lettuce. To elucidate the resistance mechanisms induced by B. velezensis SAAS-63 under nutrient stress, high-throughput sequencing and multi-omics analysis were performed. Inoculation with B. velezensis SAAS-63 altered the microbial community of the rhizosphere and increased the relative abundances of Streptomyces, Actinoallomurus, Verrucomicrobia, and Chloroflexi. It is worth noting that the inoculant SAAS-63 can affect plant rhizosphere metabolism. The inoculant changed the metabolic flow of phenylpropanoid metabolic pathway under nutrient deficiency and promoted phenylalanine to participate more in the synthesis of lignin precursors and coumarin substances by inhibiting the synthesis of flavone and isoflavone, thus improving plant resistance. This study showed that the addition of inoculant SAAS-63 could help plants recruit microorganisms to decompose and utilize trehalose and re-established the carbon metabolism of the plant rhizosphere. Additionally, microbes were found to be closely related to the accumulation of metabolites based on correlation analysis. The results indicated that the addition of PGPRs has an important role in regulating soil rhizosphere microbes and metabolism, providing valuable information for understanding how PGPRs affect complex biological processes and enhance plant adaptation to nutrient deficiency. KEY POINTS: • Inoculation with SAAS-63 significantly promoted plant growth under nutrient-deficient conditions • Inoculation with SAAS-63 affected rhizosphere microbial diversity and community structure • Inoculation with SAAS-63 affected plant rhizosphere metabolism and induced plants to synthesize substances that resist stress.},
}
@article {pmid38680650,
year = {2023},
author = {Boyes, D and Hammond, J and , and , and , and , and , and , },
title = {The genome sequence of the Crescent Bell, Epinotia bilunana (Haworth, 1811).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {163},
pmid = {38680650},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Epinotia bilunana (the Crescent Bell; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 659.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.4 kilobases in length.},
}
@article {pmid38677227,
year = {2024},
author = {Alves, RA and Santos, MMD and Rudke, AP and Francisquetti Venturin, PR and Martins, JA},
title = {Site selection for nature-based solutions for stormwater management in urban areas: An approach combining GIS and multi-criteria analysis.},
journal = {Journal of environmental management},
volume = {359},
number = {},
pages = {120999},
doi = {10.1016/j.jenvman.2024.120999},
pmid = {38677227},
issn = {1095-8630},
mesh = {*Geographic Information Systems ; Brazil ; *Conservation of Natural Resources/methods ; *Rain ; Ecosystem ; Sustainable Development ; },
abstract = {In recent years, particularly following the definition of the UN Sustainable Development Goals (SDGs) for 2030, Nature-Based Solutions (NBS) have gained considerable attention, capturing the interest of both the scientific community and policymakers committed to addressing urban environmental issues. However, the need for studies to guide decision-makers in identifying suitable locations for NBS implementation within urban stormwater management is evident. To address this gap, the present study employs a methodological approach grounded in multi-criteria analysis integrated with Geographic Information Systems (GIS) to identify areas with potential for NBS implementation. In this process, ten NBS were proposed and tested in the drainage area of a shallow tropical urban lake in Londrina, southern Brazil. Additionally, the study investigates areas hosting lower-income populations, a relevant aspect for public managers given the diverse economic subsidies required to implement NBS. Furthermore, the study incorporates a preliminary analysis that evaluates the potential ecosystem benefits to determine the most suitable NBS for a specific site. The result shows that all the ten analyzed NBS were deemed suitable for the study area. Rain barrels had the highest percentage coverage in the study area (37.1%), followed by tree pits (27.9%), and rain gardens (25.4%). Despite having the highest distribution in the basin area, rain barrels exhibited only moderate ecosystem benefits, prompting the prioritization of other NBS with more significant ecological advantages in the final integrated map. In summary, the methodology proposed showed to be a robust approach to selecting optimal solutions in densely populated urban areas.},
}
@article {pmid38672746,
year = {2024},
author = {Bakacsy, L and Kardos, LV and Szepesi, &#xc1; and Nagy, KN and Vasas, A and Feigl, G},
title = {Investigation of the Allelopathic Effect of Two Invasive Plant Species in Rhizotron System.},
journal = {Life (Basel, Switzerland)},
volume = {14},
number = {4},
pages = {},
pmid = {38672746},
issn = {2075-1729},
support = {FK129061//National Research, Development and Innovation Office (Hungary)/ ; },
abstract = {A key question in plant invasion biology is why invasive plants are more competitive in their introduced habitat than in their native habitat. Studies show that invasive species exhibit allelopathy, influencing other plants by releasing chemicals. Research on allelopathy uses in vitro tests, investigating effects on seed germination and seedling development. Although soil plays a role in modifying allelopathic effects, observations with soil are rare and almost nothing is known about the root development of test plants developing in soil and the effects of allelopathic compounds on root architecture. Our study evaluates the allelopathic effects of false indigo-bush (Amorpha fruticosa L.) and common milkweed (Asclepias syriaca L.) on oilseed rape growth as a model plant. The rhizotron system was used to study the effect of morphology and root architecture. Leaf-soil mixtures at 0.5%, 1%, and 5% concentrations were used. Shoot and root development was strongly inhibited at 5%. But there was no difference between the allelopathy of the two species, and the application of lower concentrations did not show any effect, demonstrating that soil has a significant modifying effect on their allelopathy. Our results highlight that the development of roots growing in the soil is also worth investigating in connection with allelopathy, which can strengthen the ecological importance of allelochemicals during successful invasions.},
}
@article {pmid38670119,
year = {2024},
author = {Atağ, G and Kaptan, D and Yüncü, E and Başak Vural, K and Mereu, P and Pirastru, M and Barbato, M and Leoni, GG and Güler, MN and Er, T and Eker, E and Yazıcı, TD and Kılıç, MS and Altınışık, NE and Çelik, EA and Morell Miranda, P and Dehasque, M and Floridia, V and Götherström, A and Bilgin, CC and Togan, &#x130; and Günther, T and Özer, F and Hadjisterkotis, E and Somel, M},
title = {Population Genomic History of the Endangered Anatolian and Cyprian Mouflons in Relation to Worldwide Wild, Feral, and Domestic Sheep Lineages.},
journal = {Genome biology and evolution},
volume = {16},
number = {5},
pages = {},
pmid = {38670119},
issn = {1759-6653},
support = {/ERC_/European Research Council/International ; 772390//European Union's Horizon 2020 research and innovation programme/ ; //Scientific and Technological Research Council of Turkey/ ; //National Scholarship Programme/ ; //Swedish Research Council Vetenskapsr&#xe5;det/ ; //Carl Tryggers Stiftelse f&#xf6;r Vetenskaplig Forskning/ ; 772390/ERC_/European Research Council/International ; },
mesh = {Animals ; *Endangered Species ; Sheep/genetics ; *Sheep, Domestic/genetics ; Genome ; Genetic Variation ; },
abstract = {Once widespread in their homelands, the Anatolian mouflon (Ovis gmelini anatolica) and the Cyprian mouflon (Ovis gmelini ophion) were driven to near extinction during the 20th century and are currently listed as endangered populations by the International Union for Conservation of Nature. While the exact origins of these lineages remain unclear, they have been suggested to be close relatives of domestic sheep or remnants of proto-domestic sheep. Here, we study whole genome sequences of n = 5 Anatolian mouflons and n = 10 Cyprian mouflons in terms of population history and diversity, comparing them with eight other extant sheep lineages. We find reciprocal genetic affinity between Anatolian and Cyprian mouflons and domestic sheep, higher than all other studied wild sheep genomes, including the Iranian mouflon (O. gmelini). Studying diversity indices, we detect a considerable load of short runs of homozygosity blocks (<2 Mb) in both Anatolian and Cyprian mouflons, reflecting small effective population size (Ne). Meanwhile, Ne and mutation load estimates are lower in Cyprian compared with Anatolian mouflons, suggesting the purging of recessive deleterious variants in Cyprian sheep under a small long-term Ne, possibly attributable to founder effects, island isolation, introgression from domestic lineages, or differences in their bottleneck dynamics. Expanding our analyses to worldwide wild and feral Ovis genomes, we observe varying viability metrics among different lineages and a limited consistency between viability metrics and International Union for Conservation of Nature conservation status. Factors such as recent inbreeding, introgression, and unique population dynamics may have contributed to the observed disparities.},
}
@article {pmid38668970,
year = {2024},
author = {Muthye, V and Lavrov, DV},
title = {Characterization of the Mitochondrial Proteome in the Ctenophore Mnemiopsis leidyi Using MitoPredictor.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2757},
number = {},
pages = {239-257},
pmid = {38668970},
issn = {1940-6029},
mesh = {Animals ; *Ctenophora/metabolism/genetics ; *Proteome ; *Mitochondrial Proteins/metabolism/genetics ; Computational Biology/methods ; Mitochondria/metabolism ; Proteomics/methods ; Software ; },
abstract = {Mitochondrial proteomes have been experimentally characterized for only a handful of animal species. However, the increasing availability of genomic and transcriptomic data allows one to infer mitochondrial proteins using computational tools. MitoPredictor is a novel random forest classifier, which utilizes orthology search, mitochondrial targeting signal (MTS) identification, and protein domain content to infer mitochondrial proteins in animals. MitoPredictor's output also includes an easy-to-use R Shiny applet for the visualization and analysis of the results. In this article, we provide a guide for predicting and analyzing the mitochondrial proteome of the ctenophore Mnemiopsis leidyi using MitoPredictor.},
}
@article {pmid38668514,
year = {2024},
author = {Li, Q and Yao, S and Wen, H and Li, W and Jin, L and Huang, X},
title = {Improving Lead Phytoremediation Using Endophytic Bacteria Isolated from the Pioneer Plant Ageratina adenophora (Spreng.) from a Mining Area.},
journal = {Toxics},
volume = {12},
number = {4},
pages = {},
pmid = {38668514},
issn = {2305-6304},
support = {2020KY15017//Project for Enhancing Young and Middle-aged Teacher's Research Basis Ability in Colleges of Guangxi/ ; },
abstract = {This study aimed to isolate and characterise endophytic bacteria from the pioneer plant Ageratina adenophora in a mining area. Seven strains of metal-resistant endophytic bacteria that belong to five genera were isolated from the roots of A. adenophora. These strains exhibited various plant growth-promoting (PGP) capabilities. Sphingomonas sp. ZYG-4, which exhibited the ability to secrete indoleacetic acid (IAA; 53.2 ± 8.3 mg·L[-1]), solubilize insoluble inorganic phosphates (Phosphate solubilization; 11.2 ± 2.9 mg·L[-1]), and regulate root ethylene levels (1-aminocyclopropane-1-carboxylic acid deaminase activity; 2.87 ± 0.19 µM α-KB·mg[-1]·h[-1]), had the highest PGP potential. Therefore, Sphingomonas sp. ZYG-4 was used in a pot experiment to study its effect on the biomass and Pb uptake of both host (Ageratina adenophora) and non-host (Dysphania ambrosioides) plants. Compared to the uninoculated control, Sphingomonas sp. ZYG-4 inoculation increased the biomass of shoots and roots by 59.4% and 144.4% for A. adenophora and by 56.2% and 57.1% for D. ambrosioides, respectively. In addition, Sphingomonas sp. ZYG-4 inoculation enhanced Pb accumulation in the shoot and root by 268.9% and 1187.3% for A. adenophora, and by 163.1% and 343.8% for D. ambrosioides, respectively, compared to plants without bacterial inoculation. Our research indicates that endophytic bacteria are promising candidates for enhancing plant growth and facilitating microbe-assisted phytoremediation in heavy metal-contaminated soil.},
}
@article {pmid38668506,
year = {2024},
author = {Li, S and Yang, J and Zheng, K and He, S and Liu, Z and Song, S and Zeng, T},
title = {Effective Activation of Peroxymonosulfate by Oxygen Vacancy Induced Musa Basjoo Biochar to Degrade Sulfamethoxazole: Efficiency and Mechanism.},
journal = {Toxics},
volume = {12},
number = {4},
pages = {},
pmid = {38668506},
issn = {2305-6304},
support = {2023M743772//China Postdoctoral Science Foundation/ ; 22276172//National Natural Science Foundation of China/ ; 22076168//National Natural Science Foundation of China/ ; LR21E080001//Zhejiang Provincial Natural Science Foundation of China/ ; RF-B2022005//Fundamental Research Funds for the Provincial Universities of Zhejiang/ ; 2023C03132//"Leading Goose" R&amp;D Program of Zhejiang/ ; },
abstract = {Biochar materials have garnered attention as potential catalysts for peroxymonosulfate (PMS) activation due to their cost-effectiveness, notable specific surface area, and advantageous structural properties. In this study, a suite of plantain-derived biochar (MBB-400, MBB-600, and MBB-800), possessing a well-defined pore structure and a substantial number of uniformly distributed active sites (oxygen vacancy, OVs), was synthesized through a facile calcination process at varying temperatures (400, 600, and 800 °C). These materials were designed for the activation of PMS in the degradation of sulfamethoxazole (SMX). Experimental investigations revealed that OVs not only functioned as enriched sites for pollutants, enhancing the opportunities for free radicals ([•]OH/SO4[•-]) and surface-bound radicals (SBRs) to attack pollutants, but also served as channels for intramolecular charge transfer leaps. This role contributed to a reduction in interfacial charge transfer resistance, expediting electron transfer rates with PMS, thereby accelerating the decomposition of pollutants. Capitalizing on these merits, the MBB-800/PMS system displayed a 61-fold enhancement in the conversion rate for SMX degradation compared to inactivated MBB/PMS system. Furthermore, the MBB-800 exhibited less cytotoxicity towards rat pheochromocytoma (PC12) cells. Hence, the straightforward calcination synthesis of MBB-800 emerges as a promising biochar catalyst with vast potential for sustainable and efficient wastewater treatment and environmental remediation.},
}
@article {pmid38666081,
year = {2024},
author = {Omar, KM and Kitundu, GL and Jimoh, AO and Namikelwa, DN and Lisso, FM and Babajide, AA and Olufemi, SE and Awe, OI},
title = {Investigating antimicrobial resistance genes in Kenya, Uganda and Tanzania cattle using metagenomics.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17181},
pmid = {38666081},
issn = {2167-8359},
mesh = {Animals ; Cattle ; *Metagenomics ; Kenya/epidemiology ; Uganda/epidemiology ; Tanzania ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Genes, Bacterial/genetics ; },
abstract = {Antimicrobial resistance (AMR) is a growing problem in African cattle production systems, posing a threat to human and animal health and the associated economic value chain. However, there is a poor understanding of the resistomes in small-holder cattle breeds in East African countries. This study aims to examine the distribution of antimicrobial resistance genes (ARGs) in Kenya, Tanzania, and Uganda cattle using a metagenomics approach. We used the SqueezeMeta-Abricate (assembly-based) pipeline to detect ARGs and benchmarked this approach using the Centifuge-AMRplusplus (read-based) pipeline to evaluate its efficiency. Our findings reveal a significant number of ARGs of critical medical and economic importance in all three countries, including resistance to drugs of last resort such as carbapenems, suggesting the presence of highly virulent and antibiotic-resistant bacterial pathogens (ESKAPE) circulating in East Africa. Shared ARGs such as aph(6)-id (aminoglycoside phosphotransferase), tet (tetracycline resistance gene), sul2 (sulfonamide resistance gene) and cfxA_gen (betalactamase gene) were detected. Assembly-based methods revealed fewer ARGs compared to read-based methods, indicating the sensitivity and specificity of read-based methods in resistome characterization. Our findings call for further surveillance to estimate the intensity of the antibiotic resistance problem and wider resistome classification. Effective management of livestock and antibiotic consumption is crucial in minimizing antimicrobial resistance and maximizing productivity, making these findings relevant to stakeholders, agriculturists, and veterinarians in East Africa and Africa at large.},
}
@article {pmid38662943,
year = {2024},
author = {Lu, XY and Wu, HP and Ma, H and Li, H and Li, J and Liu, YT and Pan, ZY and Xie, Y and Wang, L and Ren, B and Liu, GK},
title = {Deep Learning-Assisted Spectrum-Structure Correlation: State-of-the-Art and Perspectives.},
journal = {Analytical chemistry},
volume = {96},
number = {20},
pages = {7959-7975},
doi = {10.1021/acs.analchem.4c01639},
pmid = {38662943},
issn = {1520-6882},
abstract = {Spectrum-structure correlation is playing an increasingly crucial role in spectral analysis and has undergone significant development in recent decades. With the advancement of spectrometers, the high-throughput detection triggers the explosive growth of spectral data, and the research extension from small molecules to biomolecules accompanies massive chemical space. Facing the evolving landscape of spectrum-structure correlation, conventional chemometrics becomes ill-equipped, and deep learning assisted chemometrics rapidly emerges as a flourishing approach with superior ability of extracting latent features and making precise predictions. In this review, the molecular and spectral representations and fundamental knowledge of deep learning are first introduced. We then summarize the development of how deep learning assist to establish the correlation between spectrum and molecular structure in the recent 5 years, by empowering spectral prediction (i.e., forward structure-spectrum correlation) and further enabling library matching and de novo molecular generation (i.e., inverse spectrum-structure correlation). Finally, we highlight the most important open issues persisted with corresponding potential solutions. With the fast development of deep learning, it is expected to see ultimate solution of establishing spectrum-structure correlation soon, which would trigger substantial development of various disciplines.},
}
@article {pmid38658779,
year = {2024},
author = {Andrianova, MA and Seplyarskiy, VB and Terradas, M and Sánchez-Heras, AB and Mur, P and Soto, JL and Aiza, G and Borràs, E and Kondrashov, FA and Kondrashov, AS and Bazykin, GA and Valle, L},
title = {Discovery of recessive effect of human polymerase δ proofreading deficiency through mutational analysis of POLD1-mutated normal and cancer cells.},
journal = {European journal of human genetics : EJHG},
volume = {32},
number = {7},
pages = {837-845},
pmid = {38658779},
issn = {1476-5438},
support = {PID2020-112595RB-I00//Ministry of Economy and Competitiveness | Agencia Estatal de Investigaci&#xf3;n (Spanish Agencia Estatal de Investigaci&#xf3;n)/ ; AGAUR 2017SGR1282; CERCA Program//Government of Catalonia | Departament de Salut, Generalitat de Catalunya/ ; ISCIII-AES-2017 PI17/01082//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; I5127-B//Austrian Science Fund (Fonds zur F&#xf6;rderung der Wissenschaftlichen Forschung)/ ; 429960716//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; ERC Consolidator (771209)//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; },
mesh = {Humans ; *DNA Polymerase III/genetics/metabolism ; Female ; Male ; Pedigree ; Heterozygote ; Genes, Recessive ; Neoplasms/genetics/pathology ; Mutation ; Germ-Line Mutation ; Adult ; },
abstract = {Constitutional heterozygous pathogenic variants in the exonuclease domain of POLE and POLD1, which affect the proofreading activity of the corresponding polymerases, cause a cancer predisposition syndrome characterized by increased risk of gastrointestinal polyposis, colorectal cancer, endometrial cancer and other tumor types. The generally accepted explanation for the connection between the disruption of the proofreading activity of polymerases epsilon and delta and cancer development is through an increase in the somatic mutation rate. Here we studied an extended family with multiple members heterozygous for the pathogenic POLD1 variant c.1421T>C p.(Leu474Pro), which segregates with the polyposis and cancer phenotypes. Through the analysis of mutational patterns of patient-derived fibroblasts colonies and de novo mutations obtained by parent-offspring comparisons, we concluded that heterozygous POLD1 L474P just subtly increases the somatic and germline mutation burden. In contrast, tumors developed in individuals with a heterozygous mutation in the exonuclease domain of POLD1, including L474P, have an extremely high mutation rate (>100 mut/Mb) associated with signature SBS10d. We solved this contradiction through the observation that tumorigenesis involves somatic inactivation of the wildtype POLD1 allele. These results imply that exonuclease deficiency of polymerase delta has a recessive effect on mutation rate.},
}
@article {pmid38656485,
year = {2024},
author = {Jiménez-Madrigal, JP and Till, BJ and Gatica-Arias, A},
title = {Genetic Diversity Assessment in Plants from Reduced Representation Sequencing Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2787},
number = {},
pages = {107-122},
pmid = {38656485},
issn = {1940-6029},
mesh = {*Genetic Variation ; *Plants/genetics ; *Genome, Plant ; Software ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Genomics/methods ; },
abstract = {Genetic diversity refers to the variety of genetic traits within a population or a species. It is an essential aspect of both plant ecology and plant breeding because it contributes to the adaptability, survival, and resilience of populations in changing environments. This chapter outlines a pipeline for estimating genetic diversity statistics from reduced representation or whole genome sequencing data. The pipeline involves obtaining DNA sequence reads, mapping the corresponding reads to a reference genome, calling variants from the alignments, and generating an unbiased estimation of nucleotide diversity and divergence between populations. The pipeline is suitable for single-end Illumina reads and can be adjusted for paired-end reads. The resulting pipeline provides a comprehensive approach for aligning and analyzing sequencing data to estimate genetic diversity.},
}
@article {pmid38655208,
year = {2023},
author = {Wu, SH and Ko, JC and Lin, RS and Chang-Yang, CH and Chang, HW},
title = {Evaluating community-wide temporal sampling in passive acoustic monitoring: A comprehensive study of avian vocal patterns in subtropical montane forests.},
journal = {F1000Research},
volume = {12},
number = {},
pages = {1299},
pmid = {38655208},
issn = {2046-1402},
mesh = {Animals ; *Vocalization, Animal/physiology ; *Acoustics ; *Birds/physiology ; *Forests ; Environmental Monitoring/methods ; },
abstract = {BACKGROUND: From passive acoustic monitoring (PAM) recordings, the vocal activity rate (VAR), vocalizations per unit of time, can be calculated and is essential for assessing bird population abundance. However, VAR is subject to influences from a range of factors, including species and environmental conditions. Identifying the optimal sampling design to obtain representative acoustic data for VAR estimation is crucial for research objectives. PAM commonly uses temporal sampling strategies to decrease the volume of recordings and the resources needed for audio data management. Yet, the comprehensive impact of this sampling approach on VAR estimation remains insufficiently explored.<br><br>METHODS: In this study, we used vocalizations extracted from recordings of 12 bird species, taken at 14 PAM stations situated in subtropical montane forests over a four-month period, to assess the impact of temporal sampling on VAR across three distinct scales: short-term periodic, diel, and hourly. For short-term periodic sampling analysis, we employed hierarchical clustering analysis (HCA) and the coefficient of variation (CV). Generalized additive models (GAMs) were utilized for diel sampling analysis, and we determined the average difference in VAR values per minute for the hourly sampling analysis.<br><br>RESULTS: We identified significant day and species-specific VAR fluctuations. The survey season was divided into five segments; the earliest two showed high variability and are best avoided for surveys. Data from days with heavy rain and strong winds showed reduced VAR values and should be excluded from analysis. Continuous recordings spanning at least seven days, extending to 14 days is optimal for minimizing sampling variance. Morning chorus recordings effectively capture the majority of bird vocalizations, and hourly sampling with frequent, shorter intervals aligns closely with continuous recording outcomes.<br><br>CONCLUSIONS: While our findings are context-specific, they highlight the significance of strategic sampling in avian monitoring, optimizing resource utilization and enhancing the breadth of monitoring efforts.},
}
@article {pmid38654647,
year = {2024},
author = {Spake, L and Hassan, A and Schaffnit, SB and Alam, N and Amoah, AS and Badjie, J and Cerami, C and Crampin, A and Dube, A and Kaye, MP and Kotch, R and Liew, F and McLean, E and Munthali-Mkandawire, S and Mwalwanda, L and Petersen, AC and Prentice, AM and Zohora, FT and Watts, J and Sear, R and Shenk, MK and Sosis, R and Shaver, JH},
title = {A practical guide to cross-cultural and multi-sited data collection in the biological and behavioural sciences.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2021},
pages = {20231422},
pmid = {38654647},
issn = {1471-2954},
mesh = {Humans ; *Behavioral Sciences ; *Data Collection/methods ; Cross-Cultural Comparison ; Research Design ; Ecology/methods ; },
abstract = {Researchers in the biological and behavioural sciences are increasingly conducting collaborative, multi-sited projects to address how phenomena vary across ecologies. These types of projects, however, pose additional workflow challenges beyond those typically encountered in single-sited projects. Through specific attention to cross-cultural research projects, we highlight four key aspects of multi-sited projects that must be considered during the design phase to ensure success: (1) project and team management; (2) protocol and instrument development; (3) data management and documentation; and (4) equitable and collaborative practices. Our recommendations are supported by examples from our experiences collaborating on the Evolutionary Demography of Religion project, a mixed-methods project collecting data across five countries in collaboration with research partners in each host country. To existing discourse, we contribute new recommendations around team and project management, introduce practical recommendations for exploring the validity of instruments through qualitative techniques during piloting, highlight the importance of good documentation at all steps of the project, and demonstrate how data management workflows can be strengthened through open science practices. While this project was rooted in cross-cultural human behavioural ecology and evolutionary anthropology, lessons learned from this project are applicable to multi-sited research across the biological and behavioural sciences.},
}
@article {pmid38649162,
year = {2024},
author = {Niimura, Y and Biswa, BB and Kishida, T and Toyoda, A and Fujiwara, K and Ito, M and Touhara, K and Inoue-Murayama, M and Jenkins, SH and Adenyo, C and Kayang, BB and Koide, T},
title = {Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents.},
journal = {Molecular biology and evolution},
volume = {41},
number = {4},
pages = {},
pmid = {38649162},
issn = {1537-1719},
support = {18K06359//JSPS KAKENHI/ ; JPMJAS2017//JST aXis/ ; 1B2020//National Institute of Genetics, NIG-Joint/ ; },
mesh = {Animals ; *Evolution, Molecular ; *Multigene Family ; *Phylogeny ; Receptors, G-Protein-Coupled/genetics ; *Receptors, Odorant/genetics ; Receptors, Pheromone/genetics/metabolism ; *Rodentia/genetics ; Smell/genetics ; Taste/genetics ; *Vomeronasal Organ/metabolism ; },
abstract = {Chemical senses, including olfaction, pheromones, and taste, are crucial for the survival of most animals. There has long been a debate about whether different types of senses might influence each other. For instance, primates with a strong sense of vision are thought to have weakened olfactory abilities, although the oversimplified trade-off theory is now being questioned. It is uncertain whether such interactions between different chemical senses occur during evolution. To address this question, we examined four receptor gene families related to olfaction, pheromones, and taste: olfactory receptor (OR), vomeronasal receptor type 1 and type 2 (V1R and V2R), and bitter taste receptor (T2R) genes in Hystricomorpha, which is morphologically and ecologically the most diverse group of rodents. We also sequenced and assembled the genome of the grasscutter, Thryonomys swinderianus. By examining 16 available genome assemblies alongside the grasscutter genome, we identified orthologous gene groups among hystricomorph rodents for these gene families to separate the gene gain and loss events in each phylogenetic branch of the Hystricomorpha evolutionary tree. Our analysis revealed that the expansion or contraction of the four gene families occurred synchronously, indicating that when one chemical sense develops or deteriorates, the others follow suit. The results also showed that V1R/V2R genes underwent the fastest evolution, followed by OR genes, and T2R genes were the most evolutionarily stable. This variation likely reflects the difference in ligands of V1R/V2Rs, ORs, and T2Rs: species-specific pheromones, environment-based scents, and toxic substances common to many animals, respectively.},
}
@article {pmid38648741,
year = {2024},
author = {Crauwels, C and Heidig, SL and Díaz, A and Vranken, WF},
title = {Large-scale structure-informed multiple sequence alignment of proteins with SIMSApiper.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {5},
pages = {},
pmid = {38648741},
issn = {1367-4811},
support = {1SE5923N//Research Foundation Flanders/ ; },
mesh = {*Software ; *Proteins/chemistry ; *Sequence Alignment/methods ; *Sequence Analysis, Protein/methods ; Algorithms ; Amino Acid Sequence ; Computational Biology/methods ; Databases, Protein ; },
abstract = {SUMMARY: SIMSApiper is a Nextflow pipeline that creates reliable, structure-informed MSAs of thousands of protein sequences faster than standard structure-based alignment methods. Structural information can be provided by the user or collected by the pipeline from online resources. Parallelization with sequence identity-based subsets can be activated to significantly speed up the alignment process. Finally, the number of gaps in the final alignment can be reduced by leveraging the position of conserved secondary structure elements.<br><br>The pipeline is implemented using Nextflow, Python3, and Bash. It is publicly available on github.com/Bio2Byte/simsapiper.},
}
@article {pmid38648214,
year = {2024},
author = {Lauber, C and Zhang, X and Vaas, J and Klingler, F and Mutz, P and Dubin, A and Pietschmann, T and Roth, O and Neuman, BW and Gorbalenya, AE and Bartenschlager, R and Seitz, S},
title = {Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates.},
journal = {PLoS pathogens},
volume = {20},
number = {4},
pages = {e1012163},
pmid = {38648214},
issn = {1553-7374},
mesh = {Animals ; *Nidovirales/genetics ; *Genome, Viral ; *Coronavirus/genetics/classification ; *Phylogeny ; Vertebrates/virology/genetics ; Fishes/virology ; Evolution, Molecular ; Data Mining ; Nidovirales Infections/virology/genetics ; },
abstract = {Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization of pathogen epidemiology, and redefined our understanding of the natural genetic diversity of viruses with profound functional and structural implications. Here we employed a data-driven virus discovery approach that directly queries unprocessed sequencing data in a highly parallelized way and involves a targeted viral genome assembly strategy in a wide range of sequence similarity. By screening more than 269,000 datasets of numerous authors from the Sequence Read Archive and using two metrics that quantitatively assess assembly quality, we discovered 40 nidoviruses from six virus families whose members infect vertebrate hosts. They form 13 and 32 putative viral subfamilies and genera, respectively, and include 11 coronaviruses with bisegmented genomes from fishes and amphibians, a giant 36.1 kilobase coronavirus genome with a duplicated spike glycoprotein (S) gene, 11 tobaniviruses and 17 additional corona-, arteri-, cremega-, nanhypo- and nangoshaviruses. Genome segmentation emerged in a single evolutionary event in the monophyletic lineage encompassing the subfamily Pitovirinae. We recovered the bisegmented genome sequences of two coronaviruses from RNA samples of 69 infected fishes and validated the presence of poly(A) tails at both segments using 3'RACE PCR and subsequent Sanger sequencing. We report a genetic linkage between accessory and structural proteins whose phylogenetic relationships and evolutionary distances are incongruent with the phylogeny of replicase proteins. We rationalize these observations in a model of inter-family S recombination involving at least five ancestral corona- and tobaniviruses of aquatic hosts. In support of this model, we describe an individual fish co-infected with members from the families Coronaviridae and Tobaniviridae. Our results expand the scale of the known extraordinary evolutionary plasticity in nidoviral genome architecture and call for revisiting fundamentals of genome expression, virus particle biology, host range and ecology of vertebrate nidoviruses.},
}
@article {pmid38646766,
year = {2024},
author = {Hu, JY and Liu, LY and Dai, QL and Yang, B and Zhou, WJ},
title = {Evaluation of ecotourism suitability based on AHP-GIS: Taking Xiaoxiangling area of the Giant Panda National Park and the surrounding communities as an example.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {3},
pages = {780-788},
doi = {10.13287/j.1001-9332.202403.020},
pmid = {38646766},
issn = {1001-9332},
mesh = {Animals ; *Conservation of Natural Resources ; China ; *Parks, Recreational ; *Ecosystem ; *Ursidae ; *Geographic Information Systems ; Recreation ; },
abstract = {The primary goal of national parks is to protect ecological environment, but also with the functions of scientific research, education, and recreation. Aiming for the realization of universal sharing, we used the analytic hierarchy process (AHP) to construct an ecotourism suitability evaluation system by selecting four factors, including landscape resources, ecological environment carrying capacity, recreation utilization capacity and social condition, taking Xiaoxiangling area of Giant Panda National Park and the surrounding communities as an example. We evaluated the ecotourism suitability based on GIS, and conducted a questionnaire survey of tourists, to propose suggestions on the functional zoning in terms of ecotourism suitability and subjective choice preferences of tourists. The results showed that the ecotourism suitability of the evaluation area could be classified into five levels. The most suitable areas were located nearby the natural landscape resources and far away from the core conservation area, and the least suitable areas distributed at the edge of the core conservation area. According to the results of suitability analysis, the evaluation area was divided into suitable development area, moderate development area, and restricted development area. Combined with the tourist preferences, we divided the recreational activities in the evaluation area into seven activities, namely, ecotourism, eco-camping, science education, leisure vacation, agricultural and animal husbandry culture experience, eco-education, and mountain adventure. These findings could help provide suitable services for different tourists and offer reference for the ecotourism developmental planning of the Xiaoxiangling area of the Giant Panda National Park.},
}
@article {pmid38646687,
year = {2024},
author = {Filatov, DA},
title = {ProSeq4: A user-friendly multiplatform program for preparation and analysis of large-scale DNA polymorphism datasets.},
journal = {Molecular ecology resources},
volume = {24},
number = {5},
pages = {e13962},
pmid = {38646687},
issn = {1755-0998},
support = {BB/P009808/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Software ; *Polymorphism, Genetic ; *Computational Biology/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Preparation of DNA polymorphism datasets for analysis is an important step in evolutionary genetic and molecular ecology studies. Ever-growing dataset sizes make this step time consuming, but few convenient software tools are available to facilitate processing of large-scale datasets including thousands of sequence alignments. Here I report "processor of sequences v4" (proSeq4)-a user-friendly multiplatform software for preparation and evolutionary genetic analyses of genome- or transcriptome-scale sequence polymorphism datasets. The program has an easy-to-use graphic user interface and is designed to process and analyse many thousands of datasets. It supports over two dozen file formats, includes a flexible sequence editor and various tools for data visualization, quality control and most commonly used evolutionary genetic analyses, such as NJ-phylogeny reconstruction, DNA polymorphism analyses and coalescent simulations. Command line tools (e.g. vcf2fasta) are also provided for easier integration into bioinformatic pipelines. Apart of molecular ecology and evolution research, proSeq4 may be useful for teaching, e.g. for visual illustration of different shapes of phylogenies generated with coalescent simulations in different scenarios. ProSeq4 source code and binaries for Windows, MacOS and Ubuntu are available from https://sourceforge.net/projects/proseq/.},
}
@article {pmid38644930,
year = {2023},
author = {Boyes, D and Boyes, C and , and , and , and , and , and , },
title = {The genome sequence of the Scalloped Oak, Crocallis elinguaria (Linneas, 1758).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {426},
pmid = {38644930},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Crocallis elinguaria (the Scalloped Oak; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 430.4 megabases in span. Most of the assembly is scaffolded into 17 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.86 kilobases in length. Gene annotation of this assembly on Ensembl identified 17,741 protein coding genes.},
}
@article {pmid38644519,
year = {2024},
author = {Chen, J and Lin, JJ and Wang, W and Huang, H and Pan, Z and Ye, G and Dong, S and Lin, Y and Lin, C and Huang, Q},
title = {EV-COMM: A database of interspecies and intercellular interactions mediated by extracellular vesicles.},
journal = {Journal of extracellular vesicles},
volume = {13},
number = {4},
pages = {e12442},
pmid = {38644519},
issn = {2001-3078},
support = {2021J06037//Fujian Provincial Department of Science and Technology/ ; 2022T3063//Fujian Provincial Department of Science and Technology/ ; 32161143016//National Natural Science Foundation of China/ ; 42177362//National Natural Science Foundation of China/ ; 42250410328//National Natural Science Foundation of China/ ; CAS-WX2021SF-0302//Chinese Academy of Sciences/ ; NO. NBSDC-DB-21//National Basic Science Data Center "Environment Health DataBase"/ ; },
mesh = {Animals ; Humans ; *Cell Communication ; Databases, Factual ; *Extracellular Vesicles/metabolism ; MicroRNAs/metabolism/genetics ; },
abstract = {Intra- and inter-organismal interactions play a crucial role in the maintenance and function of individuals, as well as communities. Extracellular vesicles (EVs) have been identified as effective mediators for the communication both within and between species. They can carry and transport molecular cargoes to transmit biological messages. Several databases (ExoBCD, ExoCarta, EVpedia, EV-TRACK, Vesiclepedia) complied the cargoes information including DNA, RNA, protein, lipid and metabolite associated with EVs. Databases that refer to the complete records on both donor and recipient information are warranted to facilitate the understanding of the interaction across cells and species. In this study, we developed a database that compiled the records equipped with a structured process of EV-mediated interaction. The sources of donor and recipient were classified by cell type, tissues/organs and species, thus providing an extended knowledge of cell-cell, species-species interaction. The isolation and identification methods were presented for assessing the quality of EVs. Information on functional cargoes was included, where microRNA was linked to a prediction server to broaden its potential effects. Physiological and pathological context was marked to show the environment where EVs functioned. At present, a total of 1481 data records in our database, including 971 cell-cell interactions belonging to more than 40 different tissues/organs, and 510 cross-species records. The database provides a web interface to browse, search, visualize and download the interaction records. Users can search for interactions by selecting the context of interest or specific cells/species types, as well as functional cargoes. To the best of our knowledge, the database is the first comprehensive database focusing on interactions between donor and recipient cells or species mediated by EVs, serving as a convenient tool to explore and validate interactions. The Database, shorten as EV-COMM (EV mediated communication) is freely available at http://sdc.iue.ac.cn/evs/list/ and will be continuously updated.},
}
@article {pmid38643978,
year = {2024},
author = {Rosbakh, S and Carta, A and Fernández-Pascual, E and Phartyal, SS and Dayrell, RLC and Mattana, E and Saatkamp, A and Vandelook, F and Baskin, JM and Baskin, CC},
title = {Large dataset analyses advance knowledge of seed ecology and evolutionary biology.},
journal = {The New phytologist},
volume = {242},
number = {6},
pages = {2399-2400},
doi = {10.1111/nph.19752},
pmid = {38643978},
issn = {1469-8137},
support = {//Novo Nordisk Foundation/ ; },
mesh = {*Biological Evolution ; *Seeds/physiology/genetics ; *Ecology ; Datasets as Topic ; },
}
@article {pmid38643126,
year = {2024},
author = {Xiao, W and Chen, YL and Du, LY and Wu, J and Wang, Z and Mao, B and Wen, FQ and Gibson, PG and McDonald, VM and Yu, H and Fu, JJ},
title = {Bacterial interactome disturbance in chronic obstructive pulmonary disease clinical stability and exacerbations.},
journal = {Respiratory research},
volume = {25},
number = {1},
pages = {173},
pmid = {38643126},
issn = {1465-993X},
support = {No.82100046//National Natural Science Foundation of China/ ; No.81870014//National Natural Science Foundation of China/ ; 2023NSFSC1460//Sichuan Science and Technology Program of China/ ; 2020YFS0145//Sichuan Science and Technology Program of China/ ; },
mesh = {Humans ; *Dysbiosis ; *Pulmonary Disease, Chronic Obstructive/drug therapy ; Lung ; Haemophilus ; Sputum/microbiology ; Disease Progression ; },
abstract = {RATIONALE: Our understanding of airway dysbiosis in chronic obstructive pulmonary disease (COPD) remains incomplete, which may be improved by unraveling the complexity in microbial interactome.<br><br>OBJECTIVES: To characterize reproducible features of airway bacterial interactome in COPD at clinical stability and during exacerbation, and evaluate their associations with disease phenotypes.<br><br>METHODS: We performed weighted ensemble-based co-occurrence network analysis of 1742 sputum microbiomes from published and new microbiome datasets, comprising two case-control studies of stable COPD versus healthy control, two studies of COPD stability versus exacerbation, and one study with exacerbation-recovery time series data.<br><br>RESULTS: Patients with COPD had reproducibly lower degree of negative bacterial interactions, i.e. total number of negative interactions as a proportion of total interactions, in their airway microbiome compared with healthy controls. Evaluation of the Haemophilus interactome showed that the antagonistic interaction networks of this established pathogen rather than its abundance consistently changed in COPD. Interactome dynamic analysis revealed reproducibly reduced antagonistic interactions but not diversity loss during COPD exacerbation, which recovered after treatment. In phenotypic analysis, unsupervised network clustering showed that loss of antagonistic interactions was associated with worse clinical symptoms (dyspnea), poorer lung function, exaggerated neutrophilic inflammation, and higher exacerbation risk. Furthermore, the frequent exacerbators (&#x2265;&#x2009;2 exacerbations per year) had significantly reduced antagonistic bacterial interactions while exhibiting subtle compositional changes in their airway microbiota.<br><br>CONCLUSIONS: Bacterial interactome disturbance characterized by reduced antagonistic interactions, rather than change in pathogen abundance or diversity, is a reproducible feature of airway dysbiosis in COPD clinical stability and exacerbations, which suggests that we may target interactome rather than pathogen alone for disease treatment.},
}
@article {pmid38632407,
year = {2024},
author = {Maes, SL and Dietrich, J and Midolo, G and Schwieger, S and Kummu, M and Vandvik, V and Aerts, R and Althuizen, IHJ and Biasi, C and Björk, RG and Böhner, H and Carbognani, M and Chiari, G and Christiansen, CT and Clemmensen, KE and Cooper, EJ and Cornelissen, JHC and Elberling, B and Faubert, P and Fetcher, N and Forte, TGW and Gaudard, J and Gavazov, K and Guan, Z and Guðmundsson, J and Gya, R and Hallin, S and Hansen, BB and Haugum, SV and He, JS and Hicks Pries, C and Hovenden, MJ and Jalava, M and Jónsdóttir, IS and Juhanson, J and Jung, JY and Kaarlejärvi, E and Kwon, MJ and Lamprecht, RE and Le Moullec, M and Lee, H and Marushchak, ME and Michelsen, A and Munir, TM and Myrsky, EM and Nielsen, CS and Nyberg, M and Olofsson, J and Óskarsson, H and Parker, TC and Pedersen, EP and Petit Bon, M and Petraglia, A and Raundrup, K and Ravn, NMR and Rinnan, R and Rodenhizer, H and Ryde, I and Schmidt, NM and Schuur, EAG and Sjögersten, S and Stark, S and Strack, M and Tang, J and Tolvanen, A and Töpper, JP and Väisänen, MK and van Logtestijn, RSP and Voigt, C and Walz, J and Weedon, JT and Yang, Y and Ylänne, H and Björkman, MP and Sarneel, JM and Dorrepaal, E},
title = {Environmental drivers of increased ecosystem respiration in a warming tundra.},
journal = {Nature},
volume = {629},
number = {8010},
pages = {105-113},
pmid = {38632407},
issn = {1476-4687},
mesh = {Arctic Regions ; Carbon/metabolism/analysis ; Carbon Cycle ; Datasets as Topic ; *Ecosystem ; *Global Warming ; Hydrogen-Ion Concentration ; Nitrogen/metabolism/analysis ; Plants/metabolism ; Seasons ; Soil/chemistry ; Soil Microbiology ; Temperature ; *Tundra ; Time Factors ; *Cell Respiration ; },
abstract = {Arctic and alpine tundra ecosystems are large reservoirs of organic carbon[1,2]. Climate warming may stimulate ecosystem respiration and release carbon into the atmosphere[3,4]. The magnitude and persistency of this stimulation and the environmental mechanisms that drive its variation remain uncertain[5-7]. This hampers the accuracy of global land carbon-climate feedback projections[7,8]. Here we synthesize 136 datasets from 56 open-top chamber in situ warming experiments located at 28 arctic and alpine tundra sites which have been running for less than 1 year up to 25 years. We show that a mean rise of 1.4 °C [confidence interval (CI) 0.9-2.0 °C] in air and 0.4 °C [CI 0.2-0.7 °C] in soil temperature results in an increase in growing season ecosystem respiration by 30% [CI 22-38%] (n = 136). Our findings indicate that the stimulation of ecosystem respiration was due to increases in both plant-related and microbial respiration (n = 9) and continued for at least 25 years (n = 136). The magnitude of the warming effects on respiration was driven by variation in warming-induced changes in local soil conditions, that is, changes in total nitrogen concentration and pH and by context-dependent spatial variation in these conditions, in particular total nitrogen concentration and the carbon:nitrogen ratio. Tundra sites with stronger nitrogen limitations and sites in which warming had stimulated plant and microbial nutrient turnover seemed particularly sensitive in their respiration response to warming. The results highlight the importance of local soil conditions and warming-induced changes therein for future climatic impacts on respiration.},
}
@article {pmid38632405,
year = {2024},
author = {Swain, A and Woodhouse, A and Fagan, WF and Fraass, AJ and Lowery, CM},
title = {Biogeographic response of marine plankton to Cenozoic environmental changes.},
journal = {Nature},
volume = {629},
number = {8012},
pages = {616-623},
pmid = {38632405},
issn = {1476-4687},
mesh = {Animals ; *Aquatic Organisms/physiology/classification ; Biodiversity ; Biological Evolution ; *Climate Change/history ; Datasets as Topic ; Extinction, Biological ; *Foraminifera/classification/physiology ; History, Ancient ; *Phylogeography ; *Plankton/classification/physiology ; Spatio-Temporal Analysis ; },
abstract = {In palaeontological studies, groups with consistent ecological and morphological traits across a clade's history (functional groups)[1] afford different perspectives on biodiversity dynamics than do species and genera[2,3], which are evolutionarily ephemeral. Here we analyse Triton, a global dataset of Cenozoic macroperforate planktonic foraminiferal occurrences[4], to contextualize changes in latitudinal equitability gradients[1], functional diversity, palaeolatitudinal specialization and community equitability. We identify: global morphological communities becoming less specialized preceding the richness increase after the Cretaceous-Palaeogene extinction; ecological specialization during the Early Eocene Climatic Optimum, suggesting inhibitive equatorial temperatures during the peak of the Cenozoic hothouse; increased specialization due to circulation changes across the Eocene-Oligocene transition, preceding the loss of morphological diversity; changes in morphological specialization and richness about 19 million years ago, coeval with pelagic shark extinctions[5]; delayed onset of changing functional group richness and specialization between hemispheres during the mid-Miocene plankton diversification. The detailed nature of the Triton dataset permits a unique spatiotemporal view of Cenozoic pelagic macroevolution, in which global biogeographic responses of functional communities and richness are decoupled during Cenozoic climate events. The global response of functional groups to similar abiotic selection pressures may depend on the background climatic state (greenhouse or icehouse) to which a group is adapted.},
}
@article {pmid38629556,
year = {2024},
author = {Dai, WT and Zhang, H and Wu, X and Zhong, M and Duan, GL and Dong, JH and Zhang, PP and Fan, HM},
title = {[Pollution Characteristics and Source Analysis of Soil Heavy Metal in Coal Mine Area near the Yellow River in Shandong].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {45},
number = {5},
pages = {2952-2961},
doi = {10.13227/j.hjkx.202306029},
pmid = {38629556},
issn = {0250-3301},
abstract = {To explore the pollution characteristics and source of soil heavy metal in a coal mine area near the Yellow River in Shandong, the geo-accumulation index method and improved Nemerow pollution index method were used to evaluate the pollution characteristics of soil heavy metal. The absolute principal component-multiple linear regression model (APCS-MLR) was used to quantitatively analyze the source of soil heavy metal, and the spatial distribution of Hg and Cd were analyzed using the Kriging spatial difference method in ArcGIS. The result accuracy of the APCS-MLR model was further verified. The results showed that:The measured contents of soil heavy metal Cu, Zn, Pb, Cr, Cd, Ni, As, and Hg all exceeded the normal site, among which, Hg and Cd exceeded the background values of soil elements in Shandong. The coefficient of variation (CV) of Hg was higher than 0.500, indicating significant spatial heterogeneity. Moreover, the correlation between Hg and other heavy metals was generally low, and the possibility of the same pollution source was small. The results of the geo-accumulation index and improved Nemerow pollution index showed that the overall soil heavy metal pollution was at a moderate level, among which the Hg pollution level was the highest, and its maximum value was at a slanted-heavy pollution level; Cu, Cd, and As in soil caused local pollution, which were at a slanted-light pollution level. Soil heavy metal pollution was closely related to mining activities, rehabilitation, and engineering construction in the coal mine area. The two major pollution sources of soil heavy metal in the research area were the compound source of the parent material and industrial and mining transportation sources (known source 1) and the compound source of atmospheric sedimentation and coal production (known source 2), the contribution rates of which were 76.705% and 16.171%, respectively. The results of the APCS-MLR model were shown to be reliable by analyzing the content distribution of Hg and Cd using the Kriging space difference mode. This research can provide scientific basis for the precise control and improvement of soil heavy metal pollution, ensuring the safety of food and agricultural products and improving the quality of the ecological environment in the coal mine area in the Shandong section of the Yellow River Basin.},
}
@article {pmid38629131,
year = {2024},
author = {Reginato, M and Ordónez-Parra, CA and Messeder, JVS and Brito, VLG and Dellinger, A and Kriebel, R and Marra, C and Melo, L and Cornelissen, T and Fuzessy, L and Sperotto, P and Calderón-Hernández, M and Guerra, TJ and Kopper, C and Mancipe-Murillo, C and Pizo, MA and Posada-Herrera, JM and Hasui, &#xc9; and Silva, WR and Silveira, FAO},
title = {MelastomaTRAITs 1.0: A database of functional traits in Melastomataceae, a large pantropical angiosperm family.},
journal = {Ecology},
volume = {105},
number = {6},
pages = {e4308},
doi = {10.1002/ecy.4308},
pmid = {38629131},
issn = {1939-9170},
support = {//Conselho Nacional de Desenvolvimento Cient&#xed;fico e Tecnol&#xf3;gico/ ; FWF P-30669 T-1186//Austrian Science Fund/ ; //Funda&#xe7;&#xe3;o de Amparo &#xe0; Pesquisa do Estado de Minas Gerais/ ; //Coordena&#xe7;&#xe3;o de Aperfei&#xe7;oamento de Pessoal de N&#xed;vel Superior/ ; //Fulbright Association/ ; },
mesh = {*Databases, Factual ; Ecosystem ; *Melastomataceae/physiology/genetics ; },
abstract = {The recent availability of open-access repositories of functional traits has revolutionized trait-based approaches in ecology and evolution. Nevertheless, the underrepresentation of tropical regions and lineages remains a pervasive bias in plant functional trait databases, which constrains large-scale assessments of plant ecology, evolution, and biogeography. Here, we present MelastomaTRAITs 1.0, a comprehensive and updatable database of functional traits for the pantropical Melastomataceae, the ninth-largest angiosperm family with 177 genera and more than 5800 species. Melastomataceae encompass species with a wide diversity of growth forms (herbs, shrubs, trees, epiphytes, and woody climbers), habitats (including tropical forests, savannas, grasslands, and wetlands from sea level to montane areas above the treeline), ecological strategies (from pioneer, edge-adapted and invasive species to shade-tolerant understory species), geographic distribution (from microendemic to continental-wide distribution), reproductive, pollination, and seed dispersal systems. MelastomaTRAITs builds on 581 references, such as taxonomic monographs, ecological research, and unpublished data, and includes four whole-plant traits, six leaf traits, 11 flower traits, 18 fruit traits, and 27 seed traits for 2520 species distributed in 144 genera across all 21 tribes. Most data come from the Neotropics where the family is most species-rich. Miconieae (the largest tribe) contains the highest number of trait records (49.6%) and species (41.1%) records. The trait types with the most information in the database were whole-plant traits, flowers, and leaf traits. With the breadth of functional traits recorded, our database helps to fill a gap in information for tropical plants and will significantly improve our capacity for large-scale trait-based syntheses across levels of organization, plant-animal interactions, regeneration ecology, and thereby support conservation and restoration programs. There are no copyright restrictions on the dataset; please cite this data paper when reusing the data.},
}
@article {pmid38627476,
year = {2024},
author = {Ridley, RS and Conrad, RE and Lindner, BG and Woo, S and Konstantinidis, KT},
title = {Potential routes of plastics biotransformation involving novel plastizymes revealed by global multi-omic analysis of plastic associated microbes.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8798},
pmid = {38627476},
issn = {2045-2322},
support = {2136146//National Science Foundation/ ; },
mesh = {Humans ; *Multiomics ; *Plastics ; Polymers ; Biotransformation ; Biodegradation, Environmental ; },
abstract = {Despite increasing efforts across various disciplines, the fate, transport, and impact of synthetic plastics on the environment and public health remain poorly understood. To better elucidate the microbial ecology of plastic waste and its potential for biotransformation, we conducted a large-scale analysis of all publicly available meta-omic studies investigating plastics (n = 27) in the environment. Notably, we observed low prevalence of known plastic degraders throughout most environments, except for substantial enrichment in riverine systems. This indicates rivers may be a highly promising environment for discovery of novel plastic bioremediation products. Ocean samples associated with degrading plastics showed clear differentiation from non-degrading polymers, showing enrichment of novel putative biodegrading taxa in the degraded samples. Regarding plastisphere pathogenicity, we observed significant enrichment of antimicrobial resistance genes on plastics but not of virulence factors. Additionally, we report a co-occurrence network analysis of 10 + million proteins associated with the plastisphere. This analysis revealed a localized sub-region enriched with known and putative plastizymes-these may be useful for deeper investigation of nature's ability to biodegrade man-made plastics. Finally, the combined data from our meta-analysis was used to construct a publicly available database, the Plastics Meta-omic Database (PMDB)-accessible at plasticmdb.org. These data should aid in the integrated exploration of the microbial plastisphere and facilitate research efforts investigating the fate and bioremediation potential of environmental plastic waste.},
}
@article {pmid38627422,
year = {2024},
author = {Hammoud, R and Tognin, S and Smythe, M and Gibbons, J and Davidson, N and Bakolis, I and Mechelli, A},
title = {Smartphone-based ecological momentary assessment reveals an incremental association between natural diversity and mental wellbeing.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {7051},
pmid = {38627422},
issn = {2045-2322},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Smartphone ; *Ecological Momentary Assessment ; Mental Health ; Trees ; Biodiversity ; },
abstract = {Using smartphone-based ecological momentary assessment, this study investigated an association between natural diversity on mental wellbeing. A sample of 1,998 participants completed 41,448 assessments between April 2018 and September 2023. Environments which included a larger range of natural features, such as trees, plants and birdlife (high natural diversity) were associated with greater mental wellbeing than environments including a smaller range of natural features (low natural diversity). There was evidence of a mediating effect of natural diversity on the association between natural environments and mental wellbeing. These results highlight the importance of policies and practices that support richness of biodiversity for public mental health.},
}
@article {pmid38625737,
year = {2024},
author = {Jonathan, J and Barakabitze, AA and Fast, CD and Cox, C},
title = {Machine Learning for Prediction of Tuberculosis Detection: Case Study of Trained African Giant Pouched Rats.},
journal = {Online journal of public health informatics},
volume = {16},
number = {},
pages = {e50771},
pmid = {38625737},
issn = {1947-2579},
abstract = {BACKGROUND: Technological advancement has led to the growth and rapid increase of tuberculosis (TB) medical data generated from different health care areas, including diagnosis. Prioritizing better adoption and acceptance of innovative diagnostic technology to reduce the spread of TB significantly benefits developing countries. Trained TB-detection rats are used in Tanzania and Ethiopia for operational research to complement other TB diagnostic tools. This technology has increased new TB case detection owing to its speed, cost-effectiveness, and sensitivity.<br><br>OBJECTIVE: During the TB detection process, rats produce vast amounts of data, providing an opportunity to identify interesting patterns that influence TB detection performance. This study aimed to develop models that predict if the rat will hit (indicate the presence of TB within) the sample or not using machine learning (ML) techniques. The goal was to improve the diagnostic accuracy and performance of TB detection involving rats.<br><br>METHODS: APOPO (Anti-Persoonsmijnen Ontmijnende Product Ontwikkeling) Center in Morogoro provided data for this study from 2012 to 2019, and 366,441 observations were used to build predictive models using ML techniques, including decision tree, random forest, na&#xef;ve Bayes, support vector machine, and k-nearest neighbor, by incorporating a variety of variables, such as the diagnostic results from partner health clinics using methods endorsed by the World Health Organization (WHO).<br><br>RESULTS: The support vector machine technique yielded the highest accuracy of 83.39% for prediction compared to other ML techniques used. Furthermore, this study found that the inclusion of variables related to whether the sample contained TB or not increased the performance accuracy of the predictive model.<br><br>CONCLUSIONS: The inclusion of variables related to the diagnostic results of TB samples may improve the detection performance of the trained rats. The study results may be of importance to TB-detection rat trainers and TB decision-makers as the results may prompt them to take action to maintain the usefulness of the technology and increase the TB detection performance of trained rats.},
}
@article {pmid38622188,
year = {2024},
author = {Liu, X and Chen, J and Tang, BH and He, L and Xu, Y and Yang, C},
title = {Eco-environmental changes due to human activities in the Erhai Lake Basin from 1990 to 2020.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8646},
pmid = {38622188},
issn = {2045-2322},
support = {42301454//National Natural Science Foundation of China/ ; 42230109//National Natural Science Foundation of China/ ; 42201319//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Lakes ; *Sustainable Development ; Human Activities ; China ; Environmental Monitoring/methods ; },
abstract = {Human activities have increased with urbanisation in the Erhai Lake Basin, considerably impacting its eco-environmental quality (EEQ). This study aims to reveal the evolution and driving forces of the EEQ using water benefit-based ecological index (WBEI) in response to human activities and policy variations in the Erhai Lake Basin from 1990 to 2020. Results show that (1) the EEQ exhibited a pattern of initial degradation, subsequent improvement, further degradation and a rebound from 1990 to 2020, and the areas with poor and fair EEQ levels mainly concentrated around the Erhai Lake Basin with a high level of urbanisation and relatively flat terrain; (2) the EEQ levels were not optimistic in 1990, 1995 and 2015, and areas with poor and fair EEQ levels accounted for 43.41%, 47.01% and 40.05% of the total area, respectively; and (3) an overall improvement in the EEQ was observed in 1995-2000, 2000-2005, 2005-2009 and 2015-2020, and the improvement was most significant in 1995-2000, covering an area of 823.95 km[2] and accounting for 31.79% of the total area. Results also confirmed that the EEQ changes in the Erhai Lake Basin were primarily influenced by human activities and policy variations. Moreover, these results can provide a scientific basis for the formulation and planning of sustainable development policy in the Erhai Lake Basin.},
}
@article {pmid38621404,
year = {2024},
author = {Turtle, L and Elliot, S and Drake, TM and Thorpe, M and Khoury, EG and Greenhalf, W and Hardwick, HE and Leeming, G and Law, A and Oosthuyzen, W and Pius, R and Shaw, CA and Baillie, JK and Openshaw, PJM and Docherty, AB and Semple, MG and Harrison, EM and Palmieri, C and , },
title = {Changes in hospital mortality in patients with cancer during the COVID-19 pandemic (ISARIC-CCP-UK): a prospective, multicentre cohort study.},
journal = {The Lancet. Oncology},
volume = {25},
number = {5},
pages = {636-648},
doi = {10.1016/S1470-2045(24)00107-4},
pmid = {38621404},
issn = {1474-5488},
mesh = {Humans ; *COVID-19/mortality/epidemiology ; *Neoplasms/mortality/therapy ; Male ; Female ; Prospective Studies ; Aged ; Middle Aged ; *Hospital Mortality ; United Kingdom/epidemiology ; *SARS-CoV-2 ; Adult ; Aged, 80 and over ; Pandemics ; },
abstract = {BACKGROUND: Patients with cancer are at greater risk of dying from COVID-19 than many other patient groups. However, how this risk evolved during the pandemic remains unclear. We aimed to determine, on the basis of the UK national pandemic protocol, how factors influencing hospital mortality from COVID-19 could differentially affect patients undergoing cancer treatment. We also examined changes in hospital mortality and escalation of care in patients on cancer treatment during the first 2 years of the COVID-19 pandemic in the UK.<br><br>METHODS: We conducted a prospective cohort study of patients aged older than 19 years and admitted to 306 health-care facilities in the UK with confirmed SARS-CoV-2 infection, who were enrolled in the International Severe Acute Respiratory and emerging Infections Consortium (ISARIC) WHO Clinical Characterisation Protocol (CCP) across the UK from April 23, 2020, to Feb 28, 2022; this analysis included all patients in the complete dataset when the study closed. The primary outcome was 30-day in-hospital mortality, comparing patients on cancer treatment and those without cancer. The study was approved by the South Central-Oxford C Research Ethics Committee in England (Ref: 13/SC/0149) and the Scotland A Research Ethics Committee (Ref 20/SS/0028), and is registered on the ISRCTN Registry (ISRCTN66726260).<br><br>FINDINGS: 177&#x2008;871 eligible adult patients either with no history of cancer (n=171&#x2008;303) or on cancer treatment (n=6568) were enrolled; 93&#x2008;205 (52&#xb7;4%) were male, 84&#x2008;418 (47&#xb7;5%) were female, and in 248 (13&#xb7;9%) sex or gender details were not specified or data were missing. Patients were followed up for a median of 13 (IQR 6-21) days. Of the 6568 patients receiving cancer treatment, 2080 (31&#xb7;7%) died at 30 days, compared with 30&#x2008;901 (18&#xb7;0%) of 171&#x2008;303 patients without cancer. Patients aged younger than 50 years on cancer treatment had the highest age-adjusted relative risk (hazard ratio [HR] 5&#xb7;2 [95% CI 4&#xb7;0-6&#xb7;6], p<0&#xb7;0001; vs 50-69 years 2&#xb7;4 [2&#xb7;2-2&#xb7;6], p<0&#xb7;0001; 70-79 years 1&#xb7;8 [1&#xb7;6-2&#xb7;0], p<0&#xb7;0001; and >80 years 1&#xb7;5 [1&#xb7;3-1&#xb7;6], p<0&#xb7;0001) but a lower absolute risk (51 [6&#xb7;7%] of 763 patients <50 years died compared with 459 [30&#xb7;2%] of 1522 patients aged >80 years). In-hospital mortality decreased for all patients during the pandemic but was higher for patients on cancer treatment than for those without cancer throughout the study period.<br><br>INTERPRETATION: People with cancer have a higher risk of mortality from COVID-19 than those without cancer. Patients younger than 50 years with cancer treatment have the highest relative risk of death. Continued action is needed to mitigate the poor outcomes in patients with cancer, such as through optimising vaccination, long-acting passive immunisation, and early access to therapeutics. These findings underscore the importance of the ISARIC-WHO pandemic preparedness initiative.<br><br>FUNDING: National Institute for Health Research and the Medical Research Council.},
}
@article {pmid38618197,
year = {2023},
author = {Short, S and Green Etxabe, A and Robinson, A and Spurgeon, D and Kille, P and , and , and , and , },
title = {The genome sequence of the red compost earthworm, Lumbricus rubellus (Hoffmeister, 1843).},
journal = {Wellcome open research},
volume = {8},
number = {},
pages = {354},
pmid = {38618197},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual Lumbricus rubellus (the red compost earthworm; Annelida; Clitellata; Haplotaxida; Lumbricidae). The genome sequence is 787.5 megabases in span. Most of the assembly is scaffolded into 18 chromosomal pseudomolecules. The mitochondrial genome has also been assembled and is 15.81 kilobases in length. Gene annotation of this assembly on Ensembl identified 33,426 protein coding genes.},
}
@article {pmid38617028,
year = {2024},
author = {Liu, J and He, C and Si, Y and Li, B and Wu, Q and Ni, J and Zhao, Y and Hu, Q and Du, S and Lu, Z and Jin, J and Xu, C},
title = {Toward Better and Healthier Air Quality: Global PM2.5 and O3 Pollution Status and Risk Assessment Based on the New WHO Air Quality Guidelines for 2021.},
journal = {Global challenges (Hoboken, NJ)},
volume = {8},
number = {4},
pages = {2300258},
pmid = {38617028},
issn = {2056-6646},
abstract = {To reduce the high burden of disease caused by air pollution, the World Health Organization (WHO) released new Air Quality Guidelines (AQG) on September 22, 2021. In this study, the daily fine particulate matter (PM2.5) and surface ozone (O3) data of 618 cities around the world is collected from 2019 to 2022. Based on the new AQG, the number of attainment days for daily average concentrations of PM2.5 (≤ 15 µg m[-3]) and O3 (≤ 100 µg m[-3]) is approximately 10% and 90%, respectively. China and India exhibit a decreasing trend in the number of highly polluted days (> 75 µg m[-3]) for PM. Every year over 68% and 27% of cities in the world are exposed to harmful PM2.5 (> 35 µg m[-3]) and O3 (> 100 µg m[-3]) pollution, respectively. Combined with the United Nations Sustainable Development Goals (SDGs), it is found that more than 35% of the world's cities face PM2.5-O3 compound pollution. Furthermore, the exposure risks in these cities (China, India, etc.) are mainly categorized as "High Risk", "Risk", and "Stabilization". In contrast, economically developed cities are mainly categorized as "High Safety", "Safety", and "Deep Stabilization." These findings indicate that global implementation of the WHO's new AQG will minimize the inequitable exposure risk from air pollution.},
}
@article {pmid38616489,
year = {2024},
author = {Bleker, C and Ramšak, &#x17d; and Bittner, A and Podpečan, V and Zagorščak, M and Wurzinger, B and Baebler, &#x160; and Petek, M and Križnik, M and van Dieren, A and Gruber, J and Afjehi-Sadat, L and Weckwerth, W and Županič, A and Teige, M and Vothknecht, UC and Gruden, K},
title = {Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses.},
journal = {Plant communications},
volume = {5},
number = {6},
pages = {100920},
pmid = {38616489},
issn = {2590-3462},
mesh = {*Systems Biology ; *Stress, Physiological ; *Plants/genetics/metabolism ; Plant Physiological Phenomena/genetics ; Signal Transduction/genetics ; Databases, Factual ; },
abstract = {Stress Knowledge Map (SKM; https://skm.nib.si) is a publicly available resource containing two complementary knowledge graphs that describe the current knowledge of biochemical, signaling, and regulatory molecular interactions in plants: a highly curated model of plant stress signaling (PSS; 543 reactions) and a large comprehensive knowledge network (488 390 interactions). Both were constructed by domain experts through systematic curation of diverse literature and database resources. SKM provides a single entry point for investigations of plant stress response and related growth trade-offs, as well as interactive explorations of current knowledge. PSS is also formulated as a qualitative and quantitative model for systems biology and thus represents a starting point for a plant digital twin. Here, we describe the features of SKM and show, through two case studies, how it can be used for complex analyses, including systematic hypothesis generation and design of validation experiments, or to gain new insights into experimental observations in plant biology.},
}
@article {pmid38616247,
year = {2024},
author = {Kibet, CK and Entfellner, JD and Jjingo, D and de Villiers, EP and de Villiers, S and Wambui, K and Kinyanjui, S and Masiga, D},
title = {Designing and delivering bioinformatics project-based learning in East Africa.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {150},
pmid = {38616247},
issn = {1471-2105},
support = {U2R TW010677/TW/FIC NIH HHS/United States ; U2RTW010677/TW/FIC NIH HHS/United States ; },
mesh = {Humans ; *Learning ; Africa, Eastern ; *COVID-19/epidemiology ; Computational Biology ; Pandemics ; },
abstract = {BACKGROUND: The Eastern Africa Network for Bioinformatics Training (EANBiT) has matured through continuous evaluation, feedback, and codesign. We highlight how the program has evolved to meet challenges and achieve its goals and how experiential learning through mini projects enhances the acquisition of skills and collaboration. We continued to learn and grow through honest feedback and evaluation of the program, trainers, and modules, enabling us to provide robust training even during the Coronavirus disease 2019 (COVID-19) pandemic, when we had to redesign the program due to restricted travel and in person group meetings.<br><br>RESULTS: In response to the pandemic, we developed a program to maintain "residential" training experiences and benefits remotely. We had to answer the following questions: What must change to still achieve the RT goals? What optimal platforms should be used? How would we manage connectivity and data challenges? How could we avoid online fatigue? Going virtual presented an opportunity to reflect on the essence and uniqueness of the program and its ability to meet the objective of strengthening bioinformatics skills among the cohorts of students using different delivery approaches. It allowed an increase in the number of participants. Evaluating each program component is critical for improvement, primarily when feedback feeds into the program's continuous amendment. Initially, the participants noted that there were too many modules, insufficient time, and a lack of hands-on training as a result of too much focus on theory. In the subsequent iterations, we reduced the number of modules from 27 to five, created a harmonized repository for the materials on GitHub, and introduced project-based learning through the mini projects.<br><br>CONCLUSION: We demonstrate that implementing a program design through detailed monitoring and evaluation leads to success, especially when participants who are the best fit for the program are selected on an appropriate level of skills, motivation, and commitment.},
}
@article {pmid38614075,
year = {2024},
author = {Breeyear, JH and Mautz, BS and Keaton, JM and Hellwege, JN and Torstenson, ES and Liang, J and Bray, MJ and Giri, A and Warren, HR and Munroe, PB and Velez Edwards, DR and Zhu, X and Li, C and Edwards, TL},
title = {A new test for trait mean and variance detects unreported loci for blood-pressure variation.},
journal = {American journal of human genetics},
volume = {111},
number = {5},
pages = {954-965},
pmid = {38614075},
issn = {1537-6605},
mesh = {Humans ; *Blood Pressure/genetics ; *Quantitative Trait Loci ; *Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; Models, Genetic ; Genotype ; Genetic Variation ; Computer Simulation ; Phenotype ; },
abstract = {Variability in quantitative traits has clinical, ecological, and evolutionary significance. Most genetic variants identified for complex quantitative traits have only a detectable effect on the mean of trait. We have developed the mean-variance test (MVtest) to simultaneously model the mean and log-variance of a quantitative trait as functions of genotypes and covariates by using estimating equations. The advantages of MVtest include the facts that it can detect effect modification, that multiple testing can follow conventional thresholds, that it is robust to non-normal outcomes, and that association statistics can be meta-analyzed. In simulations, we show control of type I error of MVtest over several alternatives. We identified 51 and 37 previously unreported associations for effects on blood-pressure variance and mean, respectively, in the UK Biobank. Transcriptome-wide association studies revealed 633 significant unique gene associations with blood-pressure mean variance. MVtest is broadly applicable to studies of complex quantitative traits and provides an important opportunity to detect novel loci.},
}
@article {pmid38613584,
year = {2024},
author = {Kredics, L and Büchner, R and Balázs, D and Allaga, H and Kedves, O and Racić, G and Varga, A and Nagy, VD and Vágvölgyi, C and Sipos, G},
title = {Recent advances in the use of Trichoderma-containing multicomponent microbial inoculants for pathogen control and plant growth promotion.},
journal = {World journal of microbiology &amp; biotechnology},
volume = {40},
number = {5},
pages = {162},
pmid = {38613584},
issn = {1573-0972},
mesh = {Humans ; *Agricultural Inoculants ; *Trichoderma ; Fertilizers ; *Pesticides ; Soil ; },
abstract = {Chemical pesticides and fertilizers are used in agricultural production worldwide to prevent damage from plant pathogenic microorganisms, insects, and nematodes, to minimize crop losses and to preserve crop quality. However, the use of chemical pesticides and fertilizers can severely pollute soil, water, and air, posing risks to the environment and human health. Consequently, developing new, alternative, environment-friendly microbial soil treatment interventions for plant protection and crop yield increase has become indispensable. Members of the filamentous fungal genus Trichoderma (Ascomycota, Sordariomycetes, Hypocreales) have long been known as efficient antagonists of plant pathogenic microorganisms based on various beneficial traits and abilities of these fungi. This minireview aims to discuss the advances in the field of Trichoderma-containing multicomponent microbiological inoculants based on recent experimental updates. Trichoderma strains can be combined with each other, with other fungi and/or with beneficial bacteria. The development and field performance of such inoculants will be addressed, focusing on the complementarity, synergy, and compatibility of their microbial components.},
}
@article {pmid38613177,
year = {2024},
author = {Wan, JSH and Bonser, SP and Pang, CK and Fazlioglu, F and Rutherford, S},
title = {Adaptive responses to living in stressful habitats: Do invasive and native plant populations use different strategies?.},
journal = {Ecology letters},
volume = {27},
number = {4},
pages = {e14419},
doi = {10.1111/ele.14419},
pmid = {38613177},
issn = {1461-0248},
mesh = {Reproduction ; *Plant Physiological Phenomena ; *Stress, Physiological ; },
abstract = {Plants inhabit stressful environments characterized by a variety of stressors, including mine sites, mountains, deserts, and high latitudes. Populations from stressful and reference (non-stressful) sites often have performance differences. However, while invasive and native species may respond differently to stressful environments, there is limited understanding of the patterns in reaction norms of populations from these sites. Here, we use phylogenetically controlled meta-analysis to assess the performance of populations under stress and non-stress conditions. We ask whether stress populations of natives and invasives differ in the magnitude of lowered performance under non-stress conditions and if they vary in the degree of performance advantage under stress. We also assessed whether these distinctions differ with stress intensity. Our findings revealed that natives not only have greater adaptive advantages but also more performance reductions than invasives. Populations from very stressful sites had more efficient adaptations, and performance costs increased with stress intensity in natives only. Overall, the results support the notion that adaptation is frequently costless. Reproductive output was most closely associated with adaptive costs and benefits. Our study characterized the adaptive strategies used by invasive and native plants under stressful conditions, thereby providing important insights into the limitations of adaptation to extreme sites.},
}
@article {pmid38613081,
year = {2024},
author = {Jeong, S and Choi, YJ},
title = {Association between Socioecological Status, Nutrient Intake, and Cancer Screening Behaviors in Adults Aged 40 and Over: Insights from the Eighth Korea National Health and Nutrition Examination Survey (KNHANES, 2019).},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613081},
issn = {2072-6643},
mesh = {Adult ; Humans ; Middle Aged ; *Early Detection of Cancer ; Nutrition Surveys ; Eating ; Energy Intake ; Republic of Korea ; *Neoplasms ; },
abstract = {Cancer screening is pivotal for early detection and improved survival rates. While socio-ecological factors are known to influence screening uptake, the role of lifestyle, dietary habits, and general health in shaping these decisions remains underexplored. Utilizing the 2019 Korea National Health and Nutrition Examination Survey (KNHANES), this study examined the myriad of factors impacting cancer screening utilization. Data from 274,872 adults aged 40 years or older were scrutinized, highlighting demographics, income, lifestyle behaviors, health-related variables, nutrient intake, and dietary quality. A combination of descriptive statistics and logistic regression helped us ascertain influential determinants. Higher educational attainment and income quartiles were positively correlated with cancer screening rates. Regular walkers, those engaged in moderate physical activity, and individuals with a previous cancer diagnosis were more likely to get screened. High-risk drinkers and smokers were less inclined towards screening. Dietary habits also influenced screening decisions. Notably, participants with healthier eating behaviors, indicated by factors such as regular breakfasts and fewer meals out, were more likely to undergo screening. Additionally, nutrient intake analysis revealed that those who had undergone screening consumed greater quantities of most nutrients, bar a few exceptions. For individuals aged 50-64, nutritional assessment indicators highlighted a higher mean adequacy ratio (MAR) and index of nutritional quality (INQ) value among those who participated in screening, suggesting better nutritional quality. This study elucidates the complex socio-ecological and nutritional landscape influencing cancer screening decisions. The results underscore the importance of a holistic approach, emphasizing lifestyle, dietary habits, and socio-economic considerations. It provides a roadmap for policymakers to craft more inclusive screening programs, ensuring equal access and promoting early detection.},
}
@article {pmid38612552,
year = {2024},
author = {Jankovic, M and Knezevic, T and Tomic, A and Milicevic, O and Jovanovic, T and Djunic, I and Mihaljevic, B and Knezevic, A and Todorovic-Balint, M},
title = {Human Cytomegalovirus Oncoprotection across Diverse Populations, Tumor Histologies, and Age Groups: The Relevance for Prospective Vaccinal Therapy.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612552},
issn = {1422-0067},
support = {200110/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Cytomegalovirus ; Prospective Studies ; Seroepidemiologic Studies ; *Neoplasms/epidemiology ; *Cytomegalovirus Infections/epidemiology ; },
abstract = {The oncogenicity of the human cytomegalovirus (CMV) is currently being widely debated. Most recently, mounting clinical evidence suggests an anti-cancer effect via CMV-induced T cell-mediated tumor destruction. However, the data were mostly obtained from single-center studies and in vitro experiments. Broad geographic coverage is required to offer a global perspective. Our study examined the correlation between country-specific CMV seroprevalence (across 73 countries) and the age-standardized incidence rate (of 34 invasive tumors). The populations studied were stratified according to decadal age periods as the immunologic effects of CMV seropositivity may depend upon age at initial infection. The International Agency for Research on Cancer of the World Health Organization (IARC WHO) database was used. The multivariate linear regression analysis revealed a worldwide inverse correlation between CMV seroprevalence and the incidences of 62.8% tumors. Notably, this inverse link persists for all cancers combined (Spearman's ρ = -0.732, p < 0.001; β = -0.482, p < 0.001, adjusted R[2] = 0.737). An antithetical and significant correlation was also observed in particular age groups for the vast majority of tumors. Our results corroborate the conclusions of previous studies and indicate that this oncopreventive phenomenon holds true on a global scale. It applies to a wide spectrum of cancer histologies, additionally supporting the idea of a common underlying mechanism-CMV-stimulated T cell tumor targeting. Although these results further advance the notion of CMV-based therapies, in-depth investigation of host-virus interactions is still warranted.},
}
@article {pmid38611576,
year = {2024},
author = {Sulaiman, N and Salehi, F and Prakofjewa, J and Cavalleri, SAE and Ahmed, HM and Mattalia, G and Rastegar, A and Maghsudi, M and Amin, HM and Rasti, A and Hosseini, SH and Ghorbani, A and Pieroni, A and Sõukand, R},
title = {Cultural vs. State Borders: Plant Foraging by Hawraman and Mukriyan Kurds in Western Iran.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {38611576},
issn = {2223-7747},
abstract = {Plant foraging is a millennia-old activity still practiced by many people in the Middle East, particularly in the Fertile Crescent region, where several socioeconomic, ecological, and cultural factors shape this practice. This study seeks to understand the drivers of plant foraging in this complex region characterized by highly diverse linguistic, religious, and cultural groups. Our study aims to document the wild plants used by Kurds in Western Iran, identify similarities and differences among Hawraman and Mukriyan Kurdish groups in Iran, and compare our findings with a previous study on the Hawramani in Iraq. Forty-three semi-structured in-depth interviews were conducted in Kurdish villages of Western Iran. The results revealed the use of 44 wild food plant taxa, their preparation, and culinary uses. Among the reported taxa, 28 plant taxa were used by Mukriyani, and 33 by Hawramani. The study revealed a significant difference between the Hawraman and Mukriyan regions in Iran, whereas there is a high similarity between Hawramani Kurds in Iran and Iraq. We found that the invisible cultural border carries more weight than political divisions, and this calls for a paradigm shift in how we perceive and map the distribution of ethnobotanical knowledge.},
}
@article {pmid38609485,
year = {2024},
author = {Kazlou, A and Bornukova, K and Wickham, A and Slaykovskiy, V and Peven, K and Klepchukova, A and Ponzo, S and Garfinkel, S},
title = {Effects of stress on pain in females using a mobile health app in the Russia-Ukraine conflict.},
journal = {Npj mental health research},
volume = {3},
number = {1},
pages = {2},
pmid = {38609485},
issn = {2731-4251},
support = {MR/V037676/1//MRC/NIHR/ ; },
abstract = {The chronic and acute effects of stress can have divergent effects on health; long-term effects are associated with detrimental physical and mental health sequelae, while acute effects may be advantageous in the short-term. Stress-induced analgesia, the attenuation of pain perception due to stress, is a well-known phenomenon that has yet to be systematically investigated under ecological conditions. Using Flo, a women's health and wellbeing app and menstrual cycle tracker, with a world-wide monthly active usership of more than 57 million, women in Ukraine were monitored for their reporting of stress, pain and affective symptoms before, and immediately after, the onset of the Russian-Ukrainian conflict. To avoid potential selection (attrition) or collider bias, we rely on a sample of 87,315 users who were actively logging multiple symptoms before and after the start of the war. We found an inverse relationship between stress and pain, whereby higher reports of stress predicted lower rates of pain. Stress did not influence any other physiological symptoms with a similar magnitude, nor did any other symptom have a similar effect on pain. This relationship generally decreased in magnitude in countries neighbouring and surrounding Ukraine, with Ukraine serving as the epicentre. These findings help characterise the relationship between stress and health in a real-world setting.},
}
@article {pmid38605417,
year = {2024},
author = {Roder, T and Pimentel, G and Fuchsmann, P and Stern, MT and von Ah, U and Vergères, G and Peischl, S and Brynildsrud, O and Bruggmann, R and Bär, C},
title = {Scoary2: rapid association of phenotypic multi-omics data with microbial pan-genomes.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {93},
pmid = {38605417},
issn = {1474-760X},
support = {GRS-070/17//Gebert R&#xfc;f Stiftung/ ; },
mesh = {*Genome-Wide Association Study ; *Multiomics ; Phenotype ; Genes, Bacterial ; Genomics ; },
abstract = {Unraveling bacterial gene function drives progress in various areas, such as food production, pharmacology, and ecology. While omics technologies capture high-dimensional phenotypic data, linking them to genomic data is challenging, leaving 40-60% of bacterial genes undescribed. To address this bottleneck, we introduce Scoary2, an ultra-fast microbial genome-wide association studies (mGWAS) software. With its data exploration app and improved performance, Scoary2 is the first tool to enable the study of large phenotypic datasets using mGWAS. As proof of concept, we explore the metabolome of yogurts, each produced with a different Propionibacterium reichii strain and discover two genes affecting carnitine metabolism.},
}
@article {pmid38604487,
year = {2024},
author = {Zhang, Y and Huang, C and Zhao, J and Hu, L and Yang, L and Zhang, Y and Sang, W},
title = {Insights into tolerance mechanisms of earthworms (Eisenia fetida) in copper-contaminated soils by integrating multi-omics analyses.},
journal = {Environmental research},
volume = {252},
number = {Pt 2},
pages = {118910},
doi = {10.1016/j.envres.2024.118910},
pmid = {38604487},
issn = {1096-0953},
mesh = {*Oligochaeta/metabolism/drug effects ; Animals ; *Soil Pollutants/toxicity/metabolism ; *Copper/toxicity/metabolism ; Gastrointestinal Microbiome/drug effects ; Metabolomics ; Oxidative Stress/drug effects ; Multiomics ; },
abstract = {Earthworms can resist high levels of soil copper (Cu) contamination and play an essential role in absorbing them effectively. However, the molecular mechanisms underlying Cu tolerance in earthworms are poorly understood. To address this research gap, we studied alterations of Eisenia fetida in antioxidant enzymes, gut microbiota, metabolites, and genes under varying levels of Cu exposure soils (0, 67.58, 168.96, 337.92 mg/kg). Our results revealed a reduction in antioxidant enzyme activities across all treatment groups, indicating an adaptive response to alleviate Cu-induced oxidative stress. Analysis of gut microbiota revealed a significant increase in the abundance of bacteria associated with nutrient uptake and Cu[2+] excretion under Cu stress. Furthermore, metabolomic analysis discovered an increase in certain metabolites associated with energy metabolism, such as pyruvic acid, L-malic acid, and fumaric acid, as Cu concentration escalated. These results suggested that enhanced energy supply contributes to the elevated tolerance of E. fetida towards Cu. Additionally, transcriptome analysis not only identified crucial detoxification genes (Hsp70, CTSL, GST, CHAC, and GCLC), but also confirmed the critical role of glutathione metabolism as a key pathway in E. fetida Cu detoxification processes. These findings provide a new perspective on the molecular mechanisms of Cu tolerance in earthworms.},
}
@article {pmid38602562,
year = {2024},
author = {Nurkassimova, M and Omarova, N and Zinicovscaia, I and Yushin, N and Chaligava, O},
title = {Mosses as bioindicators of air pollution with potentially toxic elements in the Burabay State National Natural Park, Kazakhstan.},
journal = {Environmental monitoring and assessment},
volume = {196},
number = {5},
pages = {442},
pmid = {38602562},
issn = {1573-2959},
mesh = {Humans ; Environmental Biomarkers ; Parks, Recreational ; Kazakhstan ; Environmental Monitoring ; *Air Pollution ; *Bryophyta ; },
abstract = {The Burabay State National Natural Park is a national park of the great natural and historical values located in the north of Kazakhstan, which has been exposed in recent years to significant anthropogenic impact. The moss biomonitoring was performed in the Borovoye resort community, an important tourist destination in the national park, to identify the level of air pollution. Mosses collected at 29 locations were subjected to neutron activation analysis to determine 36 elements and additionally to ICP-OES to detect the level of Cu and Pb. Factor analysis was applied to check if there are any associations between identified elements and to link them with possible emission sources. According to contamination factor and pollution load indices the investigated area belongs to three classes of pollution: unpolluted, suspected and moderate. Potential ecological risk index calculated for selected elements revealed harmless risk to human health. The level of element obtained in Burabay State National Natural Park was compared with the data available for other national parks.},
}
@article {pmid38598963,
year = {2024},
author = {Shen, C and Feng, G and Zhao, F and Huang, X and Li, X},
title = {The multi-omics analysis in the hepatopancreas of Eriocheir sinensis provides novel insights into the response mechanism of heat stress.},
journal = {Comparative biochemistry and physiology. Part D, Genomics &amp; proteomics},
volume = {50},
number = {},
pages = {101232},
doi = {10.1016/j.cbd.2024.101232},
pmid = {38598963},
issn = {1878-0407},
mesh = {Animals ; *Hepatopancreas/metabolism ; *Brachyura/physiology/genetics/metabolism ; *Heat-Shock Response ; *Arthropod Proteins/genetics/metabolism ; *Proteomics ; Transcriptome ; Energy Metabolism ; Heat-Shock Proteins/genetics/metabolism ; Proteome ; Multiomics ; },
abstract = {Under global warming, heat stress can induce the excessive production of reactive oxygen species, causing irreversible damage to aquatic animals. It is essential to predict potentially harmful impacts on aquatic organisms under heat stress. Eriocheir sinensis, a typical crustacean crab, is widely distributed in China, American and Europe. Parent E. sinensis need migrate to the estuaries to reproduce in winter, and temperature is a key environmental factor. Herein, we performed a comprehensive transcriptomic and proteomic analysis in the hepatopancreas of E. sinensis under heat stress (20 °C and 30 °C), focusing on heat shock protein family, antioxidant system, energy metabolism and immune defense. The results revealed that parent E. sinensis generated adaptative responses to maintain physiological function under 20 °C stress via the transcriptional up-regulation of energy metabolism enzymes, mRNA synthesis and heat shock proteins. The transcriptional inhibition of key enzymes related to energy metabolism implied that 30 °C stress may lead to the dysfunction of energy metabolism in parent E. sinensis. Meanwhile, parent E. sinensis also enhanced the expression of ferritin and phospholipase D at translational level, and the glutathione s-transferase and heat shock protein 70 at both transcriptional and translational levels, speculating that parent E. sinensis can strengthen antioxidant and immune capacity to resist oxidative stress under 30 °C stress. This study elucidated the potential molecular mechanism in response to heat stress of parent E. sinensis hepatopancreas. The preliminary selection of heat tolerance genes or proteins in E. sinensis can provide a reference for the population prediction and the study of evolutionary mechanism under heat stress in crabs.},
}
@article {pmid38598334,
year = {2024},
author = {Wei, X and Tsai, MS and Liang, L and Jiang, L and Hung, CJ and Jelliffe-Pawlowski, L and Rand, L and Snyder, M and Jiang, C},
title = {Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process.},
journal = {Cell reports},
volume = {43},
number = {4},
pages = {114078},
doi = {10.1016/j.celrep.2024.114078},
pmid = {38598334},
issn = {2211-1247},
mesh = {Humans ; *Vagina/microbiology ; Female ; *Microbiota/genetics ; *Lactobacillus/genetics ; Adhesins, Bacterial/genetics ; Ethnicity/genetics ; Adult ; Evolution, Molecular ; Pregnancy ; Selection, Genetic ; Biological Evolution ; },
abstract = {The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.},
}
@article {pmid38597343,
year = {2024},
author = {Schwartz, LC and González, VL and Strong, EE and Truebano, M and Hilbish, TJ},
title = {Transgressive gene expression and expression plasticity under thermal stress in a stable hybrid zone.},
journal = {Molecular ecology},
volume = {33},
number = {9},
pages = {e17333},
doi = {10.1111/mec.17333},
pmid = {38597343},
issn = {1365-294X},
support = {//National Museum of Natural History/ ; //University of South Carolina/ ; },
mesh = {Animals ; *Hybridization, Genetic ; Temperature ; Climate Change ; Stress, Physiological/genetics ; Gene Expression/genetics ; Phenotype ; Mytilus/genetics ; Transcriptome ; },
abstract = {Interspecific hybridization can lead to myriad outcomes, including transgressive phenotypes in which the hybrids are more fit than either parent species. Such hybrids may display important traits in the context of climate change, able to respond to novel environmental conditions not previously experienced by the parent populations. While this has been evaluated in an agricultural context, the role of transgressive hybrids under changing conditions in the wild remains largely unexplored; this is especially true regarding transgressive gene expression. Using the blue mussel species complex (genus Mytilus) as a model system, we investigated the effects of hybridization on temperature induced gene expression plasticity by comparing expression profiles in parental species and their hybrids following a 2-week thermal challenge. Hybrid expression plasticity was most often like one parent or the other (50%). However, a large fraction of genes (26%) showed transgressive expression plasticity (i.e. the change in gene expression was either greater or lesser than that of both parent species), while only 2% were intermediately plastic in hybrids. Despite their close phylogenetic relationship, there was limited overlap in the differentially expressed genes responding to temperature, indicating interspecific differences in the responses to high temperature in which responses from hybrids are distinct from both parent species. We also identified differentially expressed long non-coding RNAs (lncRNAs), which we suggest may contribute to species-specific differences in thermal tolerance. Our findings provide important insight into the impact of hybridization on gene expression under warming. We propose transgressive hybrids may play an important role in population persistence under future warming conditions.},
}
@article {pmid38594342,
year = {2024},
author = {Brodie, JF and Mohd-Azlan, J and Chen, C and Wearn, OR and Deith, MCM and Ball, JGC and Slade, EM and Burslem, DFRP and Teoh, SW and Williams, PJ and Nguyen, A and Moore, JH and Goetz, SJ and Burns, P and Jantz, P and Hakkenberg, CR and Kaszta, ZM and Cushman, S and Coomes, D and Helmy, OE and Reynolds, G and Rodríguez, JP and Jetz, W and Luskin, MS},
title = {Author Correction: Landscape-scale benefits of protected areas for tropical biodiversity.},
journal = {Nature},
volume = {628},
number = {8009},
pages = {E5},
doi = {10.1038/s41586-024-07333-z},
pmid = {38594342},
issn = {1476-4687},
}
@article {pmid38594221,
year = {2024},
author = {Mujica, MI and Silva-Flores, P and Bueno, CG and Duchicela, J},
title = {Integrating perspectives in developing mycorrhizal trait databases: a call for inclusive and collaborative continental efforts.},
journal = {The New phytologist},
volume = {242},
number = {4},
pages = {1436-1440},
doi = {10.1111/nph.19754},
pmid = {38594221},
issn = {1469-8137},
support = {Ram&#xf3;n y Cajal fellowship #RYC2021-032533-I//Ministerio de Ciencia e Innovaci&#xf3;n/ ; 11230870//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; 3200774//Fondo Nacional de Desarrollo Cient&#xed;fico y Tecnol&#xf3;gico/ ; },
mesh = {Biodiversity ; Databases, Factual ; *Mycorrhizae/physiology ; Quantitative Trait, Heritable ; *Symbiosis ; },
abstract = {Global assessments of mycorrhizal symbiosis present large sampling gaps in rich biodiversity regions. Filling these gaps is necessary to build large-scale, unbiased mycorrhizal databases to obtain reliable analyses and prevent misleading generalizations. Underrepresented regions in mycorrhizal research are mainly in Africa, Asia, and South America. Despite the high biodiversity and endemism in these regions, many groups of organisms remain understudied, especially mycorrhizal fungi. In this Viewpoint, we emphasize the importance of inclusive and collaborative continental efforts in integrating perspectives for comprehensive trait database development and propose a conceptual framework that can help build large mycorrhizal databases in underrepresented regions. Based on the four Vs of big data (volume, variety, veracity, and velocity), we identify the main challenges of constructing a large mycorrhizal dataset and propose solutions for each challenge. We share our collaborative methodology, which involves employing open calls and working groups to engage all mycorrhizal researchers in the region to build a South American Mycorrhizal Database. By fostering interdisciplinary collaborations and embracing a continental-scale approach, we can create robust mycorrhizal trait databases that provide valuable insights into the evolution, ecology, and functioning of mycorrhizal associations, reducing the geographical biases that are so common in large-scale ecological studies.},
}
@article {pmid38589621,
year = {2024},
author = {Liew, F and Efstathiou, C and Fontanella, S and Richardson, M and Saunders, R and Swieboda, D and Sidhu, JK and Ascough, S and Moore, SC and Mohamed, N and Nunag, J and King, C and Leavy, OC and Elneima, O and McAuley, HJC and Shikotra, A and Singapuri, A and Sereno, M and Harris, VC and Houchen-Wolloff, L and Greening, NJ and Lone, NI and Thorpe, M and Thompson, AAR and Rowland-Jones, SL and Docherty, AB and Chalmers, JD and Ho, LP and Horsley, A and Raman, B and Poinasamy, K and Marks, M and Kon, OM and Howard, LS and Wootton, DG and Quint, JK and de Silva, TI and Ho, A and Chiu, C and Harrison, EM and Greenhalf, W and Baillie, JK and Semple, MG and Turtle, L and Evans, RA and Wain, LV and Brightling, C and Thwaites, RS and Openshaw, PJM and , and , },
title = {Large-scale phenotyping of patients with long COVID post-hospitalization reveals mechanistic subtypes of disease.},
journal = {Nature immunology},
volume = {25},
number = {4},
pages = {607-621},
pmid = {38589621},
issn = {1529-2916},
support = {/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; Post-Acute COVID-19 Syndrome ; *COVID-19 ; *Biomedical Research ; Hospitalization ; Immunoglobulin G ; },
abstract = {One in ten severe acute respiratory syndrome coronavirus 2 infections result in prolonged symptoms termed long coronavirus disease (COVID), yet disease phenotypes and mechanisms are poorly understood[1]. Here we profiled 368 plasma proteins in 657 participants ≥3 months following hospitalization. Of these, 426 had at least one long COVID symptom and 233 had fully recovered. Elevated markers of myeloid inflammation and complement activation were associated with long COVID. IL-1R2, MATN2 and COLEC12 were associated with cardiorespiratory symptoms, fatigue and anxiety/depression; MATN2, CSF3 and C1QA were elevated in gastrointestinal symptoms and C1QA was elevated in cognitive impairment. Additional markers of alterations in nerve tissue repair (SPON-1 and NFASC) were elevated in those with cognitive impairment and SCG3, suggestive of brain-gut axis disturbance, was elevated in gastrointestinal symptoms. Severe acute respiratory syndrome coronavirus 2-specific immunoglobulin G (IgG) was persistently elevated in some individuals with long COVID, but virus was not detected in sputum. Analysis of inflammatory markers in nasal fluids showed no association with symptoms. Our study aimed to understand inflammatory processes that underlie long COVID and was not designed for biomarker discovery. Our findings suggest that specific inflammatory pathways related to tissue damage are implicated in subtypes of long COVID, which might be targeted in future therapeutic trials.},
}
@article {pmid38587202,
year = {2024},
author = {Montfort, J and Hervas-Sotomayor, F and Le Cam, A and Murat, F},
title = {FEVER: an interactive web-based resource for evolutionary transcriptomics across fishes.},
journal = {Nucleic acids research},
volume = {52},
number = {W1},
pages = {W65-W69},
pmid = {38587202},
issn = {1362-4962},
support = {ANR-23-CE13-0008//ANR/ ; },
mesh = {Animals ; *Fishes/genetics ; *Evolution, Molecular ; *Transcriptome/genetics ; *Internet ; Gene Expression Profiling/methods ; Databases, Genetic ; Phylogeny ; Genomics/methods ; Software ; Genome/genetics ; },
abstract = {Teleost fish represent one of the largest and most diverse clades of vertebrates, which makes them great models in various research areas such as ecology and evolution. Recent sequencing endeavors provided high-quality genomes for species covering the main fish evolutionary lineages, opening up large-scale comparative genomics studies. However, transcriptomic data across fish species and organs are heterogenous and have not been integrated with newly sequenced genomes making gene expression quantification and comparative analyses particularly challenging. Thus, resources integrating genomic and transcriptomic data across fish species and organs are still lacking. Here, we present FEVER, a web-based resource allowing evolutionary transcriptomics across species and tissues. First, based on query genes FEVER reconstructs gene trees providing orthologous and paralogous relationships as well as their evolutionary dynamics across 13 species covering the major fish lineages, and 4 model species as evolutionary outgroups. Second, it provides unbiased gene expression across 11 tissues using up-to-date fish genomes. Finally, genomic and transcriptomic data are combined together allowing the exploration of gene expression evolution following speciation and duplication events. FEVER is freely accessible at https://fever.sk8.inrae.fr/.},
}
@article {pmid38584951,
year = {2024},
author = {Badiyal, A and Mahajan, R and Rana, RS and Sood, R and Walia, A and Rana, T and Manhas, S and Jayswal, DK},
title = {Synergizing biotechnology and natural farming: pioneering agricultural sustainability through innovative interventions.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1280846},
pmid = {38584951},
issn = {1664-462X},
abstract = {The world has undergone a remarkable transformation from the era of famines to an age of global food production that caters to an exponentially growing population. This transformation has been made possible by significant agricultural revolutions, marked by the intensification of agriculture through the infusion of mechanical, industrial, and economic inputs. However, this rapid advancement in agriculture has also brought about the proliferation of agricultural inputs such as pesticides, fertilizers, and irrigation, which have given rise to long-term environmental crises. Over the past two decades, we have witnessed a concerning plateau in crop production, the loss of arable land, and dramatic shifts in climatic conditions. These challenges have underscored the urgent need to protect our global commons, particularly the environment, through a participatory approach that involves countries worldwide, regardless of their developmental status. To achieve the goal of sustainability in agriculture, it is imperative to adopt multidisciplinary approaches that integrate fields such as biology, engineering, chemistry, economics, and community development. One noteworthy initiative in this regard is Zero Budget Natural Farming, which highlights the significance of leveraging the synergistic effects of both plant and animal products to enhance crop establishment, build soil fertility, and promote the proliferation of beneficial microorganisms. The ultimate aim is to create self-sustainable agro-ecosystems. This review advocates for the incorporation of biotechnological tools in natural farming to expedite the dynamism of such systems in an eco-friendly manner. By harnessing the power of biotechnology, we can increase the productivity of agro-ecology and generate abundant supplies of food, feed, fiber, and nutraceuticals to meet the needs of our ever-expanding global population.},
}
@article {pmid38581683,
year = {2024},
author = {Loos, D and Filho, APDC and Dutilh, BE and Barber, AE and Panagiotou, G},
title = {A global survey of host, aquatic, and soil microbiomes reveals shared abundance and genomic features between bacterial and fungal generalists.},
journal = {Cell reports},
volume = {43},
number = {4},
pages = {114046},
doi = {10.1016/j.celrep.2024.114046},
pmid = {38581683},
issn = {2211-1247},
mesh = {*Soil Microbiology ; *Fungi/genetics/classification ; *Microbiota/genetics ; *Bacteria/genetics/classification ; Humans ; Biodiversity ; Genomics/methods ; Phylogeny ; },
abstract = {Environmental change, coupled with alteration in human lifestyles, is profoundly impacting the microbial communities critical to the health of the Earth and its inhabitants. To identify bacteria and fungi that are resistant and susceptible to habitat change, we analyze thousands of genera detected in 1,580 host, soil, and aquatic samples. This large-scale analysis identifies 48 bacterial and 4 fungal genera that are abundant across the three biomes, demonstrating fitness in diverse environmental conditions. Samples containing these generalists have significantly higher alpha diversity. These generalists play a significant role in shaping cross-kingdom community structure, boasting larger genomes with more secondary metabolism and antimicrobial resistance genes. Conversely, 30 bacterial and 19 fungal genera are only found in a single habitat, suggesting a limited ability to adapt to different and changing environments. These findings contribute to our understanding of microbial niche breadth and its consequences for global biodiversity loss.},
}
@article {pmid38581418,
year = {2024},
author = {Chen, Z and Ain, NU and Zhao, Q and Zhang, X},
title = {From tradition to innovation: conventional and deep learning frameworks in genome annotation.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {3},
pages = {},
pmid = {38581418},
issn = {1477-4054},
support = {2021YFF1000900//National Key Research and Development Program of China/ ; RCYX20210706092103024//Shenzhen Science and Technology Program/ ; 32222019//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Deep Learning ; Genome ; Algorithms ; Software ; Computational Biology/methods ; Molecular Sequence Annotation ; },
abstract = {Following the milestone success of the Human Genome Project, the 'Encyclopedia of DNA Elements (ENCODE)' initiative was launched in 2003 to unearth information about the numerous functional elements within the genome. This endeavor coincided with the emergence of numerous novel technologies, accompanied by the provision of vast amounts of whole-genome sequences, high-throughput data such as ChIP-Seq and RNA-Seq. Extracting biologically meaningful information from this massive dataset has become a critical aspect of many recent studies, particularly in annotating and predicting the functions of unknown genes. The core idea behind genome annotation is to identify genes and various functional elements within the genome sequence and infer their biological functions. Traditional wet-lab experimental methods still rely on extensive efforts for functional verification. However, early bioinformatics algorithms and software primarily employed shallow learning techniques; thus, the ability to characterize data and features learning was limited. With the widespread adoption of RNA-Seq technology, scientists from the biological community began to harness the potential of machine learning and deep learning approaches for gene structure prediction and functional annotation. In this context, we reviewed both conventional methods and contemporary deep learning frameworks, and highlighted novel perspectives on the challenges arising during annotation underscoring the dynamic nature of this evolving scientific landscape.},
}
@article {pmid38578160,
year = {2024},
author = {Zhang, T and Peng, W and Xiao, H and Cao, S and Chen, Z and Su, X and Luo, Y and Liu, Z and Peng, Y and Yang, X and Jiang, GF and Xu, X and Ma, Z and Zhou, Y},
title = {Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape.},
journal = {Journal of integrative plant biology},
volume = {66},
number = {7},
pages = {1408-1426},
doi = {10.1111/jipb.13653},
pmid = {38578160},
issn = {1744-7909},
support = {20210020//Guangxi University, Bama Institute of Integration of Industry and Education, postgraduate joint training project/ ; 20210039//Guangxi University, Bama Institute of Integration of Industry and Education, postgraduate joint training project/ ; 2023YFF1000100//the National Key Research and Development Program of China/ ; 2023YFD2200700//the National Key Research and Development Program of China/ ; 32300191//National Natural Science Foundation of China/ ; 32372662//National Natural Science Foundation of China/ ; No.20210020;No.20210039//Guangxi University, Bama Institute of Integration of Industry and Education, postgraduate joint training project/ ; 2023YFF1000100;2023YFD2200700;//the National Key Research and Development Program of China/ ; No.32300191;No.32372662//National Natural Science Foundation of China/ ; },
mesh = {*Vitis/genetics ; Adaptation, Physiological/genetics ; Genome, Plant/genetics ; Genetics, Population ; Polymorphism, Single Nucleotide/genetics ; Salt Tolerance/genetics ; Genomic Structural Variation/genetics ; Genomics ; Genes, Plant ; },
abstract = {Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype-resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole-genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks.},
}
@article {pmid38577785,
year = {2024},
author = {Baril, T and Galbraith, J and Hayward, A},
title = {Earl Grey: A Fully Automated User-Friendly Transposable Element Annotation and Analysis Pipeline.},
journal = {Molecular biology and evolution},
volume = {41},
number = {4},
pages = {},
pmid = {38577785},
issn = {1537-1719},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; *DNA Transposable Elements/genetics ; Molecular Sequence Annotation ; *Drosophila melanogaster/genetics ; Genomics/methods ; Computational Biology ; },
abstract = {Transposable elements (TEs) are major components of eukaryotic genomes and are implicated in a range of evolutionary processes. Yet, TE annotation and characterization remain challenging, particularly for nonspecialists, since existing pipelines are typically complicated to install, run, and extract data from. Current methods of automated TE annotation are also subject to issues that reduce overall quality, particularly (i) fragmented and overlapping TE annotations, leading to erroneous estimates of TE count and coverage, and (ii) repeat models represented by short sections of total TE length, with poor capture of 5' and 3' ends. To address these issues, we present Earl Grey, a fully automated TE annotation pipeline designed for user-friendly curation and annotation of TEs in eukaryotic genome assemblies. Using nine simulated genomes and an annotation of Drosophila melanogaster, we show that Earl Grey outperforms current widely used TE annotation methodologies in ameliorating the issues mentioned above while scoring highly in benchmarking for TE annotation and classification and being robust across genomic contexts. Earl Grey provides a comprehensive and fully automated TE annotation toolkit that provides researchers with paper-ready summary figures and outputs in standard formats compatible with other bioinformatics tools. Earl Grey has a modular format, with great scope for the inclusion of additional modules focused on further quality control and tailored analyses in future releases.},
}
@article {pmid38569653,
year = {2024},
author = {Augustijn, HE and Roseboom, AM and Medema, MH and van Wezel, GP},
title = {Harnessing regulatory networks in Actinobacteria for natural product discovery.},
journal = {Journal of industrial microbiology &amp; biotechnology},
volume = {51},
number = {},
pages = {},
pmid = {38569653},
issn = {1476-5535},
support = {948770/ERC_/European Research Council/International ; },
mesh = {*Actinobacteria/metabolism/genetics ; *Biological Products/metabolism ; Biosynthetic Pathways ; Computational Biology/methods ; *Drug Discovery ; Gene Expression Regulation, Bacterial ; *Gene Regulatory Networks ; Multigene Family ; Transcription Factors/metabolism/genetics ; },
abstract = {UNLABELLED: Microbes typically live in complex habitats where they need to rapidly adapt to continuously changing growth conditions. To do so, they produce an astonishing array of natural products with diverse structures and functions. Actinobacteria stand out for their prolific production of bioactive molecules, including antibiotics, anticancer agents, antifungals, and immunosuppressants. Attention has been directed especially towards the identification of the compounds they produce and the mining of the large diversity of biosynthetic gene clusters (BGCs) in their genomes. However, the current return on investment in random screening for bioactive compounds is low, while it is hard to predict which of the millions of BGCs should be prioritized. Moreover, many of the BGCs for yet undiscovered natural products are silent or cryptic under laboratory growth conditions. To identify ways to prioritize and activate these BGCs, knowledge regarding the way their expression is controlled is crucial. Intricate regulatory networks control global gene expression in Actinobacteria, governed by a staggering number of up to 1000 transcription factors per strain. This review highlights recent advances in experimental and computational methods for characterizing and predicting transcription factor binding sites and their applications to guide natural product discovery. We propose that regulation-guided genome mining approaches will open new avenues toward eliciting the expression of BGCs, as well as prioritizing subsets of BGCs for expression using synthetic biology approaches.<br><br>ONE-SENTENCE SUMMARY: This review provides insights into advances in experimental and computational methods aimed at predicting transcription factor binding sites and their applications to guide natural product discovery.},
}
@article {pmid38560995,
year = {2024},
author = {Stiller, J and Feng, S and Chowdhury, AA and Rivas-González, I and Duchêne, DA and Fang, Q and Deng, Y and Kozlov, A and Stamatakis, A and Claramunt, S and Nguyen, JMT and Ho, SYW and Faircloth, BC and Haag, J and Houde, P and Cracraft, J and Balaban, M and Mai, U and Chen, G and Gao, R and Zhou, C and Xie, Y and Huang, Z and Cao, Z and Yan, Z and Ogilvie, HA and Nakhleh, L and Lindow, B and Morel, B and Fjeldså, J and Hosner, PA and da Fonseca, RR and Petersen, B and Tobias, JA and Székely, T and Kennedy, JD and Reeve, AH and Liker, A and Stervander, M and Antunes, A and Tietze, DT and Bertelsen, MF and Lei, F and Rahbek, C and Graves, GR and Schierup, MH and Warnow, T and Braun, EL and Gilbert, MTP and Jarvis, ED and Mirarab, S and Zhang, G},
title = {Complexity of avian evolution revealed by family-level genomes.},
journal = {Nature},
volume = {629},
number = {8013},
pages = {851-860},
pmid = {38560995},
issn = {1476-4687},
mesh = {Animals ; *Birds/genetics/classification/anatomy &amp; histology ; Brain/anatomy &amp; histology ; *Evolution, Molecular ; Extinction, Biological ; *Genome/genetics ; Genomics ; *Phylogeny ; Population Density ; Male ; Female ; },
abstract = {Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species sampled, phylogenetic method and the choice of genomic regions[1-3]. Here we address these issues by analysing the genomes of 363 bird species[4] (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a marked degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous-Palaeogene boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that are a challenge to model due to either extreme DNA composition, variable substitution rates, incomplete lineage sorting or complex evolutionary events such as ancient hybridization. Assessment of the effects of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates and relative brain size following the Cretaceous-Palaeogene extinction event, supporting the hypothesis that emerging ecological opportunities catalysed the diversification of modern birds. The resulting phylogenetic estimate offers fresh insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.},
}
@article {pmid38560613,
year = {2024},
author = {Boyes, D and Gibbs, M and , and , and , and , and , and , },
title = {The genome sequence of the Brown Oak Tortrix, Archips crataeganus (Hübner, 1796).},
journal = {Wellcome open research},
volume = {9},
number = {},
pages = {9},
pmid = {38560613},
issn = {2398-502X},
support = {/WT_/Wellcome Trust/United Kingdom ; },
abstract = {We present a genome assembly from an individual female Archips crataeganus (the Brown Oak Tortrix; Arthropoda; Insecta; Lepidoptera; Tortricidae). The genome sequence is 626.9 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 16.64 kilobases in length. Gene annotation of this assembly on Ensembl identified 19,596 protein coding genes.},
}
@article {pmid38554963,
year = {2024},
author = {Li, W and Feng, Q and Li, Z and Jin, T and Zhang, Y and Southam, G},
title = {Inhibition of iron oxidation in Acidithiobacillus ferrooxidans by low-molecular-weight organic acids: Evaluation of performance and elucidation of mechanisms.},
journal = {The Science of the total environment},
volume = {927},
number = {},
pages = {171919},
doi = {10.1016/j.scitotenv.2024.171919},
pmid = {38554963},
issn = {1879-1026},
mesh = {*Acidithiobacillus/metabolism/drug effects ; *Iron/metabolism ; *Oxidation-Reduction ; Mining ; Formates/metabolism ; Acetic Acid/metabolism ; *Propionates ; },
abstract = {The catalytic role of Acidithiobacillus ferrooxidans (A. ferrooxidans) in iron biooxidation is pivotal in the formation of Acid Mine Drainage (AMD), which poses a significant threat to the environment. To control AMD generation, treatments with low-molecular-weight organic acids are being studied, yet their exact mechanisms are unclear. In this study, AMD materials, organic acids, and molecular methods were employed to gain a deeper understanding of the inhibitory effects of low-molecular-weight organic acids on the biooxidation of iron by A. ferrooxidans. The inhibition experiments of A. ferrooxidans on the oxidation of Fe[2+] showed that to attain a 90 % inhibition efficacy within 72 h, the minimum concentrations required for formic acid, acetic acid, propionic acid, and lactic acid are 0.5, 6, 4, and 10 mmol/L, respectively. Bacterial imaging illustrated the detrimental effects of these organic acids on the cell envelope structure. This includes severe damage to the outer membrane, particularly from formic and acetic acids, which also caused cell wall damage. Coupled with alterations in the types and quantities of protein, carbohydrate, and nucleic acid content in extracellular polymeric substances (EPS), indicate the mechanisms underlying these inhibitory treatments. Transcriptomic analysis revealed interference of these organic acids with crucial metabolic pathways, particularly those related to energy metabolism. These findings establish a comprehensive theoretical basis for understanding the inhibition of A. ferrooxidans' biooxidation by low-molecular-weight organic acids, offering a novel opportunity to effectively mitigate the generation of AMD at its source.},
}
@article {pmid38554685,
year = {2024},
author = {Sfriso, AA and Juhmani, AS and Tomio, Y and Sfriso, A and Rizzolio, F and Adeel, M and Wahsha, M and Munari, C and Mistri, M},
title = {Microplastic accumulation and ecological impacts on benthic invertebrates: Insights from a microcosm experiment.},
journal = {Marine pollution bulletin},
volume = {202},
number = {},
pages = {116231},
doi = {10.1016/j.marpolbul.2024.116231},
pmid = {38554685},
issn = {1879-3363},
mesh = {Animals ; *Water Pollutants, Chemical/analysis ; *Invertebrates ; *Environmental Monitoring ; *Microplastics ; Aquatic Organisms ; Ecosystem ; },
abstract = {Microplastic (MP) pollution poses a global concern, especially for benthic invertebrates. This one-month study investigated the accumulation of small MP polymers (polypropylene and polyester resin, 3-500 μm, 250 μg L[-1]) in benthic invertebrates and on one alga species. Results revealed species-specific preferences for MP size and type, driven by ingestion, adhesion, or avoidance behaviours. Polyester resin accumulated in Mytilus galloprovincialis, Chamelea gallina, Hexaplex trunculus, and Paranemonia cinerea, while polypropylene accumulated on Ulva rigida. Over time, MP accumulation decreased in count but not size, averaging 6.2 ± 5.0 particles per individual after a month. MP were mainly found inside of the organisms, especially in the gut, gills, and gonads and externally adherent MP ranged from 11 to 35 % of the total. Biochemical energy assessments after two weeks of MP exposure indicated energy gains for water column species but energy loss for sediment-associated species, highlighting the susceptibility of infaunal benthic communities to MP contamination.},
}
@article {pmid38552719,
year = {2024},
author = {Martin, NG and Defres, S and Willis, L and Beckley, R and Hardwick, H and Coxon, A and Kadambari, S and Yu, LM and Liu, X and Galal, U and Conlin, K and Griffiths, MJ and Kneen, R and Nadel, S and Heath, PT and Kelly, DE and Solomon, T and Sadarangani, M and Pollard, AJ and , },
title = {Paediatric meningitis in the conjugate vaccine era and a novel clinical decision model to predict bacterial aetiology.},
journal = {The Journal of infection},
volume = {88},
number = {5},
pages = {106145},
doi = {10.1016/j.jinf.2024.106145},
pmid = {38552719},
issn = {1532-2742},
mesh = {Humans ; Child ; Infant ; *Meningitis, Bacterial/diagnosis/cerebrospinal fluid/microbiology ; Child, Preschool ; Adolescent ; Female ; Male ; Prospective Studies ; *Vaccines, Conjugate ; *Meningitis, Viral/diagnosis/cerebrospinal fluid ; Clinical Decision Rules ; United Kingdom/epidemiology ; Neisseria meningitidis/isolation &amp; purification ; Streptococcus pneumoniae/isolation &amp; purification ; Decision Support Techniques ; },
abstract = {OBJECTIVES: The aims of this study were to assess aetiology and clinical characteristics in childhood meningitis, and develop clinical decision rules to distinguish bacterial meningitis from other similar clinical syndromes.<br><br>METHODS: Children aged <16 years hospitalised with suspected meningitis/encephalitis were included, and prospectively recruited at 31 UK hospitals. Meningitis was defined as identification of bacteria/viruses from cerebrospinal fluid (CSF) and/or a raised CSF white blood cell count. New clinical decision rules were developed to distinguish bacterial from viral meningitis and those of alternative aetiology.<br><br>RESULTS: The cohort included 3002 children (median age 2&#xb7;4 months); 1101/3002 (36&#xb7;7%) had meningitis, including 180 bacterial, 423 viral and 280 with no pathogen identified. Enterovirus was the most common pathogen in those aged <6 months and 10-16 years, with Neisseria meningitidis and/or Streptococcus pneumoniae commonest at age 6 months to 9 years. The Bacterial Meningitis Score had a negative predictive value of 95&#xb7;3%. We developed two clinical decision rules, that could be used either before (sensitivity 82%, specificity 71%) or after lumbar puncture (sensitivity 84%, specificity 93%), to determine risk of bacterial meningitis.<br><br>CONCLUSIONS: Bacterial meningitis comprised 6% of children with suspected meningitis/encephalitis. Our clinical decision rules provide potential novel approaches to assist with identifying children with bacterial meningitis.<br><br>FUNDING: This study was funded by the Meningitis Research Foundation, Pfizer and the NIHR Programme Grants for Applied Research.},
}
@article {pmid38552245,
year = {2024},
author = {Han, B and Tian, D and Li, X and Liu, S and Tian, F and Liu, D and Wang, S and Zhao, K},
title = {Multiomics Analyses Provide New Insight into Genetic Variation of Reproductive Adaptability in Tibetan Sheep.},
journal = {Molecular biology and evolution},
volume = {41},
number = {3},
pages = {},
pmid = {38552245},
issn = {1537-1719},
support = {No. 2022-ZJ-901//Natural Science Foundation of Qinghai Province/ ; },
mesh = {Humans ; Female ; Sheep/genetics ; Animals ; Tibet ; *Genome-Wide Association Study ; *Multiomics ; Proteomics ; Reproduction ; Mutation ; },
abstract = {Domestication and artificial selection during production-oriented breeding have greatly shaped the level of genomic variability in sheep. However, the genetic variation associated with increased reproduction remains elusive. Here, two groups of samples from consecutively monotocous and polytocous sheep were collected for genome-wide association, transcriptomic, proteomic, and metabolomic analyses to explore the genetic variation in fecundity in Tibetan sheep. Genome-wide association study revealed strong associations between BMPR1B (p.Q249R) and litter size, as well as between PAPPA and lambing interval; these findings were validated in 1,130 individuals. Furthermore, we constructed the first single-cell atlas of Tibetan sheep ovary tissues and identified a specific mural granulosa cell subtype with PAPPA-specific expression and differential expression of BMPR1B between the two groups. Bulk RNA-seq indicated that BMPR1B and PAPPA expressions were similar between the two groups of sheep. 3D protein structure prediction and coimmunoprecipitation analysis indicated that mutation and mutually exclusive exons of BMPR1B are the main mechanisms for prolific Tibetan sheep. We propose that PAPPA is a key gene for stimulating ovarian follicular growth and development, and steroidogenesis. Our work reveals the genetic variation in reproductive performance in Tibetan sheep, providing insights and valuable genetic resources for the discovery of genes and regulatory mechanisms that improve reproductive success.},
}
@article {pmid38552150,
year = {2024},
author = {Howard-Varona, C and Lindback, MM and Fudyma, JD and Krongauz, A and Solonenko, NE and Zayed, AA and Andreopoulos, WB and Olson, HM and Kim, YM and Kyle, JE and Glavina Del Rio, T and Adkins, JN and Tfaily, MM and Paul, S and Sullivan, MB and Duhaime, MB},
title = {Environment-specific virocell metabolic reprogramming.},
journal = {The ISME journal},
volume = {18},
number = {1},
pages = {},
pmid = {38552150},
issn = {1751-7370},
support = {2149505//NSF Advances in Biological Informatics/ ; DE-AC05-76RL0-1830//U.S. Department of Energy/ ; //Joint Genome Institute/ ; //U.S. Department of Energy/ ; 1536989//National Science Foundation/ ; //University of Michigan/ ; 034//C-CoMP/ ; //Department of Energy/ ; T32 AI112542/AI/NIAID NIH HHS/United States ; 2055455//NSF Polar Programs/ ; 1-T32-AI-112542//National Institutes of Health (NIH)/National Institute of Allergy and Infectious Diseases (NIAID)/ ; //Facilities Integrating Collaborations for User Science/ ; 3790//Gordon and Betty Moore Foundation/ ; //EMSL/ ; //Office of Science/ ; DGE1256260//NSF Graduate Research Fellowship/ ; DE-AC02-05CH11231//Biological and Environmental Research/ ; C-CoMP NSF-STC 2019589//NSF Center for Chemical Currencies of a Microbial Planet/ ; //Environmental Molecular Sciences Laboratory/ ; DE-SC0020173//Office of Biological and Environmental Research/ ; },
mesh = {*Bacteriophages/genetics/physiology ; Proteomics ; Phosphates/metabolism ; Metabolomics ; Systems Biology ; Transcriptome ; Metabolic Reprogramming ; },
abstract = {Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell," is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.},
}
@article {pmid38547306,
year = {2024},
author = {Milić, D and Rat, M and Bokić, B and Mudri-Stojnić, S and Milošević, N and Sukur, N and Jakovetić, D and Radak, B and Tot, T and Vujanović, D and Anačkov, G and Radišić, D},
title = {Exploring the effects of habitat management on grassland biodiversity: A case study from northern Serbia.},
journal = {PloS one},
volume = {19},
number = {3},
pages = {e0301391},
pmid = {38547306},
issn = {1932-6203},
mesh = {Animals ; *Grassland ; Serbia ; *Ecosystem ; Biodiversity ; Agriculture ; Insecta ; Plants ; Birds/physiology ; },
abstract = {Grasslands represent a biodiversity hotspot in the European agricultural landscape, their restoration is necessary and offers a great opportunity to mitigate or halt harmful processes. These measures require a comprehensive knowledge of historical landscape changes, but also adequate management strategies. The required data was gathered from the sand grasslands of northern Serbia, as this habitat is of high conservation priority. This area also has a long history of different habitat management approaches (grazing and mowing versus unmanaged), which has been documented over of the last two decades. This dataset enabled us to quantify the effects of different measures across multiple taxa (plants, insect pollinators, and birds). We linked the gathered data on plants, pollinators, and birds with habitat management measures. Our results show that, at the taxon level, the adopted management strategies were beneficial for species richness, abundance, and composition, as the highest diversity of plant, insect pollinator, and bird species was found in managed areas. Thus, an innovative modelling approach was adopted in this work to identify and explain the effects of management practices on changes in habitat communities. The findings yielded can be used in the decision making as well as development of new management programmes. We thus posit that, when restoring and establishing particular communities, priority needs to be given to species with a broad ecological response. We recommend using the decision tree as a suitable machine learning model for this purpose.},
}
@article {pmid38540697,
year = {2024},
author = {Giordano, D and Bonora, S and D'Orsi, I and D'Alelio, D and Facchiano, A},
title = {Structural and Functional Characterization of Lipoxygenases from Diatoms by Bioinformatics and Modelling Studies.},
journal = {Biomolecules},
volume = {14},
number = {3},
pages = {},
pmid = {38540697},
issn = {2218-273X},
mesh = {*Lipoxygenases/chemistry/genetics ; *Diatoms/genetics ; Oxylipins ; Phylogeny ; Molecular Docking Simulation ; Ecosystem ; Computational Biology ; },
abstract = {Lipoxygenases make several biological functions in cells, based on the products of the catalyzed reactions. In diatoms, microalgae ubiquitous in aquatic ecosystems, lipoxygenases have been noted for the oxygenation of fatty acids with the production of oxylipins, which are involved in many physiological and pathological processes in marine organisms. The interest in diatoms' lipoxygenases and oxylipins has increased due to their possible biotechnological applications, ranging from ecology to medicine. We investigated using bioinformatics and molecular docking tools the lipoxygenases of diatoms and the possible interaction with substrates. A large-scale analysis of sequence resources allowed us to retrieve 45 sequences of lipoxygenases from diatoms. We compared and analyzed the sequences by multiple alignments and phylogenetic trees, suggesting the possible clustering in phylogenetic groups. Then, we modelled the 3D structure of representative enzymes from the different groups and investigated in detail the structural and functional properties by docking simulations with possible substrates. The results allowed us to propose a classification of the lipoxygenases from diatoms based on their sequence features, which may be reflected in specific structural differences and possible substrate specificity.},
}
@article {pmid38540627,
year = {2024},
author = {Santric-Milicevic, M and Pavlekic, K and Bukumiric, Z and Stevanovic, A and Nikolic, D and Matejic, B and Matanovic, D and Backovic, D and Tulic, G and Lukic, R and Zivanovic, D and Radosavljevic, S and Milovanovic, V and Zdujic, M and Stankovic, S and Asanin, M and Zdravkovic, M and Tomasevic, R},
title = {Nurses' Perception of Tension, Stress, and Pressure before and during the COVID-19 Pandemic: A Multicenter Serbian Study.},
journal = {Healthcare (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
pmid = {38540627},
issn = {2227-9032},
abstract = {The mental health of healthcare workers, especially the nursing staff in intensive care units, is crucial for the optimal functioning of healthcare systems during medical emergencies. This study implements a cross-sectional design to investigate the associations between nurses' personal characteristics, workplace challenges, and job satisfaction with the increased perception of tension, stress, and pressure at the workplace (TSPW) before and during the COVID-19 pandemic. In 2021, we surveyed 4210 nurses from 19 intensive healthcare facilities in the capital of Serbia, Belgrade, and, at that time, collected data about their perceived TSPW before and during the COVID-19 pandemic. Our study identified six predictors of the increase in TSPW, as perceived by nurses: their work in COVID-19 infectious zones (OR = 1.446), exhaustion due to work under protective equipment (OR = 1.413), uncertainty and fear of infection (OR = 1.481), a high degree of superiors' appreciation and respect (OR = 1.147), a high degree of patients' attitudes (OR = 1.111), and a low degree of work autonomy (OR = 0.889). The study's findings suggest that a solution to this issue is necessary to ensure that nurses are safe and able to alleviate the physical and mental strain that comes with prolonged use of protective equipment. Nurses on the frontline of the pandemic require better health protection, better conditions, and respect for their role. Strategies to promote mental health would help reduce nurses' stress and increase job satisfaction.},
}
@article {pmid38538788,
year = {2024},
author = {Johnson, TF and Beckerman, AP and Childs, DZ and Webb, TJ and Evans, KL and Griffiths, CA and Capdevila, P and Clements, CF and Besson, M and Gregory, RD and Thomas, GH and Delmas, E and Freckleton, RP},
title = {Revealing uncertainty in the status of biodiversity change.},
journal = {Nature},
volume = {628},
number = {8009},
pages = {788-794},
pmid = {38538788},
issn = {1476-4687},
mesh = {Animals ; *Biodiversity ; Conservation of Natural Resources/methods/trends ; Datasets as Topic ; Phylogeny ; Spatio-Temporal Analysis ; Time Factors ; *Uncertainty ; },
abstract = {Biodiversity faces unprecedented threats from rapid global change[1]. Signals of biodiversity change come from time-series abundance datasets for thousands of species over large geographic and temporal scales. Analyses of these biodiversity datasets have pointed to varied trends in abundance, including increases and decreases. However, these analyses have not fully accounted for spatial, temporal and phylogenetic structures in the data. Here, using a new statistical framework, we show across ten high-profile biodiversity datasets[2-11] that increases and decreases under existing approaches vanish once spatial, temporal and phylogenetic structures are accounted for. This is a consequence of existing approaches severely underestimating trend uncertainty and sometimes misestimating the trend direction. Under our revised average abundance trends that appropriately recognize uncertainty, we failed to observe a single increasing or decreasing trend at 95% credible intervals in our ten datasets. This emphasizes how little is known about biodiversity change across vast spatial and taxonomic scales. Despite this uncertainty at vast scales, we reveal improved local-scale prediction accuracy by accounting for spatial, temporal and phylogenetic structures. Improved prediction offers hope of estimating biodiversity change at policy-relevant scales, guiding adaptive conservation responses.},
}
@article {pmid38532952,
year = {2024},
author = {Feutz, E and Biswas, PK and Ndeketa, L and Ogwel, B and Onwuchekwa, U and Sarwar, G and Sultana, S and Peñataro Yori, P and Acebedo, A and Ahmed, N and Ahmed, I and Atlas, HE and Awuor, AO and Bhuiyan, MAI and Conteh, B and Diawara, O and Elwood, S and Fane, M and Hossen, MI and Ireen, M and Jallow, AF and Karim, M and Kosek, MN and Kotloff, KL and Lefu, C and Liu, J and Maguire, R and Qamar, FN and Ndalama, M and Ochieng, JB and Okonji, C and Paredes, LFZ and Pavlinac, PB and Perez, K and Qureshi, S and Schiaffino, F and Traore, M and Tickell, KD and Wachepa, R and Witte, D and Cornick, J and Jahangir Hossain, M and Khanam, F and Olortegui, MP and Omore, R and Sow, SO and Yousafzai, MT and Galagan, SR},
title = {Data Management in Multicountry Consortium Studies: The Enterics For Global Health (EFGH) Shigella Surveillance Study Example.},
journal = {Open forum infectious diseases},
volume = {11},
number = {Suppl 1},
pages = {S48-S57},
pmid = {38532952},
issn = {2328-8957},
support = {K43 TW012298/TW/FIC NIH HHS/United States ; },
abstract = {BACKGROUND: Rigorous data management systems and planning are essential to successful research projects, especially for large, multicountry consortium studies involving partnerships across multiple institutions. Here we describe the development and implementation of data management systems and procedures for the Enterics For Global Health (EFGH) Shigella surveillance study-a 7-country diarrhea surveillance study that will conduct facility-based surveillance concurrent with population-based enumeration and a health care utilization survey to estimate the incidence of Shigella--associated diarrhea in children 6 to 35 months old.<br><br>METHODS: The goals of EFGH data management are to utilize the knowledge and experience of consortium members to collect high-quality data and ensure equity in access and decision-making. During the planning phase before study initiation, a working group of representatives from each EFGH country site, the coordination team, and other partners met regularly to develop the data management systems for the study.<br><br>RESULTS: This resulted in the Data Management Plan, which included selecting REDCap and SurveyCTO as the primary database systems. Consequently, we laid out procedures for data processing and storage, study monitoring and reporting, data quality control and assurance activities, and data access. The data management system and associated real-time visualizations allow for rapid data cleaning activities and progress monitoring and will enable quicker time to analysis.<br><br>CONCLUSIONS: Experiences from this study will contribute toward enriching the sparse landscape of data management methods publications and serve as a case study for future studies seeking to collect and manage data consistently and rigorously while maintaining equitable access to and control of data.},
}
@article {pmid38531865,
year = {2024},
author = {Corponi, F and Li, BM and Anmella, G and Mas, A and Pacchiarotti, I and Valentí, M and Grande, I and Benabarre, A and Garriga, M and Vieta, E and Lawrie, SM and Whalley, HC and Hidalgo-Mazzei, D and Vergari, A},
title = {Automated mood disorder symptoms monitoring from multivariate time-series sensory data: getting the full picture beyond a single number.},
journal = {Translational psychiatry},
volume = {14},
number = {1},
pages = {161},
pmid = {38531865},
issn = {2158-3188},
mesh = {Humans ; *Mood Disorders/diagnosis ; *Affect ; Machine Learning ; Sleep ; },
abstract = {Mood disorders (MDs) are among the leading causes of disease burden worldwide. Limited specialized care availability remains a major bottleneck thus hindering pre-emptive interventions. MDs manifest with changes in mood, sleep, and motor activity, observable in ecological physiological recordings thanks to recent advances in wearable technology. Therefore, near-continuous and passive collection of physiological data from wearables in daily life, analyzable with machine learning (ML), could mitigate this problem, bringing MDs monitoring outside the clinician's office. Previous works predict a single label, either the disease state or a psychometric scale total score. However, clinical practice suggests that the same label may underlie different symptom profiles, requiring specific treatments. Here we bridge this gap by proposing a new task: inferring all items in HDRS and YMRS, the two most widely used standardized scales for assessing MDs symptoms, using physiological data from wearables. To that end, we develop a deep learning pipeline to score the symptoms of a large cohort of MD patients and show that agreement between predictions and assessments by an expert clinician is clinically significant (quadratic Cohen's κ and macro-average F1 score both of 0.609). While doing so, we investigate several solutions to the ML challenges associated with this task, including multi-task learning, class imbalance, ordinal target variables, and subject-invariant representations. Lastly, we illustrate the importance of testing on out-of-distribution samples.},
}
@article {pmid38531495,
year = {2024},
author = {Yuan, Q and Yao, LF and Tang, JW and Ma, ZW and Mou, JY and Wen, XR and Usman, M and Wu, X and Wang, L},
title = {Rapid discrimination and ratio quantification of mixed antibiotics in aqueous solution through integrative analysis of SERS spectra via CNN combined with NN-EN model.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.03.016},
pmid = {38531495},
issn = {2090-1224},
abstract = {INTRODUCTION: Abusing antibiotic residues in the natural environment has become a severe public health and ecological environmental problem. The side effects of its biochemical and physiological consequences are severe. To avoid antibiotic contamination in water, implementing universal and rapid antibiotic residue detection technology is critical to maintaining antibiotic safety in aquatic environments. Surface-enhanced Raman spectroscopy (SERS) provides a powerful tool for identifying small molecular components with high sensitivity and selectivity. However, it remains a challenge to identify pure antibiotics from SERS spectra due to coexisting components in the mixture.<br><br>OBJECTIVES: In this study, an intelligent analysis model for the SERS spectrum based on a deep learning algorithm was proposed for rapid identification of the antibiotic components in the mixture and quantitative determination of the ratios of these components.<br><br>METHODS: We established a water environment system containing three antibiotic residues of ciprofloxacin, doxycycline, and levofloxacin. To facilitate qualitative and quantitative analysis of the SERS spectra antibiotic mixture datasets, we developed a computational framework integrating a convolutional neural network (CNN) and a non-negative elastic network (NN-EN) method.<br><br>RESULTS: The experimental results demonstrate that the CNN model has a recognition accuracy of 98.68%, and the interpretation analysis of Shapley Additive exPlanations (SHAP) shows that our model can specifically focus on the characteristic peak distribution. In contrast, the NN-EN model can accurately quantify each component's ratio in the mixture.<br><br>CONCLUSION: Integrating the SERS technique assisted by the CNN combined with the NN-EN model exhibits great potential for rapid identification and high-precision quantification of antibiotic residues in aquatic environments.},
}
@article {pmid38531460,
year = {2024},
author = {Enjavinejad, SM and Zahedifar, M and Moosavi, AA and Khosravani, P},
title = {Integrated application of multiple indicators and geographic information system-based approaches for comprehensive assessment of environmental impacts of toxic metals-contaminated agricultural soils and vegetables.},
journal = {The Science of the total environment},
volume = {926},
number = {},
pages = {171747},
doi = {10.1016/j.scitotenv.2024.171747},
pmid = {38531460},
issn = {1879-1026},
mesh = {Adult ; Child ; Humans ; Vegetables ; Geographic Information Systems ; Environmental Monitoring ; Cadmium/analysis ; Copper/analysis ; Lead/analysis ; Risk Assessment ; *Metals, Heavy/analysis ; Soil/chemistry ; Carcinogens/analysis ; Receptors, Antigen, T-Cell ; *Soil Pollutants/analysis ; China ; },
abstract = {Conventional monitoring and mapping approaches are laborious, expensive, and time-consuming because they need a large number of data and consequently extensive sampling and experimental operations. Therefore, due to the growing concern about the potential of contamination of soils and agricultural products with heavy metals (HMs), a field experiment was conducted on 77 farm lands in an area of 2300 ha in the southeast of Shiraz (Iran) to investigate the source of metal contamination in the soils and vegetables and to model spatial distribution of HMs (iron, Fe; manganese, Mn; copper, Cu; zinc, Zn; cadmium, Cd; nickel, Ni, and lead, Pb) over the region using geographic information system (GIS) and geostatistical (Ordinary Kriging, OK) approaches and compare the results with deterministic approaches (Inverse Distance Weighting, IDW with different weighting power). Furthermore, some ecological and health risks indices including Pollution index (PI), Nemerow integrated pollution index (NIPI), pollution load index (PLI), degree of contamination (Cdeg), modified contamination degree (mCd), PIaverage and PIvector for soil quality, multi-element contamination (MEC), the probability of toxicity (MERMQ), the potential ecological index (RI), total hazard index (THI) and total carcinogenic risk index (TCR) based on ingestion, inhalation, and dermal exposure pathways for adults and children respectively for analyzing the noncarcinogenic and carcinogenic risks were calculated. Experimental semivariogram of the mentioned HMs were calculated and theoretical models (i.e., exponential, spherical, Gaussian, and linear models) were fitted in order to model their spatial structures and to investigate the most representative models. Moreover, principal component analysis (PCA) and cluster analysis (CA) were used to identify sources of HMs in the soils. Results showed that IDW method was more efficient than the OK approach to estimate the properties and HMs contents in the soils and plants. The estimated daily intake of metals (DIM) values of Pb and Ni exceeded their safe limits. In addition, Cd was the main element responsible for ecological risk. The PIave and PIvector indices showed that soil quality in the study area is not suitable. According to mCd values, the soils classified as ultra-high contaminated for Cu and Cd, extremely high for Zn and Pb, very high, high, and very low degree of contamination for Ni, Mn, and Fe, respectively. 36, 60, and 4 % of the sampling sites had high, medium, and low risk levels with 49, 21, and 9 % probability of toxicity, respectively. The maximum health risk index (HRI) value of 20.42 with extremely high risk for children was obtained for Ni and the HI for adults and children were 0.22 and 1.55, respectively. The THI values of Pb and Cd were the highest compared to the other HMs studied, revealing a possible non-cancer risk in children associated with exposure to these metals. The routes of exposure with the greatest influence on the THI and TCR indices were in the order of ingestion > inhalation > dermal. Therefore, ingestion, as the main route of exposure, is the route of greatest contribution to health risks. PCA analysis revealed that Fe, Mn, Cu, and Ni may originate from natural sources, while Fe was appeared to be controlled by fertilizer, and Cu primarily coming from pesticide, while Cd and Pb were mainly associated with the anthropogenic contamination, atmospheric depositions, and terrific in the urban soils. While, Zn mainly originated from fertilization. Findings are vital for developing remediation approaches for controlling the contaminants distribution as well as for monitoring and mapping the quality and health of soil resources.},
}
@article {pmid38528816,
year = {2024},
author = {Del Bianco, T and Haartsen, R and Mason, L and Leno, VC and Springer, C and Potter, M and Mackay, W and Smit, P and Plessis, CD and Brink, L and Johnson, MH and Murphy, D and Loth, E and Odendaal, H and Jones, EJH},
title = {The importance of decomposing periodic and aperiodic EEG signals for assessment of brain function in a global context.},
journal = {Developmental psychobiology},
volume = {66},
number = {4},
pages = {e22484},
doi = {10.1002/dev.22484},
pmid = {38528816},
issn = {1098-2302},
support = {777394//EU/EFPIA/SFARI/Autistica/AUTISM SPEAKS Innovative Medicines Initiative 2 Joint Undertaking (AIMS-2-TRIALS)/ ; 115300//Innovative Medicines Initiative 1 Joint Undertaking (AIMS-2-TRIALS)/ ; MR/K021389/1//the Medical Research Council for the projects "The Development of Social Attention and Perception Abilities in Typical and At-risk Infants"/ ; MR/T003057/1//"Human neurocognitive development: Early-stage processing, modifiers, and outcomes"/ ; 213608/Z/18/Z//Sir Henry Wellcome Postdoctoral Fellowship/ ; MR/S036423/1//UK&#xa0;Research&#xa0;and Innovation/ ; },
mesh = {Child ; Humans ; Female ; *Electroencephalography ; *Brain ; Brain Mapping ; Cognition ; },
abstract = {Measures of early neuro-cognitive development that are suitable for use in low-resource settings are needed to enable studies of the effects of early adversity on the developing brain in a global context. These measures should have high acquisition rates and good face and construct validity. Here, we investigated the feasibility of a naturalistic electroencephalography (EEG) paradigm in a low-resource context during childhood. Additionally, we examined the sensitivity of periodic and aperiodic EEG metrics to social and non-social stimuli. We recorded simultaneous 20-channel EEG and eye-tracking in 72 children aged 4-12 years (45 females) while they watched videos of women singing nursery rhymes and moving toys, selected to represent familiar childhood experiences. These measures were part of a feasibility study that assessed the feasibility and acceptability of a follow-up data collection of the South African Safe Passage Study, which tracks environmental adversity and brain and cognitive development from before birth up until childhood. We examined whether data quantity and quality varied with child characteristics and the sensitivity of varying EEG metrics (canonical band power in the theta and alpha band and periodic and aperiodic features of the power spectra). We found that children who completed the EEG and eye-tracking assessment were, in general, representative of the full cohort. Data quantity was higher in children with greater visual attention to the stimuli. Out of the tested EEG metrics, periodic measures in the theta frequency range were most sensitive to condition differences, compared to alpha range measures and canonical and aperiodic EEG measures. Our results show that measuring EEG during ecologically valid social and non-social stimuli is feasible in low-resource settings, is feasible for most children, and produces robust indices of social brain function. This work provides preliminary support for testing longitudinal links between social brain function, environmental factors, and emerging behaviors.},
}
@article {pmid38527064,
year = {2024},
author = {Barrett, C and Chiphwanya, J and Mkwanda, S and Matipula, DE and Ndhlovu, P and Chaponda, L and Turner, JD and Giorgi, E and Betts, H and Martindale, S and Taylor, MJ and Read, JM and Kelly-Hope, LA},
title = {The national distribution of lymphatic filariasis cases in Malawi using patient mapping and geostatistical modelling.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {3},
pages = {e0012056},
pmid = {38527064},
issn = {1935-2735},
mesh = {Humans ; *Elephantiasis, Filarial/epidemiology ; Malawi/epidemiology ; Prevalence ; Data Management ; Surveys and Questionnaires ; },
abstract = {BACKGROUND: In 2020 the World Health Organization (WHO) declared that