@article {pmid36704891,
year = {2023},
author = {Crandall, ED and Toczydlowski, RH and Liggins, L and Holmes, AE and Ghoojaei, M and Gaither, MR and Wham, BE and Pritt, AL and Noble, C and Anderson, TJ and Barton, RL and Berg, JT and Beskid, SG and Delgado, A and Farrell, E and Himmelsbach, N and Queeno, SR and Trinh, T and Weyand, C and Bentley, A and Deck, J and Riginos, C and Bradburd, GS and Toonen, RJ},
title = {The importance of timely metadata curation to the global surveillance of genetic diversity.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/cobi.14061},
pmid = {36704891},
issn = {1523-1739},
abstract = {Genetic diversity within species represents a fundamental yet underappreciated level of biodiversity. Because genetic diversity can indicate species resilience to changing climate, its measurement is relevant to many national and global conservation policy targets. Many studies produce large amounts of genome-scale genetic diversity data for wild populations, but most (87%) do not include the associated spatial and temporal metadata necessary for them to be reused in monitoring programs or for acknowledging the sovereignty of nations or Indigenous Peoples. We undertook a "distributed datathon" to quantify the availability of these missing metadata and to test the hypothesis that their availability decays with time. We also worked to remediate missing metadata by extracting them from associated published papers, online repositories, and from direct communication with authors. Starting with 848 candidate genomic datasets (reduced representation and whole genome) from the International Nucleotide Sequence Database Collaboration, we determined that 561 contained mostly samples from wild populations. We successfully restored spatiotemporal metadata for 78% of these 561 datasets (N = 440 datasets comprising 45,105 individuals from 762 species in 17 phyla). Looking at papers and online repositories was much more fruitful than contacting authors, who only replied to our email requests 45% of the time. Overall, 23% of our email queries to authors unearthed useful metadata. Importantly, we found that the probability of retrieving spatiotemporal metadata declined significantly with the age of the dataset, with a 13.5% yearly decrease for metadata located in published papers or online repositories and up to a 22% yearly decrease for metadata that were only available from authors. This rapid decay in metadata availability, mirrored in studies of other types of biological data, should motivate swift updates to data sharing policies and researcher practices to ensure that the valuable context provided by metadata is not lost to conservation science forever. This article is protected by copyright. All rights reserved.},
}
@article {pmid36699674,
year = {2022},
author = {Siddiqui, JA and Fan, R and Naz, H and Bamisile, BS and Hafeez, M and Ghani, MI and Wei, Y and Xu, Y and Chen, X},
title = {Insights into insecticide-resistance mechanisms in invasive species: Challenges and control strategies.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {1112278},
pmid = {36699674},
issn = {1664-042X},
abstract = {Threatening the global community is a wide variety of potential threats, most notably invasive pest species. Invasive pest species are non-native organisms that humans have either accidentally or intentionally spread to new regions. One of the most effective and first lines of control strategies for controlling pests is the application of insecticides. These toxic chemicals are employed to get rid of pests, but they pose great risks to people, animals, and plants. Pesticides are heavily used in managing invasive pests in the current era. Due to the overuse of synthetic chemicals, numerous invasive species have already developed resistance. The resistance development is the main reason for the failure to manage the invasive species. Developing pesticide resistance management techniques necessitates a thorough understanding of the mechanisms through which insects acquire insecticide resistance. Insects use a variety of behavioral, biochemical, physiological, genetic, and metabolic methods to deal with toxic chemicals, which can lead to resistance through continuous overexpression of detoxifying enzymes. An overabundance of enzymes causes metabolic resistance, detoxifying pesticides and rendering them ineffective against pests. A key factor in the development of metabolic resistance is the amplification of certain metabolic enzymes, specifically esterases, Glutathione S-transferase, Cytochromes p450 monooxygenase, and hydrolyses. Additionally, insect guts offer unique habitats for microbial colonization, and gut bacteria may serve their hosts a variety of useful services. Most importantly, the detoxification of insecticides leads to resistance development. The complete knowledge of invasive pest species and their mechanisms of resistance development could be very helpful in coping with the challenges and effectively developing effective strategies for the control of invasive species. Integrated Pest Management is particularly effective at lowering the risk of chemical and environmental contaminants and the resulting health issues, and it may also offer the most effective ways to control insect pests.},
}
@article {pmid36699126,
year = {2023},
author = {Wortel, MT and Agashe, D and Bailey, SF and Bank, C and Bisschop, K and Blankers, T and Cairns, J and Colizzi, ES and Cusseddu, D and Desai, MM and van Dijk, B and Egas, M and Ellers, J and Groot, AT and Heckel, DG and Johnson, ML and Kraaijeveld, K and Krug, J and Laan, L and Lässig, M and Lind, PA and Meijer, J and Noble, LM and Okasha, S and Rainey, PB and Rozen, DE and Shitut, S and Tans, SJ and Tenaillon, O and Teotónio, H and de Visser, JAGM and Visser, ME and Vroomans, RMA and Werner, GDA and Wertheim, B and Pennings, PS},
title = {Towards evolutionary predictions: Current promises and challenges.},
journal = {Evolutionary applications},
volume = {16},
number = {1},
pages = {3-21},
pmid = {36699126},
issn = {1752-4571},
abstract = {Evolution has traditionally been a historical and descriptive science, and predicting future evolutionary processes has long been considered impossible. However, evolutionary predictions are increasingly being developed and used in medicine, agriculture, biotechnology and conservation biology. Evolutionary predictions may be used for different purposes, such as to prepare for the future, to try and change the course of evolution or to determine how well we understand evolutionary processes. Similarly, the exact aspect of the evolved population that we want to predict may also differ. For example, we could try to predict which genotype will dominate, the fitness of the population or the extinction probability of a population. In addition, there are many uses of evolutionary predictions that may not always be recognized as such. The main goal of this review is to increase awareness of methods and data in different research fields by showing the breadth of situations in which evolutionary predictions are made. We describe how diverse evolutionary predictions share a common structure described by the predictive scope, time scale and precision. Then, by using examples ranging from SARS-CoV2 and influenza to CRISPR-based gene drives and sustainable product formation in biotechnology, we discuss the methods for predicting evolution, the factors that affect predictability and how predictions can be used to prevent evolution in undesirable directions or to promote beneficial evolution (i.e. evolutionary control). We hope that this review will stimulate collaboration between fields by establishing a common language for evolutionary predictions.},
}
@article {pmid36696549,
year = {2023},
author = {Menon, K and Sorce, LR and Argent, A and Bennett, TD and Carrol, ED and Kissoon, N and Sanchez-Pinto, LN and Schlapbach, LJ and de Souza, DC and Watson, RS and Wynn, JL and Zimmerman, JJ and Ranjit, S and , and , },
title = {Reporting of Social Determinants of Health in Pediatric Sepsis Studies.},
journal = {Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies},
volume = {},
number = {},
pages = {},
doi = {10.1097/PCC.0000000000003184},
pmid = {36696549},
issn = {1529-7535},
abstract = {OBJECTIVE: Standardized, consistent reporting of social determinants of health (SDOH) in studies on children with sepsis would allow for: 1) understanding the association of SDOH with illness severity and outcomes, 2) comparing populations and extrapolating study results, and 3) identification of potentially modifiable socioeconomic factors for policy makers. We, therefore, sought to determine how frequently data on SDOH were reported, which factors were collected and how these factors were defined in studies of sepsis in children.
DATA SOURCES AND SELECTION: We reviewed 106 articles (published between 2005 and 2020) utilized in a recent systematic review on physiologic criteria for pediatric sepsis.
DATA EXTRACTION: Data were extracted by two reviewers on variables that fell within the World Health Organization's SDOH categories.
DATA SYNTHESIS: SDOH were not the primary outcome in any of the included studies. Seventeen percent of articles (18/106) did not report on any SDOH, and a further 36.8% (39/106) only reported on gender/sex. Of the remaining 46.2% of articles, the most reported SDOH categories were preadmission nutritional status (35.8%, 38/106) and race/ethnicity (18.9%, 20/106). However, no two studies used the same definition of the variables reported within each of these categories. Six studies reported on socioeconomic status (3.8%, 6/106), including two from upper-middle-income and four from lower middle-income countries. Only three studies reported on parental education levels (2.8%, 3/106). No study reported on parental job security or structural conflict.
CONCLUSIONS: We found overall low reporting of SDOH and marked variability in categorizations and definitions of SDOH variables. Consistent and standardized reporting of SDOH in pediatric sepsis studies is needed to understand the role these factors play in the development and severity of sepsis, to compare and extrapolate study results between settings and to implement policies aimed at improving socioeconomic conditions related to sepsis.},
}
@article {pmid36692937,
year = {2023},
author = {de Angel, V and Adeleye, F and Zhang, Y and Cummins, N and Munir, S and Lewis, S and Laporta Puyal, E and Matcham, F and Sun, S and Folarin, AA and Ranjan, Y and Conde, P and Rashid, Z and Dobson, R and Hotopf, M},
title = {The Feasibility of Implementing Remote Measurement Technologies in Psychological Treatment for Depression: Mixed Methods Study on Engagement.},
journal = {JMIR mental health},
volume = {10},
number = {},
pages = {e42866},
doi = {10.2196/42866},
pmid = {36692937},
issn = {2368-7959},
abstract = {BACKGROUND: Remote measurement technologies (RMTs) such as smartphones and wearables can help improve treatment for depression by providing objective, continuous, and ecologically valid insights into mood and behavior. Engagement with RMTs is varied and highly context dependent; however, few studies have investigated their feasibility in the context of treatment.
OBJECTIVE: A mixed methods design was used to evaluate engagement with active and passive data collection via RMT in people with depression undergoing psychotherapy. We evaluated the effects of treatment on 2 different types of engagement: study attrition (engagement with study protocol) and patterns of missing data (engagement with digital devices), which we termed data availability. Qualitative interviews were conducted to help interpret the differences in engagement.
METHODS: A total of 66 people undergoing psychological therapy for depression were followed up for 7 months. Active data were gathered from weekly questionnaires and speech and cognitive tasks, and passive data were gathered from smartphone sensors and a Fitbit (Fitbit Inc) wearable device.
RESULTS: The overall retention rate was 60%. Higher-intensity treatment (χ[2]1=4.6; P=.03) and higher baseline anxiety (t56.28=-2.80, 2-tailed; P=.007) were associated with attrition, but depression severity was not (t50.4=-0.18; P=.86). A trend toward significance was found for the association between longer treatments and increased attrition (U=339.5; P=.05). Data availability was higher for active data than for passive data initially but declined at a sharper rate (90%-30% drop in 7 months). As for passive data, wearable data availability fell from a maximum of 80% to 45% at 7 months but showed higher overall data availability than smartphone-based data, which remained stable at the range of 20%-40% throughout. Missing data were more prevalent among GPS location data, followed by among Bluetooth data, then among accelerometry data. As for active data, speech and cognitive tasks had lower completion rates than clinical questionnaires. The participants in treatment provided less Fitbit data but more active data than those on the waiting list.
CONCLUSIONS: Different data streams showed varied patterns of missing data, despite being gathered from the same device. Longer and more complex treatments and clinical characteristics such as higher baseline anxiety may reduce long-term engagement with RMTs, and different devices may show opposite patterns of missingness during treatment. This has implications for the scalability and uptake of RMTs in health care settings, the generalizability and accuracy of the data collected by these methods, feature construction, and the appropriateness of RMT use in the long term.},
}
@article {pmid36690591,
year = {2023},
author = {Sambo, B and Bonato, M and Sperotto, A and Torresan, S and Furlan, E and Lambert, JH and Linkov, I and Critto, A},
title = {Framework for multirisk climate scenarios across system receptors with application to the Metropolitan City of Venice.},
journal = {Risk analysis : an official publication of the Society for Risk Analysis},
volume = {},
number = {},
pages = {},
doi = {10.1111/risa.14097},
pmid = {36690591},
issn = {1539-6924},
abstract = {Climate change influences the frequency of extreme events that affect both human and natural systems. It requires systemic climate change adaptation to address the complexity of risks across multiple domains and tackle the uncertainties of future scenarios. This paper introduces a multirisk analysis of climate hazard, exposure, vulnerability, and risk severity, specifically designed to hotspot geographic locations and prioritize system receptors that are affected by climate-related extremes. The analysis is demonstrated for the Metropolitan City of Venice. Representative scenarios (RCP4.5 and RCP8.5) of climate threats (i.e., storm surges, pluvial flood, heat waves, and drought) are selected and represented by projections of Regional Climate Models for a 30-year period (2021-2050). A sample of results is as follows. First, an increase in the risk is largely due to drought, pluvial flood, and storm surge, depending on the areas of interest, with the overall situation worsening under the RCP8.5 scenario. Second, particular locations have colocated vulnerable receptors at higher risk, concentrated in the urban centers (e.g., housing, railways, roads) and along the coast (e.g., beaches, wetlands, primary sector). Third, risk communication of potential environmental and socio-economic losses via the multirisk maps is useful to stakeholders and public administration. Fourth, the multirisk maps recommend priorities for future investigation and risk management, such as collection of sensor data, elaboration of mitigations, and adaptation plans at hotspot locations.},
}
@article {pmid36689893,
year = {2023},
author = {Werneck, RA and Meinberg, MF and Passos, MZ and Brandão, WC and de Moraes, EN and da Silva-Filho, AL},
title = {Quality of information regarding abnormal uterine bleeding available online.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {282},
number = {},
pages = {83-88},
doi = {10.1016/j.ejogrb.2023.01.020},
pmid = {36689893},
issn = {1872-7654},
abstract = {INTRODUCTION: The Internet and electronic devices with Internet access allow for a greater fluidity of information and speed of communication, especially in the field of health. Abnormal uterine bleeding (AUB) affects approximately 3-30% of women and can negatively impact their health and quality of life. Information regarding AUB that is available on the Internet may not be clear or accurate, rendering it difficult to understand and likely to result in delayed medical evaluation, which subsequently leads to worsening of the AUB.
OBJECTIVE: To evaluate the quality of the information regarding AUB currently available on the Internet, including information regarding treatments.
METHODS: The Google Trends website was searched for the most widely used English terms related to AUB. The identified descriptors were searched individually on the Google, Yahoo!, and Bing search engines. The first 10 results of each search were pre-selected and evaluated for inclusion in this study. Selected websites were categorically divided into two groups (news/magazine and academic) and individually analyzed by three experts using the DISCERN quality criteria (reliability, general quality, and quality of information) and the presence or absence of the Health on the Net Foundation Code of Conduct (HONcode®) seal.
RESULTS: Of the 168 websites included in this study, 60.1% were allocated to the news/magazine group and 39.9% were allocated to the academic group. Over half of the websites (54.2%) did not have the HONcode® quality seal. Websites in the academic group were more likely to include accurate information regarding AUB with greater reliability than websites in the news/magazine group. There were no statistical differences regarding the general quality of the websites. Most websites were rated as either moderate quality (70.8%) or low quality (28.6%). The HONcode® criterion was found to be a confounding factor of the analyses, as the grouping and quality results of websites without this seal were significantly associated. In addition, websites in the news/magazines group were 6.7 times more likely to provide low quality information than websites in the academic group (odds ratio: 6.7; 95% confidence interval: 2.1-21.4).
CONCLUSION: The information regarding AUB that is available on the Internet is of low to moderate quality. Academic websites present more reliable information of greater quality. The presence of the HONcode® seal is considered important to determine the quality of the content of a website, especially for news/magazine websites, and may help Internet users identify websites that contain more reliable information. Algorithms and applications that categorize the quality of information and the reliability of health content may be useful tools that can help patients clarify their symptoms for several conditions including AUB.},
}
@article {pmid36669842,
year = {2023},
author = {Guan, Y and Qi, Y and Zheng, L and Yang, J and Zhang, M and Zhang, Q and Ji, L},
title = {Data mining techniques for detecting signals of adverse drug reaction of cardiac therapy drugs based on Jinan adverse event reporting system database: a retrospective study.},
journal = {BMJ open},
volume = {13},
number = {1},
pages = {e068127},
doi = {10.1136/bmjopen-2022-068127},
pmid = {36669842},
issn = {2044-6055},
mesh = {Humans ; United States ; Retrospective Studies ; Bayes Theorem ; *Adverse Drug Reaction Reporting Systems ; *Drug-Related Side Effects and Adverse Reactions/diagnosis/epidemiology ; Data Mining ; Databases, Factual ; United States Food and Drug Administration ; },
abstract = {OBJECTIVE: Cardiac therapy drugs are widely used in the treatment of heart disease. However, the concern regarding adverse events (AEs) of cardiac therapy drugs have been rising. This study aimed to analyse cardiac therapy drug-related AEs using the Jinan adverse event reporting system (JAERS) database mining and conduct a comprehensive evaluation to provide safe medication information for patients.
DESIGN: Retrospective observational study.
SETTING: In this study, cardiac therapy drug-related AEs were detected using the JAERS database from January 2000 to March 2022.
METHODS: Reports of cardiac therapy drug-related AEs were extracted from JAERS database, and the basic information of patients, reports and common AEs were analysed. Four disproportionality analysis methods, proportional reporting ratio (PRR), reporting odds ratio (ROR), Bayesian Confidence Propagation Neural Network (BCPNN), Medicines and Healthcare products Regulatory Agency (MHRA), were used to detect cardiac therapy drug-related signals. We further checked whether the detected signals exist on drug labels in China and two developed countries, the USA and Japan.
RESULTS: In total, 168 314 AEs were reported, of which 4788 were associated with cardiac therapy drugs. Using the PRR, ROR, MHRA and BCPNN method, we detected 52 signals, 52 signals, 33 signals and 43 signals, respectively. Among the 52 signals, 14 were not included on the drug labels of China. One (isosorbide mononitrate-head bilges) was not included on the drug labels of the three countries.
CONCLUSION: We identified 14 new cardiac therapy drug signals that did not appear on drug labels in China and 1 new signal that did not appear on drug labels in 3 counties. A causal link between cardiac therapy drugs and AEs should be evaluated in further studies.},
}
@article {pmid36685700,
year = {2022},
author = {Jazayeri, SM and Pooralinaghi, M and Torres-Navarrete, Y and Oviedo-Bayas, B and Guerra, ÍE and Jácome, DH and Morán, CQ and Macias, CS and Escobar, KM and Ghafoor, SMHAS and Veiskarami, G and Jandaghi, P and Torres, ROV},
title = {Alkaloid production and response to natural adverse conditions in Peganum harmala: in silico transcriptome analyses.},
journal = {Biotechnologia},
volume = {103},
number = {4},
pages = {355-384},
pmid = {36685700},
issn = {2353-9461},
abstract = {Peganum harmala is a valuable wild plant that grows and survives under adverse conditions and produces pharmaceutical alkaloid metabolites. Using different assemblers to develop a transcriptome improves the quality of assembled transcriptome. In this study, a concrete and accurate method for detecting stress-responsive transcripts by comparing stress-related gene ontology (GO) terms and public domains was designed. An integrated transcriptome for P. harmala including 42 656 coding sequences was created by merging de novo assembled transcriptomes. Around 35 000 transcripts were annotated with more than 90% resemblance to three closely related species of Citrus, which confirmed the robustness of the assembled transcriptome; 4853 stress-responsive transcripts were identified. CYP82 involved in alkaloid biosynthesis showed a higher number of transcripts in P. harmala than in other plants, indicating its diverse alkaloid biosynthesis attributes. Transcription factors (TFs) and regulatory elements with 3887 transcripts comprised 9% of the transcriptome. Among the TFs of the integrated transcriptome, cystein2/histidine2 (C2H2) and WD40 repeat families were the most abundant. The Kyoto Encyclopedia of Genes and Genomes (KEGG) MAPK (mitogen-activated protein kinase) signaling map and the plant hormone signal transduction map showed the highest assigned genes to these pathways, suggesting their potential stress resistance. The P. harmala whole-transcriptome survey provides important resources and paves the way for functional and comparative genomic studies on this plant to discover stress-tolerance-related markers and response mechanisms in stress physiology, phytochemistry, ecology, biodiversity, and evolution. P. harmala can be a potential model for studying adverse environmental cues and metabolite biosynthesis and a major source for the production of various alkaloids.},
}
@article {pmid36684825,
year = {2023},
author = {Liew, CY and Labadin, J and Kok, WC and Eze, MO},
title = {A methodology framework for bipartite network modeling.},
journal = {Applied network science},
volume = {8},
number = {1},
pages = {6},
pmid = {36684825},
issn = {2364-8228},
abstract = {The graph-theoretic based studies employing bipartite network approach mostly focus on surveying the statistical properties of the structure and behavior of the network systems under the domain of complex network analysis. They aim to provide the big-picture-view insights of a networked system by looking into the dynamic interaction and relationship among the vertices. Nonetheless, incorporating the features of individual vertex and capturing the dynamic interaction of the heterogeneous local rules governing each of them in the studies is lacking. The methodology in achieving this could hardly be found. Consequently, this study intends to propose a methodology framework that considers the influence of heterogeneous features of each node to the overall network behavior in modeling real-world bipartite network system. The proposed framework consists of three main stages with principal processes detailed in each stage, and three libraries of techniques to guide the modeling activities. It is iterative and process-oriented in nature and allows future network expansion. Two case studies from the domain of communicable disease in epidemiology and habitat suitability in ecology employing this framework are also presented. The results obtained suggest that the methodology could serve as a generic framework in advancing the current state of the art of bipartite network approach.},
}
@article {pmid36682374,
year = {2023},
author = {Traore, T and Shanks, S and Haider, N and Ahmed, K and Jain, V and Rüegg, SR and Razavi, A and Kock, R and Erondu, N and Rahman-Shepherd, A and Yavlinsky, A and Mboera, L and Asogun, D and McHugh, TD and Elton, L and Oyebanji, O and Okunromade, O and Ansumana, R and Djingarey, MH and Ali Ahmed, Y and Diallo, AB and Balde, T and Talisuna, A and Ntoumi, F and Zumla, A and Heymann, D and Socé Fall, I and Dar, O},
title = {How prepared is the world? Identifying weaknesses in existing assessment frameworks for global health security through a One Health approach.},
journal = {Lancet (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1016/S0140-6736(22)01589-6},
pmid = {36682374},
issn = {1474-547X},
abstract = {The COVID-19 pandemic has exposed faults in the way we assess preparedness and response capacities for public health emergencies. Existing frameworks are limited in scope, and do not sufficiently consider complex social, economic, political, regulatory, and ecological factors. One Health, through its focus on the links among humans, animals, and ecosystems, is a valuable approach through which existing assessment frameworks can be analysed and new ways forward proposed. Although in the past few years advances have been made in assessment tools such as the International Health Regulations Joint External Evaluation, a rapid and radical increase in ambition is required. To sufficiently account for the range of complex systems in which health emergencies occur, assessments should consider how problems are defined across stakeholders and the wider sociopolitical environments in which structures and institutions operate. Current frameworks do little to consider anthropogenic factors in disease emergence or address the full array of health security hazards across the social-ecological system. A complex and interdependent set of challenges threaten human, animal, and ecosystem health, and we cannot afford to overlook important contextual factors, or the determinants of these shared threats. Health security assessment frameworks should therefore ensure that the process undertaken to prioritise and build capacity adheres to core One Health principles and that interventions and outcomes are assessed in terms of added value, trade-offs, and cobenefits across human, animal, and environmental health systems.},
}
@article {pmid36659170,
year = {2020},
author = {Gong, P and Chen, B and Li, X and Liu, H and Wang, J and Bai, Y and Chen, J and Chen, X and Fang, L and Feng, S and Feng, Y and Gong, Y and Gu, H and Huang, H and Huang, X and Jiao, H and Kang, Y and Lei, G and Li, A and Li, X and Li, X and Li, Y and Li, Z and Li, Z and Liu, C and Liu, C and Liu, M and Liu, S and Mao, W and Miao, C and Ni, H and Pan, Q and Qi, S and Ren, Z and Shan, Z and Shen, S and Shi, M and Song, Y and Su, M and Ping Suen, H and Sun, B and Sun, F and Sun, J and Sun, L and Sun, W and Tian, T and Tong, X and Tseng, Y and Tu, Y and Wang, H and Wang, L and Wang, X and Wang, Z and Wu, T and Xie, Y and Yang, J and Yang, J and Yuan, M and Yue, W and Zeng, H and Zhang, K and Zhang, N and Zhang, T and Zhang, Y and Zhao, F and Zheng, Y and Zhou, Q and Clinton, N and Zhu, Z and Xu, B},
title = {Mapping essential urban land use categories in China (EULUC-China): preliminary results for 2018.},
journal = {Science bulletin},
volume = {65},
number = {3},
pages = {182-187},
doi = {10.1016/j.scib.2019.12.007},
pmid = {36659170},
issn = {2095-9281},
}
@article {pmid36656265,
year = {2023},
author = {Yu, Y and Yu, X and Zhang, D and Jin, L and Huang, J and Zhu, X and Sun, J and Yu, M and Zhu, L},
title = {Biotransformation of Organophosphate Esters by Rice and Rhizosphere Microbiome: Multiple Metabolic Pathways, Mechanism, and Toxicity Assessment.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.2c07796},
pmid = {36656265},
issn = {1520-5851},
abstract = {The biotransformation behavior and toxicity of organophosphate esters (OPEs) in rice and rhizosphere microbiomes were comprehensively studied by hydroponic experiments. OPEs with lower hydrophobicity were liable to be translocated acropetally, and rhizosphere microbiome could reduce the uptake and translocation of OPEs in rice tissues. New metabolites were successfully identified in rice and rhizosphere microbiome, including hydrolysis, hydroxylated, methylated, and glutathione-, glucuronide-, and sulfate-conjugated products. Rhizobacteria and plants could cooperate to form a complex ecological interaction web for OPE elimination. Furthermore, active members of the rhizosphere microbiome during OPE degradation were revealed and the metagenomic analysis indicated that most of these active populations contained OPE-degrading genes. The results of metabolomics analyses for phytotoxicity assessment implied that several key function metabolic pathways of the rice plant were found perturbed by metabolites, such as diphenyl phosphate and monophenyl phosphate. In addition, the involved metabolism mechanisms, such as the carbohydrate metabolism, amino acid metabolism and synthesis, and nucleotide metabolism in Escherichia coli, were significantly altered after exposure to the products mixture of OPEs generated by rhizosphere microbiome. This work for the first time gives a comprehensive understanding of the entire metabolism of OPEs in plants and associated microbiome, and provides support for the ongoing risk assessment of emerging contaminants and, most critically, their transformation products.},
}
@article {pmid36654087,
year = {2022},
author = {Yang, L and Zou, K and Gao, K and Jiang, Z},
title = {A fuzzy DRBFNN-based information security risk assessment method in improving the efficiency of urban development.},
journal = {Mathematical biosciences and engineering : MBE},
volume = {19},
number = {12},
pages = {14232-14250},
doi = {10.3934/mbe.2022662},
pmid = {36654087},
issn = {1551-0018},
abstract = {The rapid development of urban informatization is an important way for cities to achieve a higher pattern, but the accompanying information security problem become a major challenge restricting the efficiency of urban development. Therefore, effective identification and assessment of information security risks has become a key factor to improve the efficiency of urban development. In this paper, an information security risk assessment method based on fuzzy theory and neural network technology is proposed to help identify and solve the information security problem in the development of urban informatization. Combined with the theory of information ecology, this method establishes an improved fuzzy neural network model from four aspects by using fuzzy theory, neural network model and DEMATEL method, and then constructs the information security risk assessment system of smart city. According to this method, this paper analyzed 25 smart cities in China, and provided suggestions and guidance for information security control in the process of urban informatization construction.},
}
@article {pmid36653564,
year = {2023},
author = {Battin, TJ and Lauerwald, R and Bernhardt, ES and Bertuzzo, E and Gener, LG and Hall, RO and Hotchkiss, ER and Maavara, T and Pavelsky, TM and Ran, L and Raymond, P and Rosentreter, JA and Regnier, P},
title = {River ecosystem metabolism and carbon biogeochemistry in a changing world.},
journal = {Nature},
volume = {613},
number = {7944},
pages = {449-459},
pmid = {36653564},
issn = {1476-4687},
abstract = {River networks represent the largest biogeochemical nexus between the continents, ocean and atmosphere. Our current understanding of the role of rivers in the global carbon cycle remains limited, which makes it difficult to predict how global change may alter the timing and spatial distribution of riverine carbon sequestration and greenhouse gas emissions. Here we review the state of river ecosystem metabolism research and synthesize the current best available estimates of river ecosystem metabolism. We quantify the organic and inorganic carbon flux from land to global rivers and show that their net ecosystem production and carbon dioxide emissions shift the organic to inorganic carbon balance en route from land to the coastal ocean. Furthermore, we discuss how global change may affect river ecosystem metabolism and related carbon fluxes and identify research directions that can help to develop better predictions of the effects of global change on riverine ecosystem processes. We argue that a global river observing system will play a key role in understanding river networks and their future evolution in the context of the global carbon budget.},
}
@article {pmid36648719,
year = {2023},
author = {Zhu, F and Su, T and Lei, B and Liang, Q and Zhou, Y and Liu, X and Wang, X and Zhang, D},
title = {Considerations on the impact of "source-sink" landscape pattern changes on urban thermal environment and cooling efficiency: a case study of Nanjing, China.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {36648719},
issn = {1614-7499},
abstract = {The urban heat island effect caused by rapid urbanization has had a great impact on human health and ecological environment. The evolution of landscape patterns often affects regional thermal characteristics at the local scale. How to rationally allocate land cover types from the perspective of urban planning is a huge challenge. This paper takes Nanjing, a typical "stove city" in China, as an example to study the impact of landscape pattern changes on the urban thermal environment. Firstly, based on the "source" landscape "/sink" landscape identified by the "source-sink" landscape index, on this basis, the contributions of the "source-sink" landscape and its effects are calculated, and the temporal and spatial evolution laws are analyzed. Second, we study the cooling effect of different characteristic landscapes. The results show that the change of landscape pattern is closely related to the urban thermal environment, and the expansion of built-up areas is the main reason for the urban thermal environment. With the development of urbanization, the "source-sink" landscape structure in most districts and counties has aggravated the heat island effect, and the ratios of "sink" and "source" landscape contribution ratios with strong levels are concentrated in the suburban areas. The results of cooling efficiency research show that the cooling range of forest land is larger than that of water bodies. At the same time, we found that the cooling efficiency of the sink landscape is the highest when the area of the sink landscape is 0.18-0.9 hm[2] and the shape index is between 1 and 4. The research results can provide feasible and practical scientific suggestions for the planning and ecological construction of Nanjing.},
}
@article {pmid36400569,
year = {2023},
author = {Wu, L and Yan, B and Han, J and Li, R and Xiao, J and He, S and Bo, X},
title = {TOXRIC: a comprehensive database of toxicological data and benchmarks.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D1432-D1445},
pmid = {36400569},
issn = {1362-4962},
mesh = {Humans ; Benchmarking ; *Databases, Factual ; *Toxicology/methods ; Software ; },
abstract = {The toxic effects of compounds on environment, humans, and other organisms have been a major focus of many research areas, including drug discovery and ecological research. Identifying the potential toxicity in the early stage of compound/drug discovery is critical. The rapid development of computational methods for evaluating various toxicity categories has increased the need for comprehensive and system-level collection of toxicological data, associated attributes, and benchmarks. To contribute toward this goal, we proposed TOXRIC (https://toxric.bioinforai.tech/), a database with comprehensive toxicological data, standardized attribute data, practical benchmarks, informative visualization of molecular representations, and an intuitive function interface. The data stored in TOXRIC contains 113 372 compounds, 13 toxicity categories, 1474 toxicity endpoints covering in vivo/in vitro endpoints and 39 feature types, covering structural, target, transcriptome, metabolic data, and other descriptors. All the curated datasets of endpoints and features can be retrieved, downloaded and directly used as output or input to Machine Learning (ML)-based prediction models. In addition to serving as a data repository, TOXRIC also provides visualization of benchmarks and molecular representations for all endpoint datasets. Based on these results, researchers can better understand and select optimal feature types, molecular representations, and baseline algorithms for each endpoint prediction task. We believe that the rich information on compound toxicology, ML-ready datasets, benchmarks and molecular representation distribution can greatly facilitate toxicological investigations, interpretation of toxicological mechanisms, compound/drug discovery and the development of computational methods.},
}
@article {pmid35999848,
year = {2022},
author = {Kopperud, BT and Lidgard, S and Liow, LH},
title = {Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13921},
pmid = {35999848},
issn = {2167-8359},
mesh = {Animals ; *Biodiversity ; *Bryozoa ; Information Storage and Retrieval ; },
abstract = {We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences (TMO)) in an automated procedure. We compare these results with data combined from two major public databases (DB): the Ocean Biodiversity Information System (OBIS), and the Global Biodiversity Information Facility (GBIF). Using DB and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined DB and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for extant cheilostomes for the first time, with peaks in the temperate zones. A total of 79% of the georeferenced species we retrieved from TMO (N = 1,408) and DB (N = 4,549) are non-overlapping. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that many marine latitudinal species richness patterns deviate from the canonical latitudinal diversity gradient (LDG). Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.},
}
@article {pmid36647630,
year = {2023},
author = {Watts, JD and Farina, M and Kimball, JS and Schiferl, LD and Liu, Z and Arndt, KA and Zona, D and Ballantyne, A and Euskirchen, ES and Parmentier, FW and Helbig, M and Sonnentag, O and Tagesson, T and Rinne, J and Ikawa, H and Ueyama, M and Kobayashi, H and Sachs, T and Nadeau, DF and Kochendorfer, J and Jackowicz-Korczynski, M and Virkkala, A and Aurela, M and Commane, R and Byrne, B and Birch, L and Johnson, MS and Madani, N and Rogers, B and Du, J and Endsley, A and Savage, K and Poulter, B and Zhang, Z and Bruhwiler, LM and Miller, CE and Goetz, S and Oechel, WC},
title = {Carbon uptake in Eurasian boreal forests dominates the high-latitude net ecosystem carbon budget.},
journal = {Global change biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/gcb.16553},
pmid = {36647630},
issn = {1365-2486},
support = {80NM0018D004/NASA/NASA/United States ; 80NSSC18K0770/NASA/NASA/United States ; 19-EARTH20-0105/NASA/NASA/United States ; NNX15AT74A/NASA/NASA/United States ; 80NSSC19M0113/NASA/NASA/United States ; },
abstract = {Arctic-boreal landscapes are experiencing profound warming, along with changes in ecosystem moisture status and disturbance from fire. This region is of global importance in terms of carbon feedbacks to climate, yet the sign (sink or source) and magnitude of the Arctic-boreal carbon budget within recent years remains highly uncertain. Here, we provide new estimates of recent (2003-2015) vegetation gross primary productivity (GPP), ecosystem respiration (Reco), net ecosystem CO2 exchange (NEE; Reco - GPP), and terrestrial methane (CH4) emissions for the Arctic-boreal zone using a satellite data-driven process-model for northern ecosystems (TCFM-Arctic), calibrated and evaluated using measurements from >60 tower eddy covariance (EC) sites. We used TCFM-Arctic to obtain daily 1-km[2] flux estimates and annual carbon budgets for the pan-Arctic-boreal region. Across the domain, the model indicated an overall average NEE sink of -850 Tg CO2 -C year[-1] . Eurasian boreal zones, especially those in Siberia, contributed to a majority of the net sink. In contrast, the tundra biome was relatively carbon neutral (ranging from small sink to source). Regional CH4 emissions from tundra and boreal wetlands (not accounting for aquatic CH4) were estimated at 35 Tg CH4 -C year[-1] . Accounting for additional emissions from open water aquatic bodies and from fire, using available estimates from the literature, reduced the total regional NEE sink by 21% and shifted many far northern tundra landscapes, and some boreal forests, to a net carbon source. This assessment, based on in situ observations and models, improves our understanding of the high-latitude carbon status and also indicates a continued need for integrated site-to-regional assessments to monitor the vulnerability of these ecosystems to climate change.},
}
@article {pmid36643652,
year = {2023},
author = {Mugnai, F and Costantini, F and Chenuil, A and Leduc, M and Gutiérrez Ortega, JM and Meglécz, E},
title = {Be positive: customized reference databases and new, local barcodes balance false taxonomic assignments in metabarcoding studies.},
journal = {PeerJ},
volume = {11},
number = {},
pages = {e14616},
pmid = {36643652},
issn = {2167-8359},
mesh = {Humans ; *DNA Barcoding, Taxonomic ; Databases, Factual ; Mediterranean Sea ; },
abstract = {BACKGROUND: In metabarcoding analyses, the taxonomic assignment is crucial to place sequencing data in biological and ecological contexts. This fundamental step depends on a reference database, which should have a good taxonomic coverage to avoid unassigned sequences. However, this goal is rarely achieved in many geographic regions and for several taxonomic groups. On the other hand, more is not necessarily better, as sequences in reference databases belonging to taxonomic groups out of the studied region/environment context might lead to false assignments.
METHODS: We investigated the effect of using several subsets of a cytochrome c oxidase subunit I (COI) reference database on taxonomic assignment. Published metabarcoding sequences from the Mediterranean Sea were assigned to taxa using COInr, which is a comprehensive, non-redundant and recent database of COI sequences obtained both from BOLD and NCBI, and two of its subsets: (i) all sequences except insects (COInr-WO-Insecta), which represent the overwhelming majority of COInr database, but are irrelevant for marine samples, and (ii) all sequences from taxonomic families present in the Mediterranean Sea (COInr-Med). Four different algorithms for taxonomic assignment were employed in parallel to evaluate differences in their output and data consistency.
RESULTS: The reduction of the database to more specific custom subsets increased the number of unassigned sequences. Nevertheless, since most of them were incorrectly assigned by the less specific databases, this is a positive outcome. Moreover, the taxonomic resolution (the lowest taxonomic level to which a sequence is attributed) of several sequences tended to increase when using customized databases. These findings clearly indicated the need for customized databases adapted to each study. However, the very high proportion of unassigned sequences points to the need to enrich the local database with new barcodes specifically obtained from the studied region and/or taxonomic group. Including novel local barcodes to the COI database proved to be very profitable: by adding only 116 new barcodes sequenced in our laboratory, thus increasing the reference database by only 0.04%, we were able to improve the resolution for ca. 0.6-1% of the Amplicon Sequence Variants (ASVs).},
}
@article {pmid36462728,
year = {2023},
author = {Sosa, CC and Clavijo-Buriticá, DC and García-Merchán, VH and López-Rozo, N and Riccio-Rengifo, C and Diaz, MV and Londoño, DA and Quimbaya, MA},
title = {GOCompare: An R package to compare functional enrichment analysis between two species.},
journal = {Genomics},
volume = {115},
number = {1},
pages = {110528},
doi = {10.1016/j.ygeno.2022.110528},
pmid = {36462728},
issn = {1089-8646},
mesh = {*Aluminum ; Genomics/methods ; Computational Biology/methods ; Algorithms ; Gene Ontology ; *Arabidopsis/genetics ; },
abstract = {Functional enrichment analysis is a cornerstone in bioinformatics as it makes possible to identify functional information by using a gene list as source. Different tools are available to compare gene ontology (GO) terms, based on a directed acyclic graph structure or content-based algorithms which are time-consuming and require a priori information of GO terms. Nevertheless, quantitative procedures to compare GO terms among gene lists and species are not available. Here we present a computational procedure, implemented in R, to infer functional information derived from comparative strategies. GOCompare provides a framework for functional comparative genomics starting from comparable lists from GO terms. The program uses functional enrichment analysis (FEA) results and implement graph theory to identify statistically relevant GO terms for both, GO categories and analyzed species. Thus, GOCompare allows finding new functional information complementing current FEA approaches and extending their use to a comparative perspective. To test our approach GO terms were obtained for a list of aluminum tolerance-associated genes in Oryza sativa subsp. japonica and their orthologues in Arabidopsis thaliana. GOCompare was able to detect functional similarities for reactive oxygen species and ion binding capabilities which are common in plants as molecular mechanisms to tolerate aluminum toxicity. Consequently, the R package exhibited a good performance when implemented in complex datasets, allowing to establish hypothesis that might explain a biological process from a functional perspective, and narrowing down the possible landscapes to design wet lab experiments.},
}
@article {pmid36318246,
year = {2023},
author = {Lei, B and Xu, Y and Lei, Y and Li, C and Zhou, P and Wang, L and Yang, Q and Li, X and Li, F and Liu, C and Cui, C and Chen, T and Ni, W and Hu, S},
title = {CRAMdb: a comprehensive database for composition and roles of microbiome in animals.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D700-D707},
pmid = {36318246},
issn = {1362-4962},
mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Fungi/genetics ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Databases, Factual ; },
abstract = {CRAMdb (a database for composition and roles of animal microbiome) is a comprehensive resource of curated and consistently annotated metagenomes for non-human animals. It focuses on the composition and roles of the microbiome in various animal species. The main goal of the CRAMdb is to facilitate the reuse of animal metagenomic data, and enable cross-host and cross-phenotype comparisons. To this end, we consistently annotated microbiomes (including 16S, 18S, ITS and metagenomics sequencing data) of 516 animals from 475 projects spanning 43 phenotype pairs to construct the database that is equipped with 9430 bacteria, 278 archaea, 2216 fungi and 458 viruses. CRAMdb provides two main contents: microbiome composition data, illustrating the landscape of the microbiota (bacteria, archaea, fungi, and viruses) in various animal species, and microbiome association data, revealing the relationships between the microbiota and various phenotypes across different animal species. More importantly, users can quickly compare the composition of the microbiota of interest cross-host or body site and the associated taxa that differ between phenotype pairs cross-host or cross-phenotype. CRAMdb is freely available at (http://www.ehbio.com/CRAMdb).},
}
@article {pmid36645791,
year = {2022},
author = {Marwali, EM and Kekalih, A and Yuliarto, S and Wati, DK and Rayhan, M and Valerie, IC and Cho, HJ and Jassat, W and Blumberg, L and Masha, M and Semple, C and Swann, OV and Kohns Vasconcelos, M and Popielska, J and Murthy, S and Fowler, RA and Guerguerian, AM and Streinu-Cercel, A and Pathmanathan, MD and Rojek, A and Kartsonaki, C and Gonçalves, BP and Citarella, BW and Merson, L and Olliaro, PL and Dalton, HJ and , },
title = {Paediatric COVID-19 mortality: a database analysis of the impact of health resource disparity.},
journal = {BMJ paediatrics open},
volume = {6},
number = {1},
pages = {},
doi = {10.1136/bmjpo-2022-001657},
pmid = {36645791},
issn = {2399-9772},
abstract = {BACKGROUND: The impact of the COVID-19 pandemic on paediatric populations varied between high-income countries (HICs) versus low-income to middle-income countries (LMICs). We sought to investigate differences in paediatric clinical outcomes and identify factors contributing to disparity between countries.
METHODS: The International Severe Acute Respiratory and Emerging Infections Consortium (ISARIC) COVID-19 database was queried to include children under 19 years of age admitted to hospital from January 2020 to April 2021 with suspected or confirmed COVID-19 diagnosis. Univariate and multivariable analysis of contributing factors for mortality were assessed by country group (HICs vs LMICs) as defined by the World Bank criteria.
RESULTS: A total of 12 860 children (3819 from 21 HICs and 9041 from 15 LMICs) participated in this study. Of these, 8961 were laboratory-confirmed and 3899 suspected COVID-19 cases. About 52% of LMICs children were black, and more than 40% were infants and adolescent. Overall in-hospital mortality rate (95% CI) was 3.3% [=(3.0% to 3.6%), higher in LMICs than HICs (4.0% (3.6% to 4.4%) and 1.7% (1.3% to 2.1%), respectively). There were significant differences between country income groups in intervention profile, with higher use of antibiotics, antivirals, corticosteroids, prone positioning, high flow nasal cannula, non-invasive and invasive mechanical ventilation in HICs. Out of the 439 mechanically ventilated children, mortality occurred in 106 (24.1%) subjects, which was higher in LMICs than HICs (89 (43.6%) vs 17 (7.2%) respectively). Pre-existing infectious comorbidities (tuberculosis and HIV) and some complications (bacterial pneumonia, acute respiratory distress syndrome and myocarditis) were significantly higher in LMICs compared with HICs. On multivariable analysis, LMIC as country income group was associated with increased risk of mortality (adjusted HR 4.73 (3.16 to 7.10)).
CONCLUSION: Mortality and morbidities were higher in LMICs than HICs, and it may be attributable to differences in patient demographics, complications and access to supportive and treatment modalities.},
}
@article {pmid36635306,
year = {2023},
author = {Siddik, MAB and Dickson, KE and Rising, J and Ruddell, BL and Marston, LT},
title = {Interbasin water transfers in the United States and Canada.},
journal = {Scientific data},
volume = {10},
number = {1},
pages = {27},
pmid = {36635306},
issn = {2052-4463},
mesh = {United States ; Humans ; *Ecosystem ; *Water Supply ; Canada ; Hydrology ; Surveys and Questionnaires ; },
abstract = {Interbasin water transfers (IBTs) can have a significant impact on the environment, water availability, and economies within the basins importing and exporting water, as well as basins downstream of these water transfers. The lack of comprehensive data identifying and describing IBTs inhibits understanding of the role IBTs play in supplying water for society, as well as their collective hydrologic impact. We develop three connected datasets inventorying IBTs in the United States and Canada, including their features, geospatial details, and water transfer volumes. We surveyed the academic and gray literature, as well as local, state, and federal water agencies, to collect, process, and verify IBTs in Canada and the United States. Our comprehensive IBT datasets represent all known transfers of untreated water that cross subregion (US) or subdrainage area (CA) boundaries, characterizing a total of 641 IBT projects. The infrastructure-level data made available by these data products can be used to close water budgets, connect water supplies to water use, and better represent human impacts within hydrologic and ecosystem models.},
}
@article {pmid36641462,
year = {2023},
author = {Filip, T and Michal, Š and Radoslava, J and Ivan, B and Michal, A and Lucia, Z and Gyözö, H},
title = {The impact of the striped field mouse's range expansion on communities of native small mammals.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {753},
pmid = {36641462},
issn = {2045-2322},
abstract = {Understanding species expansion as an element of the dispersal process is crucial to gaining a better comprehension of the functioning of the populations and the communities. Populations of the same species that are native in one area could be considered nonindigenous, naturalised or invasive somewhere else. The striped field mouse has been expanding its range in south-western Slovakia since 2010, although the origin of the spread has still not been clarified. In light of the striped field mouse's life history, the recent range expansion is considered to be the expansion of a native species. This study analyses the impact of the striped field mouse's expansion on the native population and small mammal communities and confronts the documented stages of striped field mouse expansion with the stages of invasion biology. Our research replicates the design and compares results from past research of small mammals prior to this expansion at the same three study areas with the same 20 study sites and control sites. Several years after expansion, the striped field mouse has a 100% frequency of occurrence in all study sites and has become the dominant species in two of the study areas. The native community is significantly affected by the striped field mouse's increasing dominance, specifically: (i) we found a re-ordering of the species rank, mainly in areas with higher dominance, and (ii) an initial positive impact on diversity and evenness during low dominance of the striped field mouse turned markedly negative after crossing the 25% dominance threshold. Results suggested that the variation in the striped field mouse's dominance is affected by the northern direction of its spread. Our findings show that establishment in a new area, spread and impact on the native community are stages possibly shared by both invasive and native species during their range expansion.},
}
@article {pmid36639402,
year = {2023},
author = {Mack, M and Stojan, R and Bock, O and Voelcker-Rehage, C},
title = {The association of executive functions and physical fitness with cognitive-motor multitasking in a street crossing scenario.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {697},
pmid = {36639402},
issn = {2045-2322},
abstract = {Age-related decline in cognitive-motor multitasking performance has been attributed to declines in executive functions and physical fitness (motor coordinative fitness and cardiovascular fitness). It has been suggested that those cognitive and physical resources strongly depend on lifestyle factors such as long-term regular physical activity and cognitive engagement. Although research suggests that there is covariation between components of executive functions and physical fitness, the interdependence between these components for cognitive-motor multitasking performance is not yet clear. The aim of the study was to examine the contribution and interrelationship between executive functions, motor coordinative fitness, and cardiovascular fitness on street crossing while multitasking. We used the more ecologically valid scenario to obtain results that might be directly transferable to daily life situation. Data from 50 healthy older adults (65-75 years, 17 females, recruited in two different cities in Germany) were analyzed. Participants' executive functions (composite score including six tests), motor coordinative fitness (composite score including five tests), and cardiovascular fitness (spiroergometry), as well as their street crossing performance while multitasking were assessed. Street crossing was tested under single-task (crossing a two-line road), and multitask conditions (crossing a two-line road while typing numbers on a keypad as simulation of mobile phone use). Street crossing performance was assessed by use of cognitive outcomes (typing, crossing failures) and motor outcomes (stay time, crossing speed). Linear mixed-effects models showed beneficial main effects of executive functions for typing (p = 0.004) and crossing failures (p = 0.023), and a beneficial main effect of motor coordinative fitness for stay time (p = 0.043). Commonality analysis revealed that the proportion of variance commonly explained by executive functions, motor coordinative fitness, and cardiovascular fitness was small for all street crossing outcomes. For typing and crossing failures (cognitive outcomes), the results further showed a higher relative contribution of executive functions compared to motor coordinative fitness and cardiovascular fitness. For stay time (motor outcome), the results correspondingly revealed a higher relative contribution of motor coordinative fitness compared to executive functions and cardiovascular fitness. The findings suggest that during cognitive-motor multitasking in everyday life, task performance is determined by the components of executive functions and physical fitness related to the specific task demands. Since multitasking in everyday life includes cognitive and motor tasks, it seems to be important to maintain both executive functions and physical fitness for independent living up to old age.},
}
@article {pmid36629615,
year = {2023},
author = {Brito, MIBDS and Oliveira, ECA and Barbosa, CS and Gomes, ECS},
title = {Factors associated with severe forms and deaths from schistosomiasis and application of probabilistic linkage in databases, state of Pernambuco, Brazil, 2007-2017.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {26},
number = {},
pages = {e230003},
doi = {10.1590/1980-549720230003.2},
pmid = {36629615},
issn = {1980-5497},
mesh = {Humans ; Brazil/epidemiology ; *Schistosomiasis/epidemiology ; Databases, Factual ; },
abstract = {OBJECTIVE: To verify the agreement of data on severe forms and deaths from schistosomiasis recorded in the Brazilian Notifiable Diseases Information System and the Mortality Information System, sociodemographic variables with the occurrence of severe forms and deaths, and the temporal trend of the disease in the state of Pernambuco, Brazil.
METHODS: This is an ecological, descriptive, time series study with data on severe forms and deaths from schistosomiasis in Pernambuco, from 2007 to 2017. For the linkage between databases, a function was developed in python programming language, using the Soundex method. To identify sociodemographic and health factors that correlated with the dependent variables, Pearson's correlation test was applied. For trend analysis, linear regression was applied.
RESULTS: We identified 9,085 severe cases, 1,956 deaths, and 186 cases in the linkage. The correlation between the average positivity rate with the general water supply and waste collection was 0.22 and 0.26 respectively. We verified a correlation of the average cumulative mortality rate with water supply by well or spring (r=0.27), water supply by the general network (r=0.3), waste collection (r=0.42), and road urbanization (r=0.29). We found 3,153 severe forms in 2007 with a decrease trend and 205 deaths in 2010, without a trend pattern.
CONCLUSION: There is a need for greater investments in disease control and in the quality of information, especially in the record of severe forms, considering that, due to the pathophysiology of the disease, death only occurs when the individual develops the chronic form, and its notification on the Notifiable Diseases Information System is imperative.},
}
@article {pmid36629614,
year = {2023},
author = {Batista, JFC and Oliveira, MR and Pereira, DLM and Matos, MLSDS and Souza, IT and Menezes, MO},
title = {Spatial distribution and temporal trends of AIDS in Brazil and regions between 2005 and 2020.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {26},
number = {},
pages = {e230002},
doi = {10.1590/1980-549720230002},
pmid = {36629614},
issn = {1980-5497},
mesh = {Humans ; Adolescent ; Young Adult ; Adult ; Brazil/epidemiology ; *Acquired Immunodeficiency Syndrome/epidemiology ; Bayes Theorem ; Information Systems ; Incidence ; },
abstract = {OBJECTIVE: To analyze the spatial distribution and the temporal trend of the AIDS incidence rate in Brazil from 2005 to 2020.
METHODS: This is an ecological, temporal, and spatial study on AIDS cases in Brazil. Data from the Notifiable Diseases Information System were stratified by year of diagnosis, region of the country/municipalities of residence, and age group (over 13 years). Incidence rates were calculated for temporal estimation using the Joinpoint model, as well as Spatial Empirical Bayes (SEB) for spatial distribution, using the Kernel density estimator.
RESULTS: The incidence rate in Brazil, in 2020, was 17.69 cases per 100 thousand inhabitants. The general trend (2005-2020) was decrease in Brazil (Annual Percent Change - APC=-2.0%), in the Southeast (APC=-4.4%) and South (APC=-3.0%) regions. The North (APC=2.3%) showed an increase trend, whereas the Southeast and Midwest regions were stationary (p>0.05). Brazil, Southeast, South, and Midwest regions showed a decrease trend in most age groups. The Northeast and North regions showed an increase in the age groups of 13-29 years and 13-24 years, respectively. The Kernel estimator showed clusters with SEB above 30/10 thousand inhabitants in the states of Paraíba, Sergipe, Alagoas, Pernambuco, São Paulo, Minas Gerais, Pará, Rio Grande do Sul, and Santa Catarina.
CONCLUSION: Brazil, the Southeast, and South regions showed a decrease in the incidence rate, whereas the North region increased and the Northeast and Midwest regions were stationary. The Southeast, South, and Northeast regions presented the largest clusters of SEB.},
}
@article {pmid35615290,
year = {2022},
author = {Adhikari, JN and Bhattarai, BP and Rokaya, MB and Thapa, TB},
title = {Land use/land cover changes in the central part of the Chitwan Annapurna Landscape, Nepal.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13435},
pmid = {35615290},
issn = {2167-8359},
mesh = {*Conservation of Natural Resources ; Nepal ; *Environmental Monitoring/methods ; Geographic Information Systems ; Remote Sensing Technology ; },
abstract = {BACKGROUND: Land use/land cover assessment and monitoring of the land cover dynamics are essential to know the ecological, physical and anthropogenic processes in the landscape. Previous studies have indicated changes in the landscape of mid-hills of Nepal in the past few decades. But there is a lack of study in the Chitwan Annapurna Landscape; hence, this study was carried out to fill in study gap that existed in the area.
METHODS: This study evaluates land use/land cover dynamics between 2000 to 2020 in the central part of the Chitwan Annapurna Landscape, Nepal by using Landsat images. The Landsat images were classified into eight different classes using remote sensing and geographic information system (GIS). The accuracy assessment of classified images was evaluated by calculating actual accuracy, producer's accuracy, user's accuracy and kappa coefficient based on the ground-truthing points for 2020 and Google Earth and topographic maps for images of 2010 and 2000.
RESULTS: The results of land use/land cover analysis of Landsat image 2020 showed that the study area was composed of grassland (1.73%), barren area (1.76%), riverine forest (1.93%), water body (1.97%), developed area (4.13%), Sal dominated forest (15.4%), cropland (28.13%) and mixed forest (44.95%). The results of land cover change between 2000 to 2020 indicated an overall increase in Sal dominated forest (7.6%), developed area (31.34%), mixed forest (37.46%) and decrease in riverine forest (11.29%), barren area (20.03%), croplands (29.87%) and grasslands (49.71%). The classification of the images of 2000, 2010 and 2020 had 81%, 81.6% and 84.77% overall accuracy, respectively. This finding can be used as a baseline information for the development of a proper management plan to protect wildlife habitats and forecasting possible future changes, if needed.},
}
@article {pmid35833012,
year = {2022},
author = {Ramirez-Delgado, D and Cicala, F and Gonzalez-Sanchez, RA and Avalos-Tellez, R and Solana-Arellano, E and Licea-Navarro, A},
title = {Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13235},
pmid = {35833012},
issn = {2167-8359},
mesh = {Animals ; *Sea Lions/genetics ; RNA, Ribosomal, 16S/genetics ; Mexico ; Bacteria/genetics ; Computational Biology ; },
abstract = {BACKGROUND: The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities.
METHODS: We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses.
RESULTS: As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6-V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6-V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.},
}
@article {pmid35791366,
year = {2022},
author = {Zheng, C and Yang, X and Liu, Z and Liu, K and Huang, Y},
title = {Spatial distribution of soil nutrients and evaluation of cultivated land in Xuwen county.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13239},
pmid = {35791366},
issn = {2167-8359},
mesh = {*Soil/chemistry ; *Agriculture ; Geographic Information Systems ; Nutrients ; Phosphorus ; Nitrogen/analysis ; },
abstract = {It is of great significance to promote the quantitative research of soil science and the implementation of precision agriculture. On this basis, taking Xuwen County as the research object, this paper comprehensively analyzed the soil characteristics of cultivated land in Xuwen County and clarify the soil nutrient content and spatial distribution characteristics of cultivated land in Xuwen County, this paper comprehensively applied the methods of geostatistics, geographic information system (GIS) and fuzzy mathematics, and referred to the cultivated land quality grade standard (GB/T 33469-2016), to analyze the soil characteristics and evaluate the soil fertility of this region. The results show that the optimal interpolation model of soil pH and available phosphorus (AP) is a Gaussian model, and the optimal interpolation model of soil organic matter (SOM), available nitrogen (AN) and available potassium (AK) is a J-Bessel model. In addition, the spatial correlation of AK is weak, whereas pH, SOM, AN and AP show moderate spatial correlation. The proportion of excellent, good, average, medium and poor comprehensive fertility index are 26.00%, 32.67%, 19.33%, 19.00% and 3.00%, respectively. The overall level of soil fertility in Xuwen County is above the average, and the fertility quality presents an obvious trend of high in the South and low in the North. Areas that above average fertility are mainly distributed in Maichen Town, Qujie Town, Nanshan Town and Chengbei Town. The results can provide theoretical basis for improving the utilization rate of chemical fertilizer, fine management of cultivated land and ecological environment in this region, which can help in decision-making of precision fertilization.},
}
@article {pmid36416261,
year = {2023},
author = {Guo, S and Xu, Z and Dong, X and Hu, D and Jiang, Y and Wang, Q and Zhang, J and Zhou, Q and Liu, S and Song, W},
title = {GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D964-D968},
pmid = {36416261},
issn = {1362-4962},
mesh = {Humans ; RNA-Seq/methods ; Cell Line ; *Databases, Genetic ; *Software ; },
abstract = {Gene knock-out/down methods are commonly used to explore the functions of genes of interest, but a database that systematically collects perturbed data is not available currently. Manual curation of all the available human cell line perturbed RNA-seq datasets enabled us to develop a comprehensive human perturbation database (GPSAdb, https://www.gpsadb.com/). The current version of GPSAdb collected 3048 RNA-seq datasets associated with 1458 genes, which were knocked out/down by siRNA, shRNA, CRISPR/Cas9, or CRISPRi. The database provides full exploration of these datasets and generated 6096 new perturbed gene sets (up and down separately). GPSAdb integrated the gene sets and developed an online tool, genetic perturbation similarity analysis (GPSA), to identify candidate causal perturbations from differential gene expression data. In summary, GPSAdb is a powerful platform that aims to assist life science researchers to easily access and analyze public perturbed data and explore differential gene expression data in depth.},
}
@article {pmid36399502,
year = {2023},
author = {Camargo, AP and Nayfach, S and Chen, IA and Palaniappan, K and Ratner, A and Chu, K and Ritter, SJ and Reddy, TBK and Mukherjee, S and Schulz, F and Call, L and Neches, RY and Woyke, T and Ivanova, NN and Eloe-Fadrosh, EA and Kyrpides, NC and Roux, S},
title = {IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D733-D743},
pmid = {36399502},
issn = {1362-4962},
mesh = {*Metadata ; Software ; Databases, Genetic ; Genome, Viral ; Metagenomics ; *Virtual Reality ; },
abstract = {Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.},
}
@article {pmid36305818,
year = {2023},
author = {Chen, Y and Zhang, X and Peng, X and Jin, Y and Ding, P and Xiao, J and Li, C and Wang, F and Chang, A and Yue, Q and Pu, M and Chen, P and Shen, J and Li, M and Jia, T and Wang, H and Huang, L and Guo, G and Zhang, W and Liu, H and Wang, X and Chen, D},
title = {SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases.},
journal = {Nucleic acids research},
volume = {51},
number = {D1},
pages = {D1150-D1159},
pmid = {36305818},
issn = {1362-4962},
mesh = {Databases, Factual ; *Single-Cell Analysis ; },
abstract = {It is a challenge to efficiently integrate and present the tremendous amounts of single-cell data generated from multiple tissues of various species. Here, we create a new database named SPEED for single-cell pan-species atlas in the light of ecology and evolution for development and diseases (freely accessible at http://8.142.154.29 or http://speedatlas.net). SPEED is an online platform with 4 data modules, 7 function modules and 2 display modules. The 'Pan' module is applied for the interactive analysis of single cell sequencing datasets from 127 species, and the 'Evo', 'Devo', and 'Diz' modules provide comprehensive analysis of single-cell atlases on 18 evolution datasets, 28 development datasets, and 85 disease datasets. The 'C2C', 'G2G' and 'S2S' modules explore intercellular communications, genetic regulatory networks, and cross-species molecular evolution. The 'sSearch', 'sMarker', 'sUp', and 'sDown' modules allow users to retrieve specific data information, obtain common marker genes for cell types, freely upload, and download single-cell datasets, respectively. Two display modules ('HOME' and 'HELP') offer easier access to the SPEED database with informative statistics and detailed guidelines. All in all, SPEED is an integrated platform for single-cell RNA sequencing (scRNA-seq) and single-cell whole-genome sequencing (scWGS) datasets to assist the deep-mining and understanding of heterogeneity among cells, tissues, and species at multi-levels, angles, and orientations, as well as provide new insights into molecular mechanisms of biological development and pathogenesis.},
}
@article {pmid36617091,
year = {2023},
author = {Abdallah, M and Joung, BG and Lee, WJ and Mousoulis, C and Raghunathan, N and Shakouri, A and Sutherland, JW and Bagchi, S},
title = {Anomaly Detection and Inter-Sensor Transfer Learning on Smart Manufacturing Datasets.},
journal = {Sensors (Basel, Switzerland)},
volume = {23},
number = {1},
pages = {},
pmid = {36617091},
issn = {1424-8220},
mesh = {*Commerce ; Databases, Factual ; Time Factors ; *Machine Learning ; },
abstract = {Smart manufacturing systems are considered the next generation of manufacturing applications. One important goal of the smart manufacturing system is to rapidly detect and anticipate failures to reduce maintenance cost and minimize machine downtime. This often boils down to detecting anomalies within the sensor data acquired from the system which has different characteristics with respect to the operating point of the environment or machines, such as, the RPM of the motor. In this paper, we analyze four datasets from sensors deployed in manufacturing testbeds. We detect the level of defect for each sensor data leveraging deep learning techniques. We also evaluate the performance of several traditional and ML-based forecasting models for predicting the time series of sensor data. We show that careful selection of training data by aggregating multiple predictive RPM values is beneficial. Then, considering the sparse data from one kind of sensor, we perform transfer learning from a high data rate sensor to perform defect type classification. We release our manufacturing database corpus (4 datasets) and codes for anomaly detection and defect type classification for the community to build on it. Taken together, we show that predictive failure classification can be achieved, paving the way for predictive maintenance.},
}
@article {pmid36612401,
year = {2022},
author = {Liu, F and Sun, D and Zhang, Y and Hong, S and Wang, M and Dong, J and Yan, C and Yang, Q},
title = {Tourist Landscape Preferences in a Historic Block Based on Spatiotemporal Big Data-A Case Study of Fuzhou, China.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {1},
pages = {},
pmid = {36612401},
issn = {1660-4601},
mesh = {*Big Data ; Surveys and Questionnaires ; China ; *Sustainable Development ; Hot Temperature ; },
abstract = {Historic blocks are valuable architectural and landscape heritage, and it is important to explore the distribution characteristics of tourists to historic blocks and their landscape preferences to realize the scientific construction and conservation of historic blocks and promote their sustainable development. At present, few studies combine the analysis of tourist distribution characteristics with landscape preferences. This study takes the historic block of Three Lanes and Seven Alleys in Fuzhou as an example, combines field research and questionnaires to construct a landscape preference evaluation indicator system for the historic block, measures the distribution characteristics of tourists in the block through the heat value of tourist flow obtained from the Tencent regional heat map, and analyses the influence of landscape preference indicators on the heat value of tourist flow in the block through stepwise multiple linear regression. The research shows that: (1) the spatial and temporal variation in the heat value of tourist flow tends to be consistent throughout the block, from 7 a.m. to 6 p.m., showing a "rising, slightly fluctuating and then stabilizing" state, both on weekdays and on weekends. (2) The factors influencing the heat value of tourist flow in the different spatial samples are various, with commercial atmosphere, plant landscape, accessibility of the road space, architecture, and the surrounding environment having a significant impact on the heat value of tourist flow. Based on the analysis of the landscape preferences of tourists in the historic block, a landscape optimization strategy is proposed to provide a reference for the management and construction of the block.},
}
@article {pmid36384190,
year = {2023},
author = {Liu, H and Wu, M and Gao, H and Gao, J and Wang, S},
title = {Application of [15]N tracing and bioinformatics for estimating microbial-mediated nitrogen cycle processes in oil-contaminated soils.},
journal = {Environmental research},
volume = {217},
number = {},
pages = {114799},
doi = {10.1016/j.envres.2022.114799},
pmid = {36384190},
issn = {1096-0953},
mesh = {Nitrogen Cycle ; Nitrogen/analysis ; Soil/chemistry ; *Microbiota ; Soil Microbiology ; Computational Biology ; *Soil Pollutants/analysis ; },
abstract = {Crude oil pollution can profoundly alter the nitrogen (N) cycle in the soil. Here, a 30-day incubation with [15]N tracer approach was performed to assess the impacts of crude oil concentrations (medium: 10,000 mg kg[-1]; heavy: 50,000 mg kg[-1]) on soil N cycling based on a numerical model. Results showed that crude oil pollution significantly increased the gross N-transformation rates, but the rates of oxidation of recalcitrant organic N, the immbolization of NO3[-] and the adsorption of NH4[+] changed differently as a function of hydrocarbon concentrations. There was no significant difference of the oxidation rate of recalcitrant organic N between the medium and heavy oil-contaminated soils (medium: 0.1149 mmol N kg[-1] d[-1]; heavy: 0.1299 mmol N kg[-1] d[-1]), but the rates of NO3[-] immobilization (0.1135 mmol N kg[-1] d[-1]) and NH4[+] adsorption were the highest (0.1148 mmol N kg[-1] d[-1]) in the moderately oil-contaminated soils than those in the heavy polluted soil (0.0849 mmol N kg[-1] d[-1] and 0.0034 mmol N kg[-1] d[-1], respectively). The NO3[-] immobilization rate was 2.5-fold higher than its reduction rate, indicating that NO3[-] immobilization played a more important role during the process of NO3[-] transformation. Microbial community structure analysis indicated that phyla of Actinobacteria and Ascomycota respectively promoted the immobilization of NO3[-] to recalcitrant organic N and the reduction of NO3[-] to NH4[+]. The genus of Aspergillus was related to net NH4[+] production, and the genera of Penicillium and Acremonium were responsible for oxidation of recalcitrant organic N to NO3[-].},
}
@article {pmid35186498,
year = {2022},
author = {Reijnders, MJMF},
title = {Wei2GO: weighted sequence similarity-based protein function prediction.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e12931},
pmid = {35186498},
issn = {2167-8359},
mesh = {*Software ; *Algorithms ; Molecular Sequence Annotation ; Proteins/genetics ; Databases, Protein ; },
abstract = {BACKGROUND: Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the form of web-servers instead of open-source locally installable versions. Such local versions are necessary to perform large scale genomics studies due to the presence of limitations imposed by web servers such as queues, prediction speed, and updatability of databases.
METHODS: This paper describes Wei2GO: a weighted sequence similarity and python-based open-source protein function prediction software. It uses DIAMOND and HMMScan sequence alignment searches against the UniProtKB and Pfam databases respectively, transfers Gene Ontology terms from the reference protein to the query protein, and uses a weighing algorithm to calculate a score for the Gene Ontology annotations.
RESULTS: Wei2GO is compared against the Argot2 and Argot2.5 web servers, which use a similar concept, and DeepGOPlus which acts as a reference. Wei2GO shows an increase in performance according to precision and recall curves, Fmax scores, and Smin scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes.
AVAILABILITY: Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO.},
}
@article {pmid36620398,
year = {2023},
author = {Gries, C and Hanson, PC and O'Brien, M and Servilla, M and Vanderbilt, K and Waide, R},
title = {The Environmental Data Initiative: Connecting the past to the future through data reuse.},
journal = {Ecology and evolution},
volume = {13},
number = {1},
pages = {e9592},
pmid = {36620398},
issn = {2045-7758},
abstract = {The Environmental Data Initiative (EDI) is a trustworthy, stable data repository, and data management support organization for the environmental scientist. In a bottom-up community process, EDI was built with the premise that freely and easily available data are necessary to advance the understanding of complex environmental processes and change, to improve transparency of research results, and to democratize ecological research. EDI provides tools and support that allow the environmental researcher to easily integrate data publishing into the research workflow. Almost ten years since going into production, we analyze metadata to provide a general description of EDI's collection of data and its data management philosophy and placement in the repository landscape. We discuss how comprehensive metadata and the repository infrastructure lead to highly findable, accessible, interoperable, and reusable (FAIR) data by evaluating compliance with specific community proposed FAIR criteria. Finally, we review measures and patterns of data (re)use, assuring that EDI is fulfilling its stated premise.},
}
@article {pmid36618211,
year = {2022},
author = {Krishnan, RA and Ravindran, RM and Vincy, VS and Arun, P and Shinu, KS and Jithesh, V and Varma, RP},
title = {Analysis of daily COVID-19 death bulletin data during the first two waves of the COVID-19 pandemic in Thiruvananthapuram district, Kerala, India.},
journal = {Journal of family medicine and primary care},
volume = {11},
number = {10},
pages = {6190-6196},
pmid = {36618211},
issn = {2249-4863},
abstract = {CONTEXT: Coronavirus disease 2019 (COVID-19) mortality trends can help discern the pattern of outbreak evolution and systemic responses.
AIM: This study aimed to explore patterns of COVID-19 deaths in Thiruvananthapuram district from 31 March 2020 to 31 December 2021.
SETTING AND DESIGN: Secondary data analysis of COVID-19 deaths in Thiruvananthapuram district was performed.
MATERIALS AND METHODS: Mortality data were obtained from the district COVID-19 control room, and deaths in the first and second waves of COVID-19 were compared.
STATISTICAL ANALYSIS: We summarised data as proportions and medians with the inter-quartile range (IQR) and performed Chi-square tests to make comparisons wherever applicable.
RESULTS: As on 31 December 2021, 4587 COVID-19 deaths were reported in Thiruvananthapuram district, with a case fatality rate of 0.91%. We observed high mortality among older persons (66.7%) and men (56.6%). The leading cause of death was bronchopneumonia (60.6%). The majority (88.5%) had co-morbidities, commonly diabetes mellitus (54.9%). The median interval from diagnosis to hospitalisation was 4 days (IQR 2-7), and that from hospitalisation to death was 2 days (IQR 0-6). The deaths reported during the second wave were four times higher than those of the first wave with a higher proportion of deaths in the absence of co-morbidities (p < 0.001). The majority of the deceased were unvaccinated. Ecological analysis with vaccine coverage data indicated 5.4 times higher mortality among unvaccinated than those who received two vaccine doses.
CONCLUSIONS: The presence of co-morbidities, an unvaccinated status, and delay in hospitalisation were important reasons for COVID-19 deaths. Primary level health providers can potentially help sustaining vaccination, expeditious referral, and monitoring of COVID-19 patients.},
}
@article {pmid36613120,
year = {2023},
author = {Qin, J and Ma, M and Shi, J and Ma, S and Wu, B and Su, X},
title = {The Time-Lag Effect of Climate Factors on the Forest Enhanced Vegetation Index for Subtropical Humid Areas in China.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {1},
pages = {},
doi = {10.3390/ijerph20010799},
pmid = {36613120},
issn = {1660-4601},
abstract = {Forests represent the greatest carbon reservoir in terrestrial ecosystems. Climate change drives the changes in forest vegetation growth, which in turn influences carbon sequestration capability. Exploring the dynamic response of forest vegetation to climate change is thus one of the most important scientific questions to be addressed in the precise monitoring of forest resources. This paper explores the relationship between climate factors and vegetation growth in typical forest ecosystems in China from 2007 to 2019 based on long-term meteorological monitoring data from six forest field stations in different subtropical ecological zones in China. The time-varying parameter vector autoregressive model (TVP-VAR) was used to analyze the temporal and spatial differences of the time-lag effects of climate factors, and the impact of climate change on vegetation was predicted. The enhanced vegetation index (EVI) was used to measure vegetation growth. Monthly meteorological observations and solar radiation data, including precipitation, air temperature, relative humidity, and photosynthetic effective radiation, were provided by the resource sharing service platform of the national ecological research data center. It was revealed that the time-lag effect of climate factors on the EVI vanished after a half year, and the lag accumulation tended to be steady over time. The TVP-VAR model was found to be more suitable than the vector autoregressive model (VAR). The predicted EVI values using the TVP-VAR model were close to the true values with the root mean squares error (RMSE) < 0.05. On average, each site improved its prediction accuracy by 14.81%. Therefore, the TVP-VAR model can be used to analyze the relationship of climate factors and forest EVI as well as the time-lag effect of climate factors on vegetation growth in subtropical China. The results can be used to improve the predictability of the EVI for forests and to encourage the development of intensive forest management.},
}
@article {pmid36612902,
year = {2022},
author = {Vlăduțu, DE and Ionescu, M and Mercuț, R and Noveri, L and Lăzărescu, G and Popescu, SM and Scrieciu, M and Manolea, HO and Iacov Crăițoiu, MM and Ionescu, AG and Mercuț, V},
title = {Ecological Momentary Assessment of Masseter Muscle Activity in Patients with Bruxism.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {1},
pages = {},
doi = {10.3390/ijerph20010581},
pmid = {36612902},
issn = {1660-4601},
abstract = {According to the International Bruxism Consensus, bruxism refers to the activity of the masticatory muscles reflecting contraction disorders, regardless of whether it is during sleep (SB) or an awake (AB) state. The objective of the present study was to evaluate the activity of the masseter muscle by surface electromyographic (sEMG) recordings. This study was performed on 20 participants with self-reported "possible bruxism" (study group) and 20 participants with no self-reported bruxism (control group); all participants underwent an evaluation of the masseter muscle activity using the dia-BRUXO device, which provides numerical parameters regarding sEMG (the total duration and the type of bruxism specific events, the effort made by the masticatory muscles during the recording period, and the personal bruxism index of each participant). Participants from the study group presented more clenching events during AB, three times more frequent than the control group (p = 0.002, Mann-Whitney U test); for SB, the frequency of clenching and grinding events was comparable within the study group, being more frequent than for the control group; the mean value of the effort index was higher for AB (1.177%) than SB (0.470%) and the same for the duration index, with a mean value of 2.788% for AB and 1.054% for SB. All participants from the control group presented reduced values for all acquired parameters. Overall, the personal bruxism index in AB was approximately four times higher for the study group (2.251%) compared to the control group (0.585%) (p < 0.005, Mann-Whitney U test). Similar values were obtained for SB. All participants with "possible bruxism" from the study group presented a higher activity of the masseter muscle, which is specific for bruxism, thus being defined as "definite bruxism".},
}
@article {pmid36612815,
year = {2022},
author = {Yang, X and Lei, S and Shi, Y and Wang, W},
title = {Effects of Ground Subsidence on Vegetation Chlorophyll Content in Semi-Arid Mining Area: From Leaf Scale to Canopy Scale.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {1},
pages = {},
doi = {10.3390/ijerph20010493},
pmid = {36612815},
issn = {1660-4601},
abstract = {Ground subsidence is the main cause of vegetation degradation in mining areas. It is of great significance to study the effects of ground subsidence on vegetation. At present, few studies have analyzed the effects of ground subsidence on vegetation from different scales. However, the conclusions on different scales may differ. In this experiment, chlorophyll content was used as an indicator of vegetation degradation. We conducted a long-term field survey in the Lijiahao coalfield in China. Based on field survey data and remote sensing images, we analyzed the effects of ground subsidence on chlorophyll content from two scales (leaf scale and canopy scale) and summarized the similarities and differences. We found that, regardless of leaf scale or canopy scale, the effects of subsidence on chlorophyll content have the following three characteristics: (1) mining had the least effect on chlorophyll content in the neutral area, followed by the compression area, and the greatest effect on chlorophyll content in the extension area; (2) subsidence had a slight effect on chlorophyll content of Caragana korshins, but a serious effect on chlorophyll content of Stipa baicalensis; (3) chlorophyll content was not immediately affected when the ground sank. It was the cumulative subsidence that affects chlorophyll content. The difference between leaf scale and canopy scale was that the chlorophyll content at canopy scale is more affected by mining. This means that when assessing vegetation degradation, the results obtained by remote sensing were more severe than those measured in the field. We believe that this is because the canopy chlorophyll content obtained by remote sensing is also affected by the plant canopy structure. We recommend that mining and ecological restoration should be carried out concurrently, and that ground fissures should be taken as the focus of ecological restoration. In addition, Caragana korshins ought to be widely planted. Most importantly, managers should assess the effects of ground subsidence on vegetation on different scales. However, managers need to be aware of differences at different scales.},
}
@article {pmid36612520,
year = {2022},
author = {Zhou, Z and Zhang, Z and Zhang, W and Luo, J and Zhang, K and Cao, Z and Wang, Z},
title = {The Impact of Residences and Roads on Wind Erosion in a Temperate Grassland Ecosystem: A Spatially Oriented Perspective.},
journal = {International journal of environmental research and public health},
volume = {20},
number = {1},
pages = {},
doi = {10.3390/ijerph20010198},
pmid = {36612520},
issn = {1660-4601},
abstract = {The existence of residences and roads is an important way in which human activity affects wind erosion in arid and semiarid environments. Studies assessing the impact of these elements on wind erosion have only focused on limited plots, and their threat of erosion to the surrounding environment has been ignored by many studies. This study was based on spatially overlayed analysis of independent wind erosion distribution simulated by the revised wind erosion equation (RWEQ) and remote-sensing-image-derived residence and road distribution data. Wind erosion at different distances from residences and roads was quantified at the landscape scale of a typical temperate grassland ecosystem, explicitly demonstrating the crucial impacts of both elements on wind erosion. The results showed that wind erosion weakened as the distance from residences and roads increased due to the priority pathways of human activities, and the wind erosion around the residence was more severe than around the road. Human activities in the buffer zones 0-200 m from the residences most frequently caused severe wind erosion, with a wind soil loss of 25 t ha[-1] yr[-1] and a wind soil loss of approximately 5.25 t ha[-1] yr[-1] for 0-60 m from the roads. The characteristics of wind erosion variation in the buffer zones were also affected by residence size and the environments in which the residences were located. The variation in wind erosion was closely related to the road levels. Human activities intensified wind erosion mainly by affecting the soil and vegetation around residences and roads. Ecological management should not be limited to residences and roads but should also protect the surrounding environments. The findings of this study are aimed towards a spatial perspective that can help implement rational and effective environmental management measures for the sustainability of wind-eroded ecosystems.},
}
@article {pmid36607160,
year = {2023},
author = {Van Sundert, K and Leuzinger, S and Bader, MK and Chang, SX and De Kauwe, MG and Dukes, JS and Langley, JA and Ma, Z and Mariën, B and Reynaert, S and Ru, J and Song, J and Stocker, B and Terrer, C and Thoresen, J and Vanuytrecht, E and Wan, S and Yue, K and Vicca, S},
title = {When things get MESI: the Manipulation Experiments Synthesis Initiative - a coordinated effort to synthesize terrestrial global change experiments.},
journal = {Global change biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/gcb.16585},
pmid = {36607160},
issn = {1365-2486},
abstract = {Responses of the terrestrial biosphere to rapidly changing environmental conditions are a major source of uncertainty in climate projections. In an effort to reduce this uncertainty, a wide range of global change experiments have been conducted that mimic future conditions in terrestrial ecosystems, manipulating CO2 , temperature, nutrient and water availability. Syntheses of results across experiments provide a more general sense of ecosystem responses to global change, and help to discern the influence of background conditions such as climate and vegetation type in determining global change responses. Several independent syntheses of published data have yielded distinct databases for specific objectives. Such parallel, uncoordinated initiatives carry the risk of producing redundant data collection efforts and have led to contrasting outcomes without clarifying the underlying reason for divergence. These problems could be avoided by creating a publicly available, updatable, curated database. Here, we report on a global effort to collect and curate 57,089 treatment responses across 3,644 manipulation experiments at 1,145 sites, simulating elevated CO2 , warming, nutrient addition and precipitation changes. In the resulting Manipulation Experiments Synthesis Initiative (MESI) database, effects of experimental global change drivers on carbon and nutrient cycles are included, as well as ancillary data such as background climate, vegetation type, treatment magnitude, duration, and, unique to our database, measured soil properties. Our analysis of the database indicates that most experiments are short-term (one or few growing seasons), conducted in the USA, Europe or China, and that the most abundantly reported variable is aboveground biomass. We provide the most comprehensive multifactor global change database to date, enabling the research community to tackle open research questions, vital to global policymaking. The MESI database, freely accessible at doi.org/10.5281/zenodo.7153253, opens new avenues for model evaluation and synthesis-based understanding of how global change affects terrestrial biomes. We welcome contributions to the database on GitHub.},
}
@article {pmid35900623,
year = {2023},
author = {Sharma, N and Kaushal, A and Yousuf, A and Sood, A and Kaur, S and Sharda, R},
title = {Geospatial technology for assessment of soil erosion and prioritization of watersheds using RUSLE model for lower Sutlej sub-basin of Punjab, India.},
journal = {Environmental science and pollution research international},
volume = {30},
number = {1},
pages = {515-531},
pmid = {35900623},
issn = {1614-7499},
mesh = {Humans ; *Soil ; *Soil Erosion ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; Geographic Information Systems ; India ; Technology ; },
abstract = {Erosion of soil by water coupled with human activities is considered as one of the most serious agents of land degradation, posing severe threat to agricultural productivity, soil health, water quality, and ecological setup. The assessment of soil erosion and recognition of problematic watersheds are pre-requisite for management of erosion hazards. In the present study, Revised Universal Soil Loss Equation (RUSLE) integrated with remote sensing (RS) and geographic information system (GIS) has been used to assess the soil erosion in lower Sutlej River basin of Punjab, India, and prioritize the watersheds for implementation of land and water conservation measures. The total basin area was about 8577 km[2] which was divided into 14 sub-watersheds with the area ranging from 357.8 to 1354 km[2]. The data on rainfall (IMD gridded data), soil characteristics (FAO soil map), topography (ALOS PALSAR DEM) and land use (ESRI land use and land cover map) were prepared in the form of raster layers and overlaid together to determine the average annual soil loss. The results revealed that the average annual soil loss varied from 1.26 to 25 t ha[-1], whereas total soil loss was estimated to be 2,441,639 tonnes. The spatial distribution map of soil erosion showed that about 94.4% and 4.7% of the total area suffered from very slight erosion (0-5 t ha[-1] year[-1]) and slight erosion (5-10 t ha[-1] year[-1]), respectively, whereas 0.11% (9.38 km[2]) experienced very severe soil loss (> 25 t ha[-1] year[-1]). Based on estimated average annual soil loss of sub-watersheds, WS8 was assigned the highest priority for implementation of soil and water conservation measures (323.5 t ha[-1] year[-1]), followed by WS9 (303.8 t ha[-1] year[-1]), whereas WS2 was given last priority owing to its lowest value of soil loss (122.02 t ha[-1] year[-1]). The present study urges that conservation strategies should be carried out in accordance with the priority ranking of diverse watersheds. These findings can certainly be used to implement soil conservation plans and management practices in order to diminish soil loss in the river basin.},
}
@article {pmid36604610,
year = {2023},
author = {Prager, M and Lundin, D and Ronquist, F and Andersson, AF},
title = {ASV portal: an interface to DNA-based biodiversity data in the Living Atlas.},
journal = {BMC bioinformatics},
volume = {24},
number = {1},
pages = {6},
pmid = {36604610},
issn = {1471-2105},
abstract = {BACKGROUND: The Living Atlas is an open source platform used to collect, visualise and analyse biodiversity data from multiple sources, and serves as the national biodiversity data hub in many countries. Although powerful, the Living Atlas has had limited functionality for species occurrence data derived from DNA sequences. As a step toward integrating this fast-growing data source into the platform, we developed the Amplicon Sequence Variant (ASV) portal: a web interface to sequence-based biodiversity observations in the Living Atlas.
RESULTS: The ASV portal allows data providers to submit denoised metabarcoding output to the Living Atlas platform via an intermediary ASV database. It also enables users to search for existing ASVs and associated Living Atlas records using the Basic Local Alignment Search Tool, or via filters on taxonomy and sequencing details. The ASV portal is a Python-Flask/jQuery web interface, implemented as a multi-container docker service, and is an integral part of the Swedish Biodiversity Data Infrastructure.
CONCLUSION: The ASV portal is a web interface that effectively integrates biodiversity data derived from DNA sequences into the Living Atlas platform.},
}
@article {pmid36602254,
year = {2023},
author = {Koenig, CJ and Vasquez, TS and Peterson, EB and Wollney, EN and Bylund, CL and Ho, EY},
title = {Mapping Uncharted Terrain: A Systematic Review of Complementary and Integrative Health Communication Using Observational Data in Biomedical Settings.},
journal = {Health communication},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/10410236.2022.2140080},
pmid = {36602254},
issn = {1532-7027},
abstract = {Complementary and integrative health (CIH) use is diverse and highly prevalent worldwide. Prior research of CIH communication in biomedical encounters address safety, efficacy, symptom management, and overall wellness. Observational methods are rarely used to study CIH communication and avoid recall bias, preserve ecological validity, and contextualize situated clinical communication. Following PRISMA guidelines, we systematically reviewed studies at the intersection of social scientific observational research and findings about CIH communication between clinicians, patients, and caregivers in biomedical settings. We identified international, peer-reviewed publications from seven databases between January 2010 and December 2020. Titles and abstracts were first screened for inclusion, then full studies were coded using explicit criteria. We used a standard checklist was modified to assess article quality. Ten of 11,793 studies examined CIH communication using observational methods for CIH communication in biomedical settings. Studies used a range of observational techniques, including participant and non-participant observation, which includes digital audio or video recordings. Results generated two broad sets of findings, one focused on methodological insights and another on CIH communication. Despite methodological and topic similarities, included studies addressed CIH communication as a process and as proximal and intermediate health outcomes. We recommend how observational studies of CIH communication can better highlight relationships between communication processes and health outcomes. Current research using observational methods offers an incomplete picture of CIH communication in biomedical settings. Future studies should standardize how observational techniques are reported to enhance consistency and comparability within and across biomedical settings to improve comparability.},
}
@article {pmid36601075,
year = {2022},
author = {Leal, JSV and Fogal, AS and Meireles, AL and Cardoso, LO and Machado, ÍE and de Menezes, MC},
title = {Health economic impacts associated with the consumption of sugar-sweetened beverages in Brazil.},
journal = {Frontiers in nutrition},
volume = {9},
number = {},
pages = {1088051},
pmid = {36601075},
issn = {2296-861X},
abstract = {INTRODUCTION: The consumption of sugar-sweetened beverages (SSBs) is among the main risk factors for non-communicable diseases (NCDs). This study aimed to estimate the financial costs of hospitalizations and procedures of high and medium complexity for NCDs attributable to the consumption of SSBs in the Brazilian Unified Health System (SUS) in 2019.
METHODS: This ecological study used data from the Global Burden of Disease (GBD) 2019 and the Department of Informatics of the Unified Health System (DATASUS). The attributable costs were estimated from the population-attributable fraction (PAF) and the costs in the treatment of chronic diseases [type 2 diabetes mellitus and ischemic heart disease (IHD)], stratified by sex, age group, level of complexity of treatment, and federative units.
RESULTS: In 2019, in Brazil, US$ 14,116,240.55 were the costs of hospitalizations and procedures of high and medium complexity in the treatment of NCDs attributable to the consumption of SSBs. These values were higher in males (US$ 8,469,265.14) and the southeast and southern regions, mainly in the state of São Paulo. However, when evaluating these results at a rate per 10,000 inhabitants, it was observed that the states of Paraná, Tocantins, and Roraima had higher costs per 10,000 inhabitants. Regarding the age groups, higher costs were observed in the older age groups.
CONCLUSION: This study revealed the high financial impact of the NCDs treatment attributed to the consumption of SSBs in Brazil and the variability among Brazilian macro-regions. The results demonstrate the urgency and need for the expansion of policies to reduce the consumption of SSBs in Brazil with strategies that consider regional particularities.},
}
@article {pmid36599936,
year = {2023},
author = {Juan, D and Santpere, G and Kelley, JL and Cornejo, OE and Marques-Bonet, T},
title = {Current advances in primate genomics: novel approaches for understanding evolution and disease.},
journal = {Nature reviews. Genetics},
volume = {},
number = {},
pages = {},
pmid = {36599936},
issn = {1471-0064},
abstract = {Primate genomics holds the key to understanding fundamental aspects of human evolution and disease. However, genetic diversity and functional genomics data sets are currently available for only a few of the more than 500 extant primate species. Concerted efforts are under way to characterize primate genomes, genetic polymorphism and divergence, and functional landscapes across the primate phylogeny. The resulting data sets will enable the connection of genotypes to phenotypes and provide new insight into aspects of the genetics of primate traits, including human diseases. In this Review, we describe the existing genome assemblies as well as genetic variation and functional genomic data sets. We highlight some of the challenges with sample acquisition. Finally, we explore how technological advances in single-cell functional genomics and induced pluripotent stem cell-derived organoids will facilitate our understanding of the molecular foundations of primate biology.},
}
@article {pmid36107138,
year = {2023},
author = {Bassing, SB and DeVivo, M and Ganz, TR and Kertson, BN and Prugh, LR and Roussin, T and Satterfield, L and Windell, RM and Wirsing, AJ and Gardner, B},
title = {Are we telling the same story? Comparing inferences made from camera trap and telemetry data for wildlife monitoring.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {33},
number = {1},
pages = {e2745},
doi = {10.1002/eap.2745},
pmid = {36107138},
issn = {1051-0761},
mesh = {Animals ; *Animals, Wild ; *Ecosystem ; Geographic Information Systems ; Surveys and Questionnaires ; Telemetry ; },
abstract = {Estimating habitat and spatial associations for wildlife is common across ecological studies and it is well known that individual traits can drive population dynamics and vice versa. Thus, it is commonly assumed that individual- and population-level data should represent the same underlying processes, but few studies have directly compared contemporaneous data representing these different perspectives. We evaluated the circumstances under which data collected from Lagrangian (individual-level) and Eulerian (population-level) perspectives could yield comparable inference to understand how scalable information is from the individual to the population. We used Global Positioning System (GPS) collar (Lagrangian) and camera trap (Eulerian) data for seven species collected simultaneously in eastern Washington (2018-2020) to compare inferences made from different survey perspectives. We fit the respective data streams to resource selection functions (RSFs) and occupancy models and compared estimated habitat- and space-use patterns for each species. Although previous studies have considered whether individual- and population-level data generated comparable information, ours is the first to make this comparison for multiple species simultaneously and to specifically ask whether inferences from the two perspectives differed depending on the focal species. We found general agreement between the predicted spatial distributions for most paired analyses, although specific habitat relationships differed. We hypothesize the discrepancies arose due to differences in statistical power associated with camera and GPS-collar sampling, as well as spatial mismatches in the data. Our research suggests data collected from individual-based sampling methods can capture coarse population-wide patterns for a diversity of species, but results differ when interpreting specific wildlife-habitat relationships.},
}
@article {pmid36239541,
year = {2023},
author = {Keck, F and Altermatt, F},
title = {Management of DNA reference libraries for barcoding and metabarcoding studies with the R package refdb.},
journal = {Molecular ecology resources},
volume = {23},
number = {2},
pages = {511-518},
doi = {10.1111/1755-0998.13723},
pmid = {36239541},
issn = {1755-0998},
mesh = {*DNA Barcoding, Taxonomic ; *DNA/genetics ; Biodiversity ; Gene Library ; Databases, Nucleic Acid ; },
abstract = {DNA barcoding and metabarcoding are revolutionizing the study and survey of biodiversity. In order to assign taxonomic labels to the DNA sequence data retrieved, these methods are strongly dependent on comprehensive and accurate reference databases. Producing reliable databases linking biological sequences and taxonomic data can be-and often has been-done using mainstream tools such as spreadsheet software. However, spreadsheets quickly become insufficient when the amount of data increases to thousands of taxa and sequences to be matched, and validation operations become more complex and are error prone if done in a manual way. Thus, there is a clear need for providing scientists with user-friendly, reliable and powerful tools to manipulate and manage DNA reference databases in tractable, sound and efficient ways. Here, we introduce the R package refdb as an environment for semi-automatic and assisted construction of DNA reference libraries. The refdb package is a reference database manager offering a set of powerful functions to import, organize, clean, filter, audit and export the data. It is broadly applicable in metabarcoding data generally obtained in biodiversity and biomonitoring studies. We present the main features of the package and outline how refdb can speed up reference database generation, management and handling, and thus contribute to standardization and repeatability in barcoding and metabarcoding studies.},
}
@article {pmid36595968,
year = {2018},
author = {Martínková, N and Pikula, J and Zukal, J and Kovacova, V and Bandouchova, H and Bartonička, T and Botvinkin, AD and Brichta, J and Dundarova, H and Kokurewicz, T and Irwin, NR and Linhart, P and Orlov, OL and Piacek, V and Škrabánek, P and Tiunov, MP and Zahradníková, A},
title = {Hibernation temperature-dependent Pseudogymnoascus destructans infection intensity in Palearctic bats.},
journal = {Virulence},
volume = {9},
number = {1},
pages = {1734-1750},
doi = {10.1080/21505594.2018.1548685},
pmid = {36595968},
issn = {2150-5608},
abstract = {White-nose syndrome (WNS) is a fungal disease caused by Pseudogymnoascus destructans that is devastating to Nearctic bat populations but tolerated by Palearctic bats. Temperature is a factor known to be important for fungal growth and bat choice of hibernation. Here we investigated the effect of temperature on the pathogenic fungal growth in the wild across the Palearctic. We modelled body surface temperature of bats with respect to fungal infection intensity and disease severity and were able to relate this to the mean annual surface temperature at the site. Bats that hibernated at lower temperatures had less fungal growth and fewer skin lesions on their wings. Contrary to expectation derived from laboratory P. destructans culture experiments, natural infection intensity peaked between 5 and 6°C and decreased at warmer hibernating temperature. We made predictive maps based on bat species distributions, temperature and infection intensity and disease severity data to determine not only where P. destructans will be found but also where the infection will be invasive to bats across the Palearctic. Together these data highlight the mechanistic model of the interplay between environmental and biological factors, which determine progression in a wildlife disease.},
}
@article {pmid36590525,
year = {2022},
author = {Prylutskyy, Y and Nozdrenko, D and Gonchar, O and Prylutska, S and Bogutska, K and Franskevych, D and Hromovyk, B and Scharff, P and Ritter, U},
title = {C60 fullerene attenuates muscle force reduction in a rat during fatigue development.},
journal = {Heliyon},
volume = {8},
number = {12},
pages = {e12449},
pmid = {36590525},
issn = {2405-8440},
abstract = {C60 fullerene (C60) as a nanocarbon particle, compatible with biological structures, capable of penetrating through cell membranes and effectively scavenging free radicals, is widely used in biomedicine. A protective effect of C60 on the biomechanics of fast (m. gastrocnemius) and slow (m. soleus) muscle contraction in rats and the pro- and antioxidant balance of muscle tissue during the development of muscle fatigue was studied compared to the same effect of the known antioxidant N-acetylcysteine (NAC). C60 and NAC were administered intraperitoneally at doses of 1 and 150 mg kg[-1], respectively, daily for 5 days and 1 h before the start of the experiment. The following quantitative markers of muscle fatigue were used: the force of muscle contraction, the level of accumulation of secondary products of lipid peroxidation (TBARS) and the oxygen metabolite H2O2, the activity of first-line antioxidant defense enzymes (superoxide dismutase (SOD) and catalase (CAT)), and the condition of the glutathione system (reduced glutathione (GSH) content and the activity of the glutathione peroxidase (GPx) enzyme). The analysis of the muscle contraction force dynamics in rats against the background of induced muscle fatigue showed, that the effect of C60, 1 h after drug administration, was (15-17)% more effective on fast muscles than on slow muscles. A further slight increase in the effect of C60 was revealed after 2 h of drug injection, (7-9)% in the case of m. gastrocnemius and (5-6)% in the case of m. soleus. An increase in the effect of using C60 occurred within 4 days (the difference between 4 and 5 days did not exceed (3-5)%) and exceeded the effect of NAC by (32-34)%. The analysis of biochemical parameters in rat muscle tissues showed that long-term application of C60 contributed to their decrease by (10-30)% and (5-20)% in fast and slow muscles, respectively, on the 5th day of the experiment. At the same time, the protective effect of C60 was higher compared to NAC by (28-44)%. The obtained results indicate the prospect of using C60 as a potential protective nano agent to improve the efficiency of skeletal muscle function by modifying the reactive oxygen species-dependent mechanisms that play an important role in the processes of muscle fatigue development.},
}
@article {pmid36581858,
year = {2022},
author = {Huang, Y and Lu, W and Zeng, M and Hu, X and Su, Z and Liu, Y and Liu, Z and Yuan, J and Li, L and Zhang, X and Huang, L and Hu, W and Wang, X and Li, S and Zhang, H},
title = {Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {245},
pmid = {36581858},
issn = {2049-2618},
mesh = {Infant, Newborn ; Humans ; *Gastrointestinal Microbiome/genetics ; Multiomics ; Inflammation ; Bacteria ; *Heart Defects, Congenital ; Dysbiosis/microbiology ; },
abstract = {BACKGROUND: The early life gut microbiome is crucial in maintaining host metabolic and immune homeostasis. Though neonates with critical congenital heart disease (CCHD) are at substantial risks of malnutrition and immune imbalance, the microbial links to CCHD pathophysiology remain poorly understood. In this study, we aimed to investigate the gut microbiome in neonates with CCHD in association with metabolomic traits. Moreover, we explored the clinical implications of the host-microbe interactions in CCHD.
METHODS: Deep metagenomic sequencing and metabolomic profiling of paired fecal samples from 45 neonates with CCHD and 50 healthy controls were performed. The characteristics of gut microbiome were investigated in three dimensions (microbial abundance, functionality, and genetic variation). An in-depth analysis of gut virome was conducted to elucidate the ecological interaction between gut viral and bacterial communities. Correlations between multilevel microbial features and fecal metabolites were determined using integrated association analysis. Finally, we conducted a subgroup analysis to examine whether the interactions between gut microbiota and metabolites could mediate inflammatory responses and poor surgical prognosis.
RESULTS: Gut microbiota dysbiosis was observed in neonates with CCHD, characterized by the depletion of Bifidobacterium and overgrowth of Enterococcus, which was highly correlated with metabolomic perturbations. Genetic variations of Bifidobacterium and Enterococcus orchestrate the metabolomic perturbations in CCHD. A temperate core virome represented by Siphoviridae was identified to be implicated in shaping the gut bacterial composition by modifying microbial adaptation. The overgrowth of Enterococcus was correlated with systemic inflammation and poor surgical prognosis in subgroup analysis. Mediation analysis indicated that the overgrowth of Enterococcus could mediate gut barrier impairment and inflammatory responses in CCHD.
CONCLUSIONS: We demonstrate for the first time that an aberrant gut microbiome associated with metabolomic perturbations is implicated in immune imbalance and adverse clinical outcomes in neonates with CCHD. Our data support the importance of reconstituting optimal gut microbiome in maintaining host metabolic and immunological homeostasis in CCHD. Video Abstract.},
}
@article {pmid36371952,
year = {2023},
author = {Zhao, H and Liu, X and Jiang, T and Cai, C and Gu, K and Liu, Y and He, P},
title = {Activated abscisic acid pathway and C4 pathway, inhibited cell cycle progression, responses of Ulva prolifera to short term high temperature elucidated by multi-omics.},
journal = {Marine environmental research},
volume = {183},
number = {},
pages = {105796},
doi = {10.1016/j.marenvres.2022.105796},
pmid = {36371952},
issn = {1879-0291},
mesh = {*Ulva/metabolism ; Temperature ; Abscisic Acid/metabolism ; Multiomics ; Cell Cycle ; Eutrophication ; China ; },
abstract = {The annual outbreak of green tides since 2007 has destroyed coastal waters' ecological environment and caused substantial economic losses. Ulva prolifera, known as the dominant species of green tides, is influenced by temperatures. Omics-based technology was used to analyze U. prolifera under 12 h of treatment at 30 °C in the work. High temperature has the following advantages, e.g., activating the abscisic acid signaling pathway, improving the heat tolerance of U. prolifera, up-regulating metabolites such as glycolipids, glyceroyl, and glutamic acid to maintain the stability and fluidity of cells, and reducing the stimulatory effect of external stress on cells. The key genes and proteins of the tricarboxylic acid cycle, glycolysis, and pentose phosphorylation pathways were inhibited; however, the key enzyme pyruvate phospho-dikinase of the C4 pathway was up-regulated. The C4 pathway was activated in U. prolifera in response to high-temperature stress and may play a key role in photosynthesis. Besides, U. prolifera metabolizing amino acids was active. High temperature inhibited genes and proteins related to DNA replication and cell cycle in the transcriptome and proteome as well as the growth and reproduction of U. prolifera.},
}
@article {pmid36576353,
year = {2022},
author = {Liu, C and Economo, EP and Guénard, B},
title = {GABI-I: The global ant biodiversity informatics-island database.},
journal = {Ecology},
volume = {},
number = {},
pages = {e3969},
doi = {10.1002/ecy.3969},
pmid = {36576353},
issn = {1939-9170},
abstract = {Island systems are known to harbor disproportionate amounts of geographically restricted biodiversity, but also for experiencing high rates of species loss, ultimately representing critical systems with significant conservation values. Knowledge of the biodiversity value of insular systems remains, however, highly fragmented and incomplete for many groups of organisms, especially insects. This gap limits our understanding of their global significance for biodiversity and inhibits prioritization for future exploration and conservation efforts. Here, we developed a new database introducing current knowledge of ants on 2678 islands globally, based on nominal species, and providing information on their native or exotic status. In total, this database contains 7,010 ant species (44.6% of the known global ant fauna) that have been recorded on islands globally from 449,232 records. In addition, this database identifies 108 large islands (area > 200km2) that have received no ant sampling efforts globally. This new data set provides the most comprehensive understanding of ant diversity and composition on islands globally, opening new opportunities to address questions on a multitude of research questions and fields related to biogeography, ecology, and evolution. This data set also provides a roadmap for future exploration and conservation actions of ants on islands as well as for overall ant diversity, with updates available as new records and taxonomic updates are published. There are no copyright restrictions on this database and users should cite this data paper in publications when using the data. This article is protected by copyright. All rights reserved.},
}
@article {pmid36575453,
year = {2022},
author = {Barone, M and Garelli, S and Rampelli, S and Agostini, A and Matysik, S and D'Amico, F and Krautbauer, S and Mazza, R and Salituro, N and Fanelli, F and Iozzo, P and Sanz, Y and Candela, M and Brigidi, P and Pagotto, U and Turroni, S},
title = {Multi-omics gut microbiome signatures in obese women: role of diet and uncontrolled eating behavior.},
journal = {BMC medicine},
volume = {20},
number = {1},
pages = {500},
pmid = {36575453},
issn = {1741-7015},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Multiomics ; Obesity/genetics ; Diet ; Feeding Behavior/physiology ; Feces/microbiology ; },
abstract = {BACKGROUND: Obesity and related co-morbidities represent a major health challenge nowadays, with a rapidly increasing incidence worldwide. The gut microbiome has recently emerged as a key modifier of human health that can affect the development and progression of obesity, largely due to its involvement in the regulation of food intake and metabolism. However, there are still few studies that have in-depth explored the functionality of the human gut microbiome in obesity and even fewer that have examined its relationship to eating behaviors.
METHODS: In an attempt to advance our knowledge of the gut-microbiome-brain axis in the obese phenotype, we thoroughly characterized the gut microbiome signatures of obesity in a well-phenotyped Italian female cohort from the NeuroFAST and MyNewGut EU FP7 projects. Fecal samples were collected from 63 overweight/obese and 37 normal-weight women and analyzed via a multi-omics approach combining 16S rRNA amplicon sequencing, metagenomics, metatranscriptomics, and lipidomics. Associations with anthropometric, clinical, biochemical, and nutritional data were then sought, with particular attention to cognitive and behavioral domains of eating.
RESULTS: We identified four compositional clusters of the gut microbiome in our cohort that, although not distinctly associated with weight status, correlated differently with eating habits and behaviors. These clusters also differed in functional features, i.e., transcriptional activity and fecal metabolites. In particular, obese women with uncontrolled eating behavior were mostly characterized by low-diversity microbial steady states, with few and poorly interconnected species (e.g., Ruminococcus torques and Bifidobacterium spp.), which exhibited low transcriptional activity, especially of genes involved in secondary bile acid biosynthesis and neuroendocrine signaling (i.e., production of neurotransmitters, indoles and ligands for cannabinoid receptors). Consistently, high amounts of primary bile acids as well as sterols were found in their feces.
CONCLUSIONS: By finding peculiar gut microbiome profiles associated with eating patterns, we laid the foundation for elucidating gut-brain axis communication in the obese phenotype. Subject to confirmation of the hypotheses herein generated, our work could help guide the design of microbiome-based precision interventions, aimed at rewiring microbial networks to support a healthy diet-microbiome-gut-brain axis, thus counteracting obesity and related complications.},
}
@article {pmid36572855,
year = {2022},
author = {Schwarz, J and Hemmerling, J and Kabisch, N and Galbusera, L and Heinze, M and von Peter, S and Wolff, J},
title = {Equal access to outreach mental health care? Exploring how the place of residence influences the use of intensive home treatment in a rural catchment area in Germany.},
journal = {BMC psychiatry},
volume = {22},
number = {1},
pages = {826},
pmid = {36572855},
issn = {1471-244X},
mesh = {Humans ; *Mental Health ; Ambulatory Care ; *Community Mental Health Services ; Catchment Area, Health ; Germany ; Health Services Accessibility ; },
abstract = {BACKGROUND: Internationally, intensive psychiatric home treatment has been increasingly implemented as a community-based alternative to inpatient admission. Since 2018, the so-called Inpatient Equivalent Home Treatment (IEHT; German: "Stationsäquivalente Behandlung", short: "StäB") has been introduced as a particularly intensive form of home treatment that provides at least one daily treatment contact in the service users' (SU) home environment. Prior research shows that this can be challenging in rural catchment areas. Our paper investigates to which extent the location of the SU home location within the catchment area as well as the distance between the home and the clinic influence the utilisation of inpatient treatment compared to IEHT.
METHOD: Routine data of one psychiatric hospital in the federal state of Brandenburg in Germany were analysed for the observational period 07/2018-06/2021. Two comparison groups were formed: SU receiving inpatient treatment and SU receiving IEHT. The SU places of residence were respectively anonymised and converted into geo-coordinates. A geographic information system (GIS) was used to visualise the places of residence, and car travel distances as well as travel times to the clinic were determined. Spatial analyses were performed to show the differences between comparison groups. In a more in-depth analysis, the proximity of SU residences to each other was examined as an indicator of possible clustering.
RESULTS: During the observational period, the location of 687 inpatient and 140 IEHT unique SU were mapped using the GIS. SU receiving treatment resided predominantly within the catchment area, and this proportion was slightly higher for SU receiving IEHT than for those treated in inpatient setting (95.3% vs. 84.7%). In the catchment area, the geographical distribution of SU place of residence was similar in the two groups. There was a general higher service provision in the more densely populated communities close to Berlin. SU with residence in peripheral communities were mainly treated within the inpatient setting. The mean travel times and distances to the place of residence only differed minimally between the two groups of SU (p > 0.05). The places of residence of SU treated with IEHT were located in greater proximity to each other than those of SU treated in inpatient setting (p < 0.1).
CONCLUSION: In especially peripheral parts of the examined catchment area, it may be more difficult to have access to IEHT rather than to inpatient services. The results raise questions regarding health equity and the planning of health care services and have important implications for the further development of intensive home treatment. Telehealth interventions such as blended-care approaches and an increase of flexibility in treatment intensity, e.g. eliminating the daily visit requirement, could ease the implementation of intensive home treatment especially in rural areas.},
}
@article {pmid36572749,
year = {2022},
author = {Kon, T and Fukuta, K and Chen, Z and Kon-Nanjo, K and Suzuki, K and Ishikawa, M and Tanaka, H and Burgess, SM and Noguchi, H and Toyoda, A and Omori, Y},
title = {Single-cell transcriptomics of the goldfish retina reveals genetic divergence in the asymmetrically evolved subgenomes after allotetraploidization.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1404},
pmid = {36572749},
issn = {2399-3642},
mesh = {Animals ; *Goldfish/genetics ; *Transcriptome ; Genome ; Evolution, Molecular ; Gene Expression Profiling ; },
abstract = {The recent whole-genome duplication (WGD) in goldfish (Carassius auratus) approximately 14 million years ago makes it a valuable model for studying gene evolution during the early stages after WGD. We analyzed the transcriptome of the goldfish retina at the level of single-cell (scRNA-seq) and open chromatin regions (scATAC-seq). We identified a group of genes that have undergone dosage selection, accounting for 5% of the total 11,444 ohnolog pairs. We also identified 306 putative sub/neo-functionalized ohnolog pairs that are likely to be under cell-type-specific genetic variation at single-cell resolution. Diversification in the expression patterns of several ohnolog pairs was observed in the retinal cell subpopulations. The single-cell level transcriptome analysis in this study uncovered the early stages of evolution in retinal cell of goldfish after WGD. Our results provide clues for understanding the relationship between the early stages of gene evolution after WGD and the evolution of diverse vertebrate retinal functions.},
}
@article {pmid36566315,
year = {2022},
author = {Dualib, PM and Fernandes, G and Taddei, CR and Carvalho, CRS and Sparvoli, LG and Bittencourt, C and Silva, IT and Mattar, R and Ferreira, SRG and Dib, SA and de Almeida-Pititto, B},
title = {The gut microbiome of obese postpartum women with and without previous gestational diabetes mellitus and the gut microbiota of their babies.},
journal = {Diabetology & metabolic syndrome},
volume = {14},
number = {1},
pages = {194},
pmid = {36566315},
issn = {1758-5996},
abstract = {BACKGROUND: The incidence of gestational diabetes mellitus (GDM) is increasing worldwide, and has been associated with some changes in the gut microbiota. Studies have shown that the maternal gut microbiota pattern with hyperglycemia can be transmitted to the offspring. The study aimed to evaluate the gut microbiota of obese postpartum women with and without previous GDM and their offspring.
METHODS: We evaluated a total of 84 puerperal women who had (n = 40) or not GDM (n = 44), and their infants were also included. Stool samples were obtained 2-6 months after delivery. The molecular profile of the fecal microbiota was obtained by sequencing V4 region of 16S rRNA gene (Illumina[®] MiSeq).
RESULTS: We found that the gut microbiota structures of the puerperal women and their infants were similar. Stratifying according to the type of delivery, the relative abundance of Victivallis genus was higher in women who had natural delivery. Exposure to exclusive breastfeeding was associated with a greater abundance of Bacteroides and Staphylococcus. The differential abundance test showed correlations to clinical and laboratory parameters. This work showed no difference in the microbiota of obese puerperal women with and without GDM and their offspring. However, breastfeeding contributed to the ecological succession of the intestinal microbiota of the offspring.
CONCLUSION: This work can contribute to understanding the potential effects of GDM and early life events on the gut microbiome of mothers and their offspring and its possible role in metabolism later in life.},
}
@article {pmid36557752,
year = {2022},
author = {Schalli, M and Inwinkl, SM and Platzer, S and Baumert, R and Reinthaler, FF and Ofner-Kopeinig, P and Haas, D},
title = {Cefsulodin and Vancomycin: A Supplement for Chromogenic Coliform Agar for Detection of Escherichia coli and Coliform Bacteria from Different Water Sources.},
journal = {Microorganisms},
volume = {10},
number = {12},
pages = {},
pmid = {36557752},
issn = {2076-2607},
abstract = {Background microorganism growth on Chromogenic Coliform Agar (CCA) can be challenging. For this reason, a new alternative method with a Cefsulodin/Vancomycin (CV)-supplemented CCA should be developed in this study. CCA supplemented with CV was validated according to ÖNORM EN ISO 16140-4:2021 using water from natural sources in Styria, Austria. Results show that the alternative method using the supplemented CCA has similar values in relation to sensitivity (82.2%), specificity (98.6%) and higher selectivity (59%) compared to the reference method. Repeatability and reproducibility were acceptable for the alternative method and showed similar results with the reference method. The alternative method shows a very low false positive rate and a low false negative rate paired with good performance regarding the inclusion study. The exclusion study shows the advantage of our method by suppressing background microorganisms and facilitating the process of enumeration of Escherichia coli and other coliform bacteria on CCA plates. Aeromonas hydrophila and Pseudomonas aeruginosa growth was inhibited using the supplement. To conclude, the coliform CV selective supplement combined with CCA is an appropriate tool for coliform bacteria detection in water samples.},
}
@article {pmid36554991,
year = {2022},
author = {Xue, Y and Lin, C and Wang, Y and Liu, W and Wan, F and Zhang, Y and Ji, L},
title = {Predicting Climate Change Effects on the Potential Distribution of Two Invasive Cryptic Species of the Bemisia tabaci Species Complex in China.},
journal = {Insects},
volume = {13},
number = {12},
pages = {},
pmid = {36554991},
issn = {2075-4450},
abstract = {Middle East-Asia Minor 1 (MEAM1) and Mediterranean (MED) are two invasive cryptic species of the Bemisia tabaci species complex (Hemiptera: Aleyrodidae) that cause serious damage to agricultural and horticultural crops worldwide. To explore the possible impact of climate change on their distribution, the maximum entropy (MaxEnt) model was used to predict the potential distribution ranges of MEAM1 and MED in China under current and four future climate scenarios, using shared socioeconomic pathways (SSPs), namely SSP1-2.6, SSP2-4.5, SSP3-7.0, and SSP5-8.5, over four time periods (2021-2040, 2041-2060, 2061-2080, and 2081-2100). The distribution ranges of MEAM1 and MED were extensive and similar in China under current climatic conditions, while their moderately and highly suitable habitat ranges differed. Under future climate scenarios, the areas of suitable habitat of different levels for MEAM1 and MED were predicted to increase to different degrees. However, the predicted expansion of suitable habitats varied between them, suggesting that these invasive cryptic species respond differently to climate change. Our results illustrate the difference in the effects of climate change on the geographical distribution of different cryptic species of B. tabaci and provide insightful information for further forecasting and managing the two invasive cryptic species in China.},
}
@article {pmid36554882,
year = {2022},
author = {Deng, F and Yang, Y and Zhao, E and Xu, N and Li, Z and Zheng, P and Han, Y and Gong, J},
title = {Urban Heat Island Intensity Changes in Guangdong-Hong Kong-Macao Greater Bay Area of China Revealed by Downscaling MODIS LST with Deep Learning.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {24},
pages = {},
pmid = {36554882},
issn = {1660-4601},
mesh = {Humans ; Macau ; Hong Kong ; Cities ; *Hot Temperature ; Temperature ; *Deep Learning ; China ; Environmental Monitoring/methods ; },
abstract = {The urban heat island (UHI) effect caused by urbanization negatively impacts the ecological environment and human health. It is crucial for urban planning and social development to monitor the urban heat island effect and study its mechanism. Due to spatial and temporal resolution limitations, existing land surface temperature (LST) data obtained from remote sensing data is challenging to meet the long-term fine-scale surface temperature mapping requirement. Given the above situation, this paper introduced the ResNet-based surface temperature downscaling method to make up for the data deficiency and applied it to the study of thermal environment change in the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) from 2000 to 2020. The results showed (1) the ResNet-based surface temperature downscaling method achieves high accuracy (R[2] above 0.85) and is suitable for generating 30 m-resolution surface temperature data from 1 km data; (2) the area of severe heat islands in the GBA continued to increase, increasing by 7.13 times within 20 years; and (3) except for Hong Kong and Macau, the heat island intensity of most cities showed an apparent upward trend, especially the cities with rapid urban expansion such as Guangzhou, Zhongshan, and Foshan. In general, the evolution of the heat island in the GBA diverges from the central urban area to the surrounding areas, with a phenomenon of local aggregation and the area of the intense heat island in the Guangzhou-Foshan metropolitan area is the largest. This study can enrich the downscaling research methods of surface temperature products in complex areas with surface heterogeneity and provide a reference for urban spatial planning in the GBA.},
}
@article {pmid36554755,
year = {2022},
author = {Chen, D and Xiong, K and Zhang, J},
title = {Progress on the Integrity Protection in the Natural World Heritage Site and Agroforestry Development in the Buffer Zone: An Implications for the World Heritage Karst.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {24},
pages = {},
pmid = {36554755},
issn = {1660-4601},
mesh = {*Conservation of Natural Resources ; China ; Databases, Factual ; *Knowledge ; },
abstract = {In the face of increasing development pressure, how to fulfill the obligations under the World Cultural and Natural Heritage Convention and maintain the integrity of the Natural World Heritage Site (NWHS) is a major problem to be solved at present. Agroforestry (AF) development in the buffer zone maintains the integrity of NWHS and promotes sustainable ecological and economic development in the buffer zone. Still, few studies on the knowledge system of integrity protection of NWHS and AF development in the buffer zone research have been conducted. To fill this gap, this study conducts a systematic literature review based on 128 related articles retrieved from the Web of Science (WoS) database and the China National Knowledge Infrastructure (CNKI) database. Firstly, quantitative studies were conducted to analyze the annual numbers, content and study regions of the published literature. Secondly, the main research progress and achievements of integrity protection of WNHS and AF development in the buffer zone are classified and summarized. On this basis, this paper proposed key scientific issues that remain to be addressed in future, as well as exploring the implications for the World Heritage (WH) karst. This study is a scientific reference for the balanced development of NWHS integrity protection and AF in the buffer zone.},
}
@article {pmid36554469,
year = {2022},
author = {Zhou, T and Zhu, Y and Sun, K and Chen, J and Wang, S and Zhu, H and Wang, X},
title = {Variance Analysis in China's Coal Mine Accident Studies Based on Data Mining.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {24},
pages = {},
pmid = {36554469},
issn = {1660-4601},
mesh = {*Accidents, Occupational/prevention & control ; *Coal Mining ; Analysis of Variance ; China ; Coal ; },
abstract = {The risk of coal mine accidents rises significantly with mining depth, making it urgent for accident prevention to be supported by both scientific analysis and advanced technologies. Hence, a comprehensive grasp of the research progress and differences in hotspots of coal mine accidents in China serves as a guide to find the shortcomings of studies in the field, promote the effectiveness of coal mine disaster management, and enhance the prevention and control ability of coal mine accidents. This paper analyzes Chinese and foreign literature based on data mining algorithms (LSI + Apriori), and the findings indicate that: (1) 99% of the available achievements are published in Chinese or English-language journals, with the research history conforming to the stage of Chinese coal industry development, which is characterized by "statistical description, risk evaluation, mechanism research, and intelligent reasoning". (2) Chinese authors are the primary contributors that lead and contribute to the continued development of coal mine accident research in China globally. Over 81% of the authors and over 60% of the new authors annually are from China. (3) The emphasis of the Chinese and English studies is different. Specifically, the Chinese studies focus on the analysis of accident patterns and causes at the macroscale, while the English studies concentrate on the occupational injuries of miners at the small-scale and the mechanism of typical coal mine disasters (gas and coal spontaneous combustion). (4) The research process in Chinese is generally later than that in English due to the joint influence of the target audience, industrial policy, and scientific research evaluation system. After 2018, the Chinese studies focus significantly on AI technology in deep mining regarding accident rules, regional variation analysis, risk monitoring and early warning, as well as knowledge intelligence services, while the hotspots of English studies remain unchanged. Furthermore, both Chinese and English studies around 2019 focus on "public opinion", with Chinese ones focusing on serving the government to guide the correct direction of public opinion while English studies focus on critical research of news authenticity and China's safety strategy.},
}
@article {pmid36554342,
year = {2022},
author = {Dantas, JDC and Marinho, CDSR and Pinheiro, YT and Silva, RARD},
title = {Temporal Trend of Gestational Syphilis between 2008 and 2018 in Brazil: Association with Socioeconomic and Health Care Factors.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {24},
pages = {},
pmid = {36554342},
issn = {1660-4601},
mesh = {Pregnancy ; Female ; Humans ; *Syphilis/epidemiology ; *Pregnancy Complications, Infectious/epidemiology ; *Syphilis, Congenital/epidemiology/prevention & control ; Brazil/epidemiology ; Literacy ; Delivery of Health Care ; Socioeconomic Factors ; },
abstract = {The increased number of cases in recent years has turned syphilis into a global public health problem. In 2020, 115,371 cases of acquired syphilis were reported (detection rate of 54.5 cases/100,000 inhabitants) in Brazil. In that same period, the country notified 61,441 cases of gestational syphilis (detection rate of 21.6 per 1000 live births). The number of syphilis cases points to the need to reinforce surveillance, prevention, and infection control actions, which is a worrying scenario for government organizations. This study aims to describe the temporal trend of gestational syphilis from 2008 to 2018 in Brazilian regions and to associate its detection rate with socioeconomic and health care indicators. We conducted an ecological study of temporal trends using secondary data from the Department of Informatics of the Unified Health System. The temporal trend was analyzed using the Joinpoint Regression program. The annual percent change (APC) and 95% confidence intervals (95%CI) were estimated and tested; statistical significance was assessed using the Monte Carlo permutation test. Correlations were assessed using Pearson's correlation coefficient, and statistical significance was calculated using Pearson's product-moment correlation. The gestational syphilis detection rate increased between 2008 and 2018. The South region showed the greatest trend, whereas the Midwest region presented the lowest trend. The following variables were significantly correlated with the gestational syphilis detection rate: Municipal Human Development Index, illiteracy rate, percentage of primary health care coverage, and proportion of doctors, nurses, and basic health units per inhabitant. Health policies are needed to mitigate social vulnerabilities and strengthen primary health care.},
}
@article {pmid36552295,
year = {2022},
author = {Sokhansanj, BA and Zhao, Z and Rosen, GL},
title = {Interpretable and Predictive Deep Neural Network Modeling of the SARS-CoV-2 Spike Protein Sequence to Predict COVID-19 Disease Severity.},
journal = {Biology},
volume = {11},
number = {12},
pages = {},
pmid = {36552295},
issn = {2079-7737},
abstract = {Through the COVID-19 pandemic, SARS-CoV-2 has gained and lost multiple mutations in novel or unexpected combinations. Predicting how complex mutations affect COVID-19 disease severity is critical in planning public health responses as the virus continues to evolve. This paper presents a novel computational framework to complement conventional lineage classification and applies it to predict the severe disease potential of viral genetic variation. The transformer-based neural network model architecture has additional layers that provide sample embeddings and sequence-wide attention for interpretation and visualization. First, training a model to predict SARS-CoV-2 taxonomy validates the architecture's interpretability. Second, an interpretable predictive model of disease severity is trained on spike protein sequence and patient metadata from GISAID. Confounding effects of changing patient demographics, increasing vaccination rates, and improving treatment over time are addressed by including demographics and case date as independent input to the neural network model. The resulting model can be interpreted to identify potentially significant virus mutations and proves to be a robust predctive tool. Although trained on sequence data obtained entirely before the availability of empirical data for Omicron, the model can predict the Omicron's reduced risk of severe disease, in accord with epidemiological and experimental data.},
}
@article {pmid36547621,
year = {2022},
author = {Jamal, QMS and Ahmad, V},
title = {Lysinibacilli: A Biological Factories Intended for Bio-Insecticidal, Bio-Control, and Bioremediation Activities.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {8},
number = {12},
pages = {},
pmid = {36547621},
issn = {2309-608X},
abstract = {Microbes are ubiquitous in the biosphere, and their therapeutic and ecological potential is not much more explored and still needs to be explored more. The bacilli are a heterogeneous group of Gram-negative and Gram-positive bacteria. Lysinibacillus are dominantly found as motile, spore-forming, Gram-positive bacilli belonging to phylum Firmicutes and the family Bacillaceae. Lysinibacillus species initially came into light due to their insecticidal and larvicidal properties. Bacillus thuringiensis, a well-known insecticidal Lysinibacillus, can control many insect vectors, including a malarial vector and another, a Plasmodium vector that transmits infectious microbes in humans. Now its potential in the environment as a piece of green machinery for remediation of heavy metal is used. Moreover, some species of Lysinibacillus have antimicrobial potential due to the bacteriocin, peptide antibiotics, and other therapeutic molecules. Thus, this review will explore the biological disease control abilities, food preservative, therapeutic, plant growth-promoting, bioremediation, and entomopathogenic potentials of the genus Lysinibacillus.},
}
@article {pmid36545372,
year = {2022},
author = {Ruttoh, RC and Obiero, JPO and Omuto, CT and Tanui, L},
title = {Assessment of Land Cover and Land Use Change Dynamics in Kibwezi Watershed, Kenya.},
journal = {TheScientificWorldJournal},
volume = {2022},
number = {},
pages = {3944810},
pmid = {36545372},
issn = {1537-744X},
mesh = {Kenya ; *Geographic Information Systems ; *Forests ; Soil ; Trees ; Environmental Monitoring/methods ; Conservation of Natural Resources ; },
abstract = {Land use and land cover (LULC) parameters influence the hydrological and ecological processes taking place in a watershed. Understanding the changes in LULC is essential in the planning and development of management strategies for water resources. The purpose of the study was to detect changes in LULC in the Kibwezi watershed in Kenya, using geospatial approaches. Supervised and unsupervised classification techniques using remote sensing (RS) and geographical information system (GIS) were used to process Landsat imagery for 1999, 2009, and 2019 while ERDAS IMAGINE™ 14 and MS Excel software were used to derive change detection, and the Soil and Water Assessment Tool (SWAT) model was used to delineate the watershed using an in-built watershed delineation tool. The watershed was classified into ten major LULC classes, namely cropland (rainfed), cropland (irrigated), cropland (perennial), crop and shrubs/trees, closed shrublands, open shrubland, shrub grasslands, wooded shrublands, riverine woodlands, and built-up land. The results showed that LULC under shrub grassland, urban areas, and crops and shrubs increased drastically by 552.5%, 366.2%, and 357.1% respectively between 1999 and 2019 with an annual increase of 35.55%, 35.38%, and 33.86% per annum. The area under open shrubland and closed shrubland declined by73.7%, and 30.4% annually. These LULC transformations pose a negative impact on the watershed resources. There is therefore a need for proper management of the watershed for sustainable socio-economic development of the Kibwezi area.},
}
@article {pmid36543718,
year = {2022},
author = {Liew, F and Talwar, S and Cross, A and Willett, BJ and Scott, S and Logan, N and Siggins, MK and Swieboda, D and Sidhu, JK and Efstathiou, C and Moore, SC and Davis, C and Mohamed, N and Nunag, J and King, C 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, L and Wootton, DG and Dunachie, S and Quint, JK and Evans, RA and Wain, LV and Fontanella, S and de Silva, TI and Ho, A and Harrison, E and Baillie, JK and Semple, MG and Brightling, C and Thwaites, RS and Turtle, L and Openshaw, PJM and , and , },
title = {SARS-CoV-2-specific nasal IgA wanes 9 months after hospitalisation with COVID-19 and is not induced by subsequent vaccination.},
journal = {EBioMedicine},
volume = {},
number = {},
pages = {104402},
pmid = {36543718},
issn = {2352-3964},
abstract = {BACKGROUND: Most studies of immunity to SARS-CoV-2 focus on circulating antibody, giving limited insights into mucosal defences that prevent viral replication and onward transmission. We studied nasal and plasma antibody responses one year after hospitalisation for COVID-19, including a period when SARS-CoV-2 vaccination was introduced.
METHODS: In this follow up study, plasma and nasosorption samples were prospectively collected from 446 adults hospitalised for COVID-19 between February 2020 and March 2021 via the ISARIC4C and PHOSP-COVID consortia. IgA and IgG responses to NP and S of ancestral SARS-CoV-2, Delta and Omicron (BA.1) variants were measured by electrochemiluminescence and compared with plasma neutralisation data.
FINDINGS: Strong and consistent nasal anti-NP and anti-S IgA responses were demonstrated, which remained elevated for nine months (p < 0.0001). Nasal and plasma anti-S IgG remained elevated for at least 12 months (p < 0.0001) with plasma neutralising titres that were raised against all variants compared to controls (p < 0.0001). Of 323 with complete data, 307 were vaccinated between 6 and 12 months; coinciding with rises in nasal and plasma IgA and IgG anti-S titres for all SARS-CoV-2 variants, although the change in nasal IgA was minimal (1.46-fold change after 10 months, p = 0.011) and the median remained below the positive threshold determined by pre-pandemic controls. Samples 12 months after admission showed no association between nasal IgA and plasma IgG anti-S responses (R = 0.05, p = 0.18), indicating that nasal IgA responses are distinct from those in plasma and minimally boosted by vaccination.
INTERPRETATION: The decline in nasal IgA responses 9 months after infection and minimal impact of subsequent vaccination may explain the lack of long-lasting nasal defence against reinfection and the limited effects of vaccination on transmission. These findings highlight the need to develop vaccines that enhance nasal immunity.
FUNDING: This study has been supported by ISARIC4C and PHOSP-COVID consortia. ISARIC4C is supported by grants from the National Institute for Health and Care Research and the Medical Research Council. Liverpool Experimental Cancer Medicine Centre provided infrastructure support for this research. The PHOSP-COVD study is jointly funded by UK Research and Innovation and National Institute of Health and Care Research. The funders were not involved in the study design, interpretation of data or the writing of this manuscript.},
}
@article {pmid36538553,
year = {2022},
author = {Vukašinović, D and Maksimović, M and Tanasković, S and Marinković, J and Gajin, P and Ilijevski, N and Vasiljević, N and Radak, Đ and Vlajinac, H},
title = {Body mass index and early outcomes after carotid endarterectomy.},
journal = {PloS one},
volume = {17},
number = {12},
pages = {e0278298},
pmid = {36538553},
issn = {1932-6203},
mesh = {Male ; Humans ; *Endarterectomy, Carotid/adverse effects ; Body Mass Index ; Cohort Studies ; Overweight/complications ; Treatment Outcome ; Risk Factors ; Retrospective Studies ; *Stroke/complications ; Hemorrhage/etiology ; Obesity/complications ; *Diabetes Mellitus, Type 2/complications ; *Carotid Stenosis/surgery ; Risk Assessment ; },
abstract = {As the existing data on the correlation of adiposity with adverse outcomes of carotid endarterectomy (CEA) are inconsistent, the aim of the present study is to examine the correlation of an increased body mass index with 30-day complications after carotid endarterectomy. The cohort study comprises 1586 CEAs, performed at the Clinic for Vascular Surgery in Belgrade, from 2012-2017. Out of them, 550 CEAs were performed in patients with normal body mass index (18.5-24.9), 750 in overweight (25.0-29.9), and 286 in obese (≥30) patients. The association of overweight and obesity with early outcomes of carotid endarterectomy was assessed using univariate and multivariate logistic regression analysis. Overweight patients, in whom CEAs were performed, were significantly more frequently males, compared to normal weight patients-Odds Ratio (OR) 1.51 (95% confidence interval- 1.19-1.89). Moreover, overweight patients significantly more frequently had non-insulin-dependent diabetes mellitus-OR 1.44 (1.09-1.90), and more frequently used ACEI in hospital discharge therapy-OR 1.41 (1.07-1.84) than normal weight patients. Additionally, the CEAs in them were less frequently followed by bleedings-OR 0.37 (0.16-0.83). Compared to normal weight patients, obese patients were significantly younger-OR 0.98 (0.96-0.99), and with insulin-dependent and non-insulin-dependent diabetes mellitus-OR 1.83 (1.09-3.06) and OR 2.13 (1.50-3.01) respectively. They also more frequently had increased triglyceride levels-OR 1.36 (1.01-1.83), and more frequently used oral anticoagulants in therapy before the surgery-OR 2.16 (1.11-4.19). According to the results obtained, overweight and obesity were not associated with an increased death rate, transient ischemic attack (TIA), stroke, myocardial infarction, or with minor complications, and the need for reoperation after carotid endarterectomy. The only exception was bleeding, which was significantly less frequent after CEA in overweight compared to normal weight patients.},
}
@article {pmid36529723,
year = {2022},
author = {Liu, X and Lu, X and Yang, S and Liu, Y and Wang, W and Wei, X and Ji, H and Zhang, B and Xin, W and Wen, J and Wang, J and Chen, Q},
title = {Role of exogenous abscisic acid in freezing tolerance of mangrove Kandelia obovata under natural frost condition at near 32[°]N.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {593},
pmid = {36529723},
issn = {1471-2229},
mesh = {*Rhizophoraceae ; Abscisic Acid/metabolism ; Antioxidants/metabolism ; Freezing ; Proline/metabolism ; Starch/metabolism ; Sucrose/metabolism ; },
abstract = {BACKGROUND: Mangroves possess substantial ecological, social, and economic functions in tropical and subtropical coastal wetlands. Kandelia obovata is the most cold-resistance species among mangrove plants, with a widespread distribution in China that ranges from Sanya (18° 12' N) to Wenzhou (28° 20' N). Here, we explored the temporal variations in physiological status and transcriptome profiling of K. obovata under natural frost conditions at ~ 32[o]N, as well as the positive role of exogenous abscisic acid (ABA) in cold resistance.
RESULTS: The soluble sugar (SS) and proline (Pro) functioned under freezing stress, of which SS was more important for K. obovata. Consistently, up-regulated DEGs responding to low temperature were significantly annotated to glycometabolism, such as starch and sucrose metabolism and amino sugar and nucleotide sugar metabolism. Notably, the top 2 pathways of KEGG enrichment were phenylpropanoid biosynthesis and flavonoid biosynthesis. For the antioxidant system, POD in conjunction with CAT removed hydrogen peroxide, and CAT appeared to be more important. The up-regulated DEGs responding to low temperature and ABA were also found to be enriched in arginine and proline metabolism, starch and sucrose metabolism, and peroxisome. Moreover, ABA triggered the expression of P5CS and P5CR, but inhibited the ProDH expression, which might contribute to Pro accumulation. Interestingly, there was no significant change in malondialdehyde (MDA) content during the cold event (P > 0.05), suggesting foliar application of ABA effectively alleviated the adverse effects of freezing stress on K. obovata by activating the antioxidant enzyme activity and increasing osmolytes accumulation, such as Pro, and the outcome was proportional to ABA concentration.
CONCLUSIONS: This study deepened our understanding of the physiological characters and molecular mechanisms underlying the response of K. obovata to natural frost conditions and exogenous ABA at the field level, which could provide a sound theoretical foundation for expanding mangroves plantations in higher latitudes, as well as the development coastal landscape.},
}
@article {pmid36528093,
year = {2022},
author = {Milan, M and Bernardini, I and Bertolini, C and Dalla Rovere, G and Manuzzi, A and Pastres, R and Peruzza, L and Smits, M and Fabrello, J and Breggion, C and Sambo, A and Boffo, L and Gallocchio, L and Carrer, C and Sorrentino, F and Bettiol, C and Lodigiulia, C and Semenzin, E and Varagnolo, M and Matozzo, V and Bargelloni, L and Patarnello, T},
title = {Multidisciplinary long-term survey of Manila clam grown in farming sites subjected to different environmental conditions.},
journal = {The Science of the total environment},
volume = {863},
number = {},
pages = {160796},
doi = {10.1016/j.scitotenv.2022.160796},
pmid = {36528093},
issn = {1879-1026},
abstract = {In recent years recurrent bivalve mass mortalities considerably increased around the world, causing the collapse of natural and farmed populations. Venice Lagoon has historically represented one of the major production areas of the Manila clam Ruditapes philippinarum in Europe. However, in the last 20 years a 75 % decrease in the annual production has been experienced. While climate change and anthropogenic interventions may have played a key role in natural and farmed stocks reductions, no studies investigated at multiple levels the environmental stressors affecting farmed Manila clam to date. In this work we carried out a long-term monitoring campaign on Manila clam reared in four farming sites located at different distances from the southern Venice Lagoon inlet, integrating (meta)genomic approaches (i.e. RNA-seq; microbiota characterization), biometric measurements and chemical-physical parameters. Our study allowed to characterize the molecular mechanisms adopted by this species to cope with the different environmental conditions characterizing farming sites and to propose hypotheses to explain mortality events observed in recent years. Among the most important findings, the disruption of clam's immune response, the spread of Vibrio spp., and the up-regulation of molecular pathways involved in xenobiotic metabolism suggested major environmental stressors affecting clams farmed in sites placed close to Chioggia's inlet, where highest mortality was also observed. Overall, our study provides knowledge-based tools for managing Manila clam farming on-growing areas. In addition, the collected data is a snapshot of the time immediately before the commissioning of MoSE, a system of mobile barriers aimed at protecting Venice from high tides, and will represent a baseline for future studies on the effects of MoSE on clams farming and more in general on the ecology of the Venice Lagoon.},
}
@article {pmid36527397,
year = {2022},
author = {Viner, A and Membe-Gadama, G and Whyte, S and Kayambo, D and Masamba, M and Martin, CJH and Magowan, B and Reynolds, RM and Stock, SJ and Freyne, B and Gadama, L},
title = {Midwife-Led Ultrasound Scanning to Date Pregnancy in Malawi: Development of a Novel Training Program.},
journal = {Journal of midwifery & women's health},
volume = {67},
number = {6},
pages = {728-734},
doi = {10.1111/jmwh.13442},
pmid = {36527397},
issn = {1542-2011},
mesh = {Female ; Pregnancy ; Humans ; *Midwifery/education ; *Nurse Midwives/education ; Malawi ; },
abstract = {The use of ultrasound to determine gestational age is fundamental to the optimum management of pregnancy and is recommended for all women by the World Health Organization. However, this modality remains unavailable to many women in low-income countries where trained practitioners are scarce. Although previous initiatives have demonstrated efficacy in training midwives and technicians to perform antenatal ultrasound, these programs have often been too long and too complex to be realistic within the specific constraints of this context, highlighting the need for a novel and pragmatic approach. We describe the development and piloting of a bespoke course to teach midwives 3 fundamental components of early antenatal ultrasound scanning: (1) to identify the number of fetuses, (2) to confirm fetal viability, and (3) to determine gestational age. Having established that 5 days is insufficient, we propose that the minimum duration required to train ultrasound-naive midwives to competency is 10 days. Our completed program therefore consists of one and one-half days of didactic teaching, followed by 8 and one-half days of supervised hands-on practical training in which trainees are assessed on their skills. This package has subsequently been successfully implemented across 6 sites in Malawi, where 28 midwives have achieved competency. By describing the processes involved in our cross-continental collaboration, we explain how unexpected challenges helped shape and improve our program, demonstrating the value of preimplementation piloting and a pragmatic and adaptive approach.},
}
@article {pmid36526212,
year = {2022},
author = {Zhang, Z and Fan, Y and Jiao, Z},
title = {Wetland ecological index and assessment of spatial-temporal changes of wetland ecological integrity.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {160741},
doi = {10.1016/j.scitotenv.2022.160741},
pmid = {36526212},
issn = {1879-1026},
abstract = {Long-term, quantitative, and dynamic monitoring of regional ecological integrity using remote sensing can provide powerful decision-making support for sustainable regional development. However, existing methods are unable to accurately evaluate the quality of the surface ecological integrity because they do not consider vegetation saturation and salinization of wetlands. In addition, the ecological fragility of wetlands is characterized by a high frequency of changes in ecological conditions over time, leading to a lack of directionality in the analysis of ecological changes over long time series. To accurately assess the surface ecological integrity, this study integrates environmental salinity (Baseline-based Soil Salinity Index, BSSI) and a new vegetation element (Improved Hyperspectral Image-based Vegetation Index, IHSVI), and proposes the wetland ecological index (WEI) for the ecological integrity assessment system. Combined with the annual ecological integrity assessment using the WEI, the Mann-Kendall test was used to obtain the nodes of long-term changes. The WEI-Mann Kendall (WEI-MK) framework indicates the direction of analysis and realizes clear long-term series change monitoring. In this study, we analyzed the spatial and temporal changes in ecological integrity in the Yellow River Delta from 1991 to 2020 based on the WEI-MK framework. The results showed that: 1) Compared with Remote Sensing-based Ecological Index (RSEI), the WEI improved the accuracy of wetland integrity evaluation to 89 %. The WEI also improved accuracy of assessments in other typical regions by approximately 10 %. 2) The selection of nodes based on the WEI-MK framework clarified the direction of environmental change analysis. The results show that although the quality of the terrestrial ecological environment has improved over the past 30 years in the Yellow River Delta, that of the marine ecological environment has gradually declined. In particular, the state of the marine ecological environment after 2016 should be of concern.},
}
@article {pmid36522390,
year = {2022},
author = {Acerbi, A and Snyder, WD and Tennie, C},
title = {The method of exclusion (still) cannot identify specific mechanisms of cultural inheritance.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {21680},
pmid = {36522390},
issn = {2045-2322},
support = {714658//European Research Council/International ; 714658//European Research Council/International ; },
mesh = {Animals ; Social Behavior ; *Social Learning ; Databases, Genetic ; *Hominidae ; *Cultural Evolution ; },
abstract = {The method of exclusion identifies patterns of distributions of behaviours and/or artefact forms among different groups, where these patterns are deemed unlikely to arise from purely genetic and/or ecological factors. The presence of such patterns is often used to establish whether a species is cultural or not-i.e. whether a species uses social learning or not. Researchers using or describing this method have often pointed out that the method cannot pinpoint which specific type(s) of social learning resulted in the observed patterns. However, the literature continues to contain such inferences. In a new attempt to warn against these logically unwarranted conclusions, we illustrate this error using a novel approach. We use an individual-based model, focused on wild ape cultural patterns-as these patterns are the best-known cases of animal culture and as they also contain the most frequent usage of the unwarranted inference for specific social learning mechanisms. We built a model that contained agents unable to copy specifics of behavioural or artefact forms beyond their individual reach (which we define as "copying"). We did so, as some of the previous inference claims related to social learning mechanisms revolve around copying defined in this way. The results of our model however show that non-copying social learning can already reproduce the defining-even iconic-features of observed ape cultural patterns detected by the method of exclusion. This shows, using a novel model approach, that copying processes are not necessary to produce the cultural patterns that are sometimes still used in an attempt to identify copying processes. Additionally, our model could fully control for both environmental and genetic factors (impossible in real life) and thus offers a new validity check for the method of exclusion as related to general cultural claims-a check that the method passed. Our model also led to new and additional findings, which we likewise discuss.},
}
@article {pmid36520387,
year = {2023},
author = {Melayah, D and Bontemps, Z and Bruto, M and Nguyen, A and Oger, P and Hugoni, M},
title = {Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2605},
number = {},
pages = {17-35},
pmid = {36520387},
issn = {1940-6029},
mesh = {*Ecosystem ; *Archaea/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Biodiversity ; },
abstract = {High-throughput amplicon sequencing, known as metabarcoding, is a powerful technique to decipher exhaustive microbial diversity considering specific gene markers. While most of the studies investigating ecosystem functioning through microbial diversity targeted only one domain of life, either bacteria, or archaea or microeukaryotes, the remaining challenge in microbial ecology is to uncover the integrated view of microbial diversity occurring in ecosystems. Indeed, interactions occurring between the different microbial counterparts are now recognized having a great impact on stability and resilience of ecosystems. Here, we summarize protocols describing sampling, molecular, and simultaneous metabarcoding of bacteria, archaea, and microeukaryotes, as well as a bioinformatic pipeline allowing the study of exhaustive microbial diversity in natural aquatic saline samples.},
}
@article {pmid36519374,
year = {2023},
author = {Seidu, S and Gillies, C and Zaccardi, F and Reeves, K and Gallier, S and Khunti, K},
title = {Temporal trends in admissions for atrial fibrillation and severe bleeding in England: an 18-year longitudinal analysis.},
journal = {Scandinavian cardiovascular journal : SCJ},
volume = {57},
number = {1},
pages = {40-47},
doi = {10.1080/14017431.2022.2156597},
pmid = {36519374},
issn = {1651-2006},
mesh = {Humans ; *Atrial Fibrillation/diagnosis/epidemiology/therapy ; Anticoagulants/therapeutic use ; Administration, Oral ; Risk Factors ; Treatment Outcome ; Time Factors ; Hemorrhage/diagnosis/epidemiology ; *Stroke ; },
abstract = {Objective. Temporal trends in admissions for atrial fibrillation (AF) and severe bleeding associated with AF vary worldwide. We aimed to explore their temporal trends in England and their relation to the introduction of DOACs in 2014 in the UK. Design. This longitudinal ecological study utilised aggregated data that was extracted from the Hospital Episode Statistics database, which captured annual admissions for AF and severe bleeding associated with AF between 2001 and 2018. Trends in admissions over the study period and across age groups, gender and regions in England were assessed. Results. In total, there were 11,292,177 admissions for AF and 324,851 admissions for severe bleeding associated with AF. There was a steady rise in admissions for AF from 2001 to 2017 (204,808 to 1,109,295; p for trend<.001). A similar trend was observed for severe bleeding (4940 to 30,169; p for trend <.001), but the increase dropped slightly between 2013 and 2014 and continued thereafter. Conclusions. There was a rise in admissions for AF and severe bleeding in England between 2001 and 2018. There is little evidence that the slight drop in admissions for severe bleeding between 2013 and 2014 may have been caused by the introduction of DOACs in 2014. Contributors to these trends need urgent exploration.},
}
@article {pmid36517756,
year = {2022},
author = {Zhang, H and Yao, G and He, M},
title = {Transcriptome analysis of gene expression profiling from the deep sea in situ to the laboratory for the cold seep mussel Gigantidas haimaensis.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {828},
pmid = {36517756},
issn = {1471-2164},
mesh = {Animals ; *Ecosystem ; *Mytilidae/genetics ; Gene Expression Profiling ; Transcriptome ; Gene Ontology ; },
abstract = {BACKGROUND: The deep-sea mussel Gigantidas haimaensis is a representative species from the Haima cold seep ecosystem in the South China Sea that establishes endosymbiosis with chemotrophic bacteria. During long-term evolution, G. haimaensis has adapted well to the local environment of cold seeps. Until now, adaptive mechanisms responding to environmental stresses have remained poorly understood.
RESULTS: In this study, transcriptomic analysis was performed for muscle tissue of G. haimaensis in the in situ environment (MH) and laboratory environment for 0 h (M0), 3 h (M3) and 9 h (M9), and 187,368 transcript sequences and 22,924 annotated differentially expressed genes (DEGs) were generated. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, these DEGs were enriched with a broad spectrum of biological processes and pathways, including those associated with antioxidants, apoptosis, chaperones, immunity and metabolism. Among these significantly enriched pathways, protein processing in the endoplasmic reticulum and metabolism were the most affected metabolic pathways. These results may imply that G. haimaensis struggles to support the life response to environmental change by changing gene expression profiles.
CONCLUSION: The present study provides a better understanding of the biological responses and survival strategies of the mussel G. haimaensis from deep sea in situ to the laboratory environment.},
}
@article {pmid36512954,
year = {2022},
author = {Kim, B and Barrington, WE and Dobra, A and Rosenberg, D and Hurvitz, P and Belza, B},
title = {Mediating role of walking between perceived and objective walkability and cognitive function in older adults.},
journal = {Health & place},
volume = {79},
number = {},
pages = {102943},
doi = {10.1016/j.healthplace.2022.102943},
pmid = {36512954},
issn = {1873-2054},
abstract = {The aim of this study was to examine the role of walking in explaining associations between perceived and objective measures of walkability and cognitive function among older adults. The study employed a cross-sectional design analyzing existing data. Data were obtained from the Adult Changes in Thought Activity Monitor study. Cognitive function and perceived walkability were measured by a survey. Objective walkability was measured using geographic information systems (GIS). Walking was measured using an accelerometer. We tested the mediating relationship based on 1,000 bootstrapped samples. Perceived walkability was associated with a 0.04 point higher cognitive function score through walking (p = 0.006). The mediating relationship accounted for 34% of the total relationship between perceived walkability and cognitive function. Walking did not have a significant indirect relationship on the association between objective walkability and cognitive function. Perceived walkability may be more relevant to walking behavior than objective walkability among older adults. Greater levels of perceived walkability may encourage older adults to undertake more walking, and more walking may in turn improve cognitive function in older adults.},
}
@article {pmid36512230,
year = {2023},
author = {Barlow, LD and Maciejowski, W and More, K and Terry, K and Vargová, R and Záhonová, K and Dacks, JB},
title = {Comparative Genomics for Evolutionary Cell Biology Using AMOEBAE: Understanding the Golgi and Beyond.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2557},
number = {},
pages = {431-452},
pmid = {36512230},
issn = {1940-6029},
mesh = {*Amoeba/genetics ; Reproducibility of Results ; Genomics/methods ; Biological Evolution ; Golgi Apparatus/metabolism ; Computational Biology/methods ; },
abstract = {Taking an evolutionary approach to cell biology can yield important new information about how the cell works and how it evolved to do so. This is true of the Golgi apparatus, as it is of all systems within the cell. Comparative genomics is one of the crucial first steps to this line of research, but comes with technical challenges that must be overcome for rigor and robustness. We here introduce AMOEBAE, a workflow for mid-range scale comparative genomic analyses. It allows for customization of parameters, queries, and taxonomic sampling of genomic and transcriptomics data. This protocol article covers the rationale for an evolutionary approach to cell biological study (i.e., when would AMOEBAE be useful), how to use AMOEBAE, and discussion of limitations. It also provides an example dataset, which demonstrates that the Golgi protein AP4 Epsilon is present as the sole retained subunit of the AP4 complex in basidiomycete fungi. AMOEBAE can facilitate comparative genomic studies by balancing reproducibility and speed with user-input and interpretation. It is hoped that AMOEBAE or similar tools will encourage cell biologists to incorporate an evolutionary context into their research.},
}
@article {pmid36504957,
year = {2022},
author = {Zhang, Y and Liu, S and Wang, Y and Wang, Y},
title = {Causal relationship between particulate matter 2.5 and hypothyroidism: A two-sample Mendelian randomization study.},
journal = {Frontiers in public health},
volume = {10},
number = {},
pages = {1000103},
pmid = {36504957},
issn = {2296-2565},
mesh = {*Particulate Matter/adverse effects ; *Genome-Wide Association Study ; Analysis of Variance ; Databases, Factual ; Polymorphism, Single Nucleotide ; },
abstract = {BACKGROUND: Epidemiological surveys have found that particulate matter 2.5 (PM2.5) plays an important role in hypothyroidism. However, due to the methodological limitations of traditional observational studies, it is difficult to make causal inferences. In the present study, we assessed the causal association between PM2.5 concentrations and risk of hypothyroidism using two-sample Mendelian randomization (TSMR).
METHODS: We performed TSMR by using aggregated data from genome-wide association studies (GWAS) on the IEU Open GWAS database. We identified seven single nucleotide polymorphisms (SNPs) associated with PM2.5 concentrations as instrumental variables (IVs). We used inverse-variance weighting (IVW) as the main analytical method, and we selected MR-Egger, weighted median, simple model, and weighted model methods for quality control.
RESULTS: MR analysis showed that PM2.5 has a positive effect on the risk of hypothyroidism: An increase of 1 standard deviation (SD) in PM2.5 concentrations increases the risk of hypothyroidism by ~10.0% (odds ratio 1.10, 95% confidence interval 1.06-1.13, P = 2.93E-08, by IVW analysis); there was no heterogeneity or pleiotropy in the results.
CONCLUSION: In conclusion, increased PM2.5 concentrations are associated with an increased risk of hypothyroidism. This study provides evidence of a causal relationship between PM2.5 and the risk of hypothyroidism, so air pollution control may have important implications for the prevention of hypothyroidism.},
}
@article {pmid36503572,
year = {2022},
author = {Yan, X and Si, H and Zhu, Y and Li, S and Han, Y and Liu, H and Du, R and Pope, PB and Qiu, Q and Li, Z},
title = {Integrated multi-omics of the gastrointestinal microbiome and ruminant host reveals metabolic adaptation underlying early life development.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {222},
pmid = {36503572},
issn = {2049-2618},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Multiomics ; *Deer/microbiology ; Rumen/microbiology ; Fatty Acids, Volatile ; },
abstract = {BACKGROUND: The gastrointestinal tract (GIT) microbiome of ruminants and its metabolic repercussions vastly influence host metabolism and growth. However, a complete understanding of the bidirectional interactions that occur across the host-microbiome axis remains elusive, particularly during the critical development stages at early life. Here, we present an integrative multi-omics approach that simultaneously resolved the taxonomic and functional attributes of microbiota from five GIT regions as well as the metabolic features of the liver, muscle, urine, and serum in sika deer (Cervus nippon) across three key early life stages.
RESULTS: Within the host, analysis of metabolites over time in serum, urine, and muscle (longissimus lumborum) showed that changes in the fatty acid profile were concurrent with gains in body weight. Additional host transcriptomic and metabolomic analysis revealed that fatty acid β-oxidation and metabolism of tryptophan and branched chain amino acids play important roles in regulating hepatic metabolism. Across the varying regions of the GIT, we demonstrated that a complex and variable community of bacteria, viruses, and archaea colonized the GIT soon after birth, whereas microbial succession was driven by the cooperative networks of hub populations. Furthermore, GIT volatile fatty acid concentrations were marked by increased microbial metabolic pathway abundances linked to mannose (rumen) and amino acids (colon) metabolism. Significant functional shifts were also revealed across varying GIT tissues, which were dominated by host fatty acid metabolism associated with reactive oxygen species in the rumen epithelium, and the intensive immune response in both small and large intestine. Finally, we reveal a possible contributing role of necroptosis and apoptosis in enhancing ileum and colon epithelium development, respectively.
CONCLUSIONS: Our findings provide a comprehensive view for the involved mechanisms in the context of GIT microbiome and ruminant metabolic growth at early life. Video Abstract.},
}
@article {pmid36498115,
year = {2022},
author = {Li, W and Liu, R and Sun, L and Guo, Z and Gao, J},
title = {An Investigation of Employees' Intention to Comply with Information Security System-A Mixed Approach Based on Regression Analysis and fsQCA.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {23},
pages = {},
pmid = {36498115},
issn = {1660-4601},
mesh = {Humans ; *Intention ; *Information Systems ; Self Efficacy ; Motivation ; Regression Analysis ; },
abstract = {Employee security compliance behavior has become an important safeguard to protect the security of corporate information assets. Focusing on human factors, this paper discusses how to regulate and guide employees' compliance with information security systems through effective methods. Based on protection motivation theory (PMT), a model of employees' intention to comply with the information security system was constructed. A questionnaire survey was adopted to obtain 224 valid data points, and SPSS 26.0 was applied to verify the hypotheses underlying the research model. Then, based on the results of a regression analysis, fuzzy set qualitative comparative analysis (fsQCA) was used to explore the conditional configurations that affect employees' intention to comply with the information security system from a holistic perspective. The empirical results demonstrated that perceived severity, perceived vulnerability, response efficacy, and self-efficacy all positively influenced the employees' intention to comply with the information security system; while rewards and response costs had a negative effect. Threat appraisal had a greater effect on employees' intention to comply with the information security system compared to response appraisal. The fsQCA results showed that individual antecedent conditions are not necessary to influence employees' intention to comply with an information security system. Seven pathways exist that influence an employees' intention to comply with an information security system, with reward, self-efficacy, and response cost being the core conditions having the highest probability of occurring in each configuration of pathways, and with perceived severity and self-efficacy appearing in the core conditions of configurations with an original coverage greater than 40%. Theoretically, this study discusses the influence of the elements of PMT on employees' intention to comply with an information security system, reveals the mechanism of influence of the combination of the influencing factors on the outcome variables, and identifies the core factors and auxiliary factors in the condition configurations, providing a new broader perspective for the study of information security compliance behavior and providing some theoretical support for strengthening enterprise security management. Practically, targeted suggestions are proposed based on the research results, to increase the intention of enterprise employees to comply with information security systems, thereby improving the effectiveness of enterprise information security management and the degree of information security in enterprises.},
}
@article {pmid36497480,
year = {2022},
author = {Islam, MM and Poly, TN and Walther, BA and Yeh, CY and Seyed-Abdul, S and Li, YJ and Lin, MC},
title = {Deep Learning for the Diagnosis of Esophageal Cancer in Endoscopic Images: A Systematic Review and Meta-Analysis.},
journal = {Cancers},
volume = {14},
number = {23},
pages = {},
pmid = {36497480},
issn = {2072-6694},
abstract = {Esophageal cancer, one of the most common cancers with a poor prognosis, is the sixth leading cause of cancer-related mortality worldwide. Early and accurate diagnosis of esophageal cancer, thus, plays a vital role in choosing the appropriate treatment plan for patients and increasing their survival rate. However, an accurate diagnosis of esophageal cancer requires substantial expertise and experience. Nowadays, the deep learning (DL) model for the diagnosis of esophageal cancer has shown promising performance. Therefore, we conducted an updated meta-analysis to determine the diagnostic accuracy of the DL model for the diagnosis of esophageal cancer. A search of PubMed, EMBASE, Scopus, and Web of Science, between 1 January 2012 and 1 August 2022, was conducted to identify potential studies evaluating the diagnostic performance of the DL model for esophageal cancer using endoscopic images. The study was performed in accordance with PRISMA guidelines. Two reviewers independently assessed potential studies for inclusion and extracted data from retrieved studies. Methodological quality was assessed by using the QUADAS-2 guidelines. The pooled accuracy, sensitivity, specificity, positive and negative predictive value, and the area under the receiver operating curve (AUROC) were calculated using a random effect model. A total of 28 potential studies involving a total of 703,006 images were included. The pooled accuracy, sensitivity, specificity, and positive and negative predictive value of DL for the diagnosis of esophageal cancer were 92.90%, 93.80%, 91.73%, 93.62%, and 91.97%, respectively. The pooled AUROC of DL for the diagnosis of esophageal cancer was 0.96. Furthermore, there was no publication bias among the studies. The findings of our study show that the DL model has great potential to accurately and quickly diagnose esophageal cancer. However, most studies developed their model using endoscopic data from the Asian population. Therefore, we recommend further validation through studies of other populations as well.},
}
@article {pmid36493775,
year = {2022},
author = {Koptekin, D and Yüncü, E and Rodríguez-Varela, R and Altınışık, NE and Psonis, N and Kashuba, N and Yorulmaz, S and George, R and Kazancı, DD and Kaptan, D and Gürün, K and Vural, KB and Gemici, HC and Vassou, D and Daskalaki, E and Karamurat, C and Lagerholm, VK and Erdal, ÖD and Kırdök, E and Marangoni, A and Schachner, A and Üstündağ, H and Shengelia, R and Bitadze, L and Elashvili, M and Stravopodi, E and Özbaşaran, M and Duru, G and Nafplioti, A and Rose, CB and Gencer, T and Darbyshire, G and Gavashelishvili, A and Pitskhelauri, K and Çevik, Ö and Vuruşkan, O and Kyparissi-Apostolika, N and Büyükkarakaya, AM and Oğuzhanoğlu, U and Günel, S and Tabakaki, E and Aliev, A and Ibrahimov, A and Shadlinski, V and Sampson, A and Kılınç, GM and Atakuman, Ç and Stamatakis, A and Poulakakis, N and Erdal, YS and Pavlidis, P and Storå, J and Özer, F and Götherström, A and Somel, M},
title = {Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2022.11.034},
pmid = {36493775},
issn = {1879-0445},
abstract = {We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.},
}
@article {pmid36478264,
year = {2022},
author = {Mairal, M and García-Verdugo, C and Le Roux, JJ and Chau, JH and van Vuuren, BJ and Hui, C and Münzbergová, Z and Chown, SL and Shaw, JD},
title = {Multiple introductions, polyploidy and mixed reproductive strategies are linked to genetic diversity and structure in the most widespread invasive plant across Southern Ocean archipelagos.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mec.16809},
pmid = {36478264},
issn = {1365-294X},
abstract = {Biological invasions in remote areas that experience low human activity provide unique opportunities to elucidate processes responsible for invasion success. Here we study the most widespread invasive plant species across the isolated islands of the Southern Ocean, the annual bluegrass, Poa annua. To analyse geographical variation in genome size, genetic diversity and reproductive strategies, we sampled all major sub-Antarctic archipelagos in this region and generated microsatellite data for 470 individual plants representing 31 populations. We also estimated genome sizes for a subset of individuals using flow cytometry. Occasional events of island colonization are expected to result in high genetic structure among islands, overall low genetic diversity and increased self-fertilization, but we show that this is not the case for P. annua. Microsatellite data indicated low population genetic structure and lack of isolation by distance among the sub-Antarctic archipelagos we sampled, but high population structure within each archipelago. We identified high levels of genetic diversity, low clonality and low selfing rates in sub-Antarctic P. annua populations (contrary to rates typical of continental populations). In turn, estimates of selfing declined in populations as genetic diversity increased. Additionally, we found that most P. annua individuals are probably tetraploid and that only slight variation exists in genome size across the Southern Ocean. Our findings suggest multiple independent introductions of P. annua into the sub-Antarctic, which promoted the establishment of genetically diverse populations. Despite multiple introductions, the adoption of convergent reproductive strategies (outcrossing) happened independently in each major archipelago. The combination of polyploidy and a mixed reproductive strategy probably benefited P. annua in the Southern Ocean by increasing genetic diversity and its ability to cope with the novel environmental conditions.},
}
@article {pmid36477523,
year = {2022},
author = {Takemura, LS and Barbosa, ÁRG and Amaral, BS and Bosco, AAD and Lourenço, DB and Apezzato, M and Barbosa, JABA and Faria, EF and Bianco, B and Lemos, GC and Carneiro, A},
title = {Radical prostatectomies for treatment of prostate cancer: trends in a ten-year period in public health services in the city of São Paulo, Brazil.},
journal = {Einstein (Sao Paulo, Brazil)},
volume = {20},
number = {},
pages = {eAO0049},
pmid = {36477523},
issn = {2317-6385},
mesh = {United States ; Humans ; Male ; Brazil/epidemiology ; *Prostatic Neoplasms/surgery ; Health Services ; },
abstract = {OBJECTIVE: To analyze the characteristics of public health services related to radical prostatectomy, according to hospital volume of surgeries and stratified as academic and non-academic centers.
METHODS: An ecological study was conducted using a database available in TabNet platform of the Unified Health System Department of Informatics. Number of surgeries, length of hospital stay, length of stay in intensive care unit, in-hospital mortality rate, and cost of hospitalization were evaluated. The hospitals were divided into three subgroups according to surgery volume (tercile), and results were compared. The same comparisons were made among academic and non-academic centers. We considered academic centers those providing Urology residency program.
RESULTS: A total of 11,259 radical prostatectomies were performed in the city of São Paulo between 2008 and 2018. We observed a significant trend of increase in radical prostatectomies for treating prostate cancer over the years (p=0.007). The length of stay in intensive care unit, and number of deaths were not statistically different among centers with diverse surgery volume, nor between academic and non-academic centers. However, length of hospital stay was significantly shorter in academic centers (p=0.043), while cost of hospitalization was significantly higher in high-volume center compared to low- (p<0.001) and intermediate-volume centers (p<0.001).
CONCLUSION: Length of hospital stay for radical prostatectomies performed in public services in the city of São Paulo was shorter in academic centers, whereas hospitals with a high volume of surgeries showed greater cost of hospitalization.},
}
@article {pmid36475098,
year = {2022},
author = {Karaarslan, F and Yılmaz, H and Akkurt, HE and Kaya, FM and Şafak Yılmaz, E},
title = {Comparison of the efficacy of mud-pack and hot-pack treatments in chronic non-specific neck pain: A single-blind, randomized-controlled study.},
journal = {Turkish journal of physical medicine and rehabilitation},
volume = {68},
number = {3},
pages = {381-390},
pmid = {36475098},
issn = {2587-1250},
abstract = {OBJECTIVES: This study aims to compare the short-term efficacy of mud-pack (MP) and hot-pack (HP) treatments with the same temperature and duration on sleep, function, depression, and quality of life for chronic non-specific neck pain (CNNP) patients.
PATIENTS AND METHODS: Between December 2018 and September 2019, a total of 70 patients with CNNP diagnosis (12 males, 58 females; mean age: 50.2±9.4 years; range, 24 to 65 years) were included. The patients were divided into two groups. The MP group (n=35) had a total of 15 sessions of MP for 20 min + transcutaneous electrical nerve stimulation (TENS) for 20 min + home exercise (HE) on five days per week for three weeks. The HP group (n=35) had 15 similar sessions of HP for 20 min + TENS for 20 min + HE. The patients were assessed with the Visual Analog Scale (VAS-pain), VAS physician's and patient's global assessments, modified Neck Disability Index (mNDI), Beck Depression Inventory (BDI), Pittsburgh Sleep Quality Index (PSQI), and Short Form-36 (SF-36) measures before treatment, at the end of post-treatment third week and one month later.
RESULTS: In the MP group, there were statistically significant improvements in all parameters at the end of treatment three-week and one-month follow-up (p<0.05), apart from SF-36 Vitality/Energy (SF-36V/E) at the end of treatment and SF-36 General Health (SF-36GH) at one month. In the HP group, there were statistically significant improvements observed for all parameters (p<0.05), apart from the SF-36 Physical Role and SF-36GH at the end of treatment third week and SF-36V/E at the first-month assessment. The VAS-pain(p<0.001), mNDI (p=0.019), BDI (p=0.002), SF-36GH (p<0.001), SF-36V/E (p<0.001) and SF-36 mental health (p<0.001) showed statistically significantly superior improvements in the MP group (p<0.05).
CONCLUSION: In CNNP patients, both MP and HP treatments are effective. However, MP therapy has more positive effects on pain, function, depression, and quality of life parameters. The MP treatment may be used in addition to TENS treatment for CNNP patients.},
}
@article {pmid36473660,
year = {2022},
author = {Simeoni, C and Furlan, E and Pham, HV and Critto, A and de Juan, S and Trégarot, E and Cornet, CC and Meesters, E and Fonseca, C and Botelho, AZ and Krause, T and N'Guetta, A and Cordova, FE and Failler, P and Marcomini, A},
title = {Evaluating the combined effect of climate and anthropogenic stressors on marine coastal ecosystems: Insights from a systematic review of cumulative impact assessment approaches.},
journal = {The Science of the total environment},
volume = {861},
number = {},
pages = {160687},
doi = {10.1016/j.scitotenv.2022.160687},
pmid = {36473660},
issn = {1879-1026},
abstract = {Cumulative impacts increasingly threaten marine and coastal ecosystems. To address this issue, the research community has invested efforts on designing and testing different methodological approaches and tools that apply cumulative impact appraisal schemes for a sound evaluation of the complex interactions and dynamics among multiple pressures affecting marine and coastal ecosystems. Through an iterative scientometric and systematic literature review, this paper provides the state of the art of cumulative impact assessment approaches and applications. It gives a specific attention to cutting-edge approaches that explore and model inter-relations among climatic and anthropogenic pressures, vulnerability and resilience of marine and coastal ecosystems to these pressures, and the resulting changes in ecosystem services flow. Despite recent advances in computer sciences and the rising availability of big data for environmental monitoring and management, this literature review evidenced that the implementation of advanced complex system methods for cumulative risk assessment remains limited. Moreover, experts have only recently started integrating ecosystem services flow into cumulative impact appraisal frameworks, but more as a general assessment endpoint within the overall evaluation process (e.g. changes in the bundle of ecosystem services against cumulative impacts). The review also highlights a lack of integrated approaches and complex tools able to frame, explain, and model spatio-temporal dynamics of marine and coastal ecosystems' response to multiple pressures, as required under relevant EU legislation (e.g., Water Framework and Marine Strategy Framework Directives). Progress in understanding cumulative impacts, exploiting the functionalities of more sophisticated machine learning-based approaches (e.g., big data integration), will support decision-makers in the achievement of environmental and sustainability objectives.},
}
@article {pmid36469956,
year = {2022},
author = {Marcusson-Clavertz, D and Persson, SD and Davidson, P and Kim, J and Cardeña, E and Kuehner, C},
title = {Mind wandering and sleep in daily life: A combined actigraphy and experience sampling study.},
journal = {Consciousness and cognition},
volume = {107},
number = {},
pages = {103447},
doi = {10.1016/j.concog.2022.103447},
pmid = {36469956},
issn = {1090-2376},
abstract = {Individuals who sleep poorly report spending more time mind wandering during the day. However, past research has relied on self-report measures of sleep or measured mind wandering during laboratory tasks, which prevents generalization to everyday contexts. We used ambulatory assessments to examine the relations between several features of sleep (duration, fragmentation, and disturbances) and mind wandering (task-unrelated, stimulus-independent, and unguided thoughts). Participants wore a wristband device that collected actigraphy and experience-sampling data across 7 days and 8 nights. Contrary to our expectations, task-unrelated and stimulus-independent thoughts were not associated with sleep either within- or between-persons (n = 164). Instead, individual differences in unguided thoughts were associated with sleep disturbances and duration, suggesting that individuals who more often experience unguided train-of-thoughts have greater sleep disturbances and sleep longer. These results highlight the need to consider the context and features of mind wandering when relating it to sleep.},
}
@article {pmid36469554,
year = {2022},
author = {Zhao, C and Goldman, M and Smith, BJ and Pollard, KS},
title = {Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.},
journal = {Current protocols},
volume = {2},
number = {12},
pages = {e604},
doi = {10.1002/cpz1.604},
pmid = {36469554},
issn = {2691-1299},
mesh = {*Metagenome/genetics ; Genotype ; Alleles ; *Microbiota/genetics ; Nucleotides ; },
abstract = {The Metagenomic Intra-Species Diversity Analysis System 2 (MIDAS2) is a scalable pipeline that identifies single nucleotide variants and gene copy number variants in metagenomes using comprehensive reference databases built from public microbial genome collections (metagenotyping). MIDAS2 is the first metagenotyping tool with functionality to control metagenomic read mapping filters and to customize the reference database to the microbial community, features that improve the precision and recall of detected variants. In this article we present four basic protocols for the most common use cases of MIDAS2, along with supporting protocols for installation and use. In addition, we provide in-depth guidance on adjusting command line parameters, editing the reference database, optimizing hardware utilization, and understanding the metagenotyping results. All the steps of metagenotyping, from raw sequencing reads to population genetic analysis, are demonstrated with example data in two downloadable sequencing libraries of single-end metagenomic reads representing a mixture of multiple bacterial species. This set of protocols empowers users to accurately genotype hundreds of species in thousands of samples, providing rich genetic data for studying the evolution and strain-level ecology of microbial communities. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Species prescreening Basic Protocol 2: Download MIDAS reference database Basic Protocol 3: Population single nucleotide variant calling Basic Protocol 4: Pan-genome copy number variant calling Support Protocol 1: Installing MIDAS2 Support Protocol 2: Command line inputs Support Protocol 3: Metagenotyping with a custom collection of genomes Support Protocol 4: Metagenotyping with advanced parameters.},
}
@article {pmid36458815,
year = {2022},
author = {Yang, B and García-Carreras, B and Lessler, J and Read, JM and Zhu, H and Metcalf, CJE and Hay, JA and Kwok, KO and Shen, R and Jiang, CQ and Guan, Y and Riley, S and Cummings, DA},
title = {Long term intrinsic cycling in human life course antibody responses to influenza A(H3N2): an observational and modeling study.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {36458815},
issn = {2050-084X},
support = {200861/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 200187/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; MR/S004793/1/MRC_/Medical Research Council/United Kingdom ; R56 AG048075/AG/NIA NIH HHS/United States ; R01 AI114703/AI/NIAID NIH HHS/United States ; R01 TW008246/TW/FIC NIH HHS/United States ; },
mesh = {Humans ; *Influenza, Human ; Influenza A Virus, H3N2 Subtype ; *Influenza Vaccines ; Antibody Formation ; Life Change Events ; Antibodies, Viral ; },
abstract = {BACKGROUND: Over a life course, human adaptive immunity to antigenically mutable pathogens exhibits competitive and facilitative interactions. We hypothesize that such interactions may lead to cyclic dynamics in immune responses over a lifetime.
METHODS: To investigate the cyclic behavior, we analyzed hemagglutination inhibition titers against 21 historical influenza A(H3N2) strains spanning 47 years from a cohort in Guangzhou, China, and applied Fourier spectrum analysis. To investigate possible biological mechanisms, we simulated individual antibody profiles encompassing known feedbacks and interactions due to generally recognized immunological mechanisms.
RESULTS: We demonstrated a long-term periodicity (about 24 years) in individual antibody responses. The reported cycles were robust to analytic and sampling approaches. Simulations suggested that individual-level cross-reaction between antigenically similar strains likely explains the reported cycle. We showed that the reported cycles are predictable at both individual and birth cohort level and that cohorts show a diversity of phases of these cycles. Phase of cycle was associated with the risk of seroconversion to circulating strains, after accounting for age and pre-existing titers of the circulating strains.
CONCLUSIONS: Our findings reveal the existence of long-term periodicities in individual antibody responses to A(H3N2). We hypothesize that these cycles are driven by preexisting antibody responses blunting responses to antigenically similar pathogens (by preventing infection and/or robust antibody responses upon infection), leading to reductions in antigen-specific responses over time until individual's increasing risk leads to an infection with an antigenically distant enough virus to generate a robust immune response. These findings could help disentangle cohort effects from individual-level exposure histories, improve our understanding of observed heterogeneous antibody responses to immunizations, and inform targeted vaccine strategy.
FUNDING: This study was supported by grants from the NIH R56AG048075 (DATC, JL), NIH R01AI114703 (DATC, BY), the Wellcome Trust 200861/Z/16/Z (SR), and 200187/Z/15/Z (SR). This work was also supported by research grants from Guangdong Government HZQB-KCZYZ-2021014 and 2019B121205009 (YG and HZ). DATC, JMR and SR acknowledge support from the National Institutes of Health Fogarty Institute (R01TW0008246). JMR acknowledges support from the Medical Research Council (MR/S004793/1) and the Engineering and Physical Sciences Research Council (EP/N014499/1). The funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.},
}
@article {pmid36456926,
year = {2022},
author = {Li, Y and Wei, CM and Li, XY and Meng, DC and Gu, ZJ and Qu, SP and Huang, MJ and Huang, HQ},
title = {De novo transcriptome sequencing of Impatiens uliginosa and the analysis of candidate genes related to spur development.},
journal = {BMC plant biology},
volume = {22},
number = {1},
pages = {553},
pmid = {36456926},
issn = {1471-2229},
mesh = {*Impatiens ; Transcriptome ; Exome Sequencing ; Cell Cycle ; Databases, Protein ; },
abstract = {BACKGROUND: Spur, a structure capable of producing and storing nectar, not only plays a vital role in the pollination process but also promotes the rapid diversification of some plant lineages, which is considered a key innovation in plants. Spur is the focus of many studies, such as evolution and ecological hypothesis, but the current understanding of spur development is limited. High-throughput sequencing of Impatiens uliginosa was carried out to study the molecular mechanism of its spur development, which is believed to provide some insights into the spur development of Impatiens.
RESULTS: Transcriptomic sequencing and analysis were performed on spurs and limbs of I. uliginosa at three developmental stages. A total of 47.83 Gb of clean data were obtained, and 49,716 unigene genes were assembled. After comparison with NR, Swiss-Prot, Pfam, COG, GO and KEGG databases, a total of 27,686 genes were annotated successfully. Through comparative analysis, 19,356 differentially expressed genes were found and enriched into 208 GO terms and 146 KEGG pathways, among which plant hormone signal transduction was the most significantly enriched pathway. One thousand thirty-two transcription factors were identified, which belonged to 33 TF families such as MYB, bHLH and TCP. Twenty candidate genes that may be involved in spur development were screened and verified by qPCR, such as SBP, IAA and ABP.
CONCLUSIONS: Transcriptome data of different developmental stages of spurs were obtained, and a series of candidate genes related to spur development were identified. The importance of genes related to cell cycle, cell division, cell elongation and hormones in spur development was clarified. This study provided valuable information and resources for understanding the molecular mechanism of spur development in Impatiens.},
}
@article {pmid36455989,
year = {2022},
author = {Van Bortel, W and Mariën, J and Jacobs, BKM and Sinzinkayo, D and Sinarinzi, P and Lampaert, E and D'hondt, R and Mafuko, JM and De Weggheleire, A and Vogt, F and Alexander, N and Wint, W and Maes, P and Vanlerberghe, V and Leclair, C},
title = {Long-lasting insecticidal nets provide protection against malaria for only a single year in Burundi, an African highland setting with marked malaria seasonality.},
journal = {BMJ global health},
volume = {7},
number = {12},
pages = {},
pmid = {36455989},
issn = {2059-7908},
mesh = {Humans ; *Insecticides ; Burundi/epidemiology ; *Malaria/epidemiology/prevention & control ; *Health Information Systems ; Time Factors ; },
abstract = {BACKGROUND: Long-lasting insecticidal nets (LLINs) are one of the key interventions in the global fight against malaria. Since 2014, mass distribution campaigns of LLINs aim for universal access by all citizens of Burundi. In this context, we assess the impact of LLINs mass distribution campaigns on malaria incidence, focusing on the endemic highland health districts. We also explored the possible correlation between observed trends in malaria incidence with any variations in climate conditions.
METHODS: Malaria cases for 2011-2019 were obtained from the National Health Information System. We developed a generalised additive model based on a time series of routinely collected data with malaria incidence as the response variable and timing of LLIN distribution as an explanatory variable to investigate the duration and magnitude of the LLIN effect on malaria incidence. We added a seasonal and continuous-time component as further explanatory variables, and health district as a random effect to account for random natural variation in malaria cases between districts.
RESULTS: Malaria transmission in Burundian highlands was clearly seasonal and increased non-linearly over the study period. Further, a fast and steep decline of malaria incidence was noted during the first year after mass LLIN distribution (p<0.0001). In years 2 and 3 after distribution, malaria cases started to rise again to levels higher than before the control intervention.
CONCLUSION: This study highlights that LLINs did reduce the incidence in the first year after a mass distribution campaign, but in the context of Burundi, LLINs lost their impact after only 1 year.},
}
@article {pmid36454025,
year = {2022},
author = {Velasco, VME and Ferreira, A and Zaman, S and Noordermeer, D and Ensminger, I and Wegrzyn, JL},
title = {A long-read and short-read transcriptomics approach provides the first high-quality reference transcriptome and genome annotation for Pseudotsuga menziesii (Douglas-fir).},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkac304},
pmid = {36454025},
issn = {2160-1836},
abstract = {Douglas-fir (Pseudotsuga menziesii) is native to western North America. It grows in a wide range of environmental conditions and is an important timber trees. Although there are several studies on the gene expression responses of Douglas-fir to abiotic cues, the absence of high-quality transcriptome and genome data is a barrier to further investigation. Like for most conifers, the available transcriptome and genome reference dataset for Douglas-fir remains fragmented and requires refinement. We aimed to generate a highly accurate, and complete reference transcriptome and genome annotation. We deep-sequenced the transcriptome of Douglas-fir needles from seedlings that were grown under non-stress control conditions or a combination of heat and drought stress conditions using long-read (LR) and short-read (SR) sequencing platforms. We used two computational approaches, namely de novo and genome-guided LR transcriptome assembly. Using the LR de novo assembly, we identified 1.3X more high-quality transcripts, 1.85X more "complete" genes, and 2.7X more functionally annotated genes compared to the genome-guided assembly approach. We predicted 666 long non-coding RNAs and 12,778 unique protein-coding transcripts including 2,016 putative transcription factors. We leveraged the LR de novo assembled transcriptome with paired-end SR and a published single-end SR transcriptome to generate an improved genome annotation. This was conducted with BRAKER2 and refined based on functional annotation, repetitive content, and transcriptome alignment. This high-quality genome annotation has 51,419 unique gene models derived from 322,631 initial predictions. Overall, our informatics approach provides a new reference Douglas-fir transcriptome assembly and genome annotation with considerably improved completeness and functional annotation.},
}
@article {pmid36451580,
year = {2022},
author = {Danneels, B and Blignaut, M and Marti, G and Sieber, S and Vandamme, P and Meyer, M and Carlier, A},
title = {Cyclitol metabolism is a central feature of Burkholderia leaf symbionts.},
journal = {Environmental microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1462-2920.16292},
pmid = {36451580},
issn = {1462-2920},
support = {203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.},
}
@article {pmid36449461,
year = {2022},
author = {van der Feltz-Cornelis, CM and Sweetman, J and Allsopp, G and Attree, E and Crooks, MG and Cuthbertson, DJ and Forshaw, D and Gabbay, M and Green, A and Heightman, M and Hillman, T and Hishmeh, L and Khunti, K and Lip, GYH and Lorgelly, P and Montgomery, H and Strain, WD and Wall, E and Watkins, C and Williams, N and Wootton, DG and Banerjee, A and , },
title = {STIMULATE-ICP-Delphi (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways Delphi): Study protocol.},
journal = {PloS one},
volume = {17},
number = {11},
pages = {e0277936},
pmid = {36449461},
issn = {1932-6203},
mesh = {Humans ; *COVID-19/epidemiology ; Critical Pathways ; Mental Health ; *Delivery of Health Care, Integrated ; Post-Acute COVID-19 Syndrome ; },
abstract = {INTRODUCTION: As mortality rates from COVID-19 disease fall, the high prevalence of long-term sequelae (Long COVID) is becoming increasingly widespread, challenging healthcare systems globally. Traditional pathways of care for Long Term Conditions (LTCs) have tended to be managed by disease-specific specialties, an approach that has been ineffective in delivering care for patients with multi-morbidity. The multi-system nature of Long COVID and its impact on physical and psychological health demands a more effective model of holistic, integrated care. The evolution of integrated care systems (ICSs) in the UK presents an important opportunity to explore areas of mutual benefit to LTC, multi-morbidity and Long COVID care. There may be benefits in comparing and contrasting ICPs for Long COVID with ICPs for other LTCs.
METHODS AND ANALYSIS: This study aims to evaluate health services requirements for ICPs for Long COVID and their applicability to other LTCs including multi-morbidity and the overlap with medically not yet explained symptoms (MNYES). The study will follow a Delphi design and involve an expert panel of stakeholders including people with lived experience, as well as clinicians with expertise in Long COVID and other LTCs. Study processes will include expert panel and moderator panel meetings, surveys, and interviews. The Delphi process is part of the overall STIMULATE-ICP programme, aimed at improving integrated care for people with Long COVID.
ETHICS AND DISSEMINATION: Ethical approval for this Delphi study has been obtained (Research Governance Board of the University of York) as have approvals for the other STIMULATE-ICP studies. Study outcomes are likely to inform policy for ICPs across LTCs. Results will be disseminated through scientific publication, conference presentation and communications with patients and stakeholders involved in care of other LTCs and Long COVID.
REGISTRATION: Researchregistry: https://www.researchregistry.com/browse-the-registry#home/registrationdetails/6246bfeeeaaed6001f08dadc/.},
}
@article {pmid36447758,
year = {2022},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the square-spot rustic, Xestia xanthographa (Schiffermuller, 1775).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {37},
pmid = {36447758},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Xestia xanthographa (the square-spot rustic; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 934 megabases in span. The majority of the assembly (99.94%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled.},
}
@article {pmid36437091,
year = {2022},
author = {Zhang, KK and He, J and Zhong, YX and Wei, QQ and Chen, F},
title = {[Identification of Soil Heavy Metal Sources Around a Copper-silver Mining Area in Ningxia Based on GIS].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {43},
number = {11},
pages = {5192-5204},
doi = {10.13227/j.hjkx.202201113},
pmid = {36437091},
issn = {0250-3301},
mesh = {Humans ; Soil ; Copper ; Silver ; *Soil Pollutants/analysis ; Geographic Information Systems ; Cadmium/analysis ; Lead/analysis ; Environmental Monitoring/methods ; *Metals, Heavy/analysis ; *Mercury/analysis ; },
abstract = {This study area was based on the catchment area of the Yaoxianzi ditch located in the arid region of western China. A total of 194 topsoil samples of 0-20 cm depth were collected using the mesh distribution method. The contents of nine heavy metals (Ni, Cu, Zn, As, Ag, Cr, Cd, Hg, and Pb) were determined using ICP-MS. The source and spatial distribution of heavy metals were analyzed using PMF and IDW. Spatial autocorrelation and clustering and outlier analysis were performed using the Spatial Statistical Analysis tool of ArcGIS. The main sources and distribution areas of heavy metals in the soil were obtained through comprehensive analysis. In the study area, the average values of Hg, Ag, Cd, and Pb were 20.48, 3.13, 2.23, and 1.12 times the background values, and the maximum values of Cd, Cu, Pb, and As were 10.92, 5.52, 2.03, and 1.39 times the filter values, respectively. The coefficients of variation of Cu, Cd, Pb, and Hg were ordered as Cu(283.23%)>Cd(224.77%)>Pb(144.40%)>Hg(67.12%) and were closely affected by human activities. The heavy metals in the soil around mining areas came from four main sources:natural parent material (32%), the mixed source of mining activities and transportation (17.1%), the mixed source of industrial activities and atmospheric sedimentation (40.3%), and the mixed source of agricultural activity and putting sandy gravel in farmland (10.6%). Cr and Ni, As and Cu, Hg, and Cd could represent these four sources of heavy metal pollution, respectively. The main sources of soil heavy metal pollution were mining activities and agricultural activities. The heavily contaminated areas were distributed in the mining areas in the south of the study area and in the planting areas in the eastern, central, and northwestern parts of the study area.},
}
@article {pmid36435969,
year = {2022},
author = {Kafkas, S and Ma, X and Zhang, X and Topçu, H and Navajas-Pérez, R and Wai, CM and Tang, H and Xu, X and Khodaeiaminjan, M and Güney, M and Paizila, A and Karcı, H and Zhang, X and Lin, J and Lin, H and Herrán, R and Rejón, CR and García-Zea, JA and Robles, F and Muñoz, CDV and Hotz-Wagenblatt, A and Min, XJ and Özkan, H and Motalebipour, EZ and Gozel, H and Çoban, N and Kafkas, NE and Kilian, A and Huang, H and Lv, X and Liu, K and Hu, Q and Jacygrad, E and Palmer, W and Michelmore, R and Ming, R},
title = {Pistachio genomes provide insights into nut tree domestication and ZW sex chromosome evolution.},
journal = {Plant communications},
volume = {},
number = {},
pages = {100497},
doi = {10.1016/j.xplc.2022.100497},
pmid = {36435969},
issn = {2590-3462},
abstract = {Pistachio is a nut crop domesticated in the Fertile Crescent and a dioecious species with ZW sex chromosomes. We sequenced the genomes of Pistacia vera cultivar (cv.) Siirt, the female parent, and P. vera cv. Bagyolu, the male parent. Two chromosome-level reference genomes of pistachio were generated, and Z and W chromosomes were assembled. The ZW chromosomes originated from an autosome following the first inversion, which occurred approximately 8.18 Mya. Three inversion events in the W chromosome led to the formation of a 12.7-Mb (22.8% of the W chromosome) non-recombining region. These W-specific sequences contain several genes of interest that may have played a pivotal role in sex determination and contributed to the initiation and evolution of a ZW sex chromosome system in pistachio. The W-specific genes, including defA, defA-like, DYT1, two PTEN1, and two tandem duplications of six VPS13A paralogs, are strong candidates for sex determination or differentiation. Demographic history analysis of resequenced genomes suggest that cultivated pistachio underwent severe domestication bottlenecks approximately 7640 years ago, dating the domestication event close to the archeological record of pistachio domestication in Iran. We identified 390, 211, and 290 potential selective sweeps in 3 cultivar subgroups that underlie agronomic traits such as nut development and quality, grafting success, flowering time shift, and drought tolerance. These findings have improved our understanding of the genomic basis of sex determination/differentiation and horticulturally important traits and will accelerate the improvement of pistachio cultivars and rootstocks.},
}
@article {pmid36429843,
year = {2022},
author = {Zhang, T and Wang, B and Ge, Y and Li, C},
title = {Research on Green Space Service Space Based on Crowd Aggregation and Activity Characteristics under Big Data-Take Tacheng City as an Example.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {22},
pages = {},
pmid = {36429843},
issn = {1660-4601},
mesh = {Humans ; *Parks, Recreational ; *Big Data ; Cities ; Personal Satisfaction ; },
abstract = {People-oriented planning has become the mainstream of urban space design. As an important research object of urban space, the accessibility and service level of accessibility and service level of green space as important indicators to evaluate the level of urban livability cannot be truly fed back to people's daily life. Therefore, based on big data and from the perspective of crowd activities and aggregation characteristics, this study analyzes the shortage of green space service space in Tacheng City and puts forward suggestions for improvement. The main conclusions are as follows: (1) The satisfaction of green space based on service scope covers up the imbalance of green space resources enjoyed by actual crowd activities and aggregation. (2) Although the accessibility of green space obtained by population density meets the needs in space, it cannot take care of the potential needs generated by daily crowd activities and aggregation, which leads to the overall spatial imbalance of accessibility. (3) The comprehensive analysis shows that the northeast and southwest regions are the focus of the later planning and construction. The southwest region echoes with the old urban area and attracts people's daily activities. The woodland in the northeast region, as the main green space supply, meets the potential needs of the daily population activities and aggregation of the new development urban area and the old urban area, and also serves as a place for rest and entertainment to meet the needs of the activities and aggregation of the accidental behavior of the people in the new and old urban areas after the opening up.},
}
@article {pmid36421254,
year = {2022},
author = {Würstle, S and Hapfelmeier, A and Karapetyan, S and Studen, F and Isaakidou, A and Schneider, T and Schmid, RM and von Delius, S and Gundling, F and Triebelhorn, J and Burgkart, R and Obermeier, A and Mayr, U and Heller, S and Rasch, S and Lahmer, T and Geisler, F and Chan, B and Turner, PE and Rothe, K and Spinner, CD and Schneider, J},
title = {A Novel Machine Learning-Based Point-Score Model as a Non-Invasive Decision-Making Tool for Identifying Infected Ascites in Patients with Hydropic Decompensated Liver Cirrhosis: A Retrospective Multicentre Study.},
journal = {Antibiotics (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
pmid = {36421254},
issn = {2079-6382},
abstract = {This study is aimed at assessing the distinctive features of patients with infected ascites and liver cirrhosis and developing a scoring system to allow for the accurate identification of patients not requiring abdominocentesis to rule out infected ascites. A total of 700 episodes of patients with decompensated liver cirrhosis undergoing abdominocentesis between 2006 and 2020 were included. Overall, 34 clinical, drug, and laboratory features were evaluated using machine learning to identify key differentiation criteria and integrate them into a point-score model. In total, 11 discriminatory features were selected using a Lasso regression model to establish a point-score model. Considering pre-test probabilities for infected ascites of 10%, 15%, and 25%, the negative and positive predictive values of the point-score model for infected ascites were 98.1%, 97.0%, 94.6% and 14.9%, 21.8%, and 34.5%, respectively. Besides the main model, a simplified model was generated, containing only features that are fast to collect, which revealed similar predictive values. Our point-score model appears to be a promising non-invasive approach to rule out infected ascites in clinical routine with high negative predictive values in patients with hydropic decompensated liver cirrhosis, but further external validation in a prospective study is needed.},
}
@article {pmid36419146,
year = {2022},
author = {Atkins, S and Heimo, L and Carter, DJ and Ribas Closa, M and Vanleeuw, L and Chenciner, L and Wambi, P and Sidney-Annerstedt, K and Egere, U and Verkuijl, S and Brands, A and Masini, T and Viney, K and Wingfield, T and Lönnroth, K and Boccia, D},
title = {The socioeconomic impact of tuberculosis on children and adolescents: a scoping review and conceptual framework.},
journal = {BMC public health},
volume = {22},
number = {1},
pages = {2153},
pmid = {36419146},
issn = {1471-2458},
support = {001/WHO_/World Health Organization/International ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Child ; Humans ; Adolescent ; *Tuberculosis/epidemiology ; Social Stigma ; Databases, Factual ; Educational Status ; Knowledge ; },
abstract = {BACKGROUND: Tuberculosis (TB) has been repeatedly shown to have socioeconomic impacts in both individual-level and ecological studies; however, much less is known about this effect among children and adolescents and the extent to which being affected by TB during childhood and adolescence can have life-course implications. This paper describes the results of the development of a conceptual framework and scoping review to review the evidence on the short- and long-term socioeconomic impact of tuberculosis on children and adolescents.
OBJECTIVES: To increase knowledge of the socioeconomic impact of TB on children and adolescents.
METHODS: We developed a conceptual framework of the socioeconomic impact of TB on children and adolescents, and used scoping review methods to search for evidence supporting or disproving it. We searched four academic databases from 1 January 1990 to 6 April 2021 and conducted targeted searches of grey literature. We extracted data using a standard form and analysed data thematically.
RESULTS: Thirty-six studies (29 qualitative, five quantitative and two mixed methods studies) were included in the review. Overall, the evidence supported the conceptual framework, suggesting a severe socioeconomic impact of TB on children and adolescents through all the postulated pathways. Effects ranged from impoverishment, stigma, and family separation, to effects on nutrition and missed education opportunities. TB did not seem to exert a different socioeconomic impact when directly or indirectly affecting children/adolescents, suggesting that TB can affect this group even when they are not affected by the disease. No study provided sufficient follow-up to observe the long-term socioeconomic effect of TB in this age group.
CONCLUSION: The evidence gathered in this review reinforces our understanding of the impact of TB on children and adolescents and highlights the importance of considering effects during the entire life course. Both ad-hoc and sustainable social protection measures and strategies are essential to mitigate the socioeconomic consequences of TB among children and adolescents.},
}
@article {pmid36418120,
year = {2022},
author = {Kumpik, DP and Santos-Rodriguez, R and Selwood, J and Coulthard, E and Twomey, N and Craddock, I and Ben-Shlomo, Y},
title = {A longitudinal observational study of home-based conversations for detecting early dementia: protocol for the CUBOId TV task.},
journal = {BMJ open},
volume = {12},
number = {11},
pages = {e065033},
pmid = {36418120},
issn = {2044-6055},
mesh = {Humans ; Pregnancy ; Female ; *Cognitive Dysfunction/diagnosis/psychology ; Neuropsychological Tests ; Longitudinal Studies ; Biomarkers ; *Dementia/diagnosis/psychology ; Observational Studies as Topic ; },
abstract = {INTRODUCTION: Limitations in effective dementia therapies mean that early diagnosis and monitoring are critical for disease management, but current clinical tools are impractical and/or unreliable, and disregard short-term symptom variability. Behavioural biomarkers of cognitive decline, such as speech, sleep and activity patterns, can manifest prodromal pathological changes. They can be continuously measured at home with smart sensing technologies, and permit leveraging of interpersonal interactions for optimising diagnostic and prognostic performance. Here we describe the ContinUous behavioural Biomarkers Of cognitive Impairment (CUBOId) study, which explores the feasibility of multimodal data fusion for in-home monitoring of mild cognitive impairment (MCI) and early Alzheimer's disease (AD). The report focuses on a subset of CUBOId participants who perform a novel speech task, the 'TV task', designed to track changes in ecologically valid conversations with disease progression.
METHODS AND ANALYSIS: CUBOId is a longitudinal observational study. Participants have diagnoses of MCI or AD, and controls are their live-in partners with no such diagnosis. Multimodal activity data were passively acquired from wearables and in-home fixed sensors over timespans of 8-25 months. At two time points participants completed the TV task over 5 days by recording audio of their conversations as they watched a favourite TV programme, with further testing to be completed after removal of the sensor installations. Behavioural testing is supported by neuropsychological assessment for deriving ground truths on cognitive status. Deep learning will be used to generate fused multimodal activity-speech embeddings for optimisation of diagnostic and predictive performance from speech alone.
ETHICS AND DISSEMINATION: CUBOId was approved by an NHS Research Ethics Committee (Wales REC; ref: 18/WA/0158) and is sponsored by University of Bristol. It is supported by the National Institute for Health Research Clinical Research Network West of England. Results will be reported at conferences and in peer-reviewed scientific journals.},
}
@article {pmid36414269,
year = {2022},
author = {Nguyen, PY and Kanukula, R and McKenzie, JE and Alqaidoom, Z and Brennan, SE and Haddaway, NR and Hamilton, DG and Karunananthan, S and McDonald, S and Moher, D and Nakagawa, S and Nunan, D and Tugwell, P and Welch, VA and Page, MJ},
title = {Changing patterns in reporting and sharing of review data in systematic reviews with meta-analysis of the effects of interventions: cross sectional meta-research study.},
journal = {BMJ (Clinical research ed.)},
volume = {379},
number = {},
pages = {e072428},
pmid = {36414269},
issn = {1756-1833},
mesh = {Humans ; Cross-Sectional Studies ; PubMed ; *Research Design ; Systematic Reviews as Topic ; *Information Dissemination ; },
abstract = {OBJECTIVES: To examine changes in completeness of reporting and frequency of sharing data, analytical code, and other review materials in systematic reviews over time; and factors associated with these changes.
DESIGN: Cross sectional meta-research study.
POPULATION: Random sample of 300 systematic reviews with meta-analysis of aggregate data on the effects of a health, social, behavioural, or educational intervention. Reviews were indexed in PubMed, Science Citation Index, Social Sciences Citation Index, Scopus, and Education Collection in November 2020.
MAIN OUTCOME MEASURES: The extent of complete reporting and the frequency of sharing review materials in the systematic reviews indexed in 2020 were compared with 110 systematic reviews indexed in February 2014. Associations between completeness of reporting and various factors (eg, self-reported use of reporting guidelines, journal policies on data sharing) were examined by calculating risk ratios and 95% confidence intervals.
RESULTS: Several items were reported suboptimally among 300 systematic reviews from 2020, such as a registration record for the review (n=113; 38%), a full search strategy for at least one database (n=214; 71%), methods used to assess risk of bias (n=185; 62%), methods used to prepare data for meta-analysis (n=101; 34%), and source of funding for the review (n=215; 72%). Only a few items not already reported at a high frequency in 2014 were reported more frequently in 2020. No evidence indicated that reviews using a reporting guideline were more completely reported than reviews not using a guideline. Reviews published in 2020 in journals that mandated either data sharing or inclusion of data availability statements were more likely to share their review materials (eg, data, code files) than reviews in journals without such mandates (16/87 (18%) v 4/213 (2%)).
CONCLUSION: Incomplete reporting of several recommended items for systematic reviews persists, even in reviews that claim to have followed a reporting guideline. Journal policies on data sharing might encourage sharing of review materials.},
}
@article {pmid36412269,
year = {2022},
author = {Ebenezer, TE and Low, RS and O'Neill, EC and Huang, I and DeSimone, A and Farrow, SC and Field, RA and Ginger, ML and Guerrero, SA and Hammond, M and Hampl, V and Horst, G and Ishikawa, T and Karnkowska, A and Linton, EW and Myler, P and Nakazawa, M and Cardol, P and Sánchez-Thomas, R and Saville, BJ and Shah, MR and Simpson, AGB and Sur, A and Suzuki, K and Tyler, KM and Zimba, PV and Hall, N and Field, MC},
title = {Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world.},
journal = {Biology open},
volume = {11},
number = {11},
pages = {},
doi = {10.1242/bio.059561},
pmid = {36412269},
issn = {2046-6390},
mesh = {*Euglena/physiology ; Biotechnology ; Symbiosis ; },
abstract = {Euglenoids (Euglenida) are unicellular flagellates possessing exceptionally wide geographical and ecological distribution. Euglenoids combine a biotechnological potential with a unique position in the eukaryotic tree of life. In large part these microbes owe this success to diverse genetics including secondary endosymbiosis and likely additional sources of genes. Multiple euglenoid species have translational applications and show great promise in production of biofuels, nutraceuticals, bioremediation, cancer treatments and more exotically as robotics design simulators. An absence of reference genomes currently limits these applications, including development of efficient tools for identification of critical factors in regulation, growth or optimization of metabolic pathways. The Euglena International Network (EIN) seeks to provide a forum to overcome these challenges. EIN has agreed specific goals, mobilized scientists, established a clear roadmap (Grand Challenges), connected academic and industry stakeholders and is currently formulating policy and partnership principles to propel these efforts in a coordinated and efficient manner.},
}
@article {pmid36408293,
year = {2022},
author = {Ebdon, S and Bisschop, G and Lohse, K and Saccheri, I and Davies, J and , and , and , and , },
title = {The genome sequence of the orange-tip butterfly, Anthocharis cardamines (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {260},
pmid = {36408293},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Anthocharis cardamines (the orange-tip; Arthropoda; Insecta; Lepidoptera; Pieridae). The genome sequence is 360 megabases in span. The majority (99.74%) of the assembly is scaffolded into 31 chromosomal pseudomolecules, with the W and Z sex chromosomes assembled. Gene annotation of this assembly on Ensembl has identified 12,477 protein coding genes.},
}
@article {pmid36407110,
year = {2022},
author = {Michel, L and Palma, K and Cerda, M and Lagadec, R and Mayeur, H and Fuentès, M and Besseau, L and Martin, P and Magnanou, E and Blader, P and Concha, ML and Mazan, S},
title = {Diversification of habenular organization and asymmetries in teleosts: Insights from the Atlantic salmon and European eel.},
journal = {Frontiers in cell and developmental biology},
volume = {10},
number = {},
pages = {1015074},
pmid = {36407110},
issn = {2296-634X},
abstract = {Habenulae asymmetries are widespread across vertebrates and analyses in zebrafish, the reference model organism for this process, have provided insight into their molecular nature, their mechanisms of formation and their important roles in the integration of environmental and internal cues with a variety of organismal adaptive responses. However, the generality of the characteristics identified in this species remains an open question, even on a relatively short evolutionary scale, in teleosts. To address this question, we have characterized the broad organization of habenulae in the Atlantic salmon and quantified the asymmetries in each of the identified subdomains. Our results show that a highly conserved partitioning into a dorsal and a ventral component is retained in the Atlantic salmon and that asymmetries are mainly observed in the former as in zebrafish. A remarkable difference is that a prominent left-restricted pax6 positive nucleus is observed in the Atlantic salmon, but undetectable in zebrafish. This nucleus is not observed outside teleosts, and harbors a complex presence/absence pattern in this group, retaining its location and cytoarchitectonic organization in an elopomorph, the European eel. These findings suggest an ancient origin and high evolvability of this trait in the taxon. Taken together, our data raise novel questions about the variability of asymmetries across teleosts and their biological significance depending on ecological contexts.},
}
@article {pmid36405737,
year = {2022},
author = {Yousaf, M and Ismail, S and Ullah, A and Bibi, S},
title = {Immuno-informatics profiling of monkeypox virus cell surface binding protein for designing a next generation multi-valent peptide-based vaccine.},
journal = {Frontiers in immunology},
volume = {13},
number = {},
pages = {1035924},
pmid = {36405737},
issn = {1664-3224},
mesh = {Humans ; *Monkeypox virus ; Molecular Docking Simulation ; Membrane Proteins ; *Monkeypox ; Vaccines, Subunit ; Epitopes, T-Lymphocyte ; },
abstract = {Monkeypox is a viral etiological agent with hallmarks analogous to those observed in smallpox cases in the past. The ongoing outbreak of Monkeypox viral infection is becoming a global health problem. Multi-valent peptide based next generation vaccines provides us a promising solution to combat these emerging infectious diseases by eliciting cell-mediated and humoral immune response. Considering the success rate of subtractive proteomics pipeline and reverse vaccinology approach, in this study, we have developed a novel, next-generation, multi-valent, in silico peptide based vaccine construct by employing cell surface binding protein. After analyzing physiochemical and biological properties of the selected target, the protein was subjected to B cell derived T cell epitope mapping. Iterative scrutinization lead to the identification of two highly antigenic, virulent, non-allergic, non-toxic, water soluble, and Interferon-gamma inducer epitopes i.e. HYITENYRN and TTSPVRENY. We estimated that the shortlisted epitopes for vaccine construction, roughly correspond to 99.74% of the world's population. UK, Finland and Sweden had the highest overall population coverage at 100% which is followed by Austria (99.99%), Germany (99.99%), France (99.98%), Poland (99.96), Croatia (99.93), Czech Republic (99.87%), Belgium (99.87), Italy (99.86%), China (97.83%), India (97.35%) and Pakistan (97.13%). The designed vaccine construct comprises of 150 amino acids with a molecular weight of 16.97242 kDa. Molecular docking studies of the modelled MEMPV (Multi-epitope Monkeypox Vaccine) with MHC I (PDB ID: 1I1Y), MHC II (PDB ID: 1KG0), and other immune mediators i.e. toll like receptors TLR3 (PDB ID: 2A0Z), and TLR4 (PDB ID: 4G8A) revealed strong binding affinity with immune receptors. Host immune simulation results predicted that the designed vaccine has strong potency to induce immune responses against target pathogen in the form of cellular and antibody-dependent immunity. Our findings suggest that the hypothesized vaccine candidate can be utilized as a potential therapeutic against Monkeypox however experimental study is required to validate the results and safe immunogenicity.},
}
@article {pmid36399496,
year = {2022},
author = {Terlouw, BR and Blin, K and Navarro-Muñoz, JC and Avalon, NE and Chevrette, MG and Egbert, S and Lee, S and Meijer, D and Recchia, MJJ and Reitz, ZL and van Santen, JA and Selem-Mojica, N and Tørring, T and Zaroubi, L and Alanjary, M and Aleti, G and Aguilar, C and Al-Salihi, SAA and Augustijn, HE and Avelar-Rivas, JA and Avitia-Domínguez, LA and Barona-Gómez, F and Bernaldo-Agüero, J and Bielinski, VA and Biermann, F and Booth, TJ and Carrion Bravo, VJ and Castelo-Branco, R and Chagas, FO and Cruz-Morales, P and Du, C and Duncan, KR and Gavriilidou, A and Gayrard, D and Gutiérrez-García, K and Haslinger, K and Helfrich, EJN and van der Hooft, JJJ and Jati, AP and Kalkreuter, E and Kalyvas, N and Kang, KB and Kautsar, S and Kim, W and Kunjapur, AM and Li, YX and Lin, GM and Loureiro, C and Louwen, JJR and Louwen, NLL and Lund, G and Parra, J and Philmus, B and Pourmohsenin, B and Pronk, LJU and Rego, A and Rex, DAB and Robinson, S and Rosas-Becerra, LR and Roxborough, ET and Schorn, MA and Scobie, DJ and Singh, KS and Sokolova, N and Tang, X and Udwary, D and Vigneshwari, A and Vind, K and Vromans, SPJM and Waschulin, V and Williams, SE and Winter, JM and Witte, TE and Xie, H and Yang, D and Yu, J and Zdouc, M and Zhong, Z and Collemare, J and Linington, RG and Weber, T and Medema, MH},
title = {MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkac1049},
pmid = {36399496},
issn = {1362-4962},
support = {GM134688/NH/NIH HHS/United States ; BBSRC/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.},
}
@article {pmid36394851,
year = {2022},
author = {Zhang, L and Gong, R and Shi, L and Wen, M and Sun, X and Yabroff, KR and Han, X},
title = {Association of Residential Racial and Economic Segregation With Cancer Mortality in the US.},
journal = {JAMA oncology},
volume = {},
number = {},
pages = {},
pmid = {36394851},
issn = {2374-2445},
abstract = {IMPORTANCE: Residential segregation is a structural risk factor for poor cancer outcomes. Previous research examining the association of residential segregation with cancer outcomes was limited by older data, restricted geographic areas, and few cancer sites. To guide targeted interventions, a comprehensive evaluation of the association between segregation and cancer outcomes is needed.
OBJECTIVE: To examine the association of residential racial and economic segregation with cancer mortality at the US county level for all cancers combined and for the 13 cancer types that represent the top 10 causes of cancer deaths in males or females.
This ecological study used county-level sociodemographic data from the 2015-2019 American Community Survey linked with 2015-2019 county-level mortality data. Data analysis was performed from September 2021 to April 2022.
EXPOSURES: Residential racial and economic segregation measured by the Index of Concentration at the Extremes (ICE) and categorized into quintiles 1 (most deprived) through 5 (most privileged).
MAIN OUTCOMES AND MEASURES: Age-adjusted cancer mortality was the outcome. Multilevel linear mixed modeling was used to calculate the adjusted mortality rate ratio (aRR).
RESULTS: A total of 3110 counties were included. The age-adjusted mortality rates of all cancers combined were 179.8, 177.3, 167.6, 159.6, and 146.1 per 100 000 population (P < .001 for trend) for the 5 ICE categories (most deprived to least deprived), respectively. Compared with the least deprived counties, aRRs for all cancers combined were 1.22 (95% CI, 1.20-1.24) for the most deprived counties, followed by 1.17 (95% CI, 1.15-1.19), 1.10 (95% CI, 1.09-1.12), and 1.06 (95% CI, 1.04-1.08) for the other 3 quintiles, respectively (P < .001 for trend). Segregation was associated with increased mortality from 12 of 13 selected cancer sites, in which aRRs ranged from 1.06 (95% CI, 1.02-1.09) for brain and other nervous system cancer to 1.49 (95% CI, 1.43-1.54) for lung and bronchus cancer.
CONCLUSIONS AND RELEVANCE: The findings of this ecological study suggest that residential racial and economic segregation is associated with higher cancer mortality at the county level, highlighting opportunities for geographically targeted cancer prevention and control efforts.},
}
@article {pmid36383289,
year = {2022},
author = {McGuinness, KN and Klau, GW and Morrison, SM and Moore, EK and Seipp, J and Falkowski, PG and Nanda, V},
title = {Evaluating Mineral Lattices as Evolutionary Proxies for Metalloprotein Evolution.},
journal = {Origins of life and evolution of the biosphere : the journal of the International Society for the Study of the Origin of Life},
volume = {52},
number = {4},
pages = {263-275},
pmid = {36383289},
issn = {1573-0875},
support = {K12GM093854/NH/NIH HHS/United States ; K12GM093854/NH/NIH HHS/United States ; },
mesh = {*Metalloproteins ; Minerals ; *Iron-Sulfur Proteins/chemistry/metabolism ; Sulfur/chemistry/metabolism ; Iron/chemistry ; },
abstract = {Protein coordinated iron-sulfur clusters drive electron flow within metabolic pathways for organisms throughout the tree of life. It is not known how iron-sulfur clusters were first incorporated into proteins. Structural analogies to iron-sulfide minerals present on early Earth, suggest a connection in the evolution of both proteins and minerals. The availability of large protein and mineral crystallographic structure data sets, provides an opportunity to explore co-evolution of proteins and minerals on a large-scale using informatics approaches. However, quantitative comparisons are confounded by the infinite, repeating nature of the mineral lattice, in contrast to metal clusters in proteins, which are finite in size. We address this problem using the Niggli reduction to transform a mineral lattice to a finite, unique structure that when translated reproduces the crystal lattice. Protein and reduced mineral structures were represented as quotient graphs with the edges and nodes corresponding to bonds and atoms, respectively. We developed a graph theory-based method to calculate the maximum common connected edge subgraph (MCCES) between mineral and protein quotient graphs. MCCES can accommodate differences in structural volumes and easily allows additional chemical criteria to be considered when calculating similarity. To account for graph size differences, we use the Tversky similarity index. Using consistent criteria, we found little similarity between putative ancient iron-sulfur protein clusters and iron-sulfur mineral lattices, suggesting these metal sites are not as evolutionarily connected as once thought. We discuss possible evolutionary implications of these findings in addition to suggesting an alternative proxy, mineral surfaces, for better understanding the coevolution of the geosphere and biosphere.},
}
@article {pmid36378489,
year = {2022},
author = {Gupta, VK and Bakshi, U and Chang, D and Lee, AR and Davis, JM and Chandrasekaran, S and Jin, YS and Freeman, MF and Sung, J},
title = {TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes.},
journal = {mSystems},
volume = {7},
number = {6},
pages = {e0092522},
pmid = {36378489},
issn = {2379-5077},
mesh = {Humans ; Metagenome/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Computational Biology ; Multigene Family/genetics ; },
abstract = {Biosynthetic gene clusters (BGCs) in microbial genomes encode bioactive secondary metabolites (SMs), which can play important roles in microbe-microbe and host-microbe interactions. Given the biological significance of SMs and the current profound interest in the metabolic functions of microbiomes, the unbiased identification of BGCs from high-throughput metagenomic data could offer novel insights into the complex chemical ecology of microbial communities. Currently available tools for predicting BGCs from shotgun metagenomes have several limitations, including the need for computationally demanding read assembly, predicting a narrow breadth of BGC classes, and not providing the SM product. To overcome these limitations, we developed taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC), a command-line tool for predicting experimentally characterized BGCs (and inferring their known SMs) in metagenomes by first pinpointing the microbial species likely to harbor them. We benchmarked TaxiBGC on various simulated metagenomes, showing that our taxonomy-guided approach could predict BGCs with much-improved performance (mean F1 score, 0.56; mean PPV score, 0.80) compared with directly identifying BGCs by mapping sequencing reads onto the BGC genes (mean F1 score, 0.49; mean PPV score, 0.41). Next, by applying TaxiBGC on 2,650 metagenomes from the Human Microbiome Project and various case-control gut microbiome studies, we were able to associate BGCs (and their SMs) with different human body sites and with multiple diseases, including Crohn's disease and liver cirrhosis. In all, TaxiBGC provides an in silico platform to predict experimentally characterized BGCs and their SM production potential in metagenomic data while demonstrating important advantages over existing techniques. IMPORTANCE Currently available bioinformatics tools to identify BGCs from metagenomic sequencing data are limited in their predictive capability or ease of use to even computationally oriented researchers. We present an automated computational pipeline called TaxiBGC, which predicts experimentally characterized BGCs (and infers their known SMs) in shotgun metagenomes by first considering the microbial species source. Through rigorous benchmarking techniques on simulated metagenomes, we show that TaxiBGC provides a significant advantage over existing methods. When demonstrating TaxiBGC on thousands of human microbiome samples, we associate BGCs encoding bacteriocins with different human body sites and diseases, thereby elucidating a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Furthermore, we report for the first time gut microbial BGC associations shared among multiple pathologies. Ultimately, we expect our tool to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.},
}
@article {pmid36378100,
year = {2022},
author = {Oh, AY and Rising, CJ and Gaysynsky, A and Tsakraklides, S and Huang, GC and Chou, WS and Blake, KD and Vanderpool, RC},
title = {Advancing multi-level health communication research: A Delphi study on barriers and opportunities.},
journal = {Translational behavioral medicine},
volume = {12},
number = {12},
pages = {1133-1145},
doi = {10.1093/tbm/ibac068},
pmid = {36378100},
issn = {1613-9860},
support = {HHSN261201800002B/CA/NCI NIH HHS/United States ; HHSN261201800002B/CA/NCI NIH HHS/United States ; },
abstract = {Adopting a multi-level perspective that considers the many interrelated contexts influencing health could make health communication interventions more effective and equitable. However, despite increasing interest in the use of multi-level approaches, multi-level health communication (MLHC) interventions are infrequently utilized. We therefore sought to conduct a modified Delphi study to better understand how researchers conceptualize MLHC interventions and identify opportunities for advancing MLHC work. Communication and health behavior experts were invited to complete two rounds of surveys about the characteristics, benefits, pitfalls, best practices, barriers, and facilitators of MLHC interventions; the role of technology in facilitating MLHC interventions; and ways to advance MLHC intervention research (46 experts completed the first survey, 44 completed both surveys). Survey data were analyzed using a mixed-methods approach. Panelists reached consensus on two components of the proposed definition of MLHC interventions and also put forward a set of best practices for these interventions. Panelists felt that most health intervention research could benefit from a multi-level approach, and generally agreed that MLHC approaches offered certain advantages over single-level approaches. However, they also expressed concern related to the time, cost, and complexity of MLHC interventions. Although panelists felt that technology could potentially support MLHC interventions, they also recognized the potential for technology to exacerbate disparities. Finally, panelists prioritized a set of methodological advances and practical supports that would be needed to facilitate future MLHC intervention research. The results of this study point to several future directions for the field, including advancing how interactions between levels are assessed, increasing the empirical evidence base demonstrating the advantages of MLHC interventions, and identifying best practices for the use of technology. The findings also suggest that researchers may need additional support to overcome the perceived practical challenges of conducting MLHC interventions.},
}
@article {pmid36374834,
year = {2022},
author = {Boyle, BL and Maitner, BS and Barbosa, GGC and Sajja, RK and Feng, X and Merow, C and Newman, EA and Park, DS and Roehrdanz, PR and Enquist, BJ},
title = {Geographic name resolution service: A tool for the standardization and indexing of world political division names, with applications to species distribution modeling.},
journal = {PloS one},
volume = {17},
number = {11},
pages = {e0268162},
pmid = {36374834},
issn = {1932-6203},
mesh = {Databases, Factual ; *Biodiversity ; *Names ; Reference Standards ; },
abstract = {Massive biological databases of species occurrences, or georeferenced locations where a species has been observed, are essential inputs for modeling present and future species distributions. Location accuracy is often assessed by determining whether the observation geocoordinates fall within the boundaries of the declared political divisions. This otherwise simple validation is complicated by the difficulty of matching political division names to the correct geospatial object. Spelling errors, abbreviations, alternative codes, and synonyms in multiple languages present daunting name disambiguation challenges. The inability to resolve political division names reduces usable data, and analysis of erroneous observations can lead to flawed results. Here, we present the Geographic Name Resolution Service (GNRS), an application for correcting, standardizing, and indexing world political division names. The GNRS resolves political division names against a reference database that combines names and codes from GeoNames with geospatial object identifiers from the Global Administrative Areas Database (GADM). In a trial resolution of political division names extracted from >270 million species occurrences, only 1.9%, representing just 6% of occurrences, matched exactly to GADM political divisions in their original form. The GNRS was able to resolve, completely or in part, 92% of the remaining 378,568 political division names, or 86% of the full biodiversity occurrence dataset. In assessing geocoordinate accuracy for >239 million species occurrences, resolution of political divisions by the GNRS enabled the detection of an order of magnitude more errors and an order of magnitude more error-free occurrences. By providing a novel solution to a significant data quality impediment, the GNRS liberates a tremendous amount of biodiversity data for quantitative biodiversity research. The GNRS runs as a web service and is accessible via an API, an R package, and a web-based graphical user interface. Its modular architecture is easily integrated into existing data validation workflows.},
}
@article {pmid36365380,
year = {2022},
author = {Ganie, IB and Ahmad, Z and Shahzad, A and Zaushintsena, A and Neverova, O and Ivanova, S and Wasi, A and Tahseen, S},
title = {Biotechnological Intervention and Secondary Metabolite Production in Centella asiatica L.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {21},
pages = {},
pmid = {36365380},
issn = {2223-7747},
abstract = {Centella asiatica L., commonly known as Gotu kola, Indian pennywort, and Asiatic pennyworts, is an herbaceous perennial plant that belongs to the family Apiaceae and has long been used in the traditional medicine system. The plant is known to produce a wide range of active metabolites such as triterpenoids including asiatic acid, asiaticoside, brahmoside, and madecassic acid along with other constituents including centellose, centelloside, and madecassoside, etc., which show immense pharmacological activity. Due to its beneficial role in neuroprotection activity, the plant has been considered as a brain tonic. However, limited cultivation, poor seed viability with low germination rate, and overexploitation for decades have led to severe depletion and threatened its wild stocks. The present review aimed to provide up-to-date information on biotechnological tools applied to this endangered medicinal plant for its in vitro propagation, direct or indirect regeneration, synthetic seed production, strategies for secondary metabolite productions including different elicitors. In addition, a proposed mechanism for the biosynthesis of triterpenoids is also discussed.},
}
@article {pmid36362326,
year = {2022},
author = {Decewicz, P and Kitowicz, M and Radlinska, M},
title = {Characteristics and Comparative Genomic Analysis of a Novel Virus, VarioGold, the First Bacteriophage of Variovorax.},
journal = {International journal of molecular sciences},
volume = {23},
number = {21},
pages = {},
pmid = {36362326},
issn = {1422-0067},
mesh = {*Bacteriophages ; Prophages/genetics ; Sequence Analysis, DNA ; Computational Biology ; Genomics ; Genome, Viral ; },
abstract = {Variovorax represents a widespread and ecologically significant genus of soil bacteria. Despite the ecological importance of these bacteria, our knowledge about the viruses infecting Variovorax spp. is quite poor. This study describes the isolation and characterization of the mitomycin-induced phage, named VarioGold. To the best of our knowledge, VarioGold represents the first characterized virus for this genus. Comparative genomic analyses suggested that VarioGold is distinct from currently known bacteriophages at both the nucleotide and protein levels; thus, it could be considered a new virus genus. In addition, another 37 prophages were distinguished in silico within the complete genomic sequences of Variovorax spp. that are available in public databases. The similarity networking analysis highlighted their general high diversity, which, despite clustering with previously described phages, shows their unique genetic load. Therefore, the novelty of Variovorax phages warrants the great enrichment of databases, which could, in turn, improve bioinformatic strategies for finding (pro)phages.},
}
@article {pmid36357425,
year = {2022},
author = {Oliveira-Rodrigues, C and Correia, AM and Valente, R and Gil, Á and Gandra, M and Liberal, M and Rosso, M and Pierce, G and Sousa-Pinto, I},
title = {Assessing data bias in visual surveys from a cetacean monitoring programme.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {682},
pmid = {36357425},
issn = {2052-4463},
mesh = {Animals ; *Cetacea/physiology ; Data Collection ; Datasets as Topic ; Bias ; },
abstract = {Long-term monitoring datasets are fundamental to understand physical and ecological responses to environmental changes, supporting management and conservation. The data should be reliable, with the sources of bias identified and quantified. CETUS Project is a cetacean monitoring programme in the Eastern North Atlantic, based on visual methods of data collection. This study aims to assess data quality and bias in the CETUS dataset, by 1) applying validation methods, through photographic confirmation of species identification; 2) creating data quality criteria to evaluate the observer's experience; and 3) assessing bias to the number of sightings collected and to the success in species identification. Through photographic validation, the species identification of 10 sightings was corrected and a new species was added to the CETUS dataset. The number of sightings collected was biased by external factors, mostly by sampling effort but also by weather conditions. Ultimately, results highlight the importance of identifying and quantifying data bias, while also yielding guidelines for data collection and processing, relevant for species monitoring programmes based on visual methods.},
}
@article {pmid36352171,
year = {2022},
author = {Mohsen, A and Zeidan, B and Elshemy, M},
title = {Water quality assessment of Lake Burullus, Egypt, utilizing statistical and GIS modeling as environmental hydrology applications.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {1},
pages = {93},
pmid = {36352171},
issn = {1573-2959},
mesh = {*Water Quality ; *Lakes ; Hydrology ; Geographic Information Systems ; Egypt ; Environmental Monitoring/methods ; },
abstract = {GIS is a very powerful tool for analyzing huge amount of data and connecting them with the geography; moreover, recently, there is great advancement in the field. The main objective of this study is to assess the water quality (WQ) and trophic status (TS) conditions of Lake Burullus, Egypt, using statistical modeling (PCA/FA and CA), WQ index (L-WQI), and trophic status index (Carlson TSI and TRIX) approaches, in addition to using GIS tools for building models able to automatically calculate the various indices and producing color coded maps for the lake. The results indicated that PCA/FA grouped the twenty-four WQ parameters into nine principal components explaining 72.6% of the total variance, domestic, and agriculture pollution were dominant. CA divided the twelve sampling stations into most and least polluted groups. The lake WQ was classified as a "Very Poor," according to L-WQI. Moreover, the results of the Carlson TSI and TRIX indices were coincided and classified the eutrophication levels in the lake as "Hyper-Eutrophic" and "Elevated Trophic," respectively. Based on the results of this study, Lake Burullus needs urgent plans for recovering its WQ. Pre-treatment for its drains' effluents and implementing of a periodical WQ monitoring program are highly recommended.},
}
@article {pmid36350456,
year = {2022},
author = {Zhang, X and Dong, X and Liu, F and Lv, T and Wu, Z and Ranagalage, M},
title = {Spatiotemporal dynamics of ecological security in a typical conservation region of southern China based on catastrophe theory and GIS.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {1},
pages = {90},
pmid = {36350456},
issn = {1573-2959},
mesh = {*Ecology/methods ; *Conservation of Natural Resources/methods ; Geographic Information Systems ; Environmental Monitoring ; Ecosystem ; China ; },
abstract = {Ecological security assessment can effectively reflect the ecological status of a region and reveal its level of sustainable development. In this paper, an ecological security-oriented evaluation system was constructed, and the ecological security level of the Dongjiangyuan region from 2000 to 2020 was evaluated based on catastrophe theory and GIS. The results were as follows: (1) As shown in the land use and cover maps, by 2020, the forestland area had decreased the most, and the artificial surface area had increased the most. (2) The ecological security index of the Dongjiangyuan region showed a low trend in the artificial surface area and its surrounding areas. The quite low values of the ecological security index in 2000 and 2010 were improved in 2020 due to the increase in ecological services capacity. The increased vegetation cover from 2000 to 2020 promoted the improved ecological service capacity. (3) The rapid urbanization process in the Dongjiangyuan region resulted in a lower ecological sensitivity index value. Notably, the ecological sensitivity index of the study area had a slightly decreasing trend. (4) The spatial autocorrelation showed that the proportion of hot and cold spots from 2000 to 2020 decreased by 2.96% and 6.91%, respectively. This study can provide a scientific basis and decision-making guidance for ecological management in the Dongjiangyuan region in the future.},
}
@article {pmid36348471,
year = {2022},
author = {Baaijens, JA and Zulli, A and Ott, IM and Nika, I and van der Lugt, MJ and Petrone, ME and Alpert, T and Fauver, JR and Kalinich, CC and Vogels, CBF and Breban, MI and Duvallet, C and McElroy, KA and Ghaeli, N and Imakaev, M and Mckenzie-Bennett, MF and Robison, K and Plocik, A and Schilling, R and Pierson, M and Littlefield, R and Spencer, ML and Simen, BB and , and Hanage, WP and Grubaugh, ND and Peccia, J and Baym, M},
title = {Lineage abundance estimation for SARS-CoV-2 in wastewater using transcriptome quantification techniques.},
journal = {Genome biology},
volume = {23},
number = {1},
pages = {236},
pmid = {36348471},
issn = {1474-760X},
support = {R35 GM133700/GM/NIGMS NIH HHS/United States ; U54 GM088558/GM/NIGMS NIH HHS/United States ; TL1 TR001864/TR/NCATS NIH HHS/United States ; },
mesh = {Humans ; *SARS-CoV-2/genetics ; Wastewater ; RNA, Viral/genetics ; Transcriptome ; *COVID-19 ; },
abstract = {Effectively monitoring the spread of SARS-CoV-2 mutants is essential to efforts to counter the ongoing pandemic. Predicting lineage abundance from wastewater, however, is technically challenging. We show that by sequencing SARS-CoV-2 RNA in wastewater and applying algorithms initially used for transcriptome quantification, we can estimate lineage abundance in wastewater samples. We find high variability in signal among individual samples, but the overall trends match those observed from sequencing clinical samples. Thus, while clinical sequencing remains a more sensitive technique for population surveillance, wastewater sequencing can be used to monitor trends in mutant prevalence in situations where clinical sequencing is unavailable.},
}
@article {pmid36344967,
year = {2022},
author = {Toh, H and Yang, C and Formenti, G and Raja, K and Yan, L and Tracey, A and Chow, W and Howe, K and Bergeron, LA and Zhang, G and Haase, B and Mountcastle, J and Fedrigo, O and Fogg, J and Kirilenko, B and Munegowda, C and Hiller, M and Jain, A and Kihara, D and Rhie, A and Phillippy, AM and Swanson, SA and Jiang, P and Clegg, DO and Jarvis, ED and Thomson, JA and Stewart, R and Chaisson, MJP and Bukhman, YV},
title = {A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes.},
journal = {BMC biology},
volume = {20},
number = {1},
pages = {245},
pmid = {36344967},
issn = {1741-7007},
mesh = {Humans ; Animals ; Haplotypes ; *Diabetes Mellitus, Type 2/genetics ; Murinae ; Genome ; Genomics ; },
abstract = {BACKGROUND: The Nile rat (Avicanthis niloticus) is an important animal model because of its robust diurnal rhythm, a cone-rich retina, and a propensity to develop diet-induced diabetes without chemical or genetic modifications. A closer similarity to humans in these aspects, compared to the widely used Mus musculus and Rattus norvegicus models, holds the promise of better translation of research findings to the clinic.
RESULTS: We report a 2.5 Gb, chromosome-level reference genome assembly with fully resolved parental haplotypes, generated with the Vertebrate Genomes Project (VGP). The assembly is highly contiguous, with contig N50 of 11.1 Mb, scaffold N50 of 83 Mb, and 95.2% of the sequence assigned to chromosomes. We used a novel workflow to identify 3613 segmental duplications and quantify duplicated genes. Comparative analyses revealed unique genomic features of the Nile rat, including some that affect genes associated with type 2 diabetes and metabolic dysfunctions. We discuss 14 genes that are heterozygous in the Nile rat or highly diverged from the house mouse.
CONCLUSIONS: Our findings reflect the exceptional level of genomic resolution present in this assembly, which will greatly expand the potential of the Nile rat as a model organism.},
}
@article {pmid36333350,
year = {2022},
author = {Zhang, X and Zhang, B and Li, J and Yao, Y and Wang, J and Liu, J and Yu, F},
title = {A database of seed plants on taxonomy, geography and ecology in the Qinling-Daba Mountains and adjacent areas.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {672},
pmid = {36333350},
issn = {2052-4463},
mesh = {Humans ; *Biodiversity ; China ; Ecology ; Ecosystem ; Geography ; Plants ; *Seeds ; Databases, Factual ; },
abstract = {The Qinling-Daba Mountains span subtropical and warm temperate zones and are one of the most remarkable biodiversity hotspots in China. Establishing a complete checklist of seed plants organized by nature reserves in the Qinling-Daba Mountains and adjacent areas is an important basis for managing and utilizing plant resources. First, we collected seed plant species data from published checklists representing 58 nature reserves in the Qinling-Daba Mountains and adjacent areas; second, we comprehensively and systematically sorted and integrated these data; third, we proofread and revised the data with the help of the R language and Flora of China dataset; and finally, we set up a seed plant database containing 96148 records, including the name, order, family, genus, life form, and endemism of each species for the entirety of the Qinling-Daba Mountains. The database contains 9491 species of seed plants belonging to 1729 genera, 211 families, and 59 orders, accounting for 39% of China's seed plants.},
}
@article {pmid36329351,
year = {2022},
author = {Pillay, R and Watson, JEM and Hansen, AJ and Jantz, PA and Aragon-Osejo, J and Armenteras, D and Atkinson, SC and Burns, P and Ervin, J and Goetz, SJ and González-Del-Pliego, P and Robinson, NP and Supples, C and Virnig, ALS and Williams, BA and Venter, O},
title = {Humid tropical vertebrates are at lower risk of extinction and population decline in forests with higher structural integrity.},
journal = {Nature ecology & evolution},
volume = {6},
number = {12},
pages = {1840-1849},
pmid = {36329351},
issn = {2397-334X},
mesh = {Animals ; Humans ; *Tropical Climate ; *Conservation of Natural Resources ; Forests ; Biodiversity ; Vertebrates ; },
abstract = {Reducing deforestation underpins global biodiversity conservation efforts. However, this focus on retaining forest cover overlooks the multitude of anthropogenic pressures that can degrade forest quality and imperil biodiversity. We use remotely sensed indices of tropical rainforest structural condition and associated human pressures to quantify the relative importance of forest cover, structural condition and integrity (the cumulative effect of condition and pressures) on vertebrate species extinction risk and population trends across the global humid tropics. We found that tropical rainforests of high integrity (structurally intact and under low pressures) were associated with lower likelihood of species being threatened and having declining populations, compared with forest cover alone (without consideration of condition and pressures). Further, species were more likely to be threatened or have declining populations if their geographic ranges contained high proportions of degraded forest than if their ranges contained lower proportions of forest cover but of high quality. Our work suggests that biodiversity conservation policies to preserve forest integrity are now urgently required alongside ongoing efforts to halt deforestation in the hyperdiverse humid tropics.},
}
@article {pmid36324785,
year = {2022},
author = {Gao, Y and Gong, L and Liu, H and Kong, Y and Wu, X and Guo, Y and Hu, D},
title = {Research on the influencing factors of users' information processing in online health communities based on heuristic-systematic model.},
journal = {Frontiers in psychology},
volume = {13},
number = {},
pages = {966033},
pmid = {36324785},
issn = {1664-1078},
abstract = {With the rapid development of the Internet and the normalization of COVID-19 epidemic prevention and control, Online health communities (OHCs) have gradually become one of the important ways for people to obtain health information, and users have to go through a series of information processing when facing the massive amount of data. Understanding the factors influencing user information processing is necessary to promote users' health literacy, health knowledge popularization and health behavior shaping. Based on the Heuristic-Systematic Model (HSM), Information Ecology Theory, Privacy Trade-Off and Self-Efficacy Theory, we constructed a model of factors influencing user information processing in online health communities. We found that information quality and emotional support had indirect effects on heuristic and systematic information processing, and these effects were mediated by privacy concerns and self-efficacy. In our research model, systematic information processing was most positively influenced directly by self-efficacy. Privacy concerns had a direct negative correlation with both dual information processing pathways. Therefore, OHCs managers should develop relevant regulations to ensure the information quality in OHCs and improve privacy protection services to promote user information processing by improving users' self-efficacy and reducing their privacy concerns. Providing a user-friendly and interactive environment for users is also recommended to create more emotional support, thus facilitating more systematic information processing.},
}
@article {pmid36324701,
year = {2022},
author = {Boyes, D and Holland, PWH and , and , and , and , and , and , },
title = {The genome sequence of the angle shades moth, Phlogophora meticulosa (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {89},
pmid = {36324701},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Phlogophora meticulosa (the angle shades; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 539 megabases in span. The majority of the assembly, 95.17%, is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. Some unassigned scaffolds are identified as belonging to the W chromosome based on half-depth coverage and comparison to other Noctuidae W chromosomes. The mitochondrial genome was also assembled and is 15.4 kilobases in length.},
}
@article {pmid36323316,
year = {2022},
author = {Vatanen, T and Ang, QY and Siegwald, L and Sarker, SA and Le Roy, CI and Duboux, S and Delannoy-Bruno, O and Ngom-Bru, C and Boulangé, CL and Stražar, M and Avila-Pacheco, J and Deik, A and Pierce, K and Bullock, K and Dennis, C and Sultana, S and Sayed, S and Rahman, M and Ahmed, T and Modesto, M and Mattarelli, P and Clish, CB and Vlamakis, H and Plichta, DR and Sakwinska, O and Xavier, RJ},
title = {A distinct clade of Bifidobacterium longum in the gut of Bangladeshi children thrives during weaning.},
journal = {Cell},
volume = {185},
number = {23},
pages = {4280-4297.e12},
doi = {10.1016/j.cell.2022.10.011},
pmid = {36323316},
issn = {1097-4172},
mesh = {Infant ; Child ; Female ; Humans ; Child, Preschool ; *Bifidobacterium longum/metabolism ; Bifidobacterium/metabolism ; Weaning ; Oligosaccharides/metabolism ; Bangladesh ; Milk, Human ; Feces/microbiology ; },
abstract = {The gut microbiome has an important role in infant health and development. We characterized the fecal microbiome and metabolome of 222 young children in Dhaka, Bangladesh during the first two years of life. A distinct Bifidobacterium longum clade expanded with introduction of solid foods and harbored enzymes for utilizing both breast milk and solid food substrates. The clade was highly prevalent in Bangladesh, present globally (at lower prevalence), and correlated with many other gut taxa and metabolites, indicating an important role in gut ecology. We also found that the B. longum clades and associated metabolites were implicated in childhood diarrhea and early growth, including positive associations between growth measures and B. longum subsp. infantis, indolelactate and N-acetylglutamate. Our data demonstrate geographic, cultural, seasonal, and ecological heterogeneity that should be accounted for when identifying microbiome factors implicated in and potentially benefiting infant development.},
}
@article {pmid36322519,
year = {2022},
author = {Wood, ALC and Kirby, KR and Ember, CR and Silbert, S and Passmore, S and Daikoku, H and McBride, J and Paulay, F and Flory, MJ and Szinger, J and D'Arcangelo, G and Bradley, KK and Guarino, M and Atayeva, M and Rifkin, J and Baron, V and El Hajli, M and Szinger, M and Savage, PE},
title = {The Global Jukebox: A public database of performing arts and culture.},
journal = {PloS one},
volume = {17},
number = {11},
pages = {e0275469},
pmid = {36322519},
issn = {1932-6203},
mesh = {Humans ; Reproducibility of Results ; *Music ; Cross-Cultural Comparison ; Language ; Databases, Factual ; Culture ; },
abstract = {Standardized cross-cultural databases of the arts are critical to a balanced scientific understanding of the performing arts, and their role in other domains of human society. This paper introduces the Global Jukebox as a resource for comparative and cross-cultural study of the performing arts and culture. The Global Jukebox adds an extensive and detailed global database of the performing arts that enlarges our understanding of human cultural diversity. Initially prototyped by Alan Lomax in the 1980s, its core is the Cantometrics dataset, encompassing standardized codings on 37 aspects of musical style for 5,776 traditional songs from 1,026 societies. The Cantometrics dataset has been cleaned and checked for reliability and accuracy, and includes a full coding guide with audio training examples (https://theglobaljukebox.org/?songsofearth). Also being released are seven additional datasets coding and describing instrumentation, conversation, popular music, vowel and consonant placement, breath management, social factors, and societies. For the first time, all digitized Global Jukebox data are being made available in open-access, downloadable format (https://github.com/theglobaljukebox), linked with streaming audio recordings (theglobaljukebox.org) to the maximum extent allowed while respecting copyright and the wishes of culture-bearers. The data are cross-indexed with the Database of Peoples, Languages, and Cultures (D-PLACE) to allow researchers to test hypotheses about worldwide coevolution of aesthetic patterns and traditions. As an example, we analyze the global relationship between song style and societal complexity, showing that they are robustly related, in contrast to previous critiques claiming that these proposed relationships were an artifact of autocorrelation (though causal mechanisms remain unresolved).},
}
@article {pmid36316770,
year = {2022},
author = {Ohashi, K and Osanai, T and Fujiwara, K and Tanikawa, T and Tani, Y and Takamiya, S and Sato, H and Morii, Y and Bando, K and Ogasawara, K},
title = {Spatial-temporal analysis of cerebral infarction mortality in Hokkaido, Japan: an ecological study using a conditional autoregressive model.},
journal = {International journal of health geographics},
volume = {21},
number = {1},
pages = {16},
pmid = {36316770},
issn = {1476-072X},
mesh = {Humans ; Bayes Theorem ; Japan/epidemiology ; *Stroke ; Socioeconomic Factors ; Cerebral Infarction/diagnosis/epidemiology/therapy ; },
abstract = {BACKGROUND: Accessibility to stroke treatments is a challenge that depends on the place of residence. However, recent advances in medical technology have improved health outcomes. Nevertheless, the geographic heterogeneity of medical resources may increase regional disparities. Therefore, evaluating spatial and temporal influences of the medical system on regional outcomes and advanced treatment of cerebral infarction are important from a health policy perspective. This spatial and temporal study aims to identify factors associated with mortality and to clarify regional disparities in cerebral infarction mortality at municipality level.
METHODS: This ecological study used public data between 2010 and 2020 from municipalities in Hokkaido, Japan. We applied spatial and temporal condition autoregression analysis in a Bayesian setting, with inference based on the Markov chain Monte Carlo simulation. The response variable was the number of deaths due to cerebral infarction (ICD-10 code: I63). The explanatory variables were healthcare accessibility and socioeconomic status.
RESULTS: The large number of emergency hospitals per 10,000 people (relative risk (RR) = 0.906, credible interval (Cr) = 0.861 to 0.954) was associated with low mortality. On the other hand, the large number of general hospitals per 10,000 people (RR = 1.123, Cr = 1.068 to 1.178) and longer distance to primary stroke centers (RR = 1.064, Cr = 1.014 to 1.110) were associated with high mortality. The standardized mortality ratio decreased from 2010 to 2020 in Hokkaido by approximately 44%. Regional disparity in mortality remained at the same level from 2010 to 2015, after which it narrowed by approximately 5% to 2020. After mapping, we identified municipalities with high mortality rates that emerged in Hokkaido's central and northeastern parts.
CONCLUSION: Cerebral infarction mortality rates and the disparity in Hokkaido improved during the study period (2010-2020). This study emphasized that healthcare accessibility through places such as emergency hospitals and primary stroke centers was important in determining cerebral infarction mortality at the municipality level. In addition, this study identified municipalities with high mortality rates that require healthcare policy changes. The impact of socioeconomic factors on stroke is a global challenge, and improving access to healthcare may reduce disparities in outcomes.},
}
@article {pmid36316345,
year = {2022},
author = {Yfantidou, S and Karagianni, C and Efstathiou, S and Vakali, A and Palotti, J and Giakatos, DP and Marchioro, T and Kazlouski, A and Ferrari, E and Girdzijauskas, Š},
title = {LifeSnaps, a 4-month multi-modal dataset capturing unobtrusive snapshots of our lives in the wild.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {663},
pmid = {36316345},
issn = {2052-4463},
mesh = {Humans ; *Ecological Momentary Assessment ; Exercise ; *Mental Health ; Sleep ; Surveys and Questionnaires ; },
abstract = {Ubiquitous self-tracking technologies have penetrated various aspects of our lives, from physical and mental health monitoring to fitness and entertainment. Yet, limited data exist on the association between in the wild large-scale physical activity patterns, sleep, stress, and overall health, and behavioral and psychological patterns due to challenges in collecting and releasing such datasets, including waning user engagement or privacy considerations. In this paper, we present the LifeSnaps dataset, a multi-modal, longitudinal, and geographically-distributed dataset containing a plethora of anthropological data, collected unobtrusively for the total course of more than 4 months by n = 71 participants. LifeSnaps contains more than 35 different data types from second to daily granularity, totaling more than 71 M rows of data. The participants contributed their data through validated surveys, ecological momentary assessments, and a Fitbit Sense smartwatch and consented to make these data available to empower future research. We envision that releasing this large-scale dataset of multi-modal real-world data will open novel research opportunities and potential applications in multiple disciplines.},
}
@article {pmid36311410,
year = {2022},
author = {Nicotra, AB and Geange, SR and Bahar, NHA and Carle, H and Catling, A and Garcia, A and Harris, RJ and Head, ML and Jin, M and Whitehead, MR and Zurcher, H and Beckmann, EA},
title = {An innovative approach to using an intensive field course to build scientific and professional skills.},
journal = {Ecology and evolution},
volume = {12},
number = {10},
pages = {e9446},
pmid = {36311410},
issn = {2045-7758},
abstract = {This paper reports on the design and evaluation of Field Studies in Functional Ecology (FSFE), a two-week intensive residential field course that enables students to master core content in functional ecology alongside skills that facilitate their transition from "student" to "scientist." We provide an overview of the course structure, showing how the constituent elements have been designed and refined over successive iterations of the course. We detail how FSFE students: (1) Work closely with discipline specialists to develop a small group project that tests an hypothesis to answer a genuine scientific question in the field; (2) Learn critical skills of data management and communication; and (3) Analyze, interpret, and present their results in the format of a scientific symposium. This process is repeated in an iterative "cognitive apprenticeship" model, supported by a series of workshops that name and explicitly instruct the students in "hard" and "soft" skills (e.g., statistics and teamwork, respectively) critically relevant for research and other careers. FSFE students develop a coherent and nuanced understanding of how to approach and execute ecological studies. The sophisticated knowledge and ecological research skills that they develop during the course is demonstrated through high-quality presentations and peer-reviewed publications in an open-access, student-led journal. We outline our course structure and evaluate its efficacy to show how this novel combination of field course elements allows students to gain maximum value from their educational journey, and to develop cognitive, affective, and reflective tools to help apply their skills as scientists.},
}
@article {pmid36302928,
year = {2022},
author = {Hammoud, R and Tognin, S and Burgess, L and Bergou, N and Smythe, M and Gibbons, J and Davidson, N and Afifi, A and Bakolis, I and Mechelli, A},
title = {Smartphone-based ecological momentary assessment reveals mental health benefits of birdlife.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {17589},
pmid = {36302928},
issn = {2045-2322},
mesh = {Humans ; *Ecological Momentary Assessment ; Smartphone ; Mental Health ; Retrospective Studies ; *Mobile Applications ; },
abstract = {The mental health benefits of everyday encounters with birdlife for mental health are poorly understood. Previous studies have typically relied on retrospective questionnaires or artificial set-ups with little ecological validity. In the present study, we used the Urban Mind smartphone application to examine the impact of seeing or hearing birds on self-reported mental wellbeing in real-life contexts. A sample of 1292 participants completed a total of 26,856 ecological momentary assessments between April 2018 and October 2021. Everyday encounters with birdlife were associated with time-lasting improvements in mental wellbeing. These improvements were evident not only in healthy people but also in those with a diagnosis of depression, the most common mental illness across the world. These findings have potential implications for both environmental and wildlife protection and mental healthcare policies. Specific measures, aimed at preserving and increasing everyday encounters with birdlife in urban areas, should be implemented.},
}
@article {pmid36300397,
year = {2022},
author = {Kulikowski, CA},
title = {50 Years of Achievements and Persistent Challenges for Biomedical and Health Informatics and John Mantas' Educational and Nursing Informatics Contributions.},
journal = {Studies in health technology and informatics},
volume = {300},
number = {},
pages = {1-11},
doi = {10.3233/SHTI220936},
pmid = {36300397},
issn = {1879-8365},
mesh = {*Nursing Informatics ; *Medical Informatics ; Cybernetics ; Expert Systems ; },
abstract = {Biomedical and Health Informatics (BMHI) have been essential catalysts for achievements in medical research and healthcare applications over the past 50 years. These include increasingly sophisticated information systems and data bases for documentation and processing, standardization of biomedical data, nomenclatures, and vocabularies to assist with large scale literature indexing and text analysis for information retrieval, and methods for computationally modeling and analyzing research and clinical data. Statistical and AI techniques for decision support, instrumentation integration, and workflow aids with improved data/information management tools are critical for scientific discoveries in the - omics revolutions with their related drug and vaccine breakthroughs and their translation to clinical and preventive healthcare. Early work on biomedical image and pattern recognition, knowledge-based expert systems, innovative database, software and simulation techniques, natural language processing and computational ontologies have all been invaluable for basic research and education. However, these methods are still in their infancy and many fundamental open scientific problems abound. Scientifically this is due to persistent limitations in understanding biological processes within complex living environments and ecologies. In clinical practice the modeling of fluid practitioner roles and methods as they adjust to novel cybernetic technologies present great opportunities but also the potential of unintended e-iatrogenic harms which must be constrained in order to adhere to ethical Hippocratic norms of responsible behavior. Balancing the art, science, and technologies of BMHI has been a hallmark of debates about the field's historical evolution. The present article reviews selected milestones, achievements, and challenges in BMHI education mainly, from a historical perspective, including some commentaries from leaders and pioneers in the field, a selection of which have been published online recently by the International Medical Informatics Association (IMIA) as the first volume of an IMIA History WG eBook. The focus of this chapter is primarily on the development of BMHI in terms of those of its educational activities which have been most significant during the first half century of IMIA, and it concentrates mainly on the leadership and contributions of John Mantas who is being honored on his retirement by the Symposia in Athens for which this chapter has been written.},
}
@article {pmid36297864,
year = {2022},
author = {Macchia, A and Biribicchi, C and Zaratti, C and Testa Chiari, K and D'Ambrosio, M and Toscano, D and Izzo, FC and La Russa, MF},
title = {Mattel's Barbie: Investigation of a Symbol-Analysis of Polymeric Matrices and Degradation Phenomena for Sixteen Dolls from 1959 to 1976.},
journal = {Polymers},
volume = {14},
number = {20},
pages = {},
pmid = {36297864},
issn = {2073-4360},
abstract = {Mattel's Barbie dolls are the most famous and iconic dolls since 1959. Today, they are being collected by individuals and often conserved in museum environments due to their cultural and historical significance reflecting everyday life and historical events. However, just like most museum objects made of plastics, both historical and more recent Barbies show evident degradation phenomena. Firstly, Barbies were made of plasticized polyvinyl chloride (PVC), affected by the migration of additives-mostly the plasticizers-from the bulk phase to the outermost layer, appearing as a tacky and glossy exudate. Over the years, Barbies' polymeric constituents were replaced with more stable ones, whose additives migration is limited compared to PVC, even though still occurring. Multispectral photography in visible (VIS) and ultraviolet (UV) light, microscopical observations in VIS and UV light, and Fourier Transform Infrared spectroscopy in the Attenuated Total Reflectance mode (FT-IR ATR) were performed to characterize the constituent materials of 15 Barbies produced between 1959 and 1976, bridging the information gap on their processing over the years. The micro-invasive multi-analytical approach also allowed for the characterization of the degradation products, permitting the reference of the exudated compound to the specific bulk polymer.},
}
@article {pmid36297101,
year = {2022},
author = {Maugeri, A and Magnano San Lio, R and Favara, G and La Rosa, MC and La Mastra, C and Riela, PM and Guarnera, L and Battiato, S and Barchitta, M and Agodi, A},
title = {Impact of Eating Context on Dietary Choices of College Students: Evidence from the HEALTHY-UNICT Project.},
journal = {Nutrients},
volume = {14},
number = {20},
pages = {},
pmid = {36297101},
issn = {2072-6643},
mesh = {Humans ; *Diet ; *Vegetables ; Feeding Behavior ; Meals ; Students ; },
abstract = {While personal characteristics have been evaluated as determinants of dietary choices over the years, only recently studies have looked at the impact of eating context. Examining eating context, however, can be challenging. Here, we propose the use of a web-app for the Ecological Momentary Assessment of dietary habits among 138 college students from Catania (Italy) and therefore for examining the impact of eating context on dietary choices. Eating away from home was associated with lower odds of consuming vegetables, fruits, and legumes and higher odds of consuming processed meat, salty snacks, and alcoholic drinks compared with eating at home. Eating in the company of other people was associated with higher odds of consuming vegetables, red meat, fish, legumes, milk, and sugar-sweetened beverages and lower odds of consuming nuts than eating alone. This study proposed a new way to capture and assess how eating environment might affect dietary habits. Based on our results, meal location and social context have significant effects on the dietary choices of college students, pointing to the need to incorporate these aspects into further epidemiological studies.},
}
@article {pmid36296237,
year = {2022},
author = {Trego, A and Keating, C and Nzeteu, C and Graham, A and O'Flaherty, V and Ijaz, UZ},
title = {Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data.},
journal = {Microorganisms},
volume = {10},
number = {10},
pages = {},
pmid = {36296237},
issn = {2076-2607},
support = {14/IA/2371/SFI_/Science Foundation Ireland/Ireland ; 16/RC/3889/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {Understanding microbial ecology through amplifying short read regions, typically 16S rRNA for prokaryotic species or 18S rRNA for eukaryotic species, remains a popular, economical choice. These methods provide relative abundances of key microbial taxa, which, depending on the experimental design, can be used to infer mechanistic ecological underpinnings. In this review, we discuss recent advancements in in situ analytical tools that have the power to elucidate ecological phenomena, unveil the metabolic potential of microbial communities, identify complex multidimensional interactions between species, and compare stability and complexity under different conditions. Additionally, we highlight methods that incorporate various modalities and additional information, which in combination with abundance data, can help us understand how microbial communities respond to change in a typical ecosystem. Whilst the field of microbial informatics continues to progress substantially, our emphasis is on popular methods that are applicable to a broad range of study designs. The application of these methods can increase our mechanistic understanding of the ongoing dynamics of complex microbial communities.},
}
@article {pmid36295335,
year = {2022},
author = {Cherevko, AG and Krygin, AS and Ivanov, AI and Soots, RA and Antonova, IV},
title = {Benefits of Printed Graphene with Variable Resistance for Flexible and Ecological 5G Band Antennas.},
journal = {Materials (Basel, Switzerland)},
volume = {15},
number = {20},
pages = {},
pmid = {36295335},
issn = {1996-1944},
abstract = {The possibility of creating antennas of the 5G standard (5.2-5.9 GHz) with specified electrodynamic characteristics by printing layers of variable thickness using a graphene suspension has been substantiated experimentally and by computer simulation. A graphene suspension for screen printing on photographic paper and other flexible substrates was prepared by means of exfoliation from graphite. The relation between the graphene layer thickness and its sheet resistance was studied with the aim of determining the required thickness of the antenna conductive layer. To create a two-sided dipole, a technology has been developed for the double-sided deposition of graphene layers on photographic paper. The electrodynamic characteristics of graphene and copper antennas of identical design are compared. The antenna design corresponds to the operating frequency of 2.4 GHz. It was found that the use of graphene as a conductive layer made it possible to suppress the fundamental (first) harmonic (2.45 GHz) and to observe radiation at the second harmonic (5.75 GHz). This effect is assumed to observe in the case when the thickness of graphene is lower than that of the skin depth. The result indicates the possibility of changing the antenna electrodynamic characteristics by adjusting the graphene layer thickness.},
}
@article {pmid36293641,
year = {2022},
author = {Zou, H and Liu, Y and Li, B and Luo, W},
title = {Sustainable Development Efficiency of Cultural Landscape Heritage in Urban Fringe Based on GIS-DEA-MI, a Case Study of Wuhan, China.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {20},
pages = {},
pmid = {36293641},
issn = {1660-4601},
mesh = {Humans ; Cities ; *Conservation of Natural Resources/methods ; *Sustainable Development ; Geographic Information Systems ; Urbanization ; China ; },
abstract = {Cultural landscape heritage refers to the rare and irreplaceable cultural landscapes recognized by UNESCO and the World Heritage Committee. It is recognized as a "common works of nature and human beings" of outstanding significance and universal value, and is a type of world heritage. Dueto construction, land isincreasingly limited in urban and rural areasin the process of urbanization, and cultural landscape heritage faces a huge threat, especially larger culturallandscapeheritagelocated at the edgesof cities. However, most of the existing studies have mainly focused on the material protection of heritage but have not paid enough attention to the non-material aspects of heritage sites, failing to reveal the inseparable nature of heritage and land. Therefore, this study takes sustainable development efficiency as its analysis tool, examines two pieces of cultural landscape heritage (the Panlongcheng site and the Tomb of the King of the Ming Dynasty) in the urban edge area of Wuhan, China as examples, innovates and establishes a multidimensional evaluation method based on the GIS-DEA-Ml model, and compares the dynamic changes of the spatial development efficiency and non-spatial development efficiency of the above two cultural landscape heritage cases. The results show that: both the spatial development efficiency and non-spatial development efficiency of Panlongcheng from 2010 to 2019 are significantly higher than that of the Tomb. This method makes up for the deficiency of traditional subjective qualitative analysis. It can be used to study the development efficiency of cultural landscape heritage more objectively and comprehensively, and promote the overall sustainable development of material and intangible cultural heritage. It can provide the basis for early decision-making and post-implementation evaluation for the preservation and utilization of cultural landscape heritage under the background of urban renewal.},
}
@article {pmid36293613,
year = {2022},
author = {Aleni, C and Rinaldi, C and Bettio, V and Mazzucco, E and Antona, A and Meini, C and Loria, E and Bonvicini, P and Cracas, SV and Caristia, S and Rimedio, A and Faggiano, F and Ferrante, D and Capello, D},
title = {Public Attitude towards Biobanking: An Italian University Survey.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {20},
pages = {},
pmid = {36293613},
issn = {1660-4601},
mesh = {Humans ; *Biological Specimen Banks ; Universities ; Attitude ; Public Opinion ; Surveys and Questionnaires ; *Biomedical Research ; },
abstract = {Biobanks have established a critical role in biomedical research by collecting, preserving, organizing, and disseminating biospecimens and related health data, contributing to precision medicine development. Participation in biobanks is influenced by several factors, such as trust in institutions and scientists, knowledge about biobanking, and the consideration of benefit sharing. Understanding public attitudes, fears, and concerns toward biobanking is fundamental to designing targeted interventions to increase trust towards biobanks. The aim of our study was to investigate the level of knowledge and perception of biobanks in students and personnel of the University of Piemonte Orientale. An online questionnaire was designed and administered via e-mail. A total of 17,758 UPO personnel and students were invited to participate in the survey, and 1521 (9.3%) subjects completed the survey. The results showed that 65.0% of the participants were aware of the term "biobank" and knew what the activity of a biobank was, and 76.3% of subjects were willing to provide biospecimens to a research biobank, whereas 67.3% of the respondents were willing to contribute, in addition to biospecimens, their health and lifestyle data. Concerns were raised about the confidentiality of the information (25.6%) and the commercial use of the samples (25.0%). In conclusion, participants were aware of the role that biobanks play in research and were eager to participate for the sake of furthering scientific research. Still, several concerns need to be addressed regarding the confidentiality of the data along with the commercial use of the samples and associated data.},
}
@article {pmid36289166,
year = {2022},
author = {Navidi, MN and Chatrenour, M and Seyedmohammadi, J and Khaki, BD and Moradi-Majd, N and Mirzaei, S},
title = {Ecological potential assessment and land use area estimation of agricultural lands based on multi-time images of Sentinel-2 using ANP-WLC and GIS in Bastam, Iran.},
journal = {Environmental monitoring and assessment},
volume = {195},
number = {1},
pages = {36},
pmid = {36289166},
issn = {1573-2959},
mesh = {Agriculture ; Conservation of Natural Resources/methods ; Environmental Monitoring/methods ; *Geographic Information Systems ; Iran ; Soil ; },
abstract = {The use of land-based ecological potential is a key management factor in achieving sustainable development and conserving soil and water resources. The purpose of this study is to use multi-time images of Sentinel-2 to determine the area of agricultural lands and evaluate their ecological potential in Bastam, Semnan Province, Iran. Therefore, in the first step, the most common agricultural lands (including apricot and grape orchards), field crops (including wheat and forage maize), and their phenological period were determined. Then, the information was classified using, namely support vector machine, maximum likelihood, and minimum distance. In the next step, soil, topography, and climate data were extracted according to expert opinions and the analysis of the basin's natural potential. The ecological evaluation models of the region were applied to homogeneous units, and after calculating the ecological potential index by the integrated ANP-WLC model, the ecological potential map was generated. The results of the land use classification showed that the support vector machine model and the minimum distance, respectively, had the best and worst performance with kappa coefficient of 0.82 and 0.61. The highest area of cultivated lands (3423 hectares) was estimated for wheat and the lowest (738 hectares) for forage maize. Moreover, the results of the ecological potential evaluation showed that 60% of apricot orchards, and 40.19% of the wheat fields, were in the class of good ecological potential. Overall, 2290 hectares were in the poor class, and 4030 hectares in the excellent class in terms of ecological potential.},
}
@article {pmid36287517,
year = {2022},
author = {Gonçalves, ICM and Freitas, RF and Aquino, EC and Carneiro, JA and Lessa, ADC},
title = {Mortality trend from falls in Brazilian older adults from 2000 to 2019.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {25},
number = {},
pages = {e220031},
doi = {10.1590/1980-549720220031.2},
pmid = {36287517},
issn = {1980-5497},
mesh = {Male ; Humans ; Female ; Aged ; *Accidental Falls ; Brazil/epidemiology ; *Quality of Life ; Retrospective Studies ; Information Systems ; Mortality ; },
abstract = {OBJECTIVE: To analyze the trend of mortality from falls among older adults in Brazil from 2000 to 2019.
METHODS: This is an epidemiological, analytical study with an ecological time-series design. A retrospective analysis was performed using secondary health data extracted from the Brazilian Mortality Information System in the specific period. Standardized rates of general and sex- and age-specific mortality were calculated. To observe the mortality trend, the Prais-Winsten model and the Annual Increase Rate (AIR) were used.
RESULTS: We identified 135,209 deaths resulting from falls in older adults in the period from 2000 to 2019. Mortality from falls in general, during the study period, had an upward trend (β=0.023; p<0.001; AIR=5.45%). We observed that both men (β=0.022; p<0.001; AIR=5.19%) and women (β=0.024; p<0.001; AIR=5.72%) had an upward trend. Regarding age group, the results also pointed to an upward mortality trend in all age strata, although higher in older people aged ≥80 years (β=0.027; p<0.001; AIR=6.38%).
CONCLUSION: There was an upward trend in mortality rates in Brazil during the time series studied. These findings suggest the importance of defining a line of care for this age group, focusing on promoting health in older adults and preventing the risk of falls, aiming at a reduction in the number of deaths from this cause and favoring the quality of life of this population.},
}
@article {pmid36287142,
year = {2022},
author = {Miller-Ter Kuile, A and Apigo, A and Bui, A and Butner, K and Childress, JN and Copeland, S and DiFiore, BP and Forbes, ES and Klope, M and Motta, CI and Orr, D and Plummer, KA and Preston, DL and Young, HS},
title = {Changes in invertebrate food web structure between high- and low-productivity environments are driven by intermediate but not top-predator diet shifts.},
journal = {Biology letters},
volume = {18},
number = {10},
pages = {20220364},
pmid = {36287142},
issn = {1744-957X},
mesh = {Animals ; *Food Chain ; *Ecosystem ; Predatory Behavior/physiology ; Invertebrates ; Diet ; },
abstract = {Predator-prey interactions shape ecosystem stability and are influenced by changes in ecosystem productivity. However, because multiple biotic and abiotic drivers shape the trophic responses of predators to productivity, we often observe patterns, but not mechanisms, by which productivity drives food web structure. One way to capture mechanisms shaping trophic responses is to quantify trophic interactions among multiple trophic groups and by using complementary metrics of trophic ecology. In this study, we combine two diet-tracing methods: diet DNA and stable isotopes, for two trophic groups (top predators and intermediate predators) in both low- and high-productivity habitats to elucidate where in the food chain trophic structure shifts in response to changes in underlying ecosystem productivity. We demonstrate that while top predators show increases in isotopic trophic position (δ[15]N) with productivity, neither their isotopic niche size nor their DNA diet composition changes. Conversely, intermediate predators show clear turnover in DNA diet composition towards a more predatory prey base in high-productivity habitats. Taking this multi-trophic approach highlights how predator identity shapes responses in predator-prey interactions across environments with different underlying productivity, building predictive power for understanding the outcomes of ongoing anthropogenic change.},
}
@article {pmid36284162,
year = {2022},
author = {Geneva, AJ and Park, S and Bock, DG and de Mello, PLH and Sarigol, F and Tollis, M and Donihue, CM and Reynolds, RG and Feiner, N and Rasys, AM and Lauderdale, JD and Minchey, SG and Alcala, AJ and Infante, CR and Kolbe, JJ and Schluter, D and Menke, DB and Losos, JB},
title = {Chromosome-scale genome assembly of the brown anole (Anolis sagrei), an emerging model species.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1126},
pmid = {36284162},
issn = {2399-3642},
mesh = {Animals ; *Lizards/genetics ; Genome ; Sex Chromosomes ; Genomics ; X Chromosome ; },
abstract = {Rapid technological improvements are democratizing access to high quality, chromosome-scale genome assemblies. No longer the domain of only the most highly studied model organisms, now non-traditional and emerging model species can be genome-enabled using a combination of sequencing technologies and assembly software. Consequently, old ideas built on sparse sampling across the tree of life have recently been amended in the face of genomic data drawn from a growing number of high-quality reference genomes. Arguably the most valuable are those long-studied species for which much is already known about their biology; what many term emerging model species. Here, we report a highly complete chromosome-scale genome assembly for the brown anole, Anolis sagrei - a lizard species widely studied across a variety of disciplines and for which a high-quality reference genome was long overdue. This assembly exceeds the vast majority of existing reptile and snake genomes in contiguity (N50 = 253.6 Mb) and annotation completeness. Through the analysis of this genome and population resequence data, we examine the history of repetitive element accumulation, identify the X chromosome, and propose a hypothesis for the evolutionary history of fusions between autosomes and the X that led to the sex chromosomes of A. sagrei.},
}
@article {pmid36270368,
year = {2023},
author = {Derx, J and Kılıç, HS and Linke, R and Cervero-Aragó, S and Frick, C and Schijven, J and Kirschner, AKT and Lindner, G and Walochnik, J and Stalder, G and Sommer, R and Saracevic, E and Zessner, M and Blaschke, AP and Farnleitner, AH},
title = {Probabilistic fecal pollution source profiling and microbial source tracking for an urban river catchment.},
journal = {The Science of the total environment},
volume = {857},
number = {Pt 2},
pages = {159533},
doi = {10.1016/j.scitotenv.2022.159533},
pmid = {36270368},
issn = {1879-1026},
mesh = {Animals ; Humans ; Rivers ; Water Pollution/analysis ; Water Microbiology ; *Cryptosporidiosis ; Escherichia coli ; Environmental Monitoring/methods ; *Cryptosporidium ; Feces/chemistry ; Giardia ; Water/analysis ; },
abstract = {We developed an innovative approach to estimate the occurrence and extent of fecal pollution sources for urban river catchments. The methodology consists of 1) catchment surveys complemented by literature data where needed for probabilistic estimates of daily produced fecal indicator (FIBs, E. coli, enterococci) and zoonotic reference pathogen numbers (Campylobacter, Cryptosporidium and Giardia) excreted by human and animal sources in a river catchment, 2) generating a hypothesis about the dominant sources of fecal pollution and selecting a source targeted monitoring design, and 3) verifying the results by comparing measured concentrations of the informed choice of parameters (i.e. chemical tracers, C. perfringensspores, and host-associated genetic microbial source tracking (MST) markers) in the river, and by multi-parametric correlation analysis. We tested the approach at a study area in Vienna, Austria. The daily produced microbial particle numbers according to the probabilistic estimates indicated that, for the dry weather scenario, the discharge of treated wastewater (WWTP) was the primary contributor to fecal pollution. For the wet weather scenario, 80-99 % of the daily produced FIBs and pathogens resulted from combined sewer overflows (CSOs) according to the probabilistic estimates. When testing our hypothesis in the river, the measured concentrations of the human genetic fecal marker were log10 4 higher than for selected animal genetic fecal markers. Our analyses showed for the first-time statistical relationships between C. perfringens spores (used as conservative microbial tracer for communal sewage) and a human genetic fecal marker (i.e. HF183/BacR287) with the reference pathogen Giardia in river water (Spearman rank correlation: 0.78-0.83, p < 0.05. The developed approach facilitates urban water safety management and provides a robust basis for microbial fate and transport models and microbial infection risk assessment.},
}
@article {pmid36263952,
year = {2023},
author = {Jensen, MA and Blatz, DJ and LaLone, CA},
title = {Defining the Biologically Plausible Taxonomic Domain of Applicability of an Adverse Outcome Pathway: A Case Study Linking Nicotinic Acetylcholine Receptor Activation to Colony Death.},
journal = {Environmental toxicology and chemistry},
volume = {42},
number = {1},
pages = {71-87},
doi = {10.1002/etc.5501},
pmid = {36263952},
issn = {1552-8618},
mesh = {Animals ; Bees ; *Adverse Outcome Pathways ; *Receptors, Nicotinic/genetics ; Ecotoxicology/methods ; Databases, Factual ; Amino Acid Sequence ; Risk Assessment ; },
abstract = {For the majority of developed adverse outcome pathways (AOPs), the taxonomic domain of applicability (tDOA) is typically narrowly defined with a single or a handful of species. Defining the tDOA of an AOP is critical for use in regulatory decision-making, particularly when considering protection of untested species. Structural and functional conservation are two elements that can be considered when defining the tDOA. Publicly accessible bioinformatics approaches, such as the Sequence Alignment to Predict Across Species Susceptibility (SeqAPASS) tool, take advantage of existing and growing databases of protein sequence and structural information to provide lines of evidence toward structural conservation of key events (KEs) and KE relationships (KERs) of an AOP. It is anticipated that SeqAPASS results could readily be combined with data derived from empirical toxicity studies to provide evidence of both structural and functional conservation, to define the tDOA for KEs, KERs, and AOPs. Such data could be incorporated in the AOP-Wiki as lines of evidence toward biological plausibility for the tDOA. We present a case study describing the process of using bioinformatics to define the tDOA of an AOP using an AOP linking the activation of the nicotinic acetylcholine receptor to colony death/failure in Apis mellifera. Although the AOP was developed to gain a particular biological understanding relative to A. mellifera health, applicability to other Apis bees, as well as non-Apis bees, has yet to be defined. The present study demonstrates how bioinformatics can be utilized to rapidly take advantage of existing protein sequence and structural knowledge to enhance and inform the tDOA of KEs, KERs, and AOPs, focusing on providing evidence of structural conservation across species. Environ Toxicol Chem 2023;42:71-87. © 2022 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.},
}
@article {pmid36261521,
year = {2022},
author = {Klunk, J and Vilgalys, TP and Demeure, CE and Cheng, X and Shiratori, M and Madej, J and Beau, R and Elli, D and Patino, MI and Redfern, R and DeWitte, SN and Gamble, JA and Boldsen, JL and Carmichael, A and Varlik, N and Eaton, K and Grenier, JC and Golding, GB and Devault, A and Rouillard, JM and Yotova, V and Sindeaux, R and Ye, CJ and Bikaran, M and Dumaine, A and Brinkworth, JF and Missiakas, D and Rouleau, GA and Steinrücken, M and Pizarro-Cerdá, J and Poinar, HN and Barreiro, LB},
title = {Evolution of immune genes is associated with the Black Death.},
journal = {Nature},
volume = {611},
number = {7935},
pages = {312-319},
pmid = {36261521},
issn = {1476-4687},
support = {F32 GM140568/GM/NIGMS NIH HHS/United States ; R01 GM146051/GM/NIGMS NIH HHS/United States ; R56 AI146556/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; Aminopeptidases/genetics/immunology ; *DNA, Ancient ; *Plague/genetics/immunology/microbiology/mortality ; *Yersinia pestis/immunology/pathogenicity ; *Selection, Genetic/immunology ; Europe/epidemiology/ethnology ; *Immunity/genetics ; Datasets as Topic ; *Genetic Predisposition to Disease ; London/epidemiology ; Denmark/epidemiology ; },
abstract = {Infectious diseases are among the strongest selective pressures driving human evolution[1,2]. This includes the single greatest mortality event in recorded history, the first outbreak of the second pandemic of plague, commonly called the Black Death, which was caused by the bacterium Yersinia pestis[3]. This pandemic devastated Afro-Eurasia, killing up to 30-50% of the population[4]. To identify loci that may have been under selection during the Black Death, we characterized genetic variation around immune-related genes from 206 ancient DNA extracts, stemming from two different European populations before, during and after the Black Death. Immune loci are strongly enriched for highly differentiated sites relative to a set of non-immune loci, suggesting positive selection. We identify 245 variants that are highly differentiated within the London dataset, four of which were replicated in an independent cohort from Denmark, and represent the strongest candidates for positive selection. The selected allele for one of these variants, rs2549794, is associated with the production of a full-length (versus truncated) ERAP2 transcript, variation in cytokine response to Y. pestis and increased ability to control intracellular Y. pestis in macrophages. Finally, we show that protective variants overlap with alleles that are today associated with increased susceptibility to autoimmune diseases, providing empirical evidence for the role played by past pandemics in shaping present-day susceptibility to disease.},
}
@article {pmid36261519,
year = {2022},
author = {Jandt, U and Bruelheide, H and Jansen, F and Bonn, A and Grescho, V and Klenke, RA and Sabatini, FM and Bernhardt-Römermann, M and Blüml, V and Dengler, J and Diekmann, M and Doerfler, I and Döring, U and Dullinger, S and Haider, S and Heinken, T and Horchler, P and Kuhn, G and Lindner, M and Metze, K and Müller, N and Naaf, T and Peppler-Lisbach, C and Poschlod, P and Roscher, C and Rosenthal, G and Rumpf, SB and Schmidt, W and Schrautzer, J and Schwabe, A and Schwartze, P and Sperle, T and Stanik, N and Storm, C and Voigt, W and Wegener, U and Wesche, K and Wittig, B and Wulf, M},
title = {More losses than gains during one century of plant biodiversity change in Germany.},
journal = {Nature},
volume = {611},
number = {7936},
pages = {512-518},
pmid = {36261519},
issn = {1476-4687},
mesh = {*Biodiversity ; Germany ; *Plants/classification ; Species Specificity ; Time Factors ; Datasets as Topic ; },
abstract = {Long-term analyses of biodiversity data highlight a 'biodiversity conservation paradox': biological communities show substantial species turnover over the past century[1,2], but changes in species richness are marginal[1,3-5]. Most studies, however, have focused only on the incidence of species, and have not considered changes in local abundance. Here we asked whether analysing changes in the cover of plant species could reveal previously unrecognized patterns of biodiversity change and provide insights into the underlying mechanisms. We compiled and analysed a dataset of 7,738 permanent and semi-permanent vegetation plots from Germany that were surveyed between 2 and 54 times from 1927 to 2020, in total comprising 1,794 species of vascular plants. We found that decrements in cover, averaged across all species and plots, occurred more often than increments; that the number of species that decreased in cover was higher than the number of species that increased; and that decrements were more equally distributed among losers than were gains among winners. Null model simulations confirmed that these trends do not emerge by chance, but are the consequence of species-specific negative effects of environmental changes. In the long run, these trends might result in substantial losses of species at both local and regional scales. Summarizing the changes by decade shows that the inequality in the mean change in species cover of losers and winners diverged as early as the 1960s. We conclude that changes in species cover in communities represent an important but understudied dimension of biodiversity change that should more routinely be considered in time-series analyses.},
}
@article {pmid36261518,
year = {2022},
author = {Jarvis, ED and Formenti, G and Rhie, A and Guarracino, A and Yang, C and Wood, J and Tracey, A and Thibaud-Nissen, F and Vollger, MR and Porubsky, D and Cheng, H and Asri, M and Logsdon, GA and Carnevali, P and Chaisson, MJP and Chin, CS and Cody, S and Collins, J and Ebert, P and Escalona, M and Fedrigo, O and Fulton, RS and Fulton, LL and Garg, S and Gerton, JL and Ghurye, J and Granat, A and Green, RE and Harvey, W and Hasenfeld, P and Hastie, A and Haukness, M and Jaeger, EB and Jain, M and Kirsche, M and Kolmogorov, M and Korbel, JO and Koren, S and Korlach, J and Lee, J and Li, D and Lindsay, T and Lucas, J and Luo, F and Marschall, T and Mitchell, MW and McDaniel, J and Nie, F and Olsen, HE and Olson, ND and Pesout, T and Potapova, T and Puiu, D and Regier, A and Ruan, J and Salzberg, SL and Sanders, AD and Schatz, MC and Schmitt, A and Schneider, VA and Selvaraj, S and Shafin, K and Shumate, A and Stitziel, NO and Stober, C and Torrance, J and Wagner, J and Wang, J and Wenger, A and Xiao, C and Zimin, AV and Zhang, G and Wang, T and Li, H and Garrison, E and Haussler, D and Hall, I and Zook, JM and Eichler, EE and Phillippy, AM and Paten, B and Howe, K and Miga, KH and , },
title = {Semi-automated assembly of high-quality diploid human reference genomes.},
journal = {Nature},
volume = {611},
number = {7936},
pages = {519-531},
pmid = {36261518},
issn = {1476-4687},
support = {U01 HG010961/HG/NHGRI NIH HHS/United States ; R01 HG010040/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; R01 HG010169/HG/NHGRI NIH HHS/United States ; R01 HG002385/HG/NHGRI NIH HHS/United States ; U01 HG010971/HG/NHGRI NIH HHS/United States ; },
mesh = {Humans ; *Chromosome Mapping/standards ; *Diploidy ; *Genome, Human/genetics ; Haplotypes/genetics ; High-Throughput Nucleotide Sequencing/methods/standards ; Sequence Analysis, DNA/methods/standards ; Reference Standards ; *Genomics/methods/standards ; Chromosomes, Human/genetics ; Genetic Variation/genetics ; },
abstract = {The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society[1,2]. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals[3,4]. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome[5]. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity[6]. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.},
}
@article {pmid36257775,
year = {2022},
author = {Peltier, DMP and Anderegg, WRL and Guo, JS and Ogle, K},
title = {Contemporary tree growth shows altered climate memory.},
journal = {Ecology letters},
volume = {25},
number = {12},
pages = {2663-2674},
doi = {10.1111/ele.14130},
pmid = {36257775},
issn = {1461-0248},
mesh = {*Trees ; *Climate Change ; Droughts ; Temperature ; },
abstract = {Trees are long-lived organisms, exhibiting temporally complex growth arising from strong climatic "memory." But conditions are becoming increasingly arid in the western USA. Using a century-long tree-ring network, we find altered climate memory across the entire range of a widespread western US conifer: growth is supported by precipitation falling further into the past (+15 months), while increasingly impacted by more recent temperature conditions (-8 months). Tree-ring datasets can be biased, so we confirm altered climate memory in a second, ecologically-sampled tree-ring network. Predicted drought responses show trees may have also become more sensitive to repeat drought. Finally, plots near sites with relatively longer precipitation memory and shorter temperature memory had significantly lower recent mortality rates (R[2] = 0.61). We argue that increased drought frequency has altered climate memory, demonstrate how non-stationarity may arise from failure to account for memory, and suggest memory length may be predictive of future tree mortality.},
}
@article {pmid36255408,
year = {2022},
author = {Sorokina, M and Ukubayev, T and Koichubekov, B},
title = {Tuberculosis incidence and its socioeconomic determinants: developing a parsimonious model.},
journal = {Annali di igiene : medicina preventiva e di comunita},
volume = {},
number = {},
pages = {},
doi = {10.7416/ai.2022.2549},
pmid = {36255408},
issn = {1120-9135},
abstract = {BACKGROUND: Tuberculosis is a widespread communicable disease, which is one of the top 10 causes of demise globally. Several regression models have been built, and then utilized for the Tuberculosis incidence projections. However, when fitting a multiple linear regression model, an analysis must account for multicollinearity aspects. The present study aimed to develop a parsimonious model that produces unbiased results based on socioeconomic variables as predictors of Tuberculosis incidence.
STUDY DESIGN: Ecological study.
METHODS: Data were collected from the Karaganda Regional Center of Phthisio-pulmonology and Bureau of National Statistics. By multiple linear regression model, we investigated associations between Tuberculosis incidence rate and socioeconomic determinants in Karaganda region, Kazakhstan, during 2001-2019. A Principal components analysis was performed on the socioeconomic variables with oblique rotation. Furthermore, associations of Tuberculosis incidence with the principal components derived from the Principal components analysis were assessed.
RESULTS: The incidence of Tuberculosis in Karaganda region decreased over the period of 2001-2019. Economic development and healthcare capacity were negatively correlated with Tuberculosis incidence. A multiple linear regression equation on Tuberculosis incidence (y) was developed with economic development (x1) and healthcare capacity (x2) clustering two components (utilizing Principal components analysis) to eliminate collinearity: y = 1442 - 454.3x1 - 211.4x2. The incidence of Tuberculosis decreased with the increase of economic development and healthcare capacity.
CONCLUSIONS: In conclusion, the study indicated that economic development and healthcare capacity are closely associated with the incidence of Tuberculosis. The findings support the implementation of optimal preventive measures for Tuberculosis control, including improving the level of economic status, increasing social protection, health expenditure, and strengthening health sector capacity, which are key determinants of the incidence of Tuberculosis.
AUTHORS’ CONTRIBUTION: M. Sorokina supervised the study, Ukubayev T. collected the data, performed statistical analysis, and drafted the manuscript; M. Sorokina and B. Koichubekov, reviewed and edited the manuscript. All authors discussed and contributed to the final manuscript.},
}
@article {pmid36254310,
year = {2022},
author = {Cui, J and Khomkrich, K},
title = {Ethnic Music Inheritance and Environmental Monitoring Using Big Data Analysis from the Cultural Perspective.},
journal = {Journal of environmental and public health},
volume = {2022},
number = {},
pages = {2485596},
pmid = {36254310},
issn = {1687-9813},
mesh = {Big Data ; China ; Data Analysis ; Environmental Monitoring ; Ethnicity/genetics ; Humans ; *Music ; },
abstract = {Ethnic music has too many expectations due to its significance to the national culture. It serves as a mirror, reflecting all the true characteristics of many geographical areas and ethnic groupings. Instilling national self-confidence and fostering national unity are essential outcomes of this. The optimal design plan for Xinjiang folk music inheritance and environmental monitoring based on big data technology is presented in this study from the standpoint of cultural ecology. Big data technology can categorize users who are interested in Xinjiang ethnic music, and after that, through customized recommendation filtering, consumers may be presented with Xinjiang ethnic music that meets their interests. Last but not least, a simulation test and analysis are performed. The algorithm's accuracy is 7.86% higher than that of the conventional algorithm, according to the simulation data. By studying and calculating the user's behavioral traits and interests, this result demonstrates in detail how the recommender system can display the user's content efficiently. However, there are numerous possibilities and varied contexts for the use of clustering techniques in recommender systems. It is crucially vital for directing the protection of ethnic music and fostering the inheritance and development of ethnic culture to conduct design study on the Xinjiang region's ethnic music heritage and development with cultural ecology as the central guiding principle. This article is from "A comprehensive study of Uygur Muqam music art with Chinese characteristics," which aims to improve the data reserve of the world and Southeast Asia on the research of Chinese Uighur Muqam art. Improve the inheritance and development of music in Xinjiang, China, and provide more detailed data to more scholars. This study adopts qualitative research methods and field survey data. The author proposes to focus on the perspective of cultural ecology, based on the use of big data technology, to improve the inheritance and development of Xinjiang national music.},
}
@article {pmid36249208,
year = {2022},
author = {Qamar, AI and Gronwald, L and Timmesfeld, N and Diebner, HH},
title = {Local socio-structural predictors of COVID-19 incidence in Germany.},
journal = {Frontiers in public health},
volume = {10},
number = {},
pages = {970092},
pmid = {36249208},
issn = {2296-2565},
mesh = {*COVID-19/epidemiology ; Germany/epidemiology ; Humans ; Incidence ; Risk Factors ; Socioeconomic Factors ; },
abstract = {Socio-economic conditions and social attitudes are known to represent epidemiological determinants. Credible knowledge on socio-economic driving factors of the COVID-19 epidemic is still incomplete. Based on linear random effects regression, an ecological model is derived to estimate COVID-19 incidence in German rural/urban districts from local socio-economic factors and popularity of political parties in terms of their share of vote. Thereby, records provided by Germany's public health institute (Robert Koch Institute) of weekly notified 7-day incidences per 100,000 inhabitants per district from the outset of the epidemic in 2020 up to December 1, 2021, are used to construct the dependent variable. Local socio-economic conditions including share of votes, retrieved from the Federal Statistical Office of Germany, have been used as potential risk factors. Socio-economic parameters like per capita income, proportions of protection seekers and social benefit claimants, and educational level have negligible impact on incidence. To the contrary, incidence significantly increases with population density and we observe a strong association with vote shares. Popularity of the right-wing party Alternative for Germany (AfD) bears a considerable risk of increasing COVID-19 incidence both in terms of predicting the maximum incidences during three epidemic periods (alternatively, cumulative incidences over the periods are used to quantify the dependent variable) and in a time-continuous sense. Thus, districts with high AfD popularity rank on top in the time-average regarding COVID-19 incidence. The impact of the popularity of the Free Democrats (FDP) is markedly intermittent in the course of time showing two pronounced peaks in incidence but also occasional drops. A moderate risk emanates from popularities of the Green Party (GRÜNE) and the Christian Democratic Union (CDU/CSU) compared to the other parties with lowest risk level. In order to effectively combat the COVID-19 epidemic, public health policymakers are well-advised to account for social attitudes and behavioral patterns reflected in local popularities of political parties, which are conceived as proper surrogates for these attitudes. Whilst causal relations between social attitudes and the presence of parties remain obscure, the political landscape in terms of share of votes constitutes at least viable predictive "markers" relevant for public health policy making.},
}
@article {pmid36248684,
year = {2022},
author = {Laroche, J and Tomassini, A and Volpe, G and Camurri, A and Fadiga, L and D'Ausilio, A},
title = {Interpersonal sensorimotor communication shapes intrapersonal coordination in a musical ensemble.},
journal = {Frontiers in human neuroscience},
volume = {16},
number = {},
pages = {899676},
pmid = {36248684},
issn = {1662-5161},
abstract = {Social behaviors rely on the coordination of multiple effectors within one's own body as well as between the interacting bodies. However, little is known about how coupling at the interpersonal level impacts coordination among body parts at the intrapersonal level, especially in ecological, complex, situations. Here, we perturbed interpersonal sensorimotor communication in violin players of an orchestra and investigated how this impacted musicians' intrapersonal movements coordination. More precisely, first section violinists were asked to turn their back to the conductor and to face the second section of violinists, who still faced the conductor. Motion capture of head and bow kinematics showed that altering the usual interpersonal coupling scheme increased intrapersonal coordination. Our perturbation also induced smaller yet more complex head movements, which spanned multiple, faster timescales that closely matched the metrical levels of the musical score. Importantly, perturbation differentially increased intrapersonal coordination across these timescales. We interpret this behavioral shift as a sensorimotor strategy that exploits periodical movements to effectively tune sensory processing in time and allows coping with the disruption in the interpersonal coupling scheme. As such, head movements, which are usually deemed to fulfill communicative functions, may possibly be adapted to help regulate own performance in time.},
}
@article {pmid36247175,
year = {2022},
author = {Sukma, P and Srinok, K and Papong, S and Supakata, N},
title = {Chula model for sustainable municipal solid waste management in university canteens.},
journal = {Heliyon},
volume = {8},
number = {10},
pages = {e10975},
pmid = {36247175},
issn = {2405-8440},
abstract = {Managing the large amount and variety of waste produced by university canteens is challenging. This study used life cycle assessment (LCA) to investigate sustainable municipal solid waste (MSW) management solutions for Chulalongkorn University (CU) canteens. This study assessed three scenarios for MSW management in CU canteens: the past scenario (prior to the Chula Zero Waste Project in 2016; S1); the current scenario (2017-2021, when the Chula Zero Waste Project's MSW management system was used; S2); and the future scenario (after 2021 with the new MSW management option for CU canteens under Chula Zero Waste; S3). The obtained results were characterized by eight impact categories: climate change, ozone depletion, terrestrial acidification, freshwater eutrophication, human toxicity, photochemical oxidant formation, particulate matter formation, and fossil depletion. The LCA results show that the future scenario (S3) under the Chula Zero Waste Project is sustainable for MSW management. The most environmentally sustainable MSW plan for CU canteens is to reduce, separate it at the source, and reuse materials instead of landfilling mixed waste.},
}
@article {pmid36228685,
year = {2023},
author = {Seyed Hashtroudi, M and Aghadadashi, V and Mehdinia, A and Sheijooni Fumani, N},
title = {Combining theoretical concepts and Geographic Information System (GIS) to highlight source, risk, and hotspots of sedimentary PAHs: A case study of Chabahar Bay.},
journal = {Environmental research},
volume = {216},
number = {Pt 1},
pages = {114540},
doi = {10.1016/j.envres.2022.114540},
pmid = {36228685},
issn = {1096-0953},
mesh = {Geographic Information Systems ; Geologic Sediments/analysis ; Bays ; Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; *Polycyclic Aromatic Hydrocarbons/analysis ; Vehicle Emissions/analysis ; China ; },
abstract = {Sedimentary PAHs are regionalized variables and their levels, source, and ecological hazards must be discussed in relation to their spatial locations. Our research targeted GIS and Chabahar Bay-Iran to trace spatial variability of PAHs, improve the diagnostic ratios and receptor models in source identification, and determine hotspot of PAH-originated hazards. The entropy Voronoi map distinguished an "entropy strip" in which ∑22PAHs levels increased sharply. Different molecular signatures were individually interpolated and the indicative ratios of distinctive sources were extracted and summed by GIS. The resulting code map reduced potential disagreement among molecular signatures and highlighted the areas where petroleum inputs are prevalent. PCA-MLR analysis extracted three potential sources including fossil fuel combustion (54.36%), petrogenic inputs (29.03%), and vehicle exhaust emissions (16.61%). Interpolated risk layers were re-arranged and overlaid via Fuzzy Membership Functions. The obtained ''Fuzzy AND" map showed the hotspot of the study area in the vicinity of a seasonal estuary.},
}
@article {pmid36226159,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Phillips, D and , },
title = {The genome sequence of the brimstone moth, Opisthograptis luteolata (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {227},
pmid = {36226159},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Opisthograptis luteolata (the brimstone moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 363 megabases in span. The majority of the assembly (99.99%) is scaffolded into 31 chromosomal pseudomolecules with the Z sex chromosome assembled. The complete mitochondrial genome was also assembled and is 16.7 kilobases in length.},
}
@article {pmid36225383,
year = {2022},
author = {Richardson, AD and Kong, GV and Taylor, KM and Le Moine, JM and Bowker, MA and Barber, JJ and Basler, D and Carbone, MS and Hayer, M and Koch, GW and Salvatore, MR and Sonnemaker, AW and Trilling, DE},
title = {Soil-atmosphere fluxes of CO2, CH4, and N2O across an experimentally-grown, successional gradient of biocrust community types.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {979825},
pmid = {36225383},
issn = {1664-302X},
abstract = {Biological soil crusts (biocrusts) are critical components of dryland and other ecosystems worldwide, and are increasingly recognized as novel model ecosystems from which more general principles of ecology can be elucidated. Biocrusts are often diverse communities, comprised of both eukaryotic and prokaryotic organisms with a range of metabolic lifestyles that enable the fixation of atmospheric carbon and nitrogen. However, how the function of these biocrust communities varies with succession is incompletely characterized, especially in comparison to more familiar terrestrial ecosystem types such as forests. We conducted a greenhouse experiment to investigate how community composition and soil-atmosphere trace gas fluxes of CO2, CH4, and N2O varied from early-successional light cyanobacterial biocrusts to mid-successional dark cyanobacteria biocrusts and late-successional moss-lichen biocrusts and as biocrusts of each successional stage matured. Cover type richness increased as biocrusts developed, and richness was generally highest in the late-successional moss-lichen biocrusts. Microbial community composition varied in relation to successional stage, but microbial diversity did not differ significantly among stages. Net photosynthetic uptake of CO2 by each biocrust type also increased as biocrusts developed but tended to be moderately greater (by up to ≈25%) for the mid-successional dark cyanobacteria biocrusts than the light cyanobacterial biocrusts or the moss-lichen biocrusts. Rates of soil C accumulation were highest for the dark cyanobacteria biocrusts and light cyanobacteria biocrusts, and lowest for the moss-lichen biocrusts and bare soil controls. Biocrust CH4 and N2O fluxes were not consistently distinguishable from the same fluxes measured from bare soil controls; the measured rates were also substantially lower than have been reported in previous biocrust studies. Our experiment, which uniquely used greenhouse-grown biocrusts to manipulate community composition and accelerate biocrust development, shows how biocrust function varies along a dynamic gradient of biocrust successional stages.},
}
@article {pmid36224329,
year = {2022},
author = {Bayer, N and Hausman, B and Pandey, RV and Deckert, F and Gail, LM and Strobl, J and Pjevac, P and Krall, C and Unterluggauer, L and Redl, A and Bachmayr, V and Kleissl, L and Nehr, M and Kirkegaard, R and Makristathis, A and Watzenboeck, ML and Nica, R and Staud, C and Hammerl, L and Wohlfarth, P and Ecker, RC and Knapp, S and Rabitsch, W and Berry, D and Stary, G},
title = {Disturbances in microbial skin recolonization and cutaneous immune response following allogeneic stem cell transfer.},
journal = {Leukemia},
volume = {36},
number = {11},
pages = {2705-2714},
pmid = {36224329},
issn = {1476-5551},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Graft vs Host Disease/etiology ; *Gastrointestinal Microbiome ; Immunity ; },
abstract = {The composition of the gut microbiome influences the clinical course after allogeneic hematopoietic stem cell transplantation (HSCT), but little is known about the relevance of skin microorganisms. In a single-center, observational study, we recruited a cohort of 50 patients before undergoing conditioning treatment and took both stool and skin samples up to one year after HSCT. We could confirm intestinal dysbiosis following HSCT and report that the skin microbiome is likewise perturbed in HSCT-recipients. Overall bacterial colonization of the skin was decreased after conditioning. Particularly patients that developed acute skin graft-versus-host disease (aGVHD) presented with an overabundance of Staphylococcus spp. In addition, a loss in alpha diversity was indicative of aGVHD development already before disease onset and correlated with disease severity. Further, co-localization of CD45[+] leukocytes and staphylococci was observed in the skin of aGVHD patients even before disease development and paralleled with upregulated genes required for antigen-presentation in mononuclear phagocytes. Overall, our data reveal disturbances of the skin microbiome as well as cutaneous immune response in HSCT recipients with changes associated with cutaneous aGVHD.},
}
@article {pmid36224130,
year = {2022},
author = {Zhao, CH and Shen, HY and Wang, ZH and Liang, YP and Zhao, Y and Xie, H and Tang, CL},
title = {[Hydrochemical and Isotopic Characteristics in the Surface Water of the Fenhe River Basin and Influence Factors].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {43},
number = {10},
pages = {4440-4448},
doi = {10.13227/j.hjkx.202201103},
pmid = {36224130},
issn = {0250-3301},
mesh = {Calcium Sulfate ; Carbonates ; Environmental Monitoring/methods ; *Groundwater/chemistry ; Hydrogen ; Minerals ; Oxygen Isotopes ; Sulfides ; *Water Pollutants, Chemical/analysis ; Water Quality ; },
abstract = {The Fenhe River Basin is the mother river of Shanxi Province. Due to the over-exploitation of water resources and the impact of social and economic development, the ecological environment has deteriorated. After a series of treatment and protection measures, the water quality has since been improved. Mathematical statistics, Piper diagrams, Gibbs model, hydrogen and oxygen isotopes, and other methods were used to analyze the characteristics and sources of hydrochemistry in the surface water of the Fenhe River basin, which revealed the evolution process of surface water quality of the Fenhe River basin. The results showed that the content of the main hydrochemical components in the main stream surface water of Fenhe River basin increased gradually along the runoff path. The hydrochemical types of surface water of Fenhe River basin were mainly HCO3·SO4·Cl-Ca·Na·Mg and SO4·HCO3·Cl-Ca·Na·Mg. There were great differences in hydrochemical components of tributaries and karst water in the basin. There were also great differences in hydrochemical components of tributaries in the basin. The hydrochemical types of surface water of karst water were mainly SO4·HCO3-Ca·Mg. The hydrochemical composition of surface water in Fenhe River basin was mainly affected by rock weathering and evaporation crystallization, whereas rainfall had little effect. Na[+] and K[+] mainly came from the dissolution of evaporated salt rocks with Na in the surrounding loess. Ca[2+], Mg[2+], and HCO3[-] mainly came from the dissolution of carbonate rocks. SO4[2-] may have also come from the dissolution of sulfide minerals in the loess layer around Fenhe River in addition to the dissolution of gypsum. The values of δD and δ[18]O of Fenhe River surface water were gradually enriched from upstream to downstream. The characteristics of hydrogen and oxygen isotopes further showed that the surface water was mainly affected by evaporation. The results of this study can provide evidence for ecological restoration and protection and ecological civilization construction in the Fenhe River basin.},
}
@article {pmid36215495,
year = {2022},
author = {Zhao, J and Jin, L and Wu, D and Xie, JW and Li, J and Fu, XW and Cong, ZY and Fu, PQ and Zhang, Y and Luo, XS and Feng, XB and Zhang, G and Tiedje, JM and Li, XD},
title = {Global airborne bacterial community-interactions with Earth's microbiomes and anthropogenic activities.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {42},
pages = {e2204465119},
pmid = {36215495},
issn = {1091-6490},
mesh = {*Air Microbiology ; Anthropogenic Effects ; Bacteria/genetics ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Airborne bacteria are an influential component of the Earth's microbiomes, but their community structure and biogeographic distribution patterns have yet to be understood. We analyzed the bacterial communities of 370 air particulate samples collected from 63 sites around the world and constructed an airborne bacterial reference catalog with more than 27 million nonredundant 16S ribosomal RNA (rRNA) gene sequences. We present their biogeographic pattern and decipher the interlacing of the microbiome co-occurrence network with surface environments of the Earth. While the total abundance of global airborne bacteria in the troposphere (1.72 × 10[24] cells) is 1 to 3 orders of magnitude lower than that of other habitats, the number of bacterial taxa (i.e., richness) in the atmosphere (4.71 × 10[8] to 3.08 × 10[9]) is comparable to that in the hydrosphere, and its maximum occurs in midlatitude regions, as is also observed in other ecosystems. The airborne bacterial community harbors a unique set of dominant taxa (24 species); however, its structure appears to be more easily perturbed, due to the more prominent role of stochastic processes in shaping community assembly. This is corroborated by the major contribution of surface microbiomes to airborne bacteria (averaging 46.3%), while atmospheric conditions such as meteorological factors and air quality also play a role. Particularly in urban areas, human impacts weaken the relative importance of plant sources of airborne bacteria and elevate the occurrence of potential pathogens from anthropogenic sources. These findings serve as a key reference for predicting planetary microbiome responses and the health impacts of inhalable microbiomes with future changes in the environment.},
}
@article {pmid36215030,
year = {2022},
author = {Yang, Z and Wang, J and Huang, Y and Wang, S and Wei, L and Liu, D and Weng, Y and Xiang, J and Zhu, Q and Yang, Z and Nie, X and Yu, Y and Yang, Z and Yang, QY},
title = {CottonMD: a multi-omics database for cotton biological study.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkac863},
pmid = {36215030},
issn = {1362-4962},
abstract = {Cotton is an important economic crop, and many loci for important traits have been identified, but it remains challenging and time-consuming to identify candidate or causal genes/variants and clarify their roles in phenotype formation and regulation. Here, we first collected and integrated the multi-omics datasets including 25 genomes, transcriptomes in 76 tissue samples, epigenome data of five species and metabolome data of 768 metabolites from four tissues, and genetic variation, trait and transcriptome datasets from 4180 cotton accessions. Then, a cotton multi-omics database (CottonMD, http://yanglab.hzau.edu.cn/CottonMD/) was constructed. In CottonMD, multiple statistical methods were applied to identify the associations between variations and phenotypes, and many easy-to-use analysis tools were provided to help researchers quickly acquire the related omics information and perform multi-omics data analysis. Two case studies demonstrated the power of CottonMD for identifying and analyzing the candidate genes, as well as the great potential of integrating multi-omics data for cotton genetic breeding and functional genomics research.},
}
@article {pmid36213026,
year = {2022},
author = {Wen, Y},
title = {Analysis of Regional Economy Development on Local Environmental Protection and Natural Resources Utilization from the Perspective of Big Data.},
journal = {Journal of environmental and public health},
volume = {2022},
number = {},
pages = {9461377},
pmid = {36213026},
issn = {1687-9813},
mesh = {Big Data ; China ; Cities ; *Conservation of Natural Resources ; *Economic Development ; Natural Resources ; Rivers ; },
abstract = {The ecological restoration and civilization construction is one of the key tasks in China. The economic development of different regions has different effects on the resource protection and utilization. In the face of complex natural conditions and resource-rich areas, how to carry out the ecological environment promotion work is put forward. The urbanization level of the Yangtze River region increases from 17.9% to 60.6%, showing the characteristics of rapid expansion. In the face of urban diseases such as unreasonable industrial layout, it is urgent to improve regional economy and promote green urban development from the perspective of big data. Adhering to the concept of ecological priority, the development of digital technology drove the development of local economy in 2019, accounting for 43% of the national population. While promoting the economic development, it is of great significance to ensure the efficiency of resource utilization and promote the high-quality development of common economy.},
}
@article {pmid36212380,
year = {2022},
author = {Shao, P and Peng, Y and Wu, Y and Wang, J and Pan, Z and Yang, Y and Aini, N and Guo, C and Shui, G and Chao, L and Tian, X and An, Q and Yang, Q and You, C and Lu, L and Zhang, X and Wang, M and Nie, X},
title = {Genome-wide association study and transcriptome analysis reveal key genes controlling fruit branch angle in cotton.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {988647},
pmid = {36212380},
issn = {1664-462X},
abstract = {Fruit branch angle (FBA), a pivotal component of cotton plant architecture, is vital for field and mechanical harvesting. However, the molecular mechanism of FBA formation is poorly understood in cotton. To uncover the genetic basis for FBA formation in cotton, we performed a genome-wide association study (GWAS) of 163 cotton accessions with re-sequencing data. A total of 55 SNPs and 18 candidate genes were significantly associated with FBA trait. By combining GWAS and transcriptome analysis, four genes underlying FBA were identified. An FBA-associated candidate gene Ghi_A09G08736, which is homologous to SAUR46 in Arabidopsis thaliana, was detected in our study. In addition, transcriptomic evidence was provided to show that gravity and light were implicated in the FBA formation. This study provides new insights into the genetic architecture of FBA that informs architecture breeding in cotton.},
}
@article {pmid36210994,
year = {2022},
author = {Ju, X},
title = {Application of Big Data Technology to Promote Agricultural Structure Adjustment and High-Quality Development of Modern Agriculture.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {5222760},
pmid = {36210994},
issn = {1687-5273},
mesh = {*Agriculture ; *Big Data ; China ; Conservation of Natural Resources ; Remote Sensing Technology ; Technology ; },
abstract = {The implementation of the strategy of rural revitalization is a major ministerial work made by the Nineteenth National Congress of the Communist Party of China and is the general grasp of contemporary agriculture, peasants, and rural work. In recent years, with the rapid development of remote sensing technology and deep learning technology, the demand for the technology for the classification of crops on satellite remote sensing images based on deep learning technology has increased in agricultural insurance and land survey. Therefore, this paper trains one, which is 85.9%-92.8%, the accuracy of corn classification is 77%-93%, and the accuracy of forest classification is 77%-87.6%. Subsequently, the overall accuracy of classifying all directories through the multi-temporal validation data set between May 2017 and October 2017 reached 92.6%. Such a multi-time combination method can be used for monthly, timely, and efficient iteration of agricultural insurance and crop yield estimation, which will be more accurate each time. These methods can also be further applied to the growth and change monitoring of large agricultural planting areas, adding bricks and tiles to China's agricultural remote sensing. If the countryside is to be revitalized, agriculture must develop rapidly at the same time, industries must flourish, ecology must be livable, rural customs must be civilized, and life must be prosperous. Modern agriculture is a comprehensive circulation system with high yield, high quality, low consumption, ecology, environmental protection, and high efficiency. The development of modern agriculture is inseparable from the industrialization of agriculture, the globalization of agriculture, the digitization of agriculture, the integration of agriculture, the adjustment of agricultural structure, and agricultural innovation. Only the continuous development of modern agriculture can make rural revitalization enter a new journey.},
}
@article {pmid36209915,
year = {2022},
author = {Chetty, M and Hallinan, J and Ruz, GA and Wipat, A},
title = {Computational intelligence and machine learning in bioinformatics and computational biology.},
journal = {Bio Systems},
volume = {222},
number = {},
pages = {104792},
doi = {10.1016/j.biosystems.2022.104792},
pmid = {36209915},
issn = {1872-8324},
mesh = {*Computational Biology ; *Artificial Intelligence ; Machine Learning ; },
}
@article {pmid36207680,
year = {2022},
author = {Asghari-Jafarabadi, M and Gholipour, K and Khodayari-Zarnaq, R and Azmin, M and Alizadeh, G},
title = {Estimation of myocardial infarction death in Iran: artificial neural network.},
journal = {BMC cardiovascular disorders},
volume = {22},
number = {1},
pages = {438},
pmid = {36207680},
issn = {1471-2261},
mesh = {Humans ; *Hypercholesterolemia/diagnosis/epidemiology ; Iran/epidemiology ; Male ; *Myocardial Infarction/diagnosis/epidemiology ; Neural Networks, Computer ; Obesity/diagnosis/epidemiology ; Overweight ; Risk Factors ; },
abstract = {BACKGROUND: Examining past trends and predicting the future helps policymakers to design effective interventions to deal with myocardial infarction (MI) with a clear understanding of the current and future situation. The aim of this study was to estimate the death rate due to MI in Iran by artificial neural network (ANN).
METHODS: In this ecological study, the prevalence of diabetes, hypercholesterolemia over 200, hypertension, overweight and obesity were estimated for the years 2017-2025. ANN and Linear regression model were used. Also, Specialists were also asked to predict the death rate due to MI by considering the conditions of 3 conditions (optimistic, pessimistic, and probable), and the predicted process was compared with the modeling process.
RESULTS: Death rate due to MI in Iran is expected to decrease on average, while there will be a significant decrease in the prevalence of hypercholesterolemia 1.031 (- 24.81, 26.88). Also, the trend of diabetes 10.48 (111.45, - 132.42), blood pressure - 110.48 (- 174.04, - 46.91) and obesity and overweight - 35.84 (- 18.66, - 5.02) are slowly increasing. MI death rate in Iran is higher in men but is decreasing on average. Experts' forecasts are different and have predicted a completely upward trend.
CONCLUSION: The trend predicted by the modeling shows that the death rate due to MI will decrease in the future with a low slope. Improving the infrastructure for providing preventive services to reduce the risk factors for cardiovascular disease in the community is one of the priority measures in the current situation.},
}
@article {pmid36202356,
year = {2023},
author = {Jones, DL and Rhymes, JM and Wade, MJ and Kevill, JL and Malham, SK and Grimsley, JMS and Rimmer, C and Weightman, AJ and Farkas, K},
title = {Suitability of aircraft wastewater for pathogen detection and public health surveillance.},
journal = {The Science of the total environment},
volume = {856},
number = {Pt 2},
pages = {159162},
pmid = {36202356},
issn = {1879-1026},
mesh = {Adult ; Male ; Humans ; *Wastewater ; Public Health Surveillance ; SARS-CoV-2 ; *COVID-19/epidemiology ; Aircraft ; },
abstract = {International air travel is now widely recognised as one of the primary mechanisms responsible for the transnational movement and global spread of SARS-CoV-2. Monitoring the viral load and novel lineages within human-derived wastewater collected from aircraft and at air transport hubs has been proposed as an effective way to monitor the importation frequency of viral pathogens. The success of this approach, however, is highly dependent on the bathroom and defecation habits of air passengers during their journey. In this study of UK adults (n = 2103), we quantified the likelihood of defecation prior to departure, on the aircraft and upon arrival on both short- and long-haul flights. The results were then used to assess the likelihood of capturing the signal from infected individuals at UK travel hubs. To obtain a representative cross-section of the population, the survey was stratified by geographical region, gender, age, parenting status, and social class. We found that an individual's likelihood to defecate on short-haul flights (< 6 h in duration) was low (< 13 % of the total), but was higher on long-haul flights (< 36 %; > 6 h in duration). This behaviour pattern was higher among males and younger age groups. The maximum likelihood of defecation was prior to departure (< 39 %). Based on known SARS-CoV-2 faecal shedding rates (30-60 %) and an equal probability of infected individuals being on short- (71 % of inbound flights) and long-haul flights (29 %), we estimate that aircraft wastewater is likely to capture ca. 8-14 % of SARS-CoV-2 cases entering the UK. Monte Carlo simulations predicted that SARS-CoV-2 would be present in wastewater on 14 % of short-haul flights and 62 % of long-haul flights under current pandemic conditions. We conclude that aircraft wastewater alone is insufficient to effectively monitor all the transboundary entries of faecal-borne pathogens but can form part of a wider strategy for public heath surveillance at national borders.},
}
@article {pmid36198068,
year = {2022},
author = {Wanchai, V and Jenjaroenpun, P and Leangapichart, T and Arrey, G and Burnham, CM and Tümmler, MC and Delgado-Calle, J and Regenberg, B and Nookaew, I},
title = {CReSIL: accurate identification of extrachromosomal circular DNA from long-read sequences.},
journal = {Briefings in bioinformatics},
volume = {23},
number = {6},
pages = {},
doi = {10.1093/bib/bbac422},
pmid = {36198068},
issn = {1477-4054},
support = {P20 GM125503/GM/NIGMS NIH HHS/United States ; R37 CA251763/CA/NCI NIH HHS/United States ; T32 GM106999/GM/NIGMS NIH HHS/United States ; },
mesh = {*DNA, Circular/genetics ; *Genome ; DNA/genetics ; Eukaryotic Cells ; },
abstract = {Extrachromosomal circular DNA (eccDNA) of chromosomal origin is found in many eukaryotic species and cell types, including cancer, where eccDNAs with oncogenes drive tumorigenesis. Most studies of eccDNA employ short-read sequencing for their identification. However, short-read sequencing cannot resolve the complexity of genomic repeats, which can lead to missing eccDNA products. Long-read sequencing technologies provide an alternative to constructing complete eccDNA maps. We present a software suite, Construction-based Rolling-circle-amplification for eccDNA Sequence Identification and Location (CReSIL), to identify and characterize eccDNA from long-read sequences. CReSIL's performance in identifying eccDNA, with a minimum F1 score of 0.98, is superior to the other bioinformatic tools based on simulated data. CReSIL provides many useful features for genomic annotation, which can be used to infer eccDNA function and Circos visualization for eccDNA architecture investigation. We demonstrated CReSIL's capability in several long-read sequencing datasets, including datasets enriched for eccDNA and whole genome datasets from cells containing large eccDNA products. In conclusion, the CReSIL suite software is a versatile tool for investigating complex and simple eccDNA in eukaryotic cells.},
}
@article {pmid36197407,
year = {2022},
author = {Cunha, APD and Cruz, MMD},
title = {Analysis of trend in mortality due to HIV/AIDS-defining and non-HIV/AIDS defining illnesses according to sociodemographic characteristics, by Federative Unit and Brazil, 2000-2018.},
journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil},
volume = {31},
number = {2},
pages = {e2022093},
doi = {10.1590/S2237-96222022000200021},
pmid = {36197407},
issn = {2237-9622},
mesh = {*Acquired Immunodeficiency Syndrome/epidemiology ; Brazil/epidemiology ; Humans ; Information Systems ; Time Factors ; },
abstract = {OBJECTIVE: To analyze the temporal trend of mortality rate due to HIV/AIDS defining and non-HIV/AIDS defining illnesses in Brazil between 2000 and 2018.
METHODS: This was an ecological time series study, using data from the Mortality Information System, in Brazil and the Federative Units. Trend analysis was performed by means of Prais-Winsten regression model, according to overall mortality rate, sex, age group, marital status and race/skin color.
RESULTS: A total of 237,435 deaths were recorded in the period. In the country, defining illnesses showed higher rates (7.4 to 4.4 deaths/100,000 inhabitants in the period) than those observed among non-defining diseases (0.4 to 0.8 death/100,000 inhabitants in the period). It could be seen a decrease in overall mortality due to defining diseases (-6.3%; 95%CI -8.8;-3.8); while it increased due to non-defining diseases (11.0%; 95%CI 6.5;15.7).
CONCLUSION: There was a change in HIV/AIDS mortality profile over the years, with a decrease in deaths due to HIV/AIDS-defining diseases.},
}
@article {pmid36197074,
year = {2022},
author = {Gonçalves, BP and Hall, M and Jassat, W and Balan, V and Murthy, S and Kartsonaki, C and Semple, MG and Rojek, A and Baruch, J and Reyes, LF and Dasgupta, A and Dunning, J and Citarella, BW and Pritchard, M and Martín-Quiros, A and Sili, U and Baillie, JK and Aryal, D and Arabi, Y and Rashan, A and Angheben, A and Caoili, J and Carrier, FM and Harrison, EM and Gómez-Junyent, J and Figueiredo-Mello, C and Douglas, JJ and Mat Nor, MB and Chow, YP and Wong, XC and Bertagnolio, S and Thwin, SS and Streinu-Cercel, A and Salazar, L and Rishu, A and Rangappa, R and Ong, DSY and Hashmi, M and Carson, G and Diaz, J and Fowler, R and Kraemer, MUG and Wils, EJ and Horby, P and Merson, L and Olliaro, PL and , },
title = {An international observational study to assess the impact of the Omicron variant emergence on the clinical epidemiology of COVID-19 in hospitalised patients.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {36197074},
issn = {2050-084X},
support = {MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; 200927/WT_/Wellcome Trust/United Kingdom ; OV2170359//CIHR/Canada ; 222410/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 001/WHO_/World Health Organization/International ; 225288/Z/22/Z/WT_/Wellcome Trust/United Kingdom ; 222048/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {*COVID-19/epidemiology/virology ; Humans ; *SARS-CoV-2/genetics ; },
abstract = {BACKGROUND: Whilst timely clinical characterisation of infections caused by novel SARS-CoV-2 variants is necessary for evidence-based policy response, individual-level data on infecting variants are typically only available for a minority of patients and settings.
METHODS: Here, we propose an innovative approach to study changes in COVID-19 hospital presentation and outcomes after the Omicron variant emergence using publicly available population-level data on variant relative frequency to infer SARS-CoV-2 variants likely responsible for clinical cases. We apply this method to data collected by a large international clinical consortium before and after the emergence of the Omicron variant in different countries.
RESULTS: Our analysis, that includes more than 100,000 patients from 28 countries, suggests that in many settings patients hospitalised with Omicron variant infection less often presented with commonly reported symptoms compared to patients infected with pre-Omicron variants. Patients with COVID-19 admitted to hospital after Omicron variant emergence had lower mortality compared to patients admitted during the period when Omicron variant was responsible for only a minority of infections (odds ratio in a mixed-effects logistic regression adjusted for likely confounders, 0.67 [95% confidence interval 0.61-0.75]). Qualitatively similar findings were observed in sensitivity analyses with different assumptions on population-level Omicron variant relative frequencies, and in analyses using available individual-level data on infecting variant for a subset of the study population.
CONCLUSIONS: Although clinical studies with matching viral genomic information should remain a priority, our approach combining publicly available data on variant frequency and a multi-country clinical characterisation dataset with more than 100,000 records allowed analysis of data from a wide range of settings and novel insights on real-world heterogeneity of COVID-19 presentation and clinical outcome.
FUNDING: Bronner P. Gonçalves, Peter Horby, Gail Carson, Piero L. Olliaro, Valeria Balan, Barbara Wanjiru Citarella, and research costs were supported by the UK Foreign, Commonwealth and Development Office (FCDO) and Wellcome [215091/Z/18/Z, 222410/Z/21/Z, 225288/Z/22/Z]; and Janice Caoili and Madiha Hashmi were supported by the UK FCDO and Wellcome [222048/Z/20/Z]. Peter Horby, Gail Carson, Piero L. Olliaro, Kalynn Kennon and Joaquin Baruch were supported by the Bill & Melinda Gates Foundation [OPP1209135]; Laura Merson was supported by University of Oxford's COVID-19 Research Response Fund - with thanks to its donors for their philanthropic support. Matthew Hall was supported by a Li Ka Shing Foundation award to Christophe Fraser. Moritz U.G. Kraemer was supported by the Branco Weiss Fellowship, Google.org, the Oxford Martin School, the Rockefeller Foundation, and the European Union Horizon 2020 project MOOD (#874850). The contents of this publication are the sole responsibility of the authors and do not necessarily reflect the views of the European Commission. Contributions from Srinivas Murthy, Asgar Rishu, Rob Fowler, James Joshua Douglas, François Martin Carrier were supported by CIHR Coronavirus Rapid Research Funding Opportunity OV2170359 and coordinated out of Sunnybrook Research Institute. Contributions from Evert-Jan Wils and David S.Y. Ong were supported by a grant from foundation Bevordering Onderzoek Franciscus; and Andrea Angheben by the Italian Ministry of Health "Fondi Ricerca corrente-L1P6" to IRCCS Ospedale Sacro Cuore-Don Calabria. The data contributions of J.Kenneth Baillie, Malcolm G. Semple, and Ewen M. Harrison were supported by grants from the National Institute for Health Research (NIHR; award CO-CIN-01), the Medical Research Council (MRC; grant MC_PC_19059), and by the NIHR Health Protection Research Unit (HPRU) in Emerging and Zoonotic Infections at University of Liverpool in partnership with Public Health England (PHE) (award 200907), NIHR HPRU in Respiratory Infections at Imperial College London with PHE (award 200927), Liverpool Experimental Cancer Medicine Centre (grant C18616/A25153), NIHR Biomedical Research Centre at Imperial College London (award IS-BRC-1215-20013), and NIHR Clinical Research Network providing infrastructure support. All funders of the ISARIC Clinical Characterisation Group are listed in the appendix.},
}
@article {pmid36195605,
year = {2022},
author = {Peters, K and König-Ries, B},
title = {Reference bioimaging to assess the phenotypic trait diversity of bryophytes within the family Scapaniaceae.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {598},
pmid = {36195605},
issn = {2052-4463},
mesh = {Biodiversity ; *Bryophyta ; Computational Biology/methods ; *Hepatophyta ; Image Processing, Computer-Assisted/methods ; },
abstract = {Macro- and microscopic images of organisms are pivotal in biodiversity research. Despite that bioimages have manifold applications such as assessing the diversity of form and function, FAIR bioimaging data in the context of biodiversity are still very scarce, especially for difficult taxonomic groups such as bryophytes. Here, we present a high-quality reference dataset containing macroscopic and bright-field microscopic images documenting various phenotypic characters of the species belonging to the liverwort family of Scapaniaceae occurring in Europe. To encourage data reuse in biodiversity and adjacent research areas, we annotated the imaging data with machine-actionable metadata using community-accepted semantics. Furthermore, raw imaging data are retained and any contextual image processing like multi-focus image fusion and stitching were documented to foster good scientific practices through source tracking and provenance. The information contained in the raw images are also of particular interest for machine learning and image segmentation used in bioinformatics and computational ecology. We expect that this richly annotated reference dataset will encourage future studies to follow our principles.},
}
@article {pmid36195601,
year = {2022},
author = {Pottier, P and Lin, HY and Oh, RRY and Pollo, P and Rivera-Villanueva, AN and Valdebenito, JO and Yang, Y and Amano, T and Burke, S and Drobniak, SM and Nakagawa, S},
title = {A comprehensive database of amphibian heat tolerance.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {600},
pmid = {36195601},
issn = {2052-4463},
mesh = {*Amphibians ; Animals ; Databases, Factual ; Hot Temperature ; Temperature ; *Thermotolerance ; },
abstract = {Rising temperatures represent a significant threat to the survival of ectothermic animals. As such, upper thermal limits represent an important trait to assess the vulnerability of ectotherms to changing temperatures. For instance, one may use upper thermal limits to estimate current and future thermal safety margins (i.e., the proximity of upper thermal limits to experienced temperatures), use this trait together with other physiological traits in species distribution models, or investigate the plasticity and evolvability of these limits for buffering the impacts of changing temperatures. While datasets on thermal tolerance limits have been previously compiled, they sometimes report single estimates for a given species, do not present measures of data dispersion, and are biased towards certain parts of the globe. To overcome these limitations, we systematically searched the literature in seven languages to produce the most comprehensive dataset to date on amphibian upper thermal limits, spanning 3,095 estimates across 616 species. This resource will represent a useful tool to evaluate the vulnerability of amphibians, and ectotherms more generally, to changing temperatures.},
}
@article {pmid36191222,
year = {2022},
author = {Yang, L and Constantino, SM and Grenfell, BT and Weber, EU and Levin, SA and Vasconcelos, VV},
title = {Sociocultural determinants of global mask-wearing behavior.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {41},
pages = {e2213525119},
pmid = {36191222},
issn = {1091-6490},
mesh = {*COVID-19/epidemiology/prevention & control ; Humans ; *Masks ; *Pandemics/prevention & control ; Public Policy ; Risk ; SARS-CoV-2 ; Social Conditions ; },
abstract = {Behavioral responses influence the trajectories of epidemics. During the COVID-19 pandemic, nonpharmaceutical interventions (NPIs) reduced pathogen transmission and mortality worldwide. However, despite the global pandemic threat, there was substantial cross-country variation in the adoption of protective behaviors that is not explained by disease prevalence alone. In particular, many countries show a pattern of slow initial mask adoption followed by sharp transitions to high acceptance rates. These patterns are characteristic of behaviors that depend on social norms or peer influence. We develop a game-theoretic model of mask wearing where the utility of wearing a mask depends on the perceived risk of infection, social norms, and mandates from formal institutions. In this model, increasing pathogen transmission or policy stringency can trigger social tipping points in collective mask wearing. We show that complex social dynamics can emerge from simple individual interactions and that sociocultural variables and local policies are important for recovering cross-country variation in the speed and breadth of mask adoption. These results have implications for public health policy and data collection.},
}
@article {pmid36188695,
year = {2022},
author = {Zhang, W},
title = {Design of Urban Garden Landscape Visualization System Based on GIS and Remote Sensing Technology.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {9592376},
pmid = {36188695},
issn = {1687-5273},
mesh = {Cities ; Environmental Monitoring/methods ; Gardens ; *Geographic Information Systems ; Hot Temperature ; *Remote Sensing Technology ; },
abstract = {Urban green ecological space is an important manifestation of the environmental characteristics of a green city. The research results show that the urban green ecological space has obvious cooling and humidity effects, which are very important for reducing the urban heat island effect. Remote sensing technology describes the slow-release effects of urban green parks in different seasons from the two perspectives of thermal slow-release intensity and thermal slow-release distance. In this paper, UAV remote sensing is used to extract the internal and external factors of the urban green environment characteristics and to identify the main factors that affect the slow-release heat effect and seasonal changes of the urban green environment. In addition, it analyzes the factors that affect the urban environmental temperature within the environmental temperature slow-release range of urban green space, establishes a model to predict the environmental temperature within the thermal slow-release range outside the park, and realizes the largest thermal slow release in the urban greening ecological space. These are new technologies created in the context of digitization, which include image understanding and synthesis, which involve the use of computer graphics and image processing technology to convert data into graphics or images displayed on the screen to achieve an interactive process.},
}
@article {pmid36187697,
year = {2022},
author = {Ekpenyong, N and Heitz Tokpa, K and Nwankwo, O and O'Donnell, D and Rodriguez Franco, D and Berté, S and Amani Kouassi, S and Eteng, G and Undelikwo, V and Auer, C and Guessan Bi, GB and Oyo-Ita, A and Bosch-Capblanch, X},
title = {Using and improving the PHISICC paper-based tools in the health facility laboratories: Examples of Human Centered Design taking systems thinking into practice, in Côte d'Ivoire and Nigeria.},
journal = {Frontiers in public health},
volume = {10},
number = {},
pages = {916397},
pmid = {36187697},
issn = {2296-2565},
mesh = {Cote d'Ivoire ; Health Facilities ; Humans ; *Laboratories ; Nigeria ; Systems Analysis ; *Universal Design ; },
abstract = {BACKGROUND: Health workers in low- and middle-income countries are increasingly demanded to collect more and more data to report them to higher levels of the health information system (HIS), in detriment of useful data for clinical and public health decision-making, potentially compromising the quality of their health care provison. In order to support health workers' decision-making, we engaged with partners in Côte d'Ivoire, Mozambique and Nigeria in a research project to conceive, design, produce, implement and test paper-based health information tools: the PHISICC tools. Our aim was to understand the use of PHISICC tools by health workers and to improve them based on their feedback.
METHODS: The design Health Facility Laboratories (HF Labs) in Côte d'Ivoire and in Nigeria were set up after months of use of PHISICC tools. Activities were structured in three phases or 'sprints' of co-creative research. We used a transdisciplinary approach, including anthropology and Human Centered Design (HCD), observations, shadowing, structured interviews and co-creation.
RESULTS: Health workers appreciated the standardization of the tools across different health care areas, with a common visual language that optimized use. Several design issues were raised, in terms of formats and contents. They strongly appreciated how the PHISICC registers guided their clinical decision-making and how it facilitated tallying and counting for monthly reporting. However, adherence to new procedures was not universal. The co-creation sessions resulted in modifications to the PHISICC tools of out-patient care and postnatal care.
DISCUSSION: Although health systems and systemic thinking allowed the teams to embrace complexity, it was the HCD approach that actually produced a shift in researchers' mind-set: from HIS as data management tools to HIS as quality of care instruments. HCD allowed navigating the complexity of health systems interventions due to its capacity to operate change: it not only allowed us to understand how the PHISICC tools were used but also how to further improve them. In the absence of (or even with) an analytical health systems framework, HCD approaches can work in real-life situations for the ideation, testing and implementation of interventions to improve health systems and health status outcomes.},
}
@article {pmid36179444,
year = {2022},
author = {Chin, JM and Growns, B and Sebastian, J and Page, MJ and Nakagawa, S},
title = {The transparency and reproducibility of systematic reviews in forensic science.},
journal = {Forensic science international},
volume = {340},
number = {},
pages = {111472},
doi = {10.1016/j.forsciint.2022.111472},
pmid = {36179444},
issn = {1872-6283},
mesh = {*Benchmarking ; Databases, Factual ; *Forensic Sciences ; Reproducibility of Results ; Systematic Reviews as Topic ; },
abstract = {Systematic reviews are indispensable tools for both reliably informing decision-makers about the state of the field and for identifying areas that need further study. Their value, however, depends on their transparency and reproducibility. Readers should be able to determine what was searched for and when, where the authors searched, and whether that search was predetermined or evolved based on what was found. In this article, we measured the transparency and reproducibility of systematic reviews in forensic science, a field where courts, policymakers, and legislators count on systematic reviews to make informed decisions. In a sample of 100 systematic reviews published between 2018 and 2021, we found that completeness of reporting varied markedly. For instance, 50 % of reviews claimed to follow a reporting guideline and such statements were only modestly related to compliance with that reporting guideline. As to specific reporting items, 82 % reported all of the databases searched, 22 % reported the review's full Boolean search logic, and just 7 % reported the review was registered. Among meta-analyses (n = 23), only one stated data was available and none stated the analytic code was available. After considering the results, we end with recommendations for improved regulation of reporting practices, especially among journals. Our results may serve as a useful benchmark as the field evolves.},
}
@article {pmid36175492,
year = {2022},
author = {Leonardi, M and Boschin, F and Boscato, P and Manica, A},
title = {Following the niche: the differential impact of the last glacial maximum on four European ungulates.},
journal = {Communications biology},
volume = {5},
number = {1},
pages = {1038},
pmid = {36175492},
issn = {2399-3642},
mesh = {Animals ; Archaeology ; Databases, Factual ; *Deer ; Ecosystem ; Horses ; Species Specificity ; Sus scrofa ; Swine ; },
abstract = {Predicting the effects of future global changes on species requires a better understanding of the ecological niche dynamics in response to climate; the large climatic fluctuations of the last 50,000 years can be used as a natural experiment to that aim. Here we test whether the realized niche of horse, aurochs, red deer, and wild boar changed between 47,000 and 7500 years ago using paleoecological modelling over an extensive archaeological database. We show that they all changed their niche, with species-specific responses to climate fluctuations. We also suggest that they survived the climatic turnovers thanks to their flexibility and by expanding their niche in response to the extinction of competitors and predators. Irrespective of the mechanism behind such processes, the fact that species with long generation times can change their niche over thousands of years cautions against assuming it to stay constant both when reconstructing the past and predicting the future.},
}
@article {pmid36174014,
year = {2022},
author = {Porter, TM and Hajibabaei, M},
title = {MetaWorks: A flexible, scalable bioinformatic pipeline for high-throughput multi-marker biodiversity assessments.},
journal = {PloS one},
volume = {17},
number = {9},
pages = {e0274260},
pmid = {36174014},
issn = {1932-6203},
mesh = {Animals ; *Biodiversity ; Biomarkers ; *Computational Biology ; Ecology ; Eukaryota ; },
abstract = {Multi-marker metabarcoding is increasingly being used to generate biodiversity information across different domains of life from microbes to fungi to animals such as for molecular ecology and biomonitoring applications in different sectors from academic research to regulatory agencies and industry. Current popular bioinformatic pipelines support microbial and fungal marker analysis, while ad hoc methods are often used to process animal metabarcode markers from the same study. MetaWorks provides a harmonized processing environment, pipeline, and taxonomic assignment approach for demultiplexed Illumina reads for all biota using a wide range of metabarcoding markers such as 16S, ITS, and COI. A Conda environment is provided to quickly gather most of the programs and dependencies for the pipeline. Several workflows are provided such as: taxonomically assigning exact sequence variants, provides an option to generate operational taxonomic units, and facilitates single-read processing. Pipelines are automated using Snakemake to minimize user intervention and facilitate scalability. All pipelines use the RDP classifier to provide taxonomic assignments with confidence measures. We extend the functionality of the RDP classifier for taxonomically assigning 16S (bacteria), ITS (fungi), and 28S (fungi), to also support COI (eukaryotes), rbcL (eukaryotes, land plants, diatoms), 12S (fish, vertebrates), 18S (eukaryotes, diatoms) and ITS (fungi, plants). MetaWorks properly handles ITS by trimming flanking conserved rRNA gene regions as well as protein coding genes by providing two options for removing obvious pseudogenes. MetaWorks can be downloaded from https://github.com/terrimporter/MetaWorks and quickstart instructions, pipeline details, and a tutorial for new users can be found at https://terrimporter.github.io/MetaWorksSite.},
}
@article {pmid36172318,
year = {2022},
author = {Yin, G and Liu, J},
title = {Research on Movement Analysis and Guidance in Dance Learning Based on Data Mining.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {9327442},
pmid = {36172318},
issn = {1687-5273},
mesh = {Data Mining ; Humans ; *Learning ; *Movement ; Students ; },
abstract = {In dance, we must understand the essential meaning of dance movements from the inside and express them on the basis of dance. Therefore, in the process of developing new dance teaching methods, it is necessary to improve the basic education of dance students, so that they can express the emotions conveyed by dance through body language and movements, and improve dance expression ability. In this context, we made the research and reached the following conclusions: (1) the number of frames of different dance types is also different, and the number of frames to be learned is also increasing. The dance with the highest number of frames is Latin2, which has 3635 frames, and the dance with the highest number of frames that need to be learned is also Latin2, which requires 2519 frames to learn. (2) The data mining method is still the highest among the three methods, and the accuracy of the complete teaching method is 82%, which is the lowest among the three methods, and the accuracy of the decentralized teaching method is 87%. No matter in the test set or the mixed test set, the curve values of deep mining are very stable. First of all, human movements emphasize that in dance, the essential meaning of dance movements needs to be understood from the inside and expressed through the foundation of dance. Therefore, when developing new dance teaching methods, it is necessary to strengthen the basic dance training of students so that students can express the emotions conveyed by dance through body language and movements and improve their dance expression ability. We conduct research in this ecological environment. Different types of dance learning process using different frames, different types of dance in the algorithm transport have different recognition methods, using better and different algorithms can achieve the best performance. Both groups in the Hip Hop dance had a shorter average learning time than both groups in the Latin dance.},
}
@article {pmid36169445,
year = {2022},
author = {Martins, ACM and Giordani, F and Gonçalves, MC and Guaraldo, L and Rozenfeld, S},
title = {[Deaths from adverse drug events in Brazil: Mortality Information System as a source of information].},
journal = {Cadernos de saude publica},
volume = {38},
number = {8},
pages = {e00291221},
doi = {10.1590/0102-311XPT291221},
pmid = {36169445},
issn = {1678-4464},
mesh = {Aged ; Brazil/epidemiology ; Child ; *Drug-Related Side Effects and Adverse Reactions ; Humans ; Information Systems ; Middle Aged ; Psychotropic Drugs/adverse effects ; Retrospective Studies ; },
abstract = {Adverse drug events (ADEs) are harmful events caused by medication, and some of which can lead to death. Death records are an important source of information when using codes from the 10th revision of the International Classification of Diseases (ICD-10) suggestive of ADE. This study aimed to identify the ADEs registered in Brazililian Mortality Information System (SIM), analyzing data distribution by year, age group, and type of event. This is an ecological study with retrospective data collection, identifying ADEs in the SIM, using the ICD-10 codes. The study included deaths that occurred in Brazil from 2008 to 2016. An increase in the number of deaths associated with ADE was observed from 2008 to 2016, with a mortality rate per 1 million inhabitants ranging from 8.70 to 14.40 in the period. Most events corresponded to mental and behavioral disorders due to the use of psychotropic drugs. Most deaths (12,311) related to ADE codes were identified in several chapters of the ICD-10. Chapter XX, about adverse events, allowed the identification of a smaller number of deaths (4,893). Higher event rates were observed among individuals aged 60 years and over (39.8/1 million) and children younger than one year (22.0/1 million). The identification of ADE-related deaths on the SIM is an important strategy for addressing undesirable drug-related events. Deaths related to the use of psychotropic drugs were the most frequent ADE-related deaths and the elderly were the age group most affected by ADEs.},
}
@article {pmid36167554,
year = {2022},
author = {Kim, J and Lee, C and Ko, BJ and Yoo, DA and Won, S and Phillippy, AM and Fedrigo, O and Zhang, G and Howe, K and Wood, J and Durbin, R and Formenti, G and Brown, S and Cantin, L and Mello, CV and Cho, S and Rhie, A and Kim, H and Jarvis, ED},
title = {False gene and chromosome losses in genome assemblies caused by GC content variation and repeats.},
journal = {Genome biology},
volume = {23},
number = {1},
pages = {204},
pmid = {36167554},
issn = {1474-760X},
support = {WT206194/WT_/Wellcome Trust/United Kingdom ; ZIA HG200398/ImNIH/Intramural NIH HHS/United States ; R03 NS115145/NS/NINDS NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; },
mesh = {Animals ; Base Composition/genetics ; Chromosomes ; *Genome/genetics ; Sequence Analysis, DNA ; *Vertebrates/genetics ; },
abstract = {BACKGROUND: Many short-read genome assemblies have been found to be incomplete and contain mis-assemblies. The Vertebrate Genomes Project has been producing new reference genome assemblies with an emphasis on being as complete and error-free as possible, which requires utilizing long reads, long-range scaffolding data, new assembly algorithms, and manual curation. A more thorough evaluation of the recent references relative to prior assemblies can provide a detailed overview of the types and magnitude of improvements.
RESULTS: Here we evaluate new vertebrate genome references relative to the previous assemblies for the same species and, in two cases, the same individuals, including a mammal (platypus), two birds (zebra finch, Anna's hummingbird), and a fish (climbing perch). We find that up to 11% of genomic sequence is entirely missing in the previous assemblies. In the Vertebrate Genomes Project zebra finch assembly, we identify eight new GC- and repeat-rich micro-chromosomes with high gene density. The impact of missing sequences is biased towards GC-rich 5'-proximal promoters and 5' exon regions of protein-coding genes and long non-coding RNAs. Between 26 and 60% of genes include structural or sequence errors that could lead to misunderstanding of their function when using the previous genome assemblies.
CONCLUSIONS: Our findings reveal novel regulatory landscapes and protein coding sequences that have been greatly underestimated in previous assemblies and are now present in the Vertebrate Genomes Project reference genomes.},
}
@article {pmid36167140,
year = {2023},
author = {Tölgyesi, C and Hábenczyus, AA and Kelemen, A and Török, P and Valkó, O and Deák, B and Erdős, L and Tóth, B and Csikós, N and Bátori, Z},
title = {How to not trade water for carbon with tree planting in water-limited temperate biomes?.},
journal = {The Science of the total environment},
volume = {856},
number = {Pt 1},
pages = {158960},
doi = {10.1016/j.scitotenv.2022.158960},
pmid = {36167140},
issn = {1879-1026},
mesh = {*Ecosystem ; *Carbon ; Water ; Sand ; Forests ; Soil ; },
abstract = {The most widespread nature-based solution for mitigating climate change is tree planting. When realized as forest restoration in historically forested biomes, it can efficiently contribute to the sequestration of atmospheric carbon and can also entail significant biodiversity and ecosystem service benefits. Conversely, tree planting in naturally open biomes can have adverse effects, of which water shortage due to increased evapotranspiration is among the most alarming ones. Here we assessed how soil texture affects the strength of the trade-off between tree cover and water balance in the forest-steppe biome, where the global pressure for afforestation is threatening with increasing tree cover above historical levels. Here we monitored vertical soil moisture dynamics in four stands in each of the most common forest types of lowland Hungary on well-drained, sandy (natural poplar groves, and Robinia and pine plantations) and on poorly drained, silty-clayey soils (natural oak stands and Robinia plantations), and neighboring grasslands. We found that forests on sand retain moisture in the topsoil (approx. 20 cm) throughout the year, but a thick dry layer develops below that during the vegetation period, significantly impeding groundwater recharge. Neighboring sandy grasslands showed an opposite pattern, with often dry topsoil but intact moisture reserves below, allowing deep percolation. In contrast, forests on silty-clayey soils did not desiccate lower soil layers compared neighboring grasslands, which in turn showed moisture patterns similar to sandy grasslands. We conclude that, in water-limited temperate biomes where landscape-wide water regime depends on deep percolation, soil texture should drive the spatial allocation of tree-based climate mitigation efforts. On sand, the establishment of new forests should be kept to a minimum and grassland restoration should be preferred. The trade-off between water and carbon is less pronounced on silty-clayey soils, making forest patches and wooded rangelands viable targets for both climate mitigation and ecosystem restoration.},
}
@article {pmid36166925,
year = {2023},
author = {Koo, SY and Hwang, KT and Hwang, S and Choi, KY and Park, YJ and Choi, JH and Truong, TQ and Kim, SM},
title = {Nanoencapsulation enhances the bioavailability of fucoxanthin in microalga Phaeodactylum tricornutum extract.},
journal = {Food chemistry},
volume = {403},
number = {},
pages = {134348},
doi = {10.1016/j.foodchem.2022.134348},
pmid = {36166925},
issn = {1873-7072},
mesh = {Humans ; Mice ; Animals ; Biological Availability ; *Microalgae/metabolism ; Caco-2 Cells ; Xanthophylls/metabolism ; },
abstract = {The marine carotenoid fucoxanthin (FX) has various health benefits but suffers from poor bioavailability. We hypothesize that the bioavailability of FX in microalga Phaeodactylum tricornutum extract (PE) could be improved through nanoencapsulation. Here, we developed two types of nanoparticles: one consisting of alginate and casein (A-C-PE, 246 nm diameter, 79.6% encapsulation efficiency) and the other A-C-PE coated with chitosan (CS-A-C-PE, 258 nm, 78.1%). Both types of nanoparticles incorporating PE showed controlled FX release during simulated gastrointestinal digestion, as well as 1.8-fold improvement of membrane permeability in Caco-2/TC7 cells compared to non-encapsulated PE. Pharmacokinetic behavior of two FX metabolites (fucoxanthinol and amarouciaxanthin A) in mouse plasma was monitored after oral administration. The results showed that 31.8-332.1% more FX metabolites from the nanoparticles were absorbed into plasma than those from PE. In conclusion, encapsulation of PE in both types of nanoparticles significantly promoted the bioavailability of FX.},
}
@article {pmid36157711,
year = {2022},
author = {Mihaljevic, JR and Borkovec, S and Ratnavale, S and Hocking, TD and Banister, KE and Eppinger, JE and Hepp, C and Doerry, E},
title = {SPARSEMODr: Rapidly simulate spatially explicit and stochastic models of COVID-19 and other infectious diseases.},
journal = {Biology methods & protocols},
volume = {7},
number = {1},
pages = {bpac022},
pmid = {36157711},
issn = {2396-8923},
abstract = {Building realistically complex models of infectious disease transmission that are relevant for informing public health is conceptually challenging and requires knowledge of coding architecture that can implement key modeling conventions. For example, many of the models built to understand COVID-19 dynamics have included stochasticity, transmission dynamics that change throughout the epidemic due to changes in host behavior or public health interventions, and spatial structures that account for important spatio-temporal heterogeneities. Here we introduce an R package, SPARSEMODr, that allows users to simulate disease models that are stochastic and spatially explicit, including a model for COVID-19 that was useful in the early phases of the epidemic. SPARSEMOD stands for SPAtial Resolution-SEnsitive Models of Outbreak Dynamics, and our goal is to demonstrate particular conventions for rapidly simulating the dynamics of more complex, spatial models of infectious disease. In this report, we outline the features and workflows of our software package that allow for user-customized simulations. We believe the example models provided in our package will be useful in educational settings, as the coding conventions are adaptable, and will help new modelers to better understand important assumptions that were built into sophisticated COVID-19 models.},
}
@article {pmid36155927,
year = {2022},
author = {Russo, A and Blettner, M and Merzenich, H and Wollschlaeger, D and Erdmann, F and Gianicolo, E},
title = {Incidence of childhood leukemia before and after shut down of nuclear power plants in Germany in 2011: A population-based register study during 2004 to 2019.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.34303},
pmid = {36155927},
issn = {1097-0215},
abstract = {The association between leukemia and proximity to nuclear-power-plants (NPPs) has been assessed in several countries with inconsistent results. A case-control study from Germany had shown an increased risk for childhood leukemia (diagnoses 1980-2003) near NPPs. Germany began shutting down nuclear reactors in 2011, following the Fukushima disaster. We tested whether the previously observed association between leukemia and proximity to NPP persisted despite the shutdown. We used an ecological study design to investigate the incidence of leukemia during 2004 to 2019 in children aged 0 to 14 years living near NPPs where at least one reactor was shut down in 2011. We defined study and control areas as municipalities whose surface area was at least 75% within 10 km or between 10 and 50 km of NPPs, respectively. We calculated age-standardized rates and incidence rate ratios (IRR) using control-areas as the reference. We also computed standardized incidence ratios (SIR) separately for each NPP using incidence rates of the German population as a reference. IRR decreased from 1.20 (95% confidence interval: 0.81-1.77) in 2004 to 2011 to 1.12 (0.75-1.68) in 2012 to 2019. Analyses of single plants showed an excess of childhood leukemia during 2004 to 2019 for the Unterweser-NPP, based only on three cases, and the Krümmel-NPP (n = 14; SIR: 1.98, 1.17-3.35). We found slightly decreasing of leukemia incidence rate ratios after the shutdown of nuclear reactors in 2011. Due to the small number of cases, risk estimates have large uncertainty. Further research including a longer follow-up is warranted. The consistent excess of incidence cases around Krümmel may require analytical epidemiological analysis.},
}
@article {pmid36149894,
year = {2022},
author = {Zhang, L and Chen, L and Yu, XA and Duvallet, C and Isazadeh, S and Dai, C and Park, S and Frois-Moniz, K and Duarte, F and Ratti, C and Alm, EJ and Ling, F},
title = {MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes.},
journal = {PLoS computational biology},
volume = {18},
number = {9},
pages = {e1010472},
pmid = {36149894},
issn = {1553-7358},
mesh = {*COVID-19 ; *Gastrointestinal Microbiome/genetics ; Humans ; Pandemics ; Population Density ; Sewage ; Wastewater ; },
abstract = {The metagenome embedded in urban sewage is an attractive new data source to understand urban ecology and assess human health status at scales beyond a single host. Analyzing the viral fraction of wastewater in the ongoing COVID-19 pandemic has shown the potential of wastewater as aggregated samples for early detection, prevalence monitoring, and variant identification of human diseases in large populations. However, using census-based population size instead of real-time population estimates can mislead the interpretation of data acquired from sewage, hindering assessment of representativeness, inference of prevalence, or comparisons of taxa across sites. Here, we show that taxon abundance and sub-species diversisty in gut-associated microbiomes are new feature space to utilize for human population estimation. Using a population-scale human gut microbiome sample of over 1,100 people, we found that taxon-abundance distributions of gut-associated multi-person microbiomes exhibited generalizable relationships with respect to human population size. Here and throughout this paper, the human population size is essentially the sample size from the wastewater sample. We present a new algorithm, MicrobiomeCensus, for estimating human population size from sewage samples. MicrobiomeCensus harnesses the inter-individual variability in human gut microbiomes and performs maximum likelihood estimation based on simultaneous deviation of multiple taxa's relative abundances from their population means. MicrobiomeCensus outperformed generic algorithms in data-driven simulation benchmarks and detected population size differences in field data. New theorems are provided to justify our approach. This research provides a mathematical framework for inferring population sizes in real time from sewage samples, paving the way for more accurate ecological and public health studies utilizing the sewage metagenome.},
}
@article {pmid36141528,
year = {2022},
author = {Emelyanova, A and Savolainen, A and Oksanen, A and Nieminen, P and Loginova, O and Abass, K and Rautio, A},
title = {Research on Selected Wildlife Infections in the Circumpolar Arctic-A Bibliometric Review.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {18},
pages = {},
pmid = {36141528},
issn = {1660-4601},
mesh = {Alaska/epidemiology ; Animals ; *Animals, Wild ; Arctic Regions ; Bibliometrics ; *Communicable Diseases/epidemiology/veterinary ; Humans ; Mammals ; },
abstract = {One Health, a multidisciplinary approach to public health, which integrates human, animal, and environmental studies, is prudent for circumpolar Arctic health research. The objective of our bibliometric review was to identify and compare research in select infectious diseases in Arctic wildlife species with importance to human health indexed in English language databases (PubMed, Scopus) and the Russian database eLibrary.ru. Included articles (in English and Russian languages) needed to meet the following criteria: (1) data comes from the Arctic, (2) articles report original research or surveillance reports, (3) articles were published between 1990 and 2018, and (4) research relates to naturally occurring infections. Of the included articles (total n = 352), most were from Russia (n = 131, 37%), Norway (n = 58, 16%), Canada (n = 39, 11%), and Alaska (n = 39, 11%). Frequently reported infectious agents among selected mammals were Trichinella spp. (n = 39), Brucella spp. (n = 25), rabies virus (n = 11), Echinococcus spp. (n = 10), and Francisella tularensis (n = 9). There were 25 articles on anthrax in eLibrary.ru, while there were none in the other two databases. We identified future directions where opportunities for further research, collaboration, systematic reviews, or monitoring programs are possible and needed.},
}
@article {pmid36138772,
year = {2022},
author = {Botella, C and Bonnet, P and Hui, C and Joly, A and Richardson, DM},
title = {Dynamic Species Distribution Modeling Reveals the Pivotal Role of Human-Mediated Long-Distance Dispersal in Plant Invasion.},
journal = {Biology},
volume = {11},
number = {9},
pages = {},
pmid = {36138772},
issn = {2079-7737},
abstract = {Plant invasions generate massive ecological and economic costs worldwide. Predicting their spatial dynamics is crucial to the design of effective management strategies and the prevention of invasions. Earlier studies highlighted the crucial role of long-distance dispersal in explaining the speed of many invasions. In addition, invasion speed depends highly on the duration of its lag phase, which may depend on the scaling of fecundity with age, especially for woody plants, even though empirical proof is still rare. Bayesian dynamic species distribution models enable the fitting of process-based models to partial and heterogeneous observations using a state-space modeling approach, thus offering a tool to test such hypotheses on past invasions over large spatial scales. We use such a model to explore the roles of long-distance dispersal and age-structured fecundity in the transient invasion dynamics of Plectranthus barbatus, a woody plant invader in South Africa. Our lattice-based model accounts for both short and human-mediated long-distance dispersal, as well as age-structured fecundity. We fitted our model on opportunistic occurrences, accounting for the spatio-temporal variations of the sampling effort and the variable detection rates across datasets. The Bayesian framework enables us to integrate a priori knowledge on demographic parameters and control identifiability issues. The model revealed a massive wave of spatial spread driven by human-mediated long-distance dispersal during the first decade and a subsequent drastic population growth, leading to a global equilibrium in the mid-1990s. Without long-distance dispersal, the maximum population would have been equivalent to 30% of the current equilibrium population. We further identified the reproductive maturity at three years old, which contributed to the lag phase before the final wave of population growth. Our results highlighted the importance of the early eradication of weedy horticultural alien plants around urban areas to hamper and delay the invasive spread.},
}
@article {pmid36130600,
year = {2022},
author = {Bidel, F and Bennett, NC and Wardill, TJ},
title = {Octopus bimaculoides' arm recruitment and use during visually evoked prey capture.},
journal = {Current biology : CB},
volume = {32},
number = {21},
pages = {4727-4733.e3},
doi = {10.1016/j.cub.2022.08.080},
pmid = {36130600},
issn = {1879-0445},
mesh = {Animals ; *Octopodiformes/physiology ; Movement/physiology ; Extremities/physiology ; Adaptation, Physiological ; },
abstract = {Octopus' limb hyper-redundancy complicates traditional motor control system theory due to its extensive sensory inputs, subsequent decision-making, and arm coordination. Octopuses are thought to reduce flexibility control complexity by relying on highly stereotypical motor primitives (e.g., reaching[1][,][2][,][3][,][4] and crawling[5]) and multi-level processes to coordinate movement,[6][,][7] utilizing extensive peripheral nervous system (PNS) processing.[2][,][8][,][9] Division of labor along the anterior-posterior axis[10] and limb specialization of the four anterior arms in T-maze food retrieval[11] further simplify control. However, specific arm recruitment and coordination during visually guided reaching behavior remains poorly understood. Here, we investigated visually evoked Octopus bimaculoides' prey capture capabilities[12][,][13] by eliciting and examining prey-specific arm recruitment. When striking crabs, octopuses preferred synchronous arm recruitment, while sequential arm recruitment with a characteristic swaying movement is employed for shrimp. Such behavioral selection aligns with specific prey escape strategies and the octopus' flexible arm biomechanical constraints. Although side bias existed, we found significant bilateral symmetry, with one side being functionally a mirror of the other rather than anterior arm use being functionally equal and differing to posterior arm use. Among arms, the second limb is unequivocally dominant for goal-directed monocularly driven prey capture. Although the eight arms share gross anatomy and are considered equipotential,[10][,][14] such arm use for specific actions could reflect subtle evolutionary adaptations. Finally, we quantitatively show, corroborating earlier observations,[10][,][15] that octopuses employ a dimension reduction strategy by actively deciding to recruit adjacent arms over other available arms during either sequential or synchronous visually evoked prey attack.},
}
@article {pmid36130260,
year = {2022},
author = {Sun, D and Ding, S and Cai, P and Zhang, D and Han, M and Hu, QN},
title = {BioBulkFoundary: a customized webserver for exploring biosynthetic potentials of bulk chemicals.},
journal = {Bioinformatics (Oxford, England)},
volume = {38},
number = {22},
pages = {5137-5138},
doi = {10.1093/bioinformatics/btac640},
pmid = {36130260},
issn = {1367-4811},
mesh = {*Metabolic Engineering/methods ; *Synthetic Biology ; Databases, Factual ; },
abstract = {SUMMARY: Advances in metabolic engineering have boosted the production of bulk chemicals, resulting in tons of production volumes of some bulk chemicals with very low prices. A decrease in the production cost and overproduction of bulk chemicals makes it necessary and desirable to explore the potential to synthesize higher-value products from them. It is also useful and important for society to explore the use of design methods involving synthetic biology to increase the economic value of these bulk chemicals. Therefore, we developed 'BioBulkFoundary', which provides an elaborate analysis of the biosynthetic potential of bulk chemicals based on the state-of-art exploration of pathways to synthesize value-added chemicals, along with associated comprehensive technology and economic database into a user-friendly framework.
Freely available on the web at http://design.rxnfinder.org/biobulkfoundary/.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid36127081,
year = {2022},
author = {Barrigon, ML and Porras-Segovia, A and Courtet, P and Lopez-Castroman, J and Berrouiguet, S and Pérez-Rodríguez, MM and Artes, A and , and Baca-Garcia, E},
title = {Smartphone-based Ecological Momentary Intervention for secondary prevention of suicidal thoughts and behaviour: protocol for the SmartCrisis V.2.0 randomised clinical trial.},
journal = {BMJ open},
volume = {12},
number = {9},
pages = {e051807},
pmid = {36127081},
issn = {2044-6055},
mesh = {Ecological Momentary Assessment ; Humans ; Randomized Controlled Trials as Topic ; Secondary Prevention ; *Smartphone ; Suicidal Ideation ; *Telemedicine ; },
abstract = {INTRODUCTION: Suicide is one of the leading public health issues worldwide. Mobile health can help us to combat suicide through monitoring and treatment. The SmartCrisis V.2.0 randomised clinical trial aims to evaluate the effectiveness of a smartphone-based Ecological Momentary Intervention to prevent suicidal thoughts and behaviour.
METHODS AND ANALYSIS: The SmartCrisis V.2.0 study is a randomised clinical trial with two parallel groups, conducted among patients with a history of suicidal behaviour treated at five sites in France and Spain. The intervention group will be monitored using Ecological Momentary Assessment (EMA) and will receive an Ecological Momentary Intervention called 'SmartSafe' in addition to their treatment as usual (TAU). TAU will consist of mental health follow-up of the patient (scheduled appointments with a psychiatrist) in an outpatient Suicide Prevention programme, with predetermined clinical appointments according to the Brief Intervention Contact recommendations (1, 2, 4, 7 and 11 weeks and 4, 6, 9 and 12 months). The control group would receive TAU and be monitored using EMA.
ETHICS AND DISSEMINATION: This study has been approved by the Ethics Committee of the University Hospital Fundación Jiménez Díaz. It is expected that, in the near future, our mobile health intervention and monitoring system can be implemented in routine clinical practice. Results will be disseminated through peer-reviewed journals and psychiatric congresses. Reference number EC005-21_FJD. Participants gave informed consent to participate in the study before taking part.
TRIAL REGISTRATION NUMBER: NCT04775160.},
}
@article {pmid36123315,
year = {2022},
author = {Fontana, F and Alessandri, G and Tarracchini, C and Bianchi, MG and Rizzo, SM and Mancabelli, L and Lugli, GA and Argentini, C and Vergna, LM and Anzalone, R and Longhi, G and Viappiani, A and Taurino, G and Chiu, M and Turroni, F and Bussolati, O and van Sinderen, D and Milani, C and Ventura, M},
title = {Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach.},
journal = {Environmental microbiology},
volume = {24},
number = {12},
pages = {5825-5839},
doi = {10.1111/1462-2920.16205},
pmid = {36123315},
issn = {1462-2920},
support = {SFI/12/RC/2273-P2/SFI_/Science Foundation Ireland/Ireland ; SFI/12/RC/2273-P1/SFI_/Science Foundation Ireland/Ireland ; },
mesh = {Humans ; Infant ; *Bifidobacterium/genetics ; *Multiomics ; Reproducibility of Results ; Feces/microbiology ; Metagenomics ; Bacteria ; },
abstract = {The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi-omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant faecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species-representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross-laboratory reproducibility and relevance of research findings.},
}
@article {pmid36120670,
year = {2022},
author = {Liu, X and Wang, J and Rui, X and Zhang, J},
title = {Application of GIS Technology-Supported Cross Media Fusion Method Based on Deep Learning in Landscape Performance Evaluation.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {8339895},
pmid = {36120670},
issn = {1687-5273},
mesh = {Algorithms ; *Deep Learning ; Geographic Information Systems ; Humans ; Neural Networks, Computer ; Technology ; },
abstract = {GIS technology can provide reasonable and sustainable data support for landscape planning and ecological development and make wetland landscape planning consider the spatial layout of landscape and the optimal allocation of resources more. The key technologies of cross media intelligence mainly focus on intelligent information retrieval, analysis and reasoning, knowledge map construction, and intelligent storage. Convolutional neural network (CNN), as one of the representative algorithms of deep learning, plays an important role in retrieving landscape data and extracting image and text features across media. Further retrieval of media data, in-depth text processing, and image feature data extraction are realized by using deep learning technology, and comprehensive in-depth analysis is carried out by combining landscape plane images, three-dimensional images, and vector information in GIS technology. Provide quantitative information for the evaluation system of human landscape, economy, history, and region, so as to formulate a scientific and reasonable performance evaluation system.},
}
@article {pmid36114727,
year = {2022},
author = {Ma, X and Zhu, X and Xie, Q and Jin, J and Zhou, Y and Luo, Y and Liu, Y and Tian, J and Zhao, Y},
title = {Monitoring nature's calendar from space: Emerging topics in land surface phenology and associated opportunities for science applications.},
journal = {Global change biology},
volume = {28},
number = {24},
pages = {7186-7204},
doi = {10.1111/gcb.16436},
pmid = {36114727},
issn = {1365-2486},
mesh = {*Ecosystem ; Seasons ; *Climate Change ; Carbon ; Water ; },
abstract = {Vegetation phenology has been viewed as the nature's calendar and an integrative indicator of plant-climate interactions. The correct representation of vegetation phenology is important for models to accurately simulate the exchange of carbon, water, and energy between the vegetated land surface and the atmosphere. Remote sensing has advanced the monitoring of vegetation phenology by providing spatially and temporally continuous data that together with conventional ground observations offers a unique contribution to our knowledge about the environmental impact on ecosystems as well as the ecological adaptations and feedback to global climate change. Land surface phenology (LSP) is defined as the use of satellites to monitor seasonal dynamics in vegetated land surfaces and to estimate phenological transition dates. LSP, as an interdisciplinary subject among remote sensing, ecology, and biometeorology, has undergone rapid development over the past few decades. Recent advances in sensor technologies, as well as data fusion techniques, have enabled novel phenology retrieval algorithms that refine phenology details at even higher spatiotemporal resolutions, providing new insights into ecosystem dynamics. As such, here we summarize the recent advances in LSP and the associated opportunities for science applications. We focus on the remaining challenges, promising techniques, and emerging topics that together we believe will truly form the very frontier of the global LSP research field.},
}
@article {pmid36112603,
year = {2022},
author = {Miller, JC and Satheesh Babu, AK and Petersen, C and Wankhade, UD and Robeson, MS and Putich, MN and Mueller, JE and O'Farrell, AS and Cho, JM and Chintapalli, SV and Jalili, T and Symons, JD and Anandh Babu, PV},
title = {Gut Microbes Are Associated with the Vascular Beneficial Effects of Dietary Strawberry on Metabolic Syndrome-Induced Vascular Inflammation.},
journal = {Molecular nutrition & food research},
volume = {66},
number = {22},
pages = {e2200112},
pmid = {36112603},
issn = {1613-4133},
support = {R01 HL141540/HL/NHLBI NIH HHS/United States ; R03AGO52848/HL/NHLBI NIH HHS/United States ; R01 AT010247/AT/NCCIH NIH HHS/United States ; },
mesh = {Male ; Mice ; Animals ; *Fragaria/chemistry ; *Metabolic Syndrome/etiology/drug therapy ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Diet, High-Fat/adverse effects ; Inflammation ; },
abstract = {SCOPE: Metabolic syndrome (MetS) alters the gut microbial ecology and increases the risk of cardiovascular disease. This study investigates whether strawberry consumption reduces vascular complications in an animal model of MetS and identifies whether this effect is associated with changes in the composition of gut microbes.
METHODS AND RESULTS: Seven-week-old male mice consume diets with 10% (C) or 60% kcal from fat (high-fat diet fed mice; HF) for 12 weeks and subgroups are fed a 2.35% freeze-dried strawberry supplemented diet (C+SB or HF+SB). This nutritional dose is equivalent to ≈160 g of strawberry. After 12 weeks treatment, vascular inflammation is enhanced in HF versus C mice as shown by an increased monocyte binding to vasculature, elevated serum chemokines, and increased mRNA expression of inflammatory molecules. However, strawberry supplementation suppresses vascular inflammation in HF+SB versus HF mice. Metabolic variables, blood pressure, and indices of vascular function were similar among the groups. Further, the abundance of opportunistic microbe is decreased in HF+SB. Importantly, circulating chemokines are positively associated with opportunistic microbes and negatively associated with the commensal microbes (Bifidobacterium and Facalibaculum).
CONCLUSION: Dietary strawberry decreases the abundance of opportunistic microbe and this is associated with a decrease in vascular inflammation resulting from MetS.},
}
@article {pmid36111781,
year = {2022},
author = {Eyre, MT and Souza, FN and Carvalho-Pereira, TSA and Nery, N and de Oliveira, D and Cruz, JS and Sacramento, GA and Khalil, H and Wunder, EA and Hacker, KP and Hagan, JE and Childs, JE and Reis, MG and Begon, M and Diggle, PJ and Ko, AI and Giorgi, E and Costa, F},
title = {Linking rattiness, geography and environmental degradation to spillover Leptospira infections in marginalised urban settings: An eco-epidemiological community-based cohort study in Brazil.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {36111781},
issn = {2050-084X},
support = {F31 AI114245/NH/NIH HHS/United States ; R25 TW009338/NH/NIH HHS/United States ; 102330/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; U01 AI088752/NH/NIH HHS/United States ; R01 AI052473/NH/NIH HHS/United States ; R01 TW009504/NH/NIH HHS/United States ; 001/WHO_/World Health Organization/International ; 964635/MRC_/Medical Research Council/United Kingdom ; },
mesh = {Adult ; Animals ; Brazil/epidemiology ; Cohort Studies ; Epidemiologic Studies ; Geography ; Humans ; *Leptospirosis/epidemiology ; Male ; *Poverty Areas ; Rats ; Zoonoses/epidemiology ; },
abstract = {BACKGROUND: Zoonotic spillover from animal reservoirs is responsible for a significant global public health burden, but the processes that promote spillover events are poorly understood in complex urban settings. Endemic transmission of Leptospira, the agent of leptospirosis, in marginalised urban communities occurs through human exposure to an environment contaminated by bacteria shed in the urine of the rat reservoir. However, it is unclear to what extent transmission is driven by variation in the distribution of rats or by the dispersal of bacteria in rainwater runoff and overflow from open sewer systems.
METHODS: We conducted an eco-epidemiological study in a high-risk community in Salvador, Brazil, by prospectively following a cohort of 1401 residents to ascertain serological evidence for leptospiral infections. A concurrent rat ecology study was used to collect information on the fine-scale spatial distribution of 'rattiness', our proxy for rat abundance and exposure of interest. We developed and applied a novel geostatistical framework for joint spatial modelling of multiple indices of disease reservoir abundance and human infection risk.
RESULTS: The estimated infection rate was 51.4 (95%CI 40.4, 64.2) infections per 1000 follow-up events. Infection risk increased with age until 30 years of age and was associated with male gender. Rattiness was positively associated with infection risk for residents across the entire study area, but this effect was stronger in higher elevation areas (OR 3.27 95% CI 1.68, 19.07) than in lower elevation areas (OR 1.14 95% CI 1.05, 1.53).
CONCLUSIONS: These findings suggest that, while frequent flooding events may disperse bacteria in regions of low elevation, environmental risk in higher elevation areas is more localised and directly driven by the distribution of local rat populations. The modelling framework developed may have broad applications in delineating complex animal-environment-human interactions during zoonotic spillover and identifying opportunities for public health intervention.
FUNDING: This work was supported by the Oswaldo Cruz Foundation and Secretariat of Health Surveillance, Brazilian Ministry of Health, the National Institutes of Health of the United States (grant numbers F31 AI114245, R01 AI052473, U01 AI088752, R01 TW009504 and R25 TW009338); the Wellcome Trust (102330/Z/13/Z), and by the Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB/JCB0020/2016). MTE was supported by a Medical Research UK doctorate studentship. FBS participated in this study under a FAPESB doctorate scholarship.},
}
@article {pmid36109660,
year = {2022},
author = {Negesse, A and Woyraw, W and Temesgen, H and Teka, Y and Yismaw, L and Akalu, TY and Deml, YA and Sume, BW and Negesse, Y and Taddege, T and Kidie, WD and Teym, A and Asmare, B and Hune, Y and Damte, D and Getaneh, T and Gebre, T and Tilahun, B and Tenagne, A and Tegegne, E and Birhanu, MY and Mekonen, H and Shiferaw, M and Kassahun, W and Desalegn, BB},
title = {Spatial exploration of non-resilience to food insecurity, its association with COVID-19 and household coping strategies in East Gojjam districts, Northwest Ethiopia, 2020.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {15511},
pmid = {36109660},
issn = {2045-2322},
mesh = {Adaptation, Psychological ; *COVID-19/epidemiology ; Cross-Sectional Studies ; Ethiopia/epidemiology ; Family Characteristics ; Food Insecurity ; *Food Supply ; Humans ; Male ; Pandemics ; Socioeconomic Factors ; },
abstract = {The coronavirus disease-2019 (COVID-19) pandemic has posed a significant multifaceted threat to the global community. Ethiopia, as a Sub-Saharan African country, is suffering from chronic food insecurity, and the emergence of such a pandemic will exacerbate the situation. As a result, this study investigated the spatial variation of non-resilience to food insecurity, its relationship with COVID-19, and household coping strategies to become resilient in the long run among households in the East Gojjam Zone of Northwest Ethiopia. From September 22 to December 24, 2020, an agro-ecological-based cross-sectional study of 3532 households was conducted to assess the spatial distribution and associated factors of non-resilience to household food insecurity. The enumeration areas (EAs) and households were chosen using a multistage sampling technique. Data were gathered using a semi-structured questionnaire and checklist using an Android device loaded with an Open Data Kit (ODK) template. Binary logistic regression was used to identify the specific factors associated with household non-resilience to food insecurity. A thematic analysis was conducted to investigate the opportunities and challenges of resilience for household food insecurity. Nearly two-thirds (62.5%) of the households were farmers, 67.9% lived in rural areas, and nearly three-quarters (73.8%) earned less than or equal to ETB 2100 per month. Males headed more than four-fifths of the households (81.7%). We found that nearly two-thirds of the households (60.02%), 95% CI 58.40, 61.64) were food insecure. After bivariate logistic regression, we found that households who were divorced (AOR = 2.54 (1.65, 3.87)), daily laborers (AOR = 2.37 (1.15, 4.87)), government employees (AOR = 2.06 (1.05, 4.05)), residents of highland and hot areas (AOR = 11.5 (5.37, 16.77)) and lowland areas (AOR = 1.35 (1.02, 3.15)) were frustrated by COVID-19 (AOR = 1.23 (1.02, 1.50)) and price inflation (1.89 (AOR = 1.42, 2.56))) were at higher odds of being non-resilient to household food insecurity at a 95% confidence level. Geospatial hot spot analysis revealed that Kurar kebele (the lowest government administrative unit) in Dejen District and Debre Markos town were the red-hotspot areas of household non-resilience to food insecurity. Less than a quarter of the households attempted to cope with food insecurity by adjusting their food consumption, while more than 60% of the households chose none of the coping strategies tested. According to the thematic analysis, the degree of poverty (lack of asset ownership), the COVID-19 pandemic, farm decreased variety, and low crop productivity were identified as challenges to coping with the hardship of resilience to food insecurity. During the COVID-19 pandemic and public emergency, the proportion of households that were unprepared for food insecurity reached its peak. It was recognized that a segment of the population with low economic capacity was more vulnerable to food insecurity and less resilient. Tough developmental gains will be undermined in this case. As a result, each responsible body and stakeholder should develop and implement solid corrective plans for the local context.},
}
@article {pmid36109545,
year = {2022},
author = {Domma, F and Condino, F and Franceschi, S and De Luca, DL and Biondi, D},
title = {On the extreme hydrologic events determinants by means of Beta-Singh-Maddala reparameterization.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {15537},
pmid = {36109545},
issn = {2045-2322},
mesh = {*Hydrology ; },
abstract = {In previous studies, beta-k distribution and distribution functions strongly related to that, have played important roles in representing extreme events. Among these distributions, the Beta-Singh-Maddala turned out to be adequate for modelling hydrological extreme events. Starting from this distribution, the aim of the paper is to express the model as a function of indexes of hydrological interest and simultaneously investigate on their dependence with a set of explanatory variables in such a way to explore on possible determinants of extreme hydrologic events. Finally, an application to a real hydrologic dataset is considered in order to show the potentiality of the proposed model in describing data and in understanding effects of covariates on frequently adopted hydrological indicators.},
}
@article {pmid36108049,
year = {2022},
author = {Tegally, H and San, JE and Cotten, M and Moir, M and Tegomoh, B and Mboowa, G and Martin, DP and Baxter, C and Lambisia, AW and Diallo, A and Amoako, DG and Diagne, MM and Sisay, A and Zekri, AN and Gueye, AS and Sangare, AK and Ouedraogo, AS and Sow, A and Musa, AO and Sesay, AK and Abias, AG and Elzagheid, AI and Lagare, A and Kemi, AS and Abar, AE and Johnson, AA and Fowotade, A and Oluwapelumi, AO and Amuri, AA and Juru, A and Kandeil, A and Mostafa, A and Rebai, A and Sayed, A and Kazeem, A and Balde, A and Christoffels, A and Trotter, AJ and Campbell, A and Keita, AK and Kone, A and Bouzid, A and Souissi, A and Agweyu, A and Naguib, A and Gutierrez, AV and Nkeshimana, A and Page, AJ and Yadouleton, A and Vinze, A and Happi, AN and Chouikha, A and Iranzadeh, A and Maharaj, A and Batchi-Bouyou, AL and Ismail, A and Sylverken, AA and Goba, A and Femi, A and Sijuwola, AE and Marycelin, B and Salako, BL and Oderinde, BS and Bolajoko, B and Diarra, B and Herring, BL and Tsofa, B and Lekana-Douki, B and Mvula, B and Njanpop-Lafourcade, BM and Marondera, BT and Khaireh, BA and Kouriba, B and Adu, B and Pool, B and McInnis, B and Brook, C and Williamson, C and Nduwimana, C and Anscombe, C and Pratt, CB and Scheepers, C and Akoua-Koffi, CG and Agoti, CN and Mapanguy, CM and Loucoubar, C and Onwuamah, CK and Ihekweazu, C and Malaka, CN and Peyrefitte, C and Grace, C and Omoruyi, CE and Rafaï, CD and Morang'a, CM and Erameh, C and Lule, DB and Bridges, DJ and Mukadi-Bamuleka, D and Park, D and Rasmussen, DA and Baker, D and Nokes, DJ and Ssemwanga, D and Tshiabuila, D and Amuzu, DSY and Goedhals, D and Grant, DS and Omuoyo, DO and Maruapula, D and Wanjohi, DW and Foster-Nyarko, E and Lusamaki, EK and Simulundu, E and Ong'era, EM and Ngabana, EN and Abworo, EO and Otieno, E and Shumba, E and Barasa, E and Ahmed, EB and Ahmed, EA and Lokilo, E and Mukantwari, E and Philomena, E and Belarbi, E and Simon-Loriere, E and Anoh, EA and Manuel, E and Leendertz, F and Taweh, FM and Wasfi, F and Abdelmoula, F and Takawira, FT and Derrar, F and Ajogbasile, FV and Treurnicht, F and Onikepe, F and Ntoumi, F and Muyembe, FM and Ragomzingba, FEZ and Dratibi, FA and Iyanu, FA and Mbunsu, GK and Thilliez, G and Kay, GL and Akpede, GO and van Zyl, GU and Awandare, GA and Kpeli, GS and Schubert, G and Maphalala, GP and Ranaivoson, HC and Omunakwe, HE and Onywera, H and Abe, H and Karray, H and Nansumba, H and Triki, H and Kadjo, HAA and Elgahzaly, H and Gumbo, H and Mathieu, H and Kavunga-Membo, H and Smeti, I and Olawoye, IB and Adetifa, IMO and Odia, I and Ben Boubaker, IB and Muhammad, IA and Ssewanyana, I and Wurie, I and Konstantinus, IS and Halatoko, JWA and Ayei, J and Sonoo, J and Makangara, JC and Tamfum, JM and Heraud, JM and Shaffer, JG and Giandhari, J and Musyoki, J and Nkurunziza, J and Uwanibe, JN and Bhiman, JN and Yasuda, J and Morais, J and Kiconco, J and Sandi, JD and Huddleston, J and Odoom, JK and Morobe, JM and Gyapong, JO and Kayiwa, JT and Okolie, JC and Xavier, JS and Gyamfi, J and Wamala, JF and Bonney, JHK and Nyandwi, J and Everatt, J and Nakaseegu, J and Ngoi, JM and Namulondo, J and Oguzie, JU and Andeko, JC and Lutwama, JJ and Mogga, JJH and O'Grady, J and Siddle, KJ and Victoir, K and Adeyemi, KT and Tumedi, KA and Carvalho, KS and Mohammed, KS and Dellagi, K and Musonda, KG and Duedu, KO and Fki-Berrajah, L and Singh, L and Kepler, LM and Biscornet, L and de Oliveira Martins, L and Chabuka, L and Olubayo, L and Ojok, LD and Deng, LL and Ochola-Oyier, LI and Tyers, L and Mine, M and Ramuth, M and Mastouri, M and ElHefnawi, M and Mbanne, M and Matsheka, MI and Kebabonye, M and Diop, M and Momoh, M and Lima Mendonça, MDL and Venter, M and Paye, MF and Faye, M and Nyaga, MM and Mareka, M and Damaris, MM and Mburu, MW and Mpina, MG and Owusu, M and Wiley, MR and Tatfeng, MY and Ayekaba, MO and Abouelhoda, M and Beloufa, MA and Seadawy, MG and Khalifa, MK and Matobo, MM and Kane, M and Salou, M and Mbulawa, MB and Mwenda, M and Allam, M and Phan, MVT and Abid, N and Rujeni, N and Abuzaid, N and Ismael, N and Elguindy, N and Top, NM and Dia, N and Mabunda, N and Hsiao, NY and Silochi, NB and Francisco, NM and Saasa, N and Bbosa, N and Murunga, N and Gumede, N and Wolter, N and Sitharam, N and Ndodo, N and Ajayi, NA and Tordo, N and Mbhele, N and Razanajatovo, NH and Iguosadolo, N and Mba, N and Kingsley, OC and Sylvanus, O and Femi, O and Adewumi, OM and Testimony, O and Ogunsanya, OA and Fakayode, O and Ogah, OE and Oludayo, OE and Faye, O and Smith-Lawrence, P and Ondoa, P and Combe, P and Nabisubi, P and Semanda, P and Oluniyi, PE and Arnaldo, P and Quashie, PK and Okokhere, PO and Bejon, P and Dussart, P and Bester, PA and Mbala, PK and Kaleebu, P and Abechi, P and El-Shesheny, R and Joseph, R and Aziz, RK and Essomba, RG and Ayivor-Djanie, R and Njouom, R and Phillips, RO and Gorman, R and Kingsley, RA and Neto Rodrigues, RMDESA and Audu, RA and Carr, RAA and Gargouri, S and Masmoudi, S and Bootsma, S and Sankhe, S and Mohamed, SI and Femi, S and Mhalla, S and Hosch, S and Kassim, SK and Metha, S and Trabelsi, S and Agwa, SH and Mwangi, SW and Doumbia, S and Makiala-Mandanda, S and Aryeetey, S and Ahmed, SS and Ahmed, SM and Elhamoumi, S and Moyo, S and Lutucuta, S and Gaseitsiwe, S and Jalloh, S and Andriamandimby, SF and Oguntope, S and Grayo, S and Lekana-Douki, S and Prosolek, S and Ouangraoua, S and van Wyk, S and Schaffner, SF and Kanyerezi, S and Ahuka-Mundeke, S and Rudder, S and Pillay, S and Nabadda, S and Behillil, S and Budiaki, SL and van der Werf, S and Mashe, T and Mohale, T and Le-Viet, T and Velavan, TP and Schindler, T and Maponga, TG and Bedford, T and Anyaneji, UJ and Chinedu, U and Ramphal, U and George, UE and Enouf, V and Nene, V and Gorova, V and Roshdy, WH and Karim, WA and Ampofo, WK and Preiser, W and Choga, WT and Ahmed, YA and Ramphal, Y and Bediako, Y and Naidoo, Y and Butera, Y and de Laurent, ZR and , and Ouma, AEO and von Gottberg, A and Githinji, G and Moeti, M and Tomori, O and Sabeti, PC and Sall, AA and Oyola, SO and Tebeje, YK and Tessema, SK and de Oliveira, T and Happi, C and Lessells, R and Nkengasong, J and Wilkinson, E},
title = {The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.},
journal = {Science (New York, N.Y.)},
volume = {378},
number = {6615},
pages = {eabq5358},
pmid = {36108049},
issn = {1095-9203},
support = {U01 HG007480/HG/NHGRI NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U19 AI089696/AI/NIAID NIH HHS/United States ; U54 HG007480/HG/NHGRI NIH HHS/United States ; U54 TW012041/TW/FIC NIH HHS/United States ; U01 AI151812/AI/NIAID NIH HHS/United States ; K24 AI131924/AI/NIAID NIH HHS/United States ; U01 AI151698/AI/NIAID NIH HHS/United States ; U19 AI129387/AI/NIAID NIH HHS/United States ; 001/WHO_/World Health Organization/International ; K24 AI131928/AI/NIAID NIH HHS/United States ; U2R TW010673/TW/FIC NIH HHS/United States ; },
mesh = {Africa/epidemiology ; *COVID-19/epidemiology/virology ; *Epidemiological Monitoring ; Genomics ; Humans ; *Pandemics ; *SARS-CoV-2/genetics ; },
abstract = {Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.},
}
@article {pmid36107252,
year = {2022},
author = {Lukasová, V and Bičárová, S and Buchholcerová, A and Adamčíková, K},
title = {Low sensitivity of Pinus mugo to surface ozone pollution in the subalpine zone of continental Europe.},
journal = {International journal of biometeorology},
volume = {66},
number = {11},
pages = {2311-2324},
pmid = {36107252},
issn = {1432-1254},
mesh = {Humans ; *Ozone/analysis ; *Air Pollutants/analysis ; *Pinus ; Environmental Monitoring ; Plant Leaves ; Polyesters/analysis/pharmacology ; },
abstract = {High altitudes have been exposed to enhanced levels of surface ozone (O3) concentrations over recent decades compared to the pre-industrial era. The responses of vegetation to this toxic pollutant are species-specific and depend on the climate conditions. In this paper, we explored the reaction of Pinus mugo (P. mugo) to O3-induced stress in the continental climate of an ozone-rich mountain area in the High Tatra Mountains (Western Carpathians). The effects of O3 doses modelled by a deposition model, O3 concentrations and other factors on P. mugo were identified from (a) satellite-based data via NDVI (normalised differenced vegetation index) over 2000-2020 and (b) visible injury on needle samples gathered from P. mugo individuals at ground-truth sites in 2019 and 2020. Analysing the NDVI trend, we observed non-significant changes (p > 0.05) in the greenness of P. mugo despite growing in an environment with the average seasonal O3 concentration around 51.6 ppbv, the maximum hourly concentrations more than 90 ppbv and increasing trend of O3 doses by 0.1 mmol m[-2] PLA (plant leaf area) year[-1]. The visible O3 injury of samples collected at study sites was low (mean injury observed on 1-10% of needles' surface), and the symptoms of injury caused by other biotic and abiotic factors prevailed over those caused by O3. In addition, the correlation analyses between NDVI and the climatic factors indicated a significant (p < 0.05) and positive relationship with photosynthetic active radiation (R = 0.45) in July, and with stomatal conductance (R = 0.52) and temperature factor (R = 0.43) in August. Therefore, we concluded that the positive effect of climate conditions, which support the growth processes of P. mugo, may suppress the negative effect of the mean O3 doses of 17.8 mmol m[-2] PLA accumulated over the growing season.},
}
@article {pmid36103465,
year = {2022},
author = {Nam, S and Jeon, S and Lee, SJ and Ash, G and Nelson, LE and Granger, DA},
title = {Real-time racial discrimination, affective states, salivary cortisol and alpha-amylase in Black adults.},
journal = {PloS one},
volume = {17},
number = {9},
pages = {e0273081},
pmid = {36103465},
issn = {1932-6203},
mesh = {Adult ; Cross-Sectional Studies ; Humans ; *Hydrocortisone ; *Racism/psychology ; Retrospective Studies ; Saliva ; Stress, Psychological/psychology ; alpha-Amylases ; },
abstract = {Perceived racial discrimination has been associated with the autonomic nervous system (ANS) and hypothalamic-pituitary-adrenal (HPA) axis activities-two major stress response systems. To date, most studies have used cross-sectional data that captured retrospective measures of the racial discrimination associated with current physiological stress responses. The purpose of this study was to examine the relationship between racial discrimination measured in real-time and physiological stress responses. Twelve healthy Black adults completed baseline surveys and self-collected saliva samples 4x/day for 4 days to measure cortisol and alpha amylase (AA) as a proxy of HPA and ANS systems, respectively. Real-time racial discrimination was measured using ecological momentary assessments (EMA) sent to participants 5x/day for 7 days. Multilevel models were conducted to examine the relationship between racial discrimination and stress responses. In multilevel models, the previous day's racial discrimination was significantly associated with the next day's cortisol level at wakening (β = 0.81, partial r = 0.74, p<0.01) and diurnal slope (β = -0.85, partial r = -0.73, p<0.01). Also, microaggressions were significantly associated with the diurnal cortisol slope in the same day, indicating that on the day when people reported more microaggressions than usual, a flatter diurnal slope of cortisol was observed (β = -0.50, partial r = -0.64, p<0.01). The concurrent use of salivary biomarkers and EMA was feasible methods to examine the temporal relationship between racial discrimination and physiological stress responses. The within-person approach may help us understand the concurrent or lagged effects of racial discrimination on the stress responses. Further studies are needed to confirm the observed findings with a large sample size and to improve stress related health outcomes in racial/ethnic minorities.},
}
@article {pmid36102834,
year = {2022},
author = {Débarre, F and Lecoeur, E and Guimier, L and Jauffret-Roustide, M and Jannot, AS},
title = {The French Covid-19 vaccination policy did not solve vaccination inequities: a nationwide study on 64.5 million people.},
journal = {European journal of public health},
volume = {32},
number = {5},
pages = {825-830},
pmid = {36102834},
issn = {1464-360X},
mesh = {*COVID-19/epidemiology/prevention & control ; *COVID-19 Vaccines ; Emigration and Immigration ; Humans ; Policy ; Vaccination ; },
abstract = {BACKGROUND: To encourage Covid-19 vaccination, France introduced during the Summer 2021 a 'Sanitary Pass', which morphed into a 'Vaccine Pass' in early 2022. While the sanitary pass led to an increase in Covid-19 vaccination rates, spatial heterogeneities in vaccination rates remained. To identify potential determinants of these heterogeneities and evaluate the French sanitary and vaccine passes' efficacies in reducing them, we used a data-driven approach on exhaustive nationwide data, gathering 141 socio-economic, political and geographic indicators.
METHODS: We considered the association between vaccination rates and each indicator at different time points: before the sanitary pass announcement (week 2021-W27), before the sanitary pass came into force (week 2021-W31) and 1 month after (week 2021-W35) and the equivalent dates for the vaccine pass (weeks 2021-W49, 2022-W03 and 2022-W07).
RESULTS: The indicators most associated with vaccination rates were the share of local income coming from unemployment benefits, overcrowded households rate, immigrants rate and vote for an 'anti-establishment' candidate at the 2017 Presidential election. These associations increase over time. Consequently, living in a district below the median of such indicator decreases the probability to be vaccinated by about 30% at the end of the studied period, and this probability gradually decreases by deciles of these indicators.
CONCLUSIONS: Our analysis reveals that factors related to poverty, immigration and trust in the government are strong determinants of vaccination rate, and that vaccination inequities tended to increase after the introduction of the French sanitary and vaccination passes.},
}
@article {pmid36100598,
year = {2022},
author = {Metz, S and Huber, P and Mateus-Barros, E and Junger, PC and de Melo, M and Bagatini, IL and Izaguirre, I and Câmara Dos Reis, M and Llames, ME and Accattatis, V and Quiroga, MV and Devercelli, M and Schiaffino, MR and Niño-García, JP and Bastidas Navarro, M and Modenutti, B and Vieira, H and Saraceno, M and Sabio Y García, CA and Pereira, E and González-Revello, A and Piccini, C and Unrein, F and Alonso, C and Sarmento, H},
title = {A georeferenced rRNA amplicon database of aquatic microbiomes from South America.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {565},
pmid = {36100598},
issn = {2052-4463},
mesh = {Bacteria/genetics ; Databases, Genetic ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; South America ; Water Microbiology ; },
abstract = {The biogeography of bacterial communities is a key topic in Microbial Ecology. Regarding continental water, most studies are carried out in the northern hemisphere, leaving a gap on microorganism's diversity patterns on a global scale. South America harbours approximately one third of the world's total freshwater resources, and is one of these understudied regions. To fill this gap, we compiled 16S rRNA amplicon sequencing data of microbial communities across South America continental water ecosystems, presenting the first database µSudAqua[db]. The database contains over 866 georeferenced samples from 9 different ecoregions with contextual environmental information. For its integration and validation we constructed a curated database (µSudAqua[db.sp]) using samples sequenced by Illumina MiSeq platform with commonly used prokaryote universal primers. This comprised ~60% of the total georeferenced samples of the µSudAqua[db]. This compilation was carried out in the scope of the µSudAqua collaborative network and represents one of the most complete databases of continental water microbial communities from South America.},
}
@article {pmid36095758,
year = {2022},
author = {Golovatch, S and Vandenspiegel, D},
title = {Carinobolus gen. nov. and Costabolus gen. nov., two new, remarkably crested, monospecific genera of spirobolidan millipedes from West Africa, with the proposal of a new tribe, Amblybolini tribus nova (Diplopoda, Spirobolida, Pachybolidae).},
journal = {Zootaxa},
volume = {5150},
number = {1},
pages = {97-110},
doi = {10.11646/zootaxa.5150.1.5},
pmid = {36095758},
issn = {1175-5334},
mesh = {Africa, Western ; Animals ; *Arthropods ; },
abstract = {Two new genera, Carinobolus gen. nov. and Costabolus gen. nov., both belonging to the very large, widespread, pantropical family Pachybolidae, are described based on Carinobolus complex sp. nov. and Costabolus baculus sp. nov., respectively. Chiefly based on the posterior gonopod being distinctly articulated at midlength, both new genera seem to be especially similar to Amblybolus Keeton, 1964a (three species in western Africa) and Atlanticobolus Hoffman, 1979 (one species from an island off the Brazilian coast), all of them meriting a separate tribal category, Amblybolini tribus nova. A key is proposed to distinguish all four presently accepted genera of the new tribe. The new genera and species are clearly distinguished in showing unusually strongly crested/ribbed metazonae, a character that is only very seldom observed in Pachybolidae generally, and apparently unique among Afrotropical members. Being rather similar in many respects, both new genera and species differ from each other sufficiently well in gonopodal and leg structure, even though both come from forests in southeastern Nigeria close to the border to Cameroon.},
}
@article {pmid36095211,
year = {2022},
author = {Still, CJ and Page, G and Rastogi, B and Griffith, DM and Aubrecht, DM and Kim, Y and Burns, SP and Hanson, CV and Kwon, H and Hawkins, L and Meinzer, FC and Sevanto, S and Roberts, D and Goulden, M and Pau, S and Detto, M and Helliker, B and Richardson, AD},
title = {No evidence of canopy-scale leaf thermoregulation to cool leaves below air temperature across a range of forest ecosystems.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {38},
pages = {e2205682119},
pmid = {36095211},
issn = {1091-6490},
mesh = {*Carbon/metabolism ; *Carbon Cycle ; *Forests ; *Plant Leaves/anatomy & histology/metabolism ; Temperature ; },
abstract = {Understanding and predicting the relationship between leaf temperature (Tleaf) and air temperature (Tair) is essential for projecting responses to a warming climate, as studies suggest that many forests are near thermal thresholds for carbon uptake. Based on leaf measurements, the limited leaf homeothermy hypothesis argues that daytime Tleaf is maintained near photosynthetic temperature optima and below damaging temperature thresholds. Specifically, leaves should cool below Tair at higher temperatures (i.e., > ∼25-30°C) leading to slopes <1 in Tleaf/Tair relationships and substantial carbon uptake when leaves are cooler than air. This hypothesis implies that climate warming will be mitigated by a compensatory leaf cooling response. A key uncertainty is understanding whether such thermoregulatory behavior occurs in natural forest canopies. We present an unprecedented set of growing season canopy-level leaf temperature (Tcan) data measured with thermal imaging at multiple well-instrumented forest sites in North and Central America. Our data do not support the limited homeothermy hypothesis: canopy leaves are warmer than air during most of the day and only cool below air in mid to late afternoon, leading to Tcan/Tair slopes >1 and hysteretic behavior. We find that the majority of ecosystem photosynthesis occurs when canopy leaves are warmer than air. Using energy balance and physiological modeling, we show that key leaf traits influence leaf-air coupling and ultimately the Tcan/Tair relationship. Canopy structure also plays an important role in Tcan dynamics. Future climate warming is likely to lead to even greater Tcan, with attendant impacts on forest carbon cycling and mortality risk.},
}
@article {pmid36094211,
year = {2022},
author = {Njoroge, SM and Madé, LF and von Mentzer, A and Kulohoma, BW and Kamanu, TK and Ouko, TT and Kiiru, J and Ward, MJ and Thomson, NR and Fèvre, EM and Woolhouse, M and Kariuki, S},
title = {Draft Genome Sequence of an Enterotoxigenic Escherichia coli Strain Carrying Genes for Colonization Surface Antigen 13 and a Heat-Labile Toxin.},
journal = {Microbiology resource announcements},
volume = {11},
number = {10},
pages = {e0041622},
pmid = {36094211},
issn = {2576-098X},
abstract = {Here, we report the draft genome of ESEI_597, an enterotoxigenic Escherichia coli (ETEC) strain harboring genes encoding colonization surface antigen 13 (CS13) and a heat-labile toxin. The ESEI_597 strain was isolated from an 8-month-old child living in Korogocho, Kenya, in 2013.},
}
@article {pmid36090080,
year = {2022},
author = {Chang, Y and Chen, F and Zhu, Y and You, Y and Cheng, Y and Ma, J},
title = {Influence of revegetation on soil microbial community and its assembly process in the open-pit mining area of the Loess Plateau, China.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {992816},
pmid = {36090080},
issn = {1664-302X},
abstract = {Vegetation recovery is an important marker of ecosystem health in the mining area. Clarifying the influence of vegetation recovery on the characteristics of soil microbial community and its assembly process can improve our understanding of the ecological resilience and self-maintaining mechanism in the open-pit mining area. For this purpose, we employed MiSeq high-throughput sequencing coupled with null model analysis to determine the composition, molecular ecological network characteristics, key bacterial and fungal clusters, and the assembly mechanism of the soil microbial communities in shrubs (BL), coniferous forest (CF), broad-leaved forests (BF), mixed forest (MF), and the control plot (CK, the poplar plantation nearby that had been continuously grown for over 30 a without disturbance). The results showed that the vegetation restoration model had a significant influence on the α-diversity of the microbial community (p < 0.05). Compared with CK, Sobs and Shannon index of MF and CF have increased by 35.29, 3.50, and 25.18%, 1.05%, respectively, whereas there was no significant difference in the α-diversity of fungal community among different vegetation restoration types, Actinobacteria, Chloroflexi, Proteobacteria, and Acidobacteria were the dominant phyla. The diversity of the first two phyla was significantly higher than those of CK. However, the diversity of the last two phyla was dramatically lower than those of CK (p < 0.05). Ascomycota and Basidiomycota were dominant phyla in the fungal community. The abundance and diversity of Ascomycota were significantly higher than those of CK, while the abundance and diversity of the latter were considerably lower than those of CK (p < 0.05). The stochastic process governed the assembly of the soil microbial community, and the contribution rate to the bacterial community construction of CK, CF, BF, and MF was 100.0%. Except for MF, where the soil fungal community assembly was governed by the deterministic process, all other fungal communities were governed by the stochastic process. Proteobacteria and Acidobacteria are key taxa of the bacterial network, while Mortierellales, Thelebolales, Chaetothyriales, and Hypocreales are the key taxa of the fungal network. All these results might provide the theoretical foundation for restoring the fragile ecosystem in the global mining region.},
}
@article {pmid36089013,
year = {2022},
author = {Lyu, Y and Wu, Z and Wu, H and Pang, X and Qin, K and Wang, B and Ding, S and Chen, D and Chen, J},
title = {Tracking long-term population exposure risks to PM2.5 and ozone in urban agglomerations of China 2015-2021.},
journal = {The Science of the total environment},
volume = {854},
number = {},
pages = {158599},
doi = {10.1016/j.scitotenv.2022.158599},
pmid = {36089013},
issn = {1879-1026},
abstract = {China has experienced severe air pollution in the past decade, especially PM2.5 and emerging ozone pollution recently. In this study, we comprehensively analyzed long-term population exposure risks to PM2.5 and ozone in urban agglomerations of China during 2015-2021 regarding two-stage clean-air actions based on the Ministry of Ecology and the Environment (MEE) air monitoring network. Overall, the ratio of the population living in the regions exceeding the Chinese National Ambient Air Quality Standard (35 μg/m[3]) decreases by 29.9 % for PM2.5 from 2015 to 2021, driven by high proportions in the Middle Plain (MP, 42.3 %) and Lan-Xi (35.0 %) regions. However, this ratio almost remains unchanged for ozone and even increases by 1.5 % in the MP region. As expected, the improved air quality leads to 234.7 × 10[3] avoided premature mortality (ΔMort), mainly ascribed to the reduction in PM2.5 concentration. COVID-19 pandemic may influence the annual variation of PM2.5-related ΔMort as it affects the shape of the population exposure curve to become much steeper. Although all eleven urban agglomerations share stroke (43.6 %) and ischaemic heart disease (IHD, 30.1 %) as the two largest contributors to total ΔMort, cause-specific ΔMort is highly regional heterogeneous, in which ozone-related ΔMort is significantly higher (21 %) in the Tibet region than other urban agglomeration. Despite ozone-related ΔMort being one order of magnitude lower than PM2.5-related ΔMort from 2015 to 2021, ozone-related ΔMort is predicted to increase in major urban agglomerations initially along with a continuous decline for PM2.5-related ΔMort from 2020 to 2060, highlighting the importance of ozone control. Coordinated controls of PM2.5 and O3 are warranted for reducing health burdens in China during achieving carbon neutrality.},
}
@article {pmid36088355,
year = {2022},
author = {Mull, CG and Pacoureau, N and Pardo, SA and Ruiz, LS and García-Rodríguez, E and Finucci, B and Haack, M and Harry, A and Judah, AB and VanderWright, W and Yin, JS and Kindsvater, HK and Dulvy, NK},
title = {Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {559},
pmid = {36088355},
issn = {2052-4463},
mesh = {Animals ; Conservation of Natural Resources ; Databases, Factual ; Internationality ; *Life History Traits ; *Sharks ; },
abstract = {A curated database of shark and ray biological data is increasingly necessary both to support fisheries management and conservation efforts, and to test the generality of hypotheses of vertebrate macroecology and macroevolution. Sharks and rays are one of the most charismatic, evolutionary distinct, and threatened lineages of vertebrates, comprising around 1,250 species. To accelerate shark and ray conservation and science, we developed Sharkipedia as a curated open-source database and research initiative to make all published biological traits and population trends accessible to everyone. Sharkipedia hosts information on 58 life history traits from 274 sources, for 170 species, from 39 families, and 12 orders related to length (n = 9 traits), age (8), growth (12), reproduction (19), demography (5), and allometric relationships (5), as well as 871 population time-series from 202 species. Sharkipedia relies on the backbone taxonomy of the IUCN Red List and the bibliography of Shark-References. Sharkipedia has profound potential to support the rapidly growing data demands of fisheries management, international trade regulation as well as anchoring vertebrate macroecology and macroevolution.},
}
@article {pmid36074761,
year = {2022},
author = {Cappellato, M and Baruzzo, G and Di Camillo, B},
title = {Investigating differential abundance methods in microbiome data: A benchmark study.},
journal = {PLoS computational biology},
volume = {18},
number = {9},
pages = {e1010467},
pmid = {36074761},
issn = {1553-7358},
mesh = {*Benchmarking ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Reproducibility of Results ; },
abstract = {The development of increasingly efficient and cost-effective high throughput DNA sequencing techniques has enhanced the possibility of studying complex microbial systems. Recently, researchers have shown great interest in studying the microorganisms that characterise different ecological niches. Differential abundance analysis aims to find the differences in the abundance of each taxa between two classes of subjects or samples, assigning a significance value to each comparison. Several bioinformatic methods have been specifically developed, taking into account the challenges of microbiome data, such as sparsity, the different sequencing depth constraint between samples and compositionality. Differential abundance analysis has led to important conclusions in different fields, from health to the environment. However, the lack of a known biological truth makes it difficult to validate the results obtained. In this work we exploit metaSPARSim, a microbial sequencing count data simulator, to simulate data with differential abundance features between experimental groups. We perform a complete comparison of recently developed and established methods on a common benchmark with great effort to the reliability of both the simulated scenarios and the evaluation metrics. The performance overview includes the investigation of numerous scenarios, studying the effect on methods' results on the main covariates such as sample size, percentage of differentially abundant features, sequencing depth, feature variability, normalisation approach and ecological niches. Mainly, we find that methods show a good control of the type I error and, generally, also of the false discovery rate at high sample size, while recall seem to depend on the dataset and sample size.},
}
@article {pmid36071746,
year = {2022},
author = {Prenzel, F and Treudler, R and Lipek, T and Vom Hove, M and Kage, P and Kuhs, S and Kaiser, T and Bastl, M and Bumberger, J and Genuneit, J and Hornick, T and Klotz, S and Zarnowski, J and Boege, M and Zebralla, V and Simon, JC and Dunker, S},
title = {Invasive Growth of Ailanthus altissima Trees is Associated with a High Rate of Sensitization in Atopic Patients.},
journal = {Journal of asthma and allergy},
volume = {15},
number = {},
pages = {1217-1226},
pmid = {36071746},
issn = {1178-6965},
abstract = {PURPOSE: Ailanthus altissima is one of the world's most invasive species with a globally problematic spread. Pollen is dispersed locally and partially airborne. We aimed at investigating if (i) A. altissima pollen can be detected in relevant quantity in the air and if (ii) sensitization to A. altissima can be detected in patients with seasonal exacerbation of atopic diseases.
PATIENTS AND METHODS: We recorded distribution of A. altissima in Leipzig, Germany. In 2019 and 2020, pollen was collected with a Hirst-type pollen trap placed on the roof of the University Hospital. Specific IgE investigations were performed in children and adults with history of atopic diseases with deterioration between May and July. We analysed specific IgE for A. altissima, Alternaria sp., birch, grasses, profilins, polcalcins and crossreacting carbohydrates.
RESULTS: We found abundant growth of A. altissima and pollen was detected from early June to mid-July with a maximum pollen concentration of 31 pollen/m[3]. Out of 138 patients (63 female, 69 children/adolescents), 95 (69%) had seasonal allergic rhinitis, 84 (61%) asthma, and 43 (31%) atopic dermatitis. Sensitization to A. altissima was shown in 59 (42%). There were no significant differences between age groups. In 59% of patients sensitized (35/59), there was no sensitization to possibly cross-reacting structures.
CONCLUSION: Sensitization to A. altissima pollen could be detected in 42% of our patients with atopic diseases, suggesting allergenic potential of this neophyte. In the context of further spread with climate change, eradication strategies and population-based sensitization studies are needed.},
}
@article {pmid36071164,
year = {2022},
author = {Arostegui, MC and Gaube, P and Woodworth-Jefcoats, PA and Kobayashi, DR and Braun, CD},
title = {Anticyclonic eddies aggregate pelagic predators in a subtropical gyre.},
journal = {Nature},
volume = {609},
number = {7927},
pages = {535-540},
pmid = {36071164},
issn = {1476-4687},
mesh = {Animals ; Cyclonic Storms ; Datasets as Topic ; *Ecosystem ; Fisheries ; Food Chain ; Nutrients/analysis ; Pacific Ocean ; *Predatory Behavior ; Tropical Climate ; *Water ; *Water Movements ; },
abstract = {Ocean eddies are coherent, rotating features that can modulate pelagic ecosystems across many trophic levels. These mesoscale features, which are ubiquitous at mid-latitudes[1], may increase productivity of nutrient-poor regions[2,3], accumulate prey[4] and modulate habitat conditions in the water column[5]. However, in nutrient-poor subtropical gyres-the largest marine biome-the role of eddies in modulating behaviour throughout the pelagic predator community remains unknown despite predictions for these gyres to expand[6] and pelagic predators to become increasingly important for food security[7]. Using a large-scale fishery dataset in the North Pacific Subtropical Gyre, we show a pervasive pattern of increased pelagic predator catch inside anticyclonic eddies relative to cyclones and non-eddy areas. Our results indicate that increased mesopelagic prey abundance in anticyclone cores[4,8] may be attracting diverse predators, forming ecological hotspots where these predators aggregate and exhibit increased abundance. In this energetically quiescent gyre, we expect that isolated mesoscale features (and the habitat conditions in them) exhibit primacy over peripheral submesoscale dynamics in structuring the foraging opportunities of pelagic predators. Our finding that eddies influence coupling of epi- to mesopelagic communities corroborates the growing evidence that deep scattering layer organisms are vital prey for a suite of commercially important predator species[9] and, thus, provide valuable ecosystem services.},
}
@article {pmid36071118,
year = {2022},
author = {Brown, JM and Bossomaier, T and Barnett, L},
title = {Information flow in first-order potts model phase transition.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {15145},
pmid = {36071118},
issn = {2045-2322},
mesh = {Entropy ; *Hot Temperature ; Phase Transition ; Thermodynamics ; },
abstract = {Phase transitions abound in nature and society, and, from species extinction to stock market collapse, their prediction is of widespread importance. In earlier work we showed that Global Transfer Entropy, a general measure of information flow, was found to peaks away from the transition on the disordered side for the Ising model, a canonical second order transition. Here we show that (a) global transfer entropy also peaks on the disordered side of the transition of finite first order transitions, such as ecology dynamics on coral reefs, which have latent heat and no correlation length divergence, and (b) analysis of information flow across state boundaries unifies both transition orders. We obtain the first information-theoretic result for the high-order Potts model and the first demonstration of early warning of a first order transition. The unexpected earlier finding that global transfer entropy peaks on the disordered side of a transition is also found for finite first order systems, albeit not in the thermodynamic limit. By noting that the interface length of clusters in each phase is the dominant region of information flow, we unify the information theoretic behaviour of first and second order transitions.},
}
@article {pmid36058075,
year = {2022},
author = {Maloney, KO and Buchanan, C and Jepsen, RD and Krause, KP and Cashman, MJ and Gressler, BP and Young, JA and Schmid, M},
title = {Explainable machine learning improves interpretability in the predictive modeling of biological stream conditions in the Chesapeake Bay Watershed, USA.},
journal = {Journal of environmental management},
volume = {322},
number = {},
pages = {116068},
doi = {10.1016/j.jenvman.2022.116068},
pmid = {36058075},
issn = {1095-8630},
mesh = {Agriculture ; *Bays ; Ecosystem ; Environmental Monitoring/methods ; Machine Learning ; *Rivers ; },
abstract = {Anthropogenic alterations have resulted in widespread degradation of stream conditions. To aid in stream restoration and management, baseline estimates of conditions and improved explanation of factors driving their degradation are needed. We used random forests to model biological conditions using a benthic macroinvertebrate index of biotic integrity for small, non-tidal streams (upstream area ≤200 km[2]) in the Chesapeake Bay watershed (CBW) of the mid-Atlantic coast of North America. We utilized several global and local model interpretation tools to improve average and site-specific model inferences, respectively. The model was used to predict condition for 95,867 individual catchments for eight periods (2001, 2004, 2006, 2008, 2011, 2013, 2016, 2019). Predicted conditions were classified as Poor, FairGood, or Uncertain to align with management needs and individual reach lengths and catchment areas were summed by condition class for the CBW for each period. Global permutation and local Shapley importance values indicated percent of forest, development, and agriculture in upstream catchments had strong impacts on predictions. Development and agriculture negatively influenced stream condition for model average (partial dependence [PD] and accumulated local effect [ALE] plots) and local (individual condition expectation and Shapley value plots) levels. Friedman's H-statistic indicated large overall interactions for these three land covers, and bivariate global plots (PD and ALE) supported interactions among agriculture and development. Total stream length and catchment area predicted in FairGood conditions decreased then increased over the 19-years (length/area: 66.6/65.4% in 2001, 66.3/65.2% in 2011, and 66.6/65.4% in 2019). Examination of individual catchment predictions between 2001 and 2019 showed those predicted to have the largest decreases in condition had large increases in development; whereas catchments predicted to exhibit the largest increases in condition showed moderate increases in forest cover. Use of global and local interpretative methods together with watershed-wide and individual catchment predictions support conservation practitioners that need to identify widespread and localized patterns, especially acknowledging that management actions typically take place at individual-reach scales.},
}
@article {pmid36053136,
year = {2022},
author = {Kelleher, K and McGinnity, P and Howard, BJ and Boyer, P and Vidal, M and Bildstein, OM},
title = {The use of the IAEA MARIS database in determining the variability of sediment distribution coefficients in the marine environment and potential implications for marine dispersion modelling.},
journal = {Journal of radiological protection : official journal of the Society for Radiological Protection},
volume = {42},
number = {3},
pages = {},
doi = {10.1088/1361-6498/ac8a53},
pmid = {36053136},
issn = {1361-6498},
mesh = {Geologic Sediments ; Information Systems ; *Radioactivity ; Seawater ; *Water Pollutants, Radioactive/analysis ; },
abstract = {A prototype tool has been developed for deriving sediment distribution coefficients,Kd, in the marine environment by harvesting simultaneous measurements of activity concentrations of radionuclides in seawater and sediments based on the International Atomic Energy Agency's Marine Radioactivity Information System (MARIS). As a case study, theKdvariability in the Baltic Sea was investigated as this region has been extensively monitored by HELCOM since 1984 resulting in a comprehensive dataset with good spatial and temporal coverage and required ancillary parameters. The prototype tool was used to derive a dataset ofin-situapparentKd(a)values derived from measurements of seawater and sediment in quasi-equilibrium conditions from the Baltic Sea over a period of approximately 35 years. For Cs, a comprehensive analysis of the Baltic SeaKd(a)dataset was undertaken, focusing on the temporal trend ofKd(a)and comparing the results toKdvalues derived elsewhere. For Sr and Pu, for which there were fewer data records available a more rudimentary analysis was carried out. The CsKd(a)median values derived from[137]Cs data in this study were estimated to be 2154 l kg[-1]for seabed sediment and 10 000 l kg[-1]for suspended sediment. The value derived for seabed sediment is in good agreement with the previously recommended ocean margin CsKdvalue of 4000 l kg[-1]. The analysis demonstrated the important distinction in the Baltic Sea betweenKdvalues for seabed sediment and suspended sediments, which differed by an order of magnitude. The analysis also highlighted the dependence ofKdvalues on the variation in both the salinity of seawater and the type of seabed sediment. Such variability can significantly influence outcomes when modelling the behaviour of radionuclides in marine dispersion modelling.},
}
@article {pmid36051895,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Gibbs, M and , },
title = {The genome sequence of the clay, Mythimna ferrago (Fabricius, 1787).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {177},
pmid = {36051895},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual female Mythimna ferrago (the clay; Arthropoda; Insecta; Lepidoptera; Noctuidae). The genome sequence is 861 megabases in span. The majority of the assembly (99.98%) is scaffolded into 32 chromosomal pseudomolecules, with the W and Z chromosomes assembled. The complete mitochondrial genome was also assembled and is 15.3 kilobases in length. Gene annotation of this assembly on Ensembl has identified 14,075 protein coding genes.},
}
@article {pmid36050321,
year = {2022},
author = {Young, WJ and Lahrouchi, N and Isaacs, A and Duong, T and Foco, L and Ahmed, F and Brody, JA and Salman, R and Noordam, R and Benjamins, JW and Haessler, J and Lyytikäinen, LP and Repetto, L and Concas, MP and van den Berg, ME and Weiss, S and Baldassari, AR and Bartz, TM and Cook, JP and Evans, DS and Freudling, R and Hines, O and Isaksen, JL and Lin, H and Mei, H and Moscati, A and Müller-Nurasyid, M and Nursyifa, C and Qian, Y and Richmond, A and Roselli, C and Ryan, KA and Tarazona-Santos, E and Thériault, S and van Duijvenboden, S and Warren, HR and Yao, J and Raza, D and Aeschbacher, S and Ahlberg, G and Alonso, A and Andreasen, L and Bis, JC and Boerwinkle, E and Campbell, A and Catamo, E and Cocca, M and Cutler, MJ and Darbar, D and De Grandi, A and De Luca, A and Ding, J and Ellervik, C and Ellinor, PT and Felix, SB and Froguel, P and Fuchsberger, C and Gögele, M and Graff, C and Graff, M and Guo, X and Hansen, T and Heckbert, SR and Huang, PL and Huikuri, HV and Hutri-Kähönen, N and Ikram, MA and Jackson, RD and Junttila, J and Kavousi, M and Kors, JA and Leal, TP and Lemaitre, RN and Lin, HJ and Lind, L and Linneberg, A and Liu, S and MacFarlane, PW and Mangino, M and Meitinger, T and Mezzavilla, M and Mishra, PP and Mitchell, RN and Mononen, N and Montasser, ME and Morrison, AC and Nauck, M and Nauffal, V and Navarro, P and Nikus, K and Pare, G and Patton, KK and Pelliccione, G and Pittman, A and Porteous, DJ and Pramstaller, PP and Preuss, MH and Raitakari, OT and Reiner, AP and Ribeiro, ALP and Rice, KM and Risch, L and Schlessinger, D and Schotten, U and Schurmann, C and Shen, X and Shoemaker, MB and Sinagra, G and Sinner, MF and Soliman, EZ and Stoll, M and Strauch, K and Tarasov, K and Taylor, KD and Tinker, A and Trompet, S and Uitterlinden, A and Völker, U and Völzke, H and Waldenberger, M and Weng, LC and Whitsel, EA and Wilson, JG and Avery, CL and Conen, D and Correa, A and Cucca, F and Dörr, M and Gharib, SA and Girotto, G and Grarup, N and Hayward, C and Jamshidi, Y and Järvelin, MR and Jukema, JW and Kääb, S and Kähönen, M and Kanters, JK and Kooperberg, C and Lehtimäki, T and Lima-Costa, MF and Liu, Y and Loos, RJF and Lubitz, SA and Mook-Kanamori, DO and Morris, AP and O'Connell, JR and Olesen, MS and Orini, M and Padmanabhan, S and Pattaro, C and Peters, A and Psaty, BM and Rotter, JI and Stricker, B and van der Harst, P and van Duijn, CM and Verweij, N and Wilson, JF and Arking, DE and Ramirez, J and Lambiase, PD and Sotoodehnia, N and Mifsud, B and Newton-Cheh, C and Munroe, PB},
title = {Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {5144},
pmid = {36050321},
issn = {2041-1723},
support = {R01 HL128914/HL/NHLBI NIH HHS/United States ; MR/N025083/1/MRC_/Medical Research Council/United Kingdom ; R01 HL139731/HL/NHLBI NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; MC_UU_00007/10/MRC_/Medical Research Council/United Kingdom ; U24 AG051129/AG/NIA NIH HHS/United States ; R01 HL105756/HL/NHLBI NIH HHS/United States ; T32 HL007604/HL/NHLBI NIH HHS/United States ; U01 HG007416/HG/NHGRI NIH HHS/United States ; R01 DK107786/DK/NIDDK NIH HHS/United States ; K23 HL127704/HL/NHLBI NIH HHS/United States ; R01 DK124097/DK/NIDDK NIH HHS/United States ; R01 DK110113/DK/NIDDK NIH HHS/United States ; R01 HL141989/HL/NHLBI NIH HHS/United States ; R01 HL143070/HL/NHLBI NIH HHS/United States ; U54 GM115428/GM/NIGMS NIH HHS/United States ; MR/R017468/1/MRC_/Medical Research Council/United Kingdom ; T32 HL139439/HL/NHLBI NIH HHS/United States ; R01 HL142302/HL/NHLBI NIH HHS/United States ; R01 HL138737/HL/NHLBI NIH HHS/United States ; K24 HL105780/HL/NHLBI NIH HHS/United States ; K24 HL148521/HL/NHLBI NIH HHS/United States ; R01 HL142825/HL/NHLBI NIH HHS/United States ; },
mesh = {*Arrhythmias, Cardiac/genetics ; Death, Sudden, Cardiac ; *Electrocardiography/methods ; Genetic Testing ; Humans ; Male ; },
abstract = {The QT interval is an electrocardiographic measure representing the sum of ventricular depolarization and repolarization, estimated by QRS duration and JT interval, respectively. QT interval abnormalities are associated with potentially fatal ventricular arrhythmia. Using genome-wide multi-ancestry analyses (>250,000 individuals) we identify 177, 156 and 121 independent loci for QT, JT and QRS, respectively, including a male-specific X-chromosome locus. Using gene-based rare-variant methods, we identify associations with Mendelian disease genes. Enrichments are observed in established pathways for QT and JT, and previously unreported genes indicated in insulin-receptor signalling and cardiac energy metabolism. In contrast for QRS, connective tissue components and processes for cell growth and extracellular matrix interactions are significantly enriched. We demonstrate polygenic risk score associations with atrial fibrillation, conduction disease and sudden cardiac death. Prioritization of druggable genes highlight potential therapeutic targets for arrhythmia. Together, these results substantially advance our understanding of the genetic architecture of ventricular depolarization and repolarization.},
}
@article {pmid36048827,
year = {2022},
author = {Omoru, OB and Pereira, F and Janga, SC and Manzourolajdad, A},
title = {A Putative long-range RNA-RNA interaction between ORF8 and Spike of SARS-CoV-2.},
journal = {PloS one},
volume = {17},
number = {9},
pages = {e0260331},
pmid = {36048827},
issn = {1932-6203},
support = {R01 GM123314/GM/NIGMS NIH HHS/United States ; },
mesh = {*COVID-19 ; Genome, Viral ; Humans ; RNA, Viral/genetics ; *SARS-CoV-2/genetics ; *Spike Glycoprotein, Coronavirus/genetics ; *Viral Proteins/genetics ; },
abstract = {SARS-CoV-2 has affected people worldwide as the causative agent of COVID-19. The virus is related to the highly lethal SARS-CoV-1 responsible for the 2002-2003 SARS outbreak in Asia. Research is ongoing to understand why both viruses have different spreading capacities and mortality rates. Like other beta coronaviruses, RNA-RNA interactions occur between different parts of the viral genomic RNA, resulting in discontinuous transcription and production of various sub-genomic RNAs. These sub-genomic RNAs are then translated into other viral proteins. In this work, we performed a comparative analysis for novel long-range RNA-RNA interactions that may involve the Spike region. Comparing in-silico fragment-based predictions between reference sequences of SARS-CoV-1 and SARS-CoV-2 revealed several predictions amongst which a thermodynamically stable long-range RNA-RNA interaction between (23660-23703 Spike) and (28025-28060 ORF8) unique to SARS-CoV-2 was observed. The patterns of sequence variation using data gathered worldwide further supported the predicted stability of the sub-interacting region (23679-23690 Spike) and (28031-28042 ORF8). Such RNA-RNA interactions can potentially impact viral life cycle including sub-genomic RNA production rates.},
}
@article {pmid36044830,
year = {2022},
author = {Niestroj, SC and Steden, S and Boecker, M and Brodkin, ES and Konrad, K},
title = {The Development and Validation of the First German Open Scale of Social Information Processing.},
journal = {Psychopathology},
volume = {},
number = {},
pages = {1-12},
doi = {10.1159/000525950},
pmid = {36044830},
issn = {1423-033X},
abstract = {INTRODUCTION: This study introduces the first German Open Scale of Social Information Processing (GOSSIP) and evaluates its psychometric properties. Even though social information processing (SIP) and its important role in developmental psychopathology is a rising field of interest, model-based standardized assessment tools are still scarce.
METHODS: GOSSIP was developed to assess SI processes in boys and girls aged eight to 21 years. First, 61 vignettes (combinations of pictures and short written descriptions of the situation depicted) were evaluated by an expert group and piloted with 48 healthy participants (aged 8-21). The best-rated vignettes were then implemented in a Web-based application. 191 participants completed GOSSIP. Of those, 76 answered additional questionnaires to assess their social skills and psychopathology. Internal consistencies for the emotional and cognitive GOSSIP scales were determined. Latent profile analysis (LPA) was used to identify subgroups of children and adolescents characterized by specific SIP profiles (i.e., patterns of emotional, cognitive, and behavioral responses to the GOSSIP). Furthermore, the external validity of the participants' attribution tendencies in GOSSIP was evaluated in real life by smartphone-based Ecological Momentary Assessments (EMA).
RESULTS: The internal consistencies for the emotional and cognitive scales (angry, ashamed, physical aggression, pro-social response, revenge, and outcome expectancy) were good to excellent. The scales of hostile interpretation, relation aggression, sadness, and exclusion showed borderline/acceptable internal consistency. Correlation analysis confirmed convergent validity with self-reported social skills and external validity with ratings of aggressive and pro-social behaviors. The LPA revealed three profiles as the best fit of the data. The first group is named "aggressors," the second "social-emotional group," and a third named "ashamed-internalizing group." However, no significant association was found between the attribution tendencies derived from GOSSIP and EMA data.
DISCUSSION/CONCLUSION: GOSSIP is the first model-based German Web-based assessment for several SIP mechanisms that showed overall adequate psychometric properties. GOSSIP can be used to classify individuals into SIP profiles that differ in terms of their cognitive and emotional response tendencies and therefore could contribute to the development of targeted interventions. Integrating assessments of emotional responses into GOSSIP revealed an important role of "shame" in SIP and the development of psychopathology. Furthermore, the lack of external validity between GOSSIP and EMA calls into question how attribution tendencies are best assessed in future studies.},
}
@article {pmid36041271,
year = {2022},
author = {Sokhansanj, BA and Rosen, GL},
title = {Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning.},
journal = {Computers in biology and medicine},
volume = {149},
number = {},
pages = {105969},
pmid = {36041271},
issn = {1879-0534},
mesh = {*COVID-19/epidemiology ; Humans ; Machine Learning ; Mutation ; Phylogeny ; Retrospective Studies ; SARS-CoV-2 ; Severity of Illness Index ; *Spike Glycoprotein, Coronavirus/genetics ; },
abstract = {Epidemiological studies show that COVID-19 variants-of-concern, like Delta and Omicron, pose different risks for severe disease, but they typically lack sequence-level information for the virus. Studies which do obtain viral genome sequences are generally limited in time, location, and population scope. Retrospective meta-analyses require time-consuming data extraction from heterogeneous formats and are limited to publicly available reports. Fortuitously, a subset of GISAID, the global SARS-CoV-2 sequence repository, includes "patient status" metadata that can indicate whether a sequence record is associated with mild or severe disease. While GISAID lacks data on comorbidities relevant to severity, such as obesity and chronic disease, it does include metadata for age and sex to use as additional attributes in modeling. With these caveats, previous efforts have demonstrated that genotype-patient status models can be fit to GISAID data, particularly when country-of-origin is used as an additional feature. But are these models robust and biologically meaningful? This paper shows that, in fact, temporal and geographic biases in sequences submitted to GISAID, as well as the evolving pandemic response, particularly reduction in severe disease due to vaccination, create complex issues for model development and interpretation. This paper poses a potential solution: efficient mixed effects machine learning using GPBoost, treating country as a random effect group. Training and validation using temporally split GISAID data and emerging Omicron variants demonstrates that GPBoost models are more predictive of the impact of spike protein mutations on patient outcomes than fixed effect XGBoost, LightGBM, random forests, and elastic net logistic regression models.},
}
@article {pmid36039768,
year = {2022},
author = {De Calheiros Velozo, J and Habets, J and George, SV and Niemeijer, K and Minaeva, O and Hagemann, N and Herff, C and Kuppens, P and Rintala, A and Vaessen, T and Riese, H and Delespaul, P},
title = {Designing daily-life research combining experience sampling method with parallel data.},
journal = {Psychological medicine},
volume = {},
number = {},
pages = {1-10},
doi = {10.1017/S0033291722002367},
pmid = {36039768},
issn = {1469-8978},
abstract = {BACKGROUND: Ambulatory monitoring is gaining popularity in mental and somatic health care to capture an individual's wellbeing or treatment course in daily-life. Experience sampling method collects subjective time-series data of patients' experiences, behavior, and context. At the same time, digital devices allow for less intrusive collection of more objective time-series data with higher sampling frequencies and for prolonged sampling periods. We refer to these data as parallel data. Combining these two data types holds the promise to revolutionize health care. However, existing ambulatory monitoring guidelines are too specific to each data type, and lack overall directions on how to effectively combine them.
METHODS: Literature and expert opinions were integrated to formulate relevant guiding principles.
RESULTS: Experience sampling and parallel data must be approached as one holistic time series right from the start, at the study design stage. The fluctuation pattern and volatility of the different variables of interest must be well understood to ensure that these data are compatible. Data have to be collected and operationalized in a manner that the minimal common denominator is able to answer the research question with regard to temporal and disease severity resolution. Furthermore, recommendations are provided for device selection, data management, and analysis. Open science practices are also highlighted throughout. Finally, we provide a practical checklist with the delineated considerations and an open-source example demonstrating how to apply it.
CONCLUSIONS: The provided considerations aim to structure and support researchers as they undertake the new challenges presented by this exciting multidisciplinary research field.},
}
@article {pmid36039277,
year = {2022},
author = {Stokes, J and Bower, P and Guthrie, B and Mercer, SW and Rice, N and Ryan, AM and Sutton, M},
title = {Cuts to local government spending, multimorbidity and health-related quality of life: A longitudinal ecological study in England.},
journal = {The Lancet regional health. Europe},
volume = {19},
number = {},
pages = {100436},
pmid = {36039277},
issn = {2666-7762},
support = {MR/T027517/1/MRC_/Medical Research Council/United Kingdom ; },
abstract = {BACKGROUND: Population health has stagnated or is declining in many high-income countries. We analysed whether nationally administered austerity cuts in England were associated with prevalence of multimorbidity (individuals with two or more long-term conditions) and health-related quality of life.
METHODS: We conducted an observational, longitudinal study on 147 local authorities in England. We examined associations of changes in spending over time (2009/10-2017/18), in total and by budget line, with (i) prevalence of multimorbidity, 2+ conditions (2011/12-2017/18), and (ii) health-related quality of life (EQ-5D-5L) score (2012/13-2016/17). We estimated linear, log-log regression models, incorporating local authority fixed-effects, time-varying demographic and socio-economic confounders, and time trends.
FINDINGS: All local authorities experienced real spending cuts, varying from 42% (Barking and Dagenham) to 0·3% (Sefton). A 1% cut in per capita total service expenditure was associated with a 0·10% (95% CI 0·03 to 0·16) increase in prevalence of multimorbidity. We found no association (0·003%; 95% CI -0·01 to 0·01) with health-related quality of life. By budget line, after controlling for other spending, a 1% cut in public health expenditure was associated with a 0·15% (95% CI 0·11 to 0·20) increase in prevalence of multimorbidity, and a 1% cut in adult social care expenditure was associated with a 0·01% (95% CI 0·002 to 0·02) decrease in average health-related quality of life.
INTERPRETATION: Fiscal austerity is associated with worse multimorbidity and health-related quality of life. Policymakers should consider the potential health consequences of local government expenditure cuts and knock-on effects for health systems.
FUNDING: Medical Research Council.},
}
@article {pmid36037884,
year = {2022},
author = {Luoma, E and Laurila-Pant, M and Altarriba, E and Nevalainen, L and Helle, I and Granhag, L and Lehtiniemi, M and Srėbalienė, G and Olenin, S and Lehikoinen, A},
title = {A multi-criteria decision analysis model for ship biofouling management in the Baltic Sea.},
journal = {The Science of the total environment},
volume = {852},
number = {},
pages = {158316},
doi = {10.1016/j.scitotenv.2022.158316},
pmid = {36037884},
issn = {1879-1026},
mesh = {*Biofouling/prevention & control ; Ships ; Carbon Dioxide ; Bayes Theorem ; Water ; Decision Support Techniques ; },
abstract = {Biofouling of ship hulls form a vector for the introduction of non-indigenous organisms worldwide. Through increasing friction, the organisms attached to ships' hulls increase the fuel consumption, leading to both higher fuel costs and air emissions. At the same time, ship biofouling management causes both ecological risks and monetary costs. All these aspects should be considered case-specifically in the search of sustainable management strategies. Applying Bayesian networks, we developed a multi-criteria decision analysis model to compare biofouling management strategies in the Baltic Sea, given the characteristics of a ship, its operating profile and operational environment, considering the comprehensive environmental impact and the monetary costs. The model is demonstrated for three scenarios (SC1-3) and sub-scenarios (A-C), comparing the alternative biofouling management strategies in relation to NIS (non-indigenous species) introduction risk, eco-toxicological risk due to biocidal coating, carbon dioxide emissions and costs related to fuel consumption, in-water cleaning and hull coating. The scenarios demonstrate that by the careful consideration of the hull fouling management strategy, both money and environment can be saved. We suggest biocidal-free coating with a regular in-water cleaning using a capture system is generally the lowest-risk option. The best biocidal-free coating type and the optimal in-water cleaning interval should be evaluated case-specifically, though. In some cases, however, biocidal coating remains a justifiable option.},
}
@article {pmid36036236,
year = {2022},
author = {Strobl, MR and Vollmann, U and Eckl-Dorna, J and Radakovics, A and Ibl, V and Schnurer, M and Brenner, M and Dermendjiev, G and Weckwerth, W and Neumüller, M and Frommlet, F and Demir, H and Bublin, M and Müller, C and Bohle, B},
title = {Identification of apple cultivars hypoallergenic for birch pollen-allergic individuals by a multidisciplinary in vitro and in vivo approach.},
journal = {Clinical and translational allergy},
volume = {12},
number = {8},
pages = {e12186},
pmid = {36036236},
issn = {2045-7022},
abstract = {BACKGROUND: Birch pollen-related apple allergy is the most frequent IgE-mediated food allergy in Central-Northern Europe with Mal d 1 as major allergen. Its concentration in apples varies with the cultivar and storage time. Year-round appealing, hypoallergenic cultivars still are needed to satisfy the nutritional needs of affected individuals. We characterized three promising cultivars by multidisciplinary in vitro assays including long-term storage and by clinical challenges of allergic individuals before and after the birch pollen season.
METHODS: Proteins were extracted from fruits of 'Santana', 'Golden Delicious' (GD), and three genuine cultivars in November 2018 and April 2019. Mal d 1-levels were analysed by mass spectrometry, SDS-PAGE, immunoblotting, competitive ELISA, and basophil activation tests. Twenty-eight allergic individuals underwent single-blinded open food challenges and skin testing with the cultivars and birch pollen in November 2018 and May 2019. Allergen-specific IgE-levels were determined.
RESULTS: After storage all cultivars except 'Santana' were of appealing appearance and taste. Their Mal d 1 content had increased, also reflected by significantly amplified basophil activation and stronger reactions in clinical challenges. Besides, individuals showed boosted reactivity after pollen exposure indicated by enhanced allergen-specific IgE-levels and skin reactions to birch pollen. Still, all cultivars remained significantly less allergenic than GD and comparable to Santana in November 2018 in all assessments except for skin testing.
CONCLUSIONS: Combined expertise in pomology and allergology identified promising new cultivars for allergic consumers. The evaluation of hypoallergenic apples should incorporate long-term storage and birch pollen exposure. Basophil activation tests may be suitable in the selection of promising cultivars for oral challenges.},
}
@article {pmid36035686,
year = {2022},
author = {Del Vecchio, S and Sharma, SK and Pavan, M and Acosta, ATR and Bacchetta, G and de Bello, F and Isermann, M and Michalet, R and Buffa, G},
title = {Within-species variation of seed traits of dune engineering species across a European climatic gradient.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {978205},
pmid = {36035686},
issn = {1664-462X},
abstract = {Within-species variation is a key component of biodiversity and linking it to climatic gradients may significantly improve our understanding of ecological processes. High variability can be expected in plant traits, but it is unclear to which extent it varies across populations under different climatic conditions. Here, we investigated seed trait variability and its environmental dependency across a latitudinal gradient of two widely distributed dune-engineering species (Thinopyrum junceum and Calamagrostis arenaria). Seed germination responses against temperature and seed mass were compared within and among six populations exposed to a gradient of temperature and precipitation regimes (Spiekeroog, DE; Bordeaux, FR; Valencia, ES; Cagliari, IT, Rome, IT; Venice, IT). Seed germination showed opposite trends in response to temperature experienced during emergence in both species: with some expectation, in populations exposed to severe winters, seed germination was warm-cued, whereas in populations from warm sites with dry summer, seed germination was cold-cued. In C. arenaria, variability in seed germination responses disappeared once the seed coat was incised. Seed mass from sites with low precipitation was smaller than that from sites with higher precipitation and was better explained by rainfall continentality than by aridity in summer. Within-population variability in seed germination accounted for 5 to 54%, while for seed mass it was lower than 40%. Seed trait variability can be considerable both within- and among-populations even at broad spatial scale. The variability may be hardly predictable since it only partially correlated with the analyzed climatic variables, and with expectation based on the climatic features of the seed site of origin. Considering seed traits variability in the analysis of ecological processes at both within- and among-population levels may help elucidate unclear patterns of species dynamics, thereby contributing to plan adequate measures to counteract biodiversity loss.},
}
@article {pmid36033213,
year = {2022},
author = {Pho, AT and Mangal, S and Bakken, S},
title = {Human Papillomavirus Vaccination Among Transgender and Gender Diverse People in the United States: An Integrative Review.},
journal = {Transgender health},
volume = {7},
number = {4},
pages = {303-313},
pmid = {36033213},
issn = {2688-4887},
abstract = {OBJECTIVE: This integrative review explores the barriers to and facilitators for human papillomavirus (HPV) vaccination among adult transgender and gender diverse (TGD) people in the United States.
DATA SOURCE: A systematic search of electronic databases included PubMed/MEDLINE, CINAHL, and EMBASE from 1985 to 2020.
Inclusion criteria included studies from the United States that described HPV vaccination barriers or facilitators and included adult TGD participants, both quantitative and qualitative studies. Exclusion criteria were studies that reported only HPV vaccine prevalence, non-English/non-U.S. studies, and studies limited to pediatric populations.
DATA EXTRACTION: Two investigators used Covidence software to screen studies and manage data extraction. Quality of the quantitative studies was appraised using a checklist proposed by the Joanna Briggs Institute (JBI); qualitative studies were appraised using quality criteria informed by the literature.
DATA SYNTHESIS: The Social Ecological Model guided the review to organize barriers to and facilitators for HPV vaccination at the patient-, provider-, and system-levels.
RESULTS: Database searches and hand-searching yielded 843 citations. After screening, eight articles were retained in the review. Seven were cross-sectional studies and one was a qualitative focus-group. All retained quantitative studies met six of the eight JBI quality checklist items.
CONCLUSION: The low proportion of TGD participants in the retained studies highlights a gap in knowledge about HPV vaccination among this population. Future studies of HPV vaccination should recruit TGD people to better represent their perspectives.},
}
@article {pmid36032727,
year = {2022},
author = {Kenzie, ES and Parks, EL and Carney, N and Wakeland, W},
title = {System dynamics modeling for traumatic brain injury: Mini-review of applications.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {10},
number = {},
pages = {854358},
pmid = {36032727},
issn = {2296-4185},
abstract = {Traumatic brain injury (TBI) is a highly complex phenomenon involving a cascade of disruptions across biomechanical, neurochemical, neurological, cognitive, emotional, and social systems. Researchers and clinicians urgently need a rigorous conceptualization of brain injury that encompasses nonlinear and mutually causal relations among the factors involved, as well as sources of individual variation in recovery trajectories. System dynamics, an approach from systems science, has been used for decades in fields such as management and ecology to model nonlinear feedback dynamics in complex systems. In this mini-review, we summarize some recent uses of this approach to better understand acute injury mechanisms, recovery dynamics, and care delivery for TBI. We conclude that diagram-based approaches like causal-loop diagramming have the potential to support the development of a shared paradigm of TBI that incorporates social support aspects of recovery. When developed using adequate data from large-scale studies, simulation modeling presents opportunities for improving individualized treatment and care delivery.},
}
@article {pmid36030325,
year = {2022},
author = {Cooney, DB and Rossine, FW and Morris, DH and Levin, SA},
title = {A PDE Model for Protocell Evolution and the Origin of Chromosomes via Multilevel Selection.},
journal = {Bulletin of mathematical biology},
volume = {84},
number = {10},
pages = {109},
doi = {10.1007/s11538-022-01062-y},
pmid = {36030325},
issn = {1522-9602},
mesh = {*Artificial Cells ; Chromosomes ; Genome ; Mathematical Concepts ; Models, Biological ; },
abstract = {The evolution of complex cellular life involved two major transitions: the encapsulation of self-replicating genetic entities into cellular units and the aggregation of individual genes into a collectively replicating genome. In this paper, we formulate a minimal model of the evolution of proto-chromosomes within protocells. We model a simple protocell composed of two types of genes: a "fast gene" with an advantage for gene-level self-replication and a "slow gene" that replicates more slowly at the gene level, but which confers an advantage for protocell-level reproduction. Protocell-level replication capacity depends on cellular composition of fast and slow genes. We use a partial differential equation to describe how the composition of genes within protocells evolves over time under within-cell and between-cell competition, considering an infinite population of protocells that each contain infinitely many genes. We find that the gene-level advantage of fast replicators casts a long shadow on the multilevel dynamics of protocell evolution: no level of between-protocell competition can produce coexistence of the fast and slow replicators when the two genes are equally needed for protocell-level reproduction. By introducing a "dimer replicator" consisting of a linked pair of the slow and fast genes, we show analytically that coexistence between the two genes can be promoted in pairwise multilevel competition between fast and dimer replicators, and provide numerical evidence for coexistence in trimorphic competition between fast, slow, and dimer replicators. Our results suggest that dimerization, or the formation of a simple chromosome-like dimer replicator, can help to overcome the shadow of lower-level selection and work in concert with deterministic multilevel selection in protocells featuring high gene copy number to allow for the coexistence of two genes that are complementary at the protocell level but compete at the level of individual gene-level replication. These results for the PDE model complement existing results on the benefits of dimerization in the case of low genetic copy number, for which it has been shown that genetic linkage can help to overcome the stochastic loss of necessary genetic templates.},
}
@article {pmid36016080,
year = {2022},
author = {Yousaf, M and Ullah, A and Sarosh, N and Abbasi, SW and Ismail, S and Bibi, S and Hasan, MM and Albadrani, GM and Talaat Nouh, NA and Abdulhakim, JA and Abdel-Daim, MM and Bin Emran, T},
title = {Design of Multi-Epitope Vaccine for Staphylococcus saprophyticus: Pan-Genome and Reverse Vaccinology Approach.},
journal = {Vaccines},
volume = {10},
number = {8},
pages = {},
pmid = {36016080},
issn = {2076-393X},
abstract = {Staphylococcus saprophyticus is a Gram-positive coccus responsible for the occurrence of cystitis in sexually active, young females. While effective antibiotics against this organism exist, resistant strains are on the rise. Therefore, prevention via vaccines appears to be a viable solution to address this problem. In comparison to traditional techniques of vaccine design, computationally aided vaccine development demonstrates marked specificity, efficiency, stability, and safety. In the present study, a novel, multi-epitope vaccine construct was developed against S. saprophyticus by targeting fully sequenced proteomes of its five different strains, which were examined using a pangenome and subtractive proteomic strategy to characterize prospective vaccination targets. The three immunogenic vaccine targets which were utilized to map the probable immune epitopes were verified by annotating the entire proteome. The predicted epitopes were further screened on the basis of antigenicity, allergenicity, water solubility, toxicity, virulence, and binding affinity towards the DRB*0101 allele, resulting in 11 potential epitopes, i.e., DLKKQKEKL, NKDLKKQKE, QDKLKDKSD, NVMDNKDLE, TSGTPDSQA, NANSDGSSS, GSDSSSSNN, DSSSSNNDS, DSSSSDRNN, SSSDRNNGD, and SSDDKSKDS. All these epitopes have the efficacy to cover 99.74% of populations globally. Finally, shortlisted epitopes were joined together with linkers and three different adjuvants to find the most stable and immunogenic vaccine construct. The top-ranked vaccine construct was further scrutinized on the basis of its physicochemical characterization and immunological profile. The non-allergenic and antigenic features of modeled vaccine constructs were initially validated and then subjected to docking with immune receptor major histocompatibility complex I and II (MHC-I and II), resulting in strong contact. In silico cloning validations yielded a codon adaptation index (CAI) value of 1 and an ideal percentage of GC contents (46.717%), indicating a putative expression of the vaccine in E. coli. Furthermore, immune simulation demonstrated that, after injecting the proposed MEVC, powerful antibodies were produced, resulting in the sharpest peaks of IgM + IgG formation (>11,500) within 5 to 15 days. Experimental testing against S. saprophyticus can evaluate the safety and efficacy of these prophylactic vaccination designs.},
}
@article {pmid36016053,
year = {2022},
author = {Tropea, M and Fedele, G and De Luca, R and Miriello, D and De Rango, F},
title = {Automatic Stones Classification through a CNN-Based Approach.},
journal = {Sensors (Basel, Switzerland)},
volume = {22},
number = {16},
pages = {},
pmid = {36016053},
issn = {1424-8220},
mesh = {Bayes Theorem ; Cluster Analysis ; Machine Learning ; *Neural Networks, Computer ; *Support Vector Machine ; },
abstract = {This paper presents an automatic recognition system for classifying stones belonging to different Calabrian quarries (Southern Italy). The tool for stone recognition has been developed in the SILPI project (acronym of "Sistema per l'Identificazione di Lapidei Per Immagini"), financed by POR Calabria FESR-FSE 2014-2020. Our study is based on the Convolutional Neural Network (CNNs) that is used in literature for many different tasks such as speech recognition, neural language processing, bioinformatics, image classification and much more. In particular, we propose a two-stage hybrid approach based on the use of a model of Deep Learning (DL), in our case the CNN, in the first stage and a model of Machine Learning (ML) in the second one. In this work, we discuss a possible solution to stones classification which uses a CNN for the feature extraction phase and the Softmax or Multinomial Logistic Regression (MLR), Support Vector Machine (SVM), k-Nearest Neighbors (kNN), Random Forest (RF) and Gaussian Naive Bayes (GNB) ML techniques in order to perform the classification phase basing our study on the approach called Transfer Learning (TL). We show the image acquisition process in order to collect adequate information for creating an opportune database of the stone typologies present in the Calabrian quarries, also performing the identification of quarries in the considered region. Finally, we show a comparison of different DL and ML combinations in our Two-Stage Hybrid Model solution.},
}
@article {pmid36007741,
year = {2022},
author = {Ali, A and Farhan, SB and Zhang, Y and Nasir, J and Farhan, H and Zamir, UB and Gao, H},
title = {Changes in temporal pattern and spatial distribution of environmental pollutants in 8 Asian countries owing to COVID-19 pandemic.},
journal = {Chemosphere},
volume = {308},
number = {Pt 1},
pages = {136075},
pmid = {36007741},
issn = {1879-1298},
mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; *COVID-19/epidemiology ; Carbon Monoxide/analysis ; Environmental Monitoring/methods ; *Environmental Pollutants ; Formaldehyde ; Humans ; Nitrogen Dioxide/analysis ; *Ozone/analysis ; Pakistan ; Pandemics ; Particulate Matter/analysis ; Sulfur Dioxide/analysis ; },
abstract = {This study investigated the changes in air pollutant's concentration, spatio-temporal distribution and sensitivity of changes in air pollutant's concentration during pre and post COVID-19 outbreak. We employed Google Earth Engine Platform to access remote sensing datasets of air pollutants across Asian continent. Air pollution and cumulative confirmed-COVID cases data of Asian countries (Afghanistan, Bangladesh, China, India, Iran, Iraq, Pakistan, and Saudi Arabia) have been collected and analyzed for 2019 and 2020. The results indicate that aerosol index (AI) and nitrogen dioxide (NO2) is significantly reduced during COVID outbreak i.e. in year 2020. In addition, we found significantly positive (P < 0.05, 95% confidence interval, two-tailed) correlation between changes in AI and NO2 concentration for net active-COVID case increment in almost each country. For other atmospheric gases i.e. carbon monoxide (CO), formaldehyde (HCHO), ozone (O3), and Sulfur dioxide (SO2), insignificant and/or significant negative correlation is also observed. These results suggest that the atmospheric concentration of AI and NO2 are good indicators of human activities. Furthermore, the changes in O3 shows significantly negative correlation for net active-COVID case increment. In conclusion, we observed significant positive environmental impact of COVID-19 restrictions in Asia. This study would help and assist environmentalist and policy makers in restraining air pollution by implementing efficient restrictions on human activities with minimal economic loss.},
}
@article {pmid36007087,
year = {2022},
author = {Wang, Y and Cai, G and Yang, L and Zhang, N and Du, M},
title = {Monitoring of urban ecological environment including air quality using satellite imagery.},
journal = {PloS one},
volume = {17},
number = {8},
pages = {e0266759},
pmid = {36007087},
issn = {1932-6203},
mesh = {*Air Pollution ; China ; Environment ; Environmental Monitoring/methods ; Remote Sensing Technology ; *Satellite Imagery ; },
abstract = {Rapid urbanisation has highlighted problems in the urban ecological environment and stimulated research on the evaluation of urban environments. In previous studies, key factors such as greenness, wetness, and temperature were extracted from satellite images to assess the urban ecological environment. Although air pollution has become increasingly serious as urbanisation proceeds, information on air pollution is not included in existing models. The Sentinel-5P satellite launched by the European Space Agency in 2017 is a reliable data source for monitoring air quality. By making full use of images from Landsat 8, Sentinel-2A, and Sentinel-5P, this work attempts to construct a new remote sensing monitoring index for urban ecology by adding air quality information to the existing remote sensing ecological index. The proposed index was tested in the Beijing metropolitan area using satellite data from 2020. The results obtained using the proposed index differ greatly in the central urban region and near large bodies of water from those obtained using the existing remote sensing monitoring model, indicating that air quality plays a significant role in evaluating the urban ecological environment. Because the model constructed in this study integrates information on vegetation, soil, humidity, heat, and air quality, it can comprehensively and objectively reflect the quality of the urban ecological environment. Consequently, the proposed remote sensing index provides a new approach to effectively monitoring the urban ecological environment.},
}
@article {pmid35999898,
year = {2021},
author = {Waterhouse, RM and Adam-Blondon, AF and Agosti, D and Baldrian, P and Balech, B and Corre, E and Davey, RP and Lantz, H and Pesole, G and Quast, C and Glöckner, FO and Raes, N and Sandionigi, A and Santamaria, M and Addink, W and Vohradsky, J and Nunes-Jorge, A and Willassen, NP and Lanfear, J},
title = {Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR.},
journal = {F1000Research},
volume = {10},
number = {},
pages = {},
pmid = {35999898},
issn = {2046-1402},
support = {BB/CSP1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P016855/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9783/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9814/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Biodiversity ; *Biological Science Disciplines ; Computational Biology ; Europe ; },
abstract = {Threats to global biodiversity are increasingly recognised by scientists and the public as a critical challenge. Molecular sequencing technologies offer means to catalogue, explore, and monitor the richness and biogeography of life on Earth. However, exploiting their full potential requires tools that connect biodiversity infrastructures and resources. As a research infrastructure developing services and technical solutions that help integrate and coordinate life science resources across Europe, ELIXIR is a key player. To identify opportunities, highlight priorities, and aid strategic thinking, here we survey approaches by which molecular technologies help inform understanding of biodiversity. We detail example use cases to highlight how DNA sequencing is: resolving taxonomic issues; Increasing knowledge of marine biodiversity; helping understand how agriculture and biodiversity are critically linked; and playing an essential role in ecological studies. Together with examples of national biodiversity programmes, the use cases show where progress is being made but also highlight common challenges and opportunities for future enhancement of underlying technologies and services that connect molecular and wider biodiversity domains. Based on emerging themes, we propose key recommendations to guide future funding for biodiversity research: biodiversity and bioinformatic infrastructures need to collaborate closely and strategically; taxonomic efforts need to be aligned and harmonised across domains; metadata needs to be standardised and common data management approaches widely adopted; current approaches need to be scaled up dramatically to address the anticipated explosion of molecular data; bioinformatics support for biodiversity research needs to be enabled and sustained; training for end users of biodiversity research infrastructures needs to be prioritised; and community initiatives need to be proactive and focused on enabling solutions. For sequencing data to deliver their full potential they must be connected to knowledge: together, molecular sequence data collection initiatives and biodiversity research infrastructures can advance global efforts to prevent further decline of Earth's biodiversity.},
}
@article {pmid36002452,
year = {2022},
author = {Yang, C and Liu, H and Li, Q and Wang, X and Ma, W and Liu, C and Fang, X and Tang, Y and Shi, T and Wang, Q and Xu, Y and Zhang, J and Li, X and Xu, G and Chen, J and Su, M and Wang, S and Wu, J and Huang, L and Li, X and Wu, G},
title = {Human expansion into Asian highlands in the 21st Century and its effects.},
journal = {Nature communications},
volume = {13},
number = {1},
pages = {4955},
pmid = {36002452},
issn = {2041-1723},
mesh = {Asia ; Asia, Southeastern ; *Asian People ; *Ecosystem ; Humans ; },
abstract = {Most intensive human activities occur in lowlands. However, sporadic reports indicate that human activities are expanding in some Asian highlands. Here we investigate the expansions of human activities in highlands and their effects over Asia from 2000 to 2020 by combining earth observation data and socioeconomic data. We find that ∼23% of human activity expansions occur in Asian highlands and ∼76% of these expansions in highlands comes from ecological lands, reaching 95% in Southeast Asia. The expansions of human activities in highlands intensify habitat fragmentation and result in large ecological costs in low and lower-middle income countries, and they also support Asian developments. We estimate that cultivated land net growth in the Asian highlands contributed approximately 54% in preventing the net loss of the total cultivated land. Moreover, the growth of highland artificial surfaces may provide living and working spaces for ∼40 million people. Our findings suggest that highland developments hold dual effects and provide new insight for regional sustainable developments.},
}
@article {pmid36001546,
year = {2022},
author = {Diodato, N and Borrelli, P and Panagos, P and Bellocchi, G},
title = {Global assessment of storm disaster-prone areas.},
journal = {PloS one},
volume = {17},
number = {8},
pages = {e0272161},
pmid = {36001546},
issn = {1932-6203},
mesh = {*Disasters ; Geographic Information Systems ; Humans ; Hydrology ; *Rain ; Soil ; },
abstract = {BACKGROUND: Advances in climate change research contribute to improved forecasts of hydrological extremes with potentially severe impacts on human societies and natural landscapes. Rainfall erosivity density (RED), i.e. rainfall erosivity (MJ mm hm-2 h-1 yr-1) per rainfall unit (mm), is a measure of rainstorm aggressiveness and a proxy indicator of damaging hydrological events.
METHODS AND FINDINGS: Here, using downscaled RED data from 3,625 raingauges worldwide and log-normal ordinary kriging with probability mapping, we identify damaging hydrological hazard-prone areas that exceed warning and alert thresholds (1.5 and 3.0 MJ hm-2 h-1, respectively). Applying exceedance probabilities in a geographical information system shows that, under current climate conditions, hazard-prone areas exceeding a 50% probability cover ~31% and ~19% of the world's land at warning and alert states, respectively.
CONCLUSION: RED is identified as a key driver behind the spatial growth of environmental disruption worldwide (with tropical Latin America, South Africa, India and the Indian Archipelago most affected).},
}
@article {pmid36001047,
year = {2023},
author = {Shaffer, M and Thurimella, K and Sterrett, JD and Lozupone, CA},
title = {SCNIC: Sparse correlation network investigation for compositional data.},
journal = {Molecular ecology resources},
volume = {23},
number = {1},
pages = {312-325},
pmid = {36001047},
issn = {1755-0998},
support = {T15 LM009451/LM/NLM NIH HHS/United States ; },
mesh = {*Software ; Algorithms ; *Microbiota ; },
abstract = {Microbiome studies are often limited by a lack of statistical power due to small sample sizes and a large number of features. This problem is exacerbated in correlative studies of multi-omic datasets. Statistical power can be increased by finding and summarizing modules of correlated observations, which is one dimensionality reduction method. Additionally, modules provide biological insight as correlated groups of microbes can have relationships among themselves. To address these challenges, we developed SCNIC: Sparse Cooccurrence Network Investigation for compositional data. SCNIC is open-source software that can generate correlation networks and detect and summarize modules of highly correlated features. Modules can be formed using either the Louvain Modularity Maximization (LMM) algorithm or a Shared Minimum Distance algorithm (SMD) that we newly describe here and relate to LMM using simulated data. We applied SCNIC to two published datasets and we achieved increased statistical power and identified microbes that not only differed across groups, but also correlated strongly with each other, suggesting shared environmental drivers or cooperative relationships among them. SCNIC provides an easy way to generate correlation networks, identify modules of correlated features and summarize them for downstream statistical analysis. Although SCNIC was designed considering properties of microbiome data, such as compositionality and sparsity, it can be applied to a variety of data types including metabolomics data and used to integrate multiple data types. SCNIC allows for the identification of functional microbial relationships at scale while increasing statistical power through feature reduction.},
}
@article {pmid36000659,
year = {2022},
author = {Santos, JS and Cruz, AJS and Ruas, CM and Pereira Júnior, EA and Mattos, FF and Klevens, M and Abreu, MHNG},
title = {Factors associated with the use of a public information system of dentist-prescribed antibiotics in Minas Gerais, Brazil.},
journal = {Ciencia & saude coletiva},
volume = {27},
number = {9},
pages = {3741-3750},
doi = {10.1590/1413-81232022279.07422022},
pmid = {36000659},
issn = {1678-4561},
mesh = {*Anti-Bacterial Agents ; Brazil ; *Dentists ; Humans ; Information Systems ; Socioeconomic Factors ; },
abstract = {This article aims to investigate the association between socioeconomic factors, health care organizations, and the use of a management and monitoring system for the dispensing of antibiotics prescribed by dentists in public health services in Minas Gerais, Brazil. This is an ecological-epidemiological study that analyzed secondary data from the Integrated Pharmaceutical Care Management System (SIGAF) of the Department of Health of the state of MG, Brazil, in 2017. Thirteen independent variables were analyzed to assess their influence on municipal adherence to SIGAF system considering dental prescriptions of antibiotics. Descriptive statistical analyses were performed, and the Classification and Regression Tree technique was used to identify the municipal variables associated with the outcome. A total of 57,279 antibiotic courses prescribed by dentists and recorded in SIGAF were examined. Socioeconomic factors were not associated with the use of SIGAF to record these prescriptions. Oral healthcare coverage was positively associated with the use of SIGAF for the dispensing of antibiotics prescribed by dentists. Dental Specialties Center were negatively associated with the outcome. Municipalities with high oral healthcare coverage and those without a Dental Specialties Center were more likely to use SIGAF.},
}
@article {pmid35990172,
year = {2022},
author = {Xiao, H and Xu, Z and Ren, J and Zhou, Y and Lin, R and Bao, S and Zhang, L and Lu, S and Lee, CKM and Liu, J},
title = {Navigating Chinese cities to achieve sustainable development goals by 2030.},
journal = {Innovation (Cambridge (Mass.))},
volume = {3},
number = {5},
pages = {100288},
pmid = {35990172},
issn = {2666-6758},
abstract = {Achieving the 17 United Nations sustainable development goals (SDGs) in China largely depends on the transition of cities toward sustainable development. However, significant knowledge gaps exist in evaluating the SDG index at the city scale and in understanding how to simulate pathways to achieve the 17 SDGs for Chinese cities by 2030. This study aimed to quantify the SDG index of 285 Chinese cities and developed a forecasting model to simulate the performance of each SDG in each city until 2030 using varied scenarios. The results indicated that although the SDG index in Chinese cities increased by 33.97% during 2005-2016, Chinese cities, which continued their past paths, achieved an average of only five SDGs by 2030. To promote the joint achievement of all SDGs, we designed different paths for all SDGs of each of the 285 cities and simulated their SDG index until 2030. Under the scenarios, 216 Chinese cities (75.79%) could achieve 9-13 more SDGs in 2030 and the overall SDG index can improve from 74.57 in 2030 to 97.49 (target score 100) by adopting more intensive path adjustment. We lastly determined a cost-effective path for each SDG of each city to promote joint achievement of all SDGs by 2030. The proposed simulation model and cost-effective path serve as a foundation for other countries to simulate SDG progress and develop pathways for achieving SDGs in the future.},
}
@article {pmid35990120,
year = {2022},
author = {Zhang, H},
title = {The Impact of Tax Reduction and Fee Reduction Based on Big Data Algorithm on the High-Quality Development of the Real Economy under the Action of Coupling Effect or Substitution Effect.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {2828687},
pmid = {35990120},
issn = {1687-5273},
mesh = {Algorithms ; *Big Data ; China ; Ecology ; *Economic Development ; },
abstract = {The basic idea of the mass of medical growth is to adhere to local market price thinking with a Chinese touch and follow the development policy of "quality first, efficiency first." It insists on properly handling a series of important relationships betwixt socialism and market economy, the first to drive the rich later, the government and the market, equality and efficiency, short-term growth and long-term development, China and the international economy, ecology and growth of the region. Under the guidance of the qualitative thinking theory, it combines the strategic goals of China's economic qualitative development and actively draws on the research results of other countries. It uses big data algorithms to focus on the impact of qualitative development on tax and income reduction in the real economy. It conducts research experiments on the impact of tax reduction and fee reduction based on big data algorithms on the top-notch growth of the real economy. Its experimental data show that: in 2018, the share of primary, tertiary, and primary sector in China's dimensional economy top-notch growth coordination index was 7.2%, 40.7%, and 52.2%, respectively. Its contribution rate to economic growth was 4.2%, 36.1%, and 59.7%, respectively. From these data, it can be concluded that the top-notch growth of the real economy is getting better and better under the influence of tax reduction and fee reduction by big data algorithms.},
}
@article {pmid35983321,
year = {2022},
author = {Zhu, Y and Ge, X and Wang, L and You, Y and Cheng, Y and Ma, J and Chen, F},
title = {Biochar rebuilds the network complexity of rare and abundant microbial taxa in reclaimed soil of mining areas to cooperatively avert cadmium stress.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {972300},
pmid = {35983321},
issn = {1664-302X},
abstract = {Understanding the interactions between the soil microbial communities and species is critical in the remediation of heavy metal-contaminated soil. Biochar has been widely applied as a stabilizer in the in situ remediation of cadmium (Cd)-contaminated soils in mining areas. However, the rebuilding of the microbial taxa of rare and abundant species by biochar and their cooperative resistance to Cd stress remains elusive. In this pursuit, the present study envisaged the effects of two types of biochars viz., poplar bark biochar (PB) and thiourea-modified poplar bark biochar (TP) on the rare and abundant bacterial and fungal taxa by using pot experiments. The results demonstrated that the PB and TP treatments significantly reduced the leached Cd content, by 35.13 and 68.05%, respectively, compared with the control group (CK), in the reclaimed soil of the mining area. The application of biochar significantly improved the physicochemical properties like pH and Soil Organic Matter (SOM) of the soil. It was observed that TP treatment was superior to the PB and CK groups in increasing the diversity of the soil abundant and rare species of microbial taxa. Compared with the CK group, the application of PB and TP enhanced and elevated the complexity of the microbial networks of rare and abundant taxa, increased the number and types of network core microorganisms, reshaped the network core microorganisms and hubs, and boosted the microbial resistance to Cd stress. Our results indicate the response of rare and abundant microbial taxa to biochar application and the mechanism of their synergistic remediation of Cd-contaminated soil, thereby providing technical feasibility for in situ remediation of Cd-contaminated soil in mining areas.},
}
@article {pmid35977400,
year = {2022},
author = {IJdema, F and De Smet, J and Crauwels, S and Lievens, B and Van Campenhout, L},
title = {Meta-analysis of larvae of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing.},
journal = {FEMS microbiology ecology},
volume = {98},
number = {9},
pages = {},
pmid = {35977400},
issn = {1574-6941},
mesh = {Animals ; Bacteria/genetics ; *Diptera/microbiology ; Genes, rRNA ; Larva/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Black soldier fly larvae (BSFL) belong to the most widely reared insects as an alternative protein source at industrial scale. Bacteria in the larval gut can provide benefits for the animal, though some bacteria can also be pathogenic for the insect. Accurate characterization of the BSFL microbiota is important for the production of BSFL in terms of yield and microbiological safety. In this study, 16S ribosomal RNA gene sequence data sets from 11 studies were re-analysed to gain better insights in the BSFL gut microbiota, potential factors that influence their composition, and differences between the gut and the whole larvae microbiota. A core gut microbiota was found consisting of members of Enterococcus, Klebsiella, Morganella, Providencia, and Scrofimicrobium. Further, the factors 'Study', 'Age' and 'Feed' (i.e. rearing substrate of the larvae) significantly affected the microbiota gut composition. When compared to whole larvae, a significantly lower diversity was found for gut samples, suggesting that the larvae harboured additional microbes on their cuticle or in the insect body. Universal choices in insect sample type, primer selection and bio-informatics analysis pipeline can strengthen future meta-analyses and improve our understanding of the BSFL gut microbiota towards the optimization of insect rearing conditions and substrates.},
}
@article {pmid35975694,
year = {2022},
author = {Orlando, CG and Possell, M and Price, C and Banks, PB and Mercorelli, L and McArthur, C},
title = {A new conceptual and quantitative approach to exploring and defining potential open-access olfactory information.},
journal = {The New phytologist},
volume = {236},
number = {4},
pages = {1605-1619},
doi = {10.1111/nph.18432},
pmid = {35975694},
issn = {1469-8137},
mesh = {*Odorants ; *Plants/chemistry ; Reproducibility of Results ; Trees/chemistry ; },
abstract = {All organisms emit odour, providing 'open-access' olfactory information for any receiver with the right sensory apparatus. Characterizing open-access information emitted by groups of organisms, such as plant species, provides the means to answer significant questions about ecological interactions and their evolution. We present a new conceptual framework defining information reliability and a practical method to characterize and recover information from amongst olfactory noise. We quantified odour emissions from two tree species, one focal group and one outgroup, to demonstrate our approach using two new R statistical functions. We explore the consequences of relaxing or tightening criteria defining information and, from thousands of odour combinations, we identify and quantify those few likely to be informative. Our method uses core general principles characterizing information while incorporating knowledge of how receivers detect and discriminate odours. We can now map information in consistency-precision reliability space, explore the concept of information, and test information-noise boundaries, and between cues and signals.},
}
@article {pmid35974327,
year = {2022},
author = {Garza, DR and von Meijenfeldt, FAB and van Dijk, B and Boleij, A and Huynen, MA and Dutilh, BE},
title = {Nutrition or nature: using elementary flux modes to disentangle the complex forces shaping prokaryote pan-genomes.},
journal = {BMC ecology and evolution},
volume = {22},
number = {1},
pages = {101},
pmid = {35974327},
issn = {2730-7182},
mesh = {Archaea/genetics ; Bacteria/genetics ; *Evolution, Molecular ; *Genome, Bacterial/genetics ; Genomics ; Humans ; Phylogeny ; Prokaryotic Cells ; },
abstract = {BACKGROUND: Microbial pan-genomes are shaped by a complex combination of stochastic and deterministic forces. Even closely related genomes exhibit extensive variation in their gene content. Understanding what drives this variation requires exploring the interactions of gene products with each other and with the organism's external environment. However, to date, conceptual models of pan-genome dynamics often represent genes as independent units and provide limited information about their mechanistic interactions.
RESULTS: We simulated the stochastic process of gene-loss using the pooled genome-scale metabolic reaction networks of 46 taxonomically diverse bacterial and archaeal families as proxies for their pan-genomes. The frequency by which reactions are retained in functional networks when stochastic gene loss is simulated in diverse environments allowed us to disentangle the metabolic reactions whose presence depends on the metabolite composition of the external environment (constrained by "nutrition") from those that are independent of the environment (constrained by "nature"). By comparing the frequency of reactions from the first group with their observed frequencies in bacterial and archaeal families, we predicted the metabolic niches that shaped the genomic composition of these lineages. Moreover, we found that the lineages that were shaped by a more diverse metabolic niche also occur in more diverse biomes as assessed by global environmental sequencing datasets.
CONCLUSION: We introduce a computational framework for analyzing and interpreting pan-reactomes that provides novel insights into the ecological and evolutionary drivers of pan-genome dynamics.},
}
@article {pmid35972961,
year = {2022},
author = {Ramírez-Castañeda, V and Westeen, EP and Frederick, J and Amini, S and Wait, DR and Achmadi, AS and Andayani, N and Arida, E and Arifin, U and Bernal, MA and Bonaccorso, E and Bonachita Sanguila, M and Brown, RM and Che, J and Condori, FP and Hartiningtias, D and Hiller, AE and Iskandar, DT and Jiménez, RA and Khelifa, R and Márquez, R and Martínez-Fonseca, JG and Parra, JL and Peñalba, JV and Pinto-García, L and Razafindratsima, OH and Ron, SR and Souza, S and Supriatna, J and Bowie, RCK and Cicero, C and McGuire, JA and Tarvin, RD},
title = {A set of principles and practical suggestions for equitable fieldwork in biology.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {34},
pages = {e2122667119},
pmid = {35972961},
issn = {1091-6490},
mesh = {*Bioethical Issues ; *Biology/ethics ; Humans ; },
abstract = {Field biology is an area of research that involves working directly with living organisms in situ through a practice known as "fieldwork." Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of the core team members. However, existing power imbalances stemming from geopolitical history, discrimination, and professional position, among other factors, perpetuate inequities when conducting these research endeavors. After reflecting on our own research programs, we propose four general principles to guide equitable, inclusive, ethical, and safe practices in field biology: be collaborative, be respectful, be legal, and be safe. Although many biologists already structure their field programs around these principles or similar values, executing equitable research practices can prove challenging and requires careful consideration, especially by those in positions with relatively greater privilege. Based on experiences and input from a diverse group of global collaborators, we provide suggestions for action-oriented approaches to make field biology more equitable, with particular attention to how those with greater privilege can contribute. While we acknowledge that not all suggestions will be applicable to every institution or program, we hope that they will generate discussions and provide a baseline for training in proactive, equitable fieldwork practices.},
}
@article {pmid35972940,
year = {2022},
author = {Vimercati, G and Probert, AF and Volery, L and Bernardo-Madrid, R and Bertolino, S and Céspedes, V and Essl, F and Evans, T and Gallardo, B and Gallien, L and González-Moreno, P and Grange, MC and Hui, C and Jeschke, JM and Katsanevakis, S and Kühn, I and Kumschick, S and Pergl, J and Pyšek, P and Rieseberg, L and Robinson, TB and Saul, WC and Sorte, CJB and Vilà, M and Wilson, JRU and Bacher, S},
title = {The EICAT+ framework enables classification of positive impacts of alien taxa on native biodiversity.},
journal = {PLoS biology},
volume = {20},
number = {8},
pages = {e3001729},
pmid = {35972940},
issn = {1545-7885},
mesh = {*Biodiversity ; Ecosystem ; Human Activities ; Humans ; *Introduced Species ; },
abstract = {Species introduced through human-related activities beyond their native range, termed alien species, have various impacts worldwide. The IUCN Environmental Impact Classification for Alien Taxa (EICAT) is a global standard to assess negative impacts of alien species on native biodiversity. Alien species can also positively affect biodiversity (for instance, through food and habitat provisioning or dispersal facilitation) but there is currently no standardized and evidence-based system to classify positive impacts. We fill this gap by proposing EICAT+, which uses 5 semiquantitative scenarios to categorize the magnitude of positive impacts, and describes underlying mechanisms. EICAT+ can be applied to all alien taxa at different spatial and organizational scales. The application of EICAT+ expands our understanding of the consequences of biological invasions and can inform conservation decisions.},
}
@article {pmid35969597,
year = {2022},
author = {Ramasawmy, M and Mu, Y and Clutterbuck, D and Pantelic, M and Lip, GYH and van der Feltz-Cornelis, C and Wootton, D and Williams, NH and Montgomery, H and Mallinson Cookson, R and Attree, E and Gabbay, M and Heightman, M and Alwan, NA and Banerjee, A and Lorgelly, P and , },
title = {STIMULATE-ICP-CAREINEQUAL (Symptoms, Trajectory, Inequalities and Management: Understanding Long-COVID to Address and Transform Existing Integrated Care Pathways) study protocol: Defining usual care and examining inequalities in Long Covid support.},
journal = {PloS one},
volume = {17},
number = {8},
pages = {e0271978},
pmid = {35969597},
issn = {1932-6203},
support = {COV-LT2-0043/DH_/Department of Health/United Kingdom ; },
mesh = {*COVID-19/complications/epidemiology/therapy ; Critical Pathways ; *Delivery of Health Care, Integrated ; Humans ; Longitudinal Studies ; Post-Acute COVID-19 Syndrome ; },
abstract = {INTRODUCTION: Individuals with Long Covid represent a new and growing patient population. In England, fewer than 90 Long Covid clinics deliver assessment and treatment informed by NICE guidelines. However, a paucity of clinical trials or longitudinal cohort studies means that the epidemiology, clinical trajectory, healthcare utilisation and effectiveness of current Long Covid care are poorly documented, and that neither evidence-based treatments nor rehabilitation strategies exist. In addition, and in part due to pre-pandemic health inequalities, access to referral and care varies, and patient experience of the Long Covid care pathways can be poor. In a mixed methods study, we therefore aim to: (1) describe the usual healthcare, outcomes and resource utilisation of individuals with Long Covid; (2) assess the extent of inequalities in access to Long Covid care, and specifically to understand Long Covid patients' experiences of stigma and discrimination.
METHODS AND ANALYSIS: A mixed methods study will address our aims. Qualitative data collection from patients and health professionals will be achieved through surveys, interviews and focus group discussions, to understand their experience and document the function of clinics. A patient cohort study will provide an understanding of outcomes and costs of care. Accessible data will be further analysed to understand the nature of Long Covid, and the care received.
ETHICS AND DISSEMINATION: Ethical approval was obtained from South Central-Berkshire Research Ethics Committee (reference 303958). The dissemination plan will be decided by the patient and public involvement and engagement (PPIE) group members and study Co-Is, but will target 1) policy makers, and those responsible for commissioning and delivering Long Covid services, 2) patients and the public, and 3) academics.},
}
@article {pmid35964757,
year = {2022},
author = {Loli, M and Kefalas, G and Dafis, S and Mitoulis, SA and Schmidt, F},
title = {Bridge-specific flood risk assessment of transport networks using GIS and remotely sensed data.},
journal = {The Science of the total environment},
volume = {850},
number = {},
pages = {157976},
doi = {10.1016/j.scitotenv.2022.157976},
pmid = {35964757},
issn = {1879-1026},
mesh = {*Floods ; *Geographic Information Systems ; Hydrology ; Reproducibility of Results ; Risk Assessment ; },
abstract = {A novel framework for the expedient assessment of flood risk to transportation networks focused on the response of the most critical and vulnerable infrastructure assets, the bridges, is developed, validated and applied. Building upon the recent French guidelines on scour risk (CEREMA, 2019), this paper delivers a thorough methodology, that incorporates three key, risk parameters: (i) the hydrodynamic loading, a hazard component of equal significance to scour, for the assessment of hazard; (ii) the correlation of select scour indicators with a new index relating to flow velocity, a primary measure of the adverse impacts of flow-structure interaction, enabling a more accurate and automated, assessment of bridge susceptibility to scour; (iii) the use of a new, comprehensive indicator, namely the Indicator of Flood Hazard Intensity (IFHI) which incorporates, in a simple yet efficient way, the key parameters controlling the severity of flood impact on bridges, namely flow velocity, floodwater height, flow obstruction, and sediment type. The framework is implemented for the analysis of flood risk in a case study area, considering an inventory of 117 bridges of diverse construction characteristics, which were affected by a major flood that impacted Greece in September 2020. The reliability of the method is validated against an extensive record of inspected and documented bridge damages. Regional scale analysis is facilitated by the adoption of the Multi-Criteria Decision-Making method for flood hazard indexing, considering geomorphological, meteorological, hydrological, and land use/cover data, based on the processing of remotely sensed imagery and openly available geospatial datasets in GIS.},
}
@article {pmid35964726,
year = {2022},
author = {Karimian, H and Zou, W and Chen, Y and Xia, J and Wang, Z},
title = {Landscape ecological risk assessment and driving factor analysis in Dongjiang river watershed.},
journal = {Chemosphere},
volume = {307},
number = {Pt 3},
pages = {135835},
doi = {10.1016/j.chemosphere.2022.135835},
pmid = {35964726},
issn = {1879-1298},
mesh = {China ; *Environmental Monitoring/methods ; Factor Analysis, Statistical ; Humans ; Risk Assessment ; *Rivers ; Urbanization ; },
abstract = {The ecological and environmental quality of Dongjiang river watershed has great influence on Guangdong, Hong Kong and Macao. The landscape ecological risk assessment model could effectively monitor and assess environmental quality. In this study, spatial autocorrelation and geographic detector methods were used to explore the spatial characteristics of landscape ecological risk and their driving factors in the Dongjiang river watershed for four decades. The results showed that the ecological risks of Dongjiang River Source Watershed are mainly classified as low and intermediate, which are distributed in the hilly regions and the marginal mountainous regions at the junction of the Xunwu and Dingnan counties. From 1980 to 2018, the area of regions with the low ecological risk increased by 587.01 km [2]. The size of regions with moderate, high and severe ecological risk decreased by 165.6 km [2], 258.82 km[2] and 162.58 km[2], respectively. Moreover, landscape ecological risk values exhibited an apparent spatial dependency, and high-risk areas cluster together. Among influencing factors, population density has the most significant impact on the change of landscape ecological risk in the Dongjiang river watershed, followed by elevation (DEM), human interface, vegetation index (NDVI), and urbanization level. However, the interaction of driving factors has a greater impact on the ecological risk of the Dongjiang river watershed than a single driving factor. The research provides good knowledge for environmental quality management, and the proposed methods can be used for other regions.},
}
@article {pmid35960845,
year = {2022},
author = {Amend, AS and Swift, SOI and Darcy, JL and Belcaid, M and Nelson, CE and Buchanan, J and Cetraro, N and Fraiola, KMS and Frank, K and Kajihara, K and McDermot, TG and McFall-Ngai, M and Medeiros, M and Mora, C and Nakayama, KK and Nguyen, NH and Rollins, RL and Sadowski, P and Sparagon, W and Téfit, MA and Yew, JY and Yogi, D and Hynson, NA},
title = {A ridge-to-reef ecosystem microbial census reveals environmental reservoirs for animal and plant microbiomes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {33},
pages = {e2204146119},
pmid = {35960845},
issn = {1091-6490},
support = {P20 GM125508/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Bacteria ; *Ecosystem ; *Microbiota ; *Plants/microbiology ; },
abstract = {Microbes are found in nearly every habitat and organism on the planet, where they are critical to host health, fitness, and metabolism. In most organisms, few microbes are inherited at birth; instead, acquiring microbiomes generally involves complicated interactions between the environment, hosts, and symbionts. Despite the criticality of microbiome acquisition, we know little about where hosts' microbes reside when not in or on hosts of interest. Because microbes span a continuum ranging from generalists associating with multiple hosts and habitats to specialists with narrower host ranges, identifying potential sources of microbial diversity that can contribute to the microbiomes of unrelated hosts is a gap in our understanding of microbiome assembly. Microbial dispersal attenuates with distance, so identifying sources and sinks requires data from microbiomes that are contemporary and near enough for potential microbial transmission. Here, we characterize microbiomes across adjacent terrestrial and aquatic hosts and habitats throughout an entire watershed, showing that the most species-poor microbiomes are partial subsets of the most species-rich and that microbiomes of plants and animals are nested within those of their environments. Furthermore, we show that the host and habitat range of a microbe within a single ecosystem predicts its global distribution, a relationship with implications for global microbial assembly processes. Thus, the tendency for microbes to occupy multiple habitats and unrelated hosts enables persistent microbiomes, even when host populations are disjunct. Our whole-watershed census demonstrates how a nested distribution of microbes, following the trophic hierarchies of hosts, can shape microbial acquisition.},
}
@article {pmid35960769,
year = {2022},
author = {Ali, MA and Iqbal, MS and Ahmad, KS and Akbar, M and Mehmood, A and Hussain, SA and Arshad, N and Munir, S and Masood, H and Ahmad, T and Kaloi, GM and Islam, M},
title = {Plant species diversity assessment and monitoring in catchment areas of River Chenab, Punjab, Pakistan.},
journal = {PloS one},
volume = {17},
number = {8},
pages = {e0272654},
pmid = {35960769},
issn = {1932-6203},
mesh = {Biodiversity ; *Ecosystem ; Humans ; Pakistan ; Plants ; Potassium ; *Rivers ; Soil/chemistry ; Trees ; },
abstract = {BACKGROUND: Biodiversity data is crucial for sustainable development and making decisions regarding natural resources and its conservation. The study goal was to use quantitative ecological approaches to determine the species richness and diversity of wild flora and the ultimate impact of environmental factors on vegetation dynamics.
METHODS: Quadrats having sizes of 1×1 for herbs, 5×5 for shrubs, and 10×10 m2 for trees were used. Various phytosociological characteristics were investigated in association with a wide variety of environmental variables. Soil analysis based on texture, moisture, pH, electrical conductivity (EC), organic matter (OM), available potassium (K), and phosphorus (P) were examined. The existing state of vegetation along the River Chenab was assessed using SWOT analysis and a future conservation strategy was devised.
RESULTS: One hundred twenty different plant speies were divided into 51 families including 92 dicots, 17 monocots, 6 pteridophytes and 1 bryophyte species. Herbs accounted for 89 followed by shrubs (16 species) and trees (15 species). Correlation analysis revealed a highly positive correlation between relative density and relative frequency (0.956**). Shannon and Simpson's diversity indices elaborated that site 3 and 7 with clay loamy soil had non-significant alpha diversity and varies from site to site. Diversity analysis showed that site 10 was most diverse (22.25) in terms of species richness. The principal coordinate analysis expressed that different environmental variables including OM, soil pH, P, K, and EC affect vegetation significantly, therefore, loamy soil showed presence and dispersal of more vegetation as compared to loam, sandy and sandy loam soils. Further, 170 ppm of available potassium had significant affect on plant diversity and distribution.
CONCLUSION: Asteraceae family was found dominant as dicot while poaceae among monocot. Adhatoda vasica was one of the unique species and found in Head Maralla site. For evenness, site 3 had maximum value 0.971. Most of the soil represented loamy soil texture where site 2 and 4 possess high soil moisture content. SWOT analysis revealed strengths as people prefered plants for medicine, food and economic purposes. In weakness, agricultural practices, soil erosion and flooding affected the vegetation. In opportunities, Forest and Irrigation Departments were planting plants for the restoration of ecosystem. Threats include anthropogenic activities overgrazing, urbanization and road infrastructure at Head Maralla, habitat fragmentation at Head Khanki, and extensive fish farming at Head Qadirabad. Future conservation efforts should be concentrated on SWOT analysis outcome in terms of stopping illegal consumption of natural resources, restoration of plant biodiversity through reforestation, designating protected areas and multiplying rare species locally.},
}
@article {pmid35959935,
year = {2022},
author = {Stahlke, AR and Chang, J and Tembrock, LR and Sim, SB and Chudalayandi, S and Geib, SM and Scheffler, BE and Perera, OP and Gilligan, TM and Childers, AK and Hackett, KJ and Coates, BS},
title = {A chromosome-scale genome assembly of a Helicoverpa zea strain resistant to Bacillus thuringiensis Cry1Ac insecticidal protein.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evac131},
pmid = {35959935},
issn = {1759-6653},
abstract = {Helicoverpa zea (Lepidoptera: Noctuidae) is an insect pest of major cultivated crops in North and South America. The species has adapted to different host plants and developed resistance to several insecticidal agents, including Bacillus thuringiensis (Bt) insecticidal proteins in transgenic cotton and maize. H. zea populations persist year-round in tropical and subtropical regions, but seasonal migrations into temperate zones increase the geographic range of associated crop damage. To better understand the genetic basis of these physiological and ecological characteristics, we generated a high-quality chromosome-level assembly for a single H. zea male from Bt resistant strain, HzStark_Cry1AcR. Hi-C data were used to scaffold an initial 375.2 Mb contig assembly into 30 autosomes and the Z sex chromosome (scaffold N50 = 12.8 Mb and L50 = 14). The scaffolded assembly was error-corrected with a novel pipeline, polishCLR. The mitochondrial genome was assembled through an improved pipeline and annotated. Assessment of this genome assembly indicated 98.8% of the Lepidopteran Benchmark Universal Single-Copy Ortholog set were complete (98.5% as complete single-copy). Repetitive elements comprised approximately 29.5% of the assembly with the plurality (11.2%) classified as retroelements. This chromosome-scale reference assembly for H. zea, ilHelZeax1.1, will facilitate future research to evaluate and enhance sustainable crop production practices.},
}
@article {pmid35955104,
year = {2022},
author = {Zhou, X and Shen, D and Gu, X},
title = {Influences of Land Policy on Urban Ecological Corridors Governance: A Case Study from Shanghai.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {15},
pages = {},
pmid = {35955104},
issn = {1660-4601},
mesh = {Agriculture ; China ; Cities ; Conservation of Natural Resources ; Ecosystem ; *Forests ; *Policy ; },
abstract = {The analysis of land use change (LUC) characteristics and the impact of policies related to urban ecological space is required to improve spatial planning and to support decision making regarding green infrastructure (GI) investment. This study employed Geo-informatic Tupu analysis and Fluctuation Potential Tupu analysis methods to analyze the characteristics of LUC in an urban ecological corridor (EC). To help understand the influence of land use policy on GI governance and support the optimization of spatial planning, we proposed a situation-structure-implementation-outcome (SSIO) policy cascade analysis framework. SSIO takes "place" as its starting point, then couples the local policy with the governance structure to promote the sustainability of urban commons governance. The results show that the land use type within an EC in the city is mainly cultivated land. However, between 2009 and 2019, cultivated land, construction land, and facility agricultural land all showed a decreasing trend, while forest land and garden land types underwent increasing trends. The LUC Tupu unit highlights the transition from cultivated land to forest land. Forest land has the greatest increase in area and accounts for 52.34% of the area of increasing land use. Cultivated land shows the greatest decrease in area and accounts for 70.30% of the area of decreasing trends. Based on the local policy situation of the metropolis, a land policy governance mechanism can be constructed by the establishment of a governance structure with local government as the core, using land consolidation as the platform, taking ecological spatial planning and inefficient construction land reduction as typical policy tools, and experimentally integrating the concept of Nature-based Solutions (NbS). In general, these findings may be applicable to other rapidly urbanizing cities around the world that are developing complex land use policies for ecological space governance.},
}
@article {pmid35954991,
year = {2022},
author = {Wang, Q and Yang, K and Li, L and Zhu, Y},
title = {Assessing the Terrain Gradient Effect of Landscape Ecological Risk in the Dianchi Lake Basin of China Using Geo-Information Tupu Method.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {15},
pages = {},
pmid = {35954991},
issn = {1660-4601},
mesh = {China ; *Conservation of Natural Resources ; Ecosystem ; Geographic Information Systems ; *Lakes ; Risk Assessment/methods ; },
abstract = {The assessment of landscape ecological risk (LER) in different terrain gradients is beneficial to ecological environmental protection and risk management in different terrain gradients. Due to the impact of urban expansion, the landscape pattern of the Dianchi Lake basin (DLB) changed obviously, resulting in significant spatial difference of LER. At present, the LER assessment of the DLB is not clear, and the evolution mechanism of LER in different terrain gradients has not been revealed. Based on the LER assessment model, the geo-information Tupu method, the terrain niche gradient, and distribution index, this paper analyzed the LER and its terrain gradient effect in the DLB of China. The conclusions are as follows: (1) Since 1995, the land use type has mainly changed from grassland and cultivated land to construction land in the DLB of China. (2) The LERs in the DLB of China were mainly low, med low, and med high due to the transformation of land use type. The dominance distribution of the low and high LER was obviously constrained by terrain gradient. While the dominance distribution of med-low LER expanded to med-high terrain gradient, the dominance distribution of the med-high LER decreased to med-low terrain gradient. (3) The Tupu LERs were mainly a stable type of "medium" risk and anaphase change type of "med-high to medium" risk. The dominant distribution regions of the stable type, the prophase change type, and the continuous change type were relatively stable; the anaphase and middle change type expanded to the higher terrain gradient, and the repeated change type decreased to the med-high terrain gradient. In the process of ecological risk management and protection in the DLB, attention should be paid to the water area structure and LER control in med-high and high terrain gradients.},
}
@article {pmid35954559,
year = {2022},
author = {Lamberti-Castronuovo, A and Valente, M and Aleni, C and Hubloue, I and Ragazzoni, L and Barone-Adesi, F},
title = {Using Ambulatory Care Sensitive Conditions to Assess Primary Health Care Performance during Disasters: A Systematic Review.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {15},
pages = {},
pmid = {35954559},
issn = {1660-4601},
mesh = {Ambulatory Care ; Ambulatory Care Sensitive Conditions ; Databases, Factual ; *Disasters ; Hospitalization ; Humans ; *Primary Health Care ; },
abstract = {Ambulatory care sensitive conditions (ACSCs) are health conditions for which appropriate primary care intervention could prevent hospital admission. ACSC hospitalization rates are a well-established parameter for assessing the performance of primary health care (PHC). Although this indicator has been extensively used to monitor the performance of PHC systems in peacetime, its consideration during disasters has been neglected. The World Health Organization (WHO) has acknowledged the importance of PHC in guaranteeing continuity of care during and after a disaster for avoiding negative health outcomes. We conducted a systematic review to evaluate the extent and nature of research activity on the use of ACSCs during disasters, with an eye toward finding innovative ways to assess the level of PHC function at times of crisis. Online databases were searched to identify papers. A final list of nine publications was retrieved. The analysis of the reviewed articles confirmed that ACSCs can serve as a useful indicator of PHC performance during disasters, with several caveats that must be considered. The reviewed articles cover several disaster scenarios and a wide variety of methodologies showing the connection between ACSCs and health system performance. The strengths and weaknesses of using different methodologies are explored and recommendations are given for using ACSCs to assess PHC performance during disasters.},
}
@article {pmid35951711,
year = {2022},
author = {Nishimura, T and Tokuda, IT and Miyachi, S and Dunn, JC and Herbst, CT and Ishimura, K and Kaneko, A and Kinoshita, Y and Koda, H and Saers, JPP and Imai, H and Matsuda, T and Larsen, ON and Jürgens, U and Hirabayashi, H and Kojima, S and Fitch, WT},
title = {Evolutionary loss of complexity in human vocal anatomy as an adaptation for speech.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6607},
pages = {760-763},
doi = {10.1126/science.abm1574},
pmid = {35951711},
issn = {1095-9203},
mesh = {Animals ; *Biological Evolution ; Humans ; *Larynx/anatomy & histology ; *Phonation ; Phonetics ; *Primates ; *Speech ; Speech Acoustics ; *Vocal Cords/anatomy & histology ; },
abstract = {Human speech production obeys the same acoustic principles as vocal production in other animals but has distinctive features: A stable vocal source is filtered by rapidly changing formant frequencies. To understand speech evolution, we examined a wide range of primates, combining observations of phonation with mathematical modeling. We found that source stability relies upon simplifications in laryngeal anatomy, specifically the loss of air sacs and vocal membranes. We conclude that the evolutionary loss of vocal membranes allows human speech to mostly avoid the spontaneous nonlinear phenomena and acoustic chaos common in other primate vocalizations. This loss allows our larynx to produce stable, harmonic-rich phonation, ideally highlighting formant changes that convey most phonetic information. Paradoxically, the increased complexity of human spoken language thus followed simplification of our laryngeal anatomy.},
}
@article {pmid35946638,
year = {2022},
author = {Andrade, GM and Gil, AO and Barbosa, ARG and Teles, SB and Amaral, BS and Monteiro, J and Apezzato, M and Bianco, B and Lemos, GC and Carneiro, A},
title = {Analysis of adrenalectomy for the treatment of adrenal diseases performed by the Public Health Service in São Paulo between 2008 and 2019.},
journal = {Revista do Colegio Brasileiro de Cirurgioes},
volume = {49},
number = {},
pages = {e20223320},
doi = {10.1590/0100-6991e-20223320-en},
pmid = {35946638},
issn = {1809-4546},
mesh = {*Adrenalectomy/methods ; Brazil ; Hospitals, High-Volume ; Humans ; Length of Stay ; *Surgeons ; },
abstract = {INTRODUCTION: treating benign (hormonally active or nonfunctional) and malignant adrenal cancer includes adrenalectomy. The expertise of surgeons and surgery performed by high-volume surgeons were associated with fewer complications and lower cost. We aimed to describe and compare the number of surgeries, mortality rate, and length of hospital stay for adrenalectomies performed between 2008 and 2019 in the public health system of São Paulo.
METHODS: this was an ecological study. The data were collected using the TabNet Platform of the Unified Health System Department of Informatics. Outcomes analyzed included the number of surgeries performed, mortality rate during hospital stay, and length of hospital stay. Public hospitals in Sao Paulo were divided into three subgroups according to the surgical volume of adrenalectomies performed as well as hospitals with and without a residency program in Urology, and the results were compared among them.
RESULTS: a total of 943 adrenalectomies were performed in Sao Paulo between 2008 and 2019. Mortality rates during hospital stay according to hospital surgical volume were no reported deaths in low-volume, 0.015% in intermediate-volume, and 0.004% in high-volume hospitals. The average length of the ICU stay was 1.03 days in low-volume, 2.8 in intermediate-volume, and 1.12 in high-volume hospitals (analysis between intermediate and high volume centers with statistical significance, p=0.016).
CONCLUSIONS: despite no statistically significant differences among the groups analyzed, mortality rates were very low in all groups. ICU stay was shorter in high-volume centers than in intermediate-volume centers.},
}
@article {pmid35933453,
year = {2022},
author = {Wang, Z and Yang, S and Luo, L and Guo, X and Deng, B and Zhao, Z and Rui, J and Yu, S and Zhao, B and Wang, Y and Chen, J and Sun, Y and Chen, T and Feng, X},
title = {Epidemiological characteristics of severe fever with thrombocytopenia syndrome and its relationship with meteorological factors in Liaoning Province, China.},
journal = {Parasites & vectors},
volume = {15},
number = {1},
pages = {283},
pmid = {35933453},
issn = {1756-3305},
mesh = {China/epidemiology ; Humans ; Incidence ; Male ; Meteorological Concepts ; *Severe Fever with Thrombocytopenia Syndrome ; Temperature ; },
abstract = {BACKGROUND: Severe fever with thrombocytopenia syndrome (SFTS), one kind of tick-borne acute infectious disease, is caused by a novel bunyavirus. The relationship between meteorological factors and infectious diseases is a hot topic of current research. Liaoning Province has reported a high incidence of SFTS in recent years. However, the epidemiological characteristics of SFTS and its relationship with meteorological factors in the province remain largely unexplored.
METHODS: Data on reported SFTS cases were collected from 2011 to 2019. Epidemiological characteristics of SFTS were analyzed. Spearman's correlation test and generalized linear models (GLM) were used to identify the relationship between meteorological factors and the number of SFTS cases.
RESULTS: From 2011 to 2019, the incidence showed an overall upward trend in Liaoning Province, with the highest incidence in 2019 (0.35/100,000). The incidence was slightly higher in males (55.9%, 438/783), and there were more SFTS patients in the 60-69 age group (31.29%, 245/783). Dalian City and Dandong City had the largest number of cases of SFTS (87.99%, 689/783). The median duration from the date of illness onset to the date of diagnosis was 8 days [interquartile range (IQR): 4-13 days]. Spearman correlation analysis and GLM showed that the number of SFTS cases was positively correlated with monthly average rainfall (rs = 0.750, P < 0.001; β = 0.285, P < 0.001), monthly average relative humidity (rs = 0.683, P < 0.001; β = 0.096, P < 0.001), monthly average temperature (rs = 0.822, P < 0.001; β = 0.154, P < 0.001), and monthly average ground temperature (rs = 0.810, P < 0.001; β = 0.134, P < 0.001), while negatively correlated with monthly average air pressure (rs = -0.728, P < 0.001; β = -0.145, P < 0.001), and monthly average wind speed (rs = -0.272, P < 0.05; β = -1.048, P < 0.001). By comparing both correlation coefficients and regression coefficients between the number of SFTS cases (dependent variable) and meteorological factors (independent variables), no significant differences were observed when considering immediate cases and cases with lags of 1 to 5 weeks for dependent variables. Based on the forward and backward stepwise GLM regression, the monthly average air pressure, monthly average temperature, monthly average wind speed, and time sequence were selected as relevant influences on the number of SFTS cases.
CONCLUSION: The annual incidence of SFTS increased year on year in Liaoning Province. Incidence of SFTS was affected by several meteorological factors, including monthly average air pressure, monthly average temperature, and monthly average wind speed.},
}
@article {pmid35933090,
year = {2022},
author = {Sun, Z and Wang, Y and Song, Z and Zhang, H and Wang, Y and Liu, K and Ma, M and Wang, P and Fang, Y and Cai, D and Li, G and Fang, Y},
title = {DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication.},
journal = {Journal of advanced research},
volume = {42},
number = {},
pages = {41-53},
pmid = {35933090},
issn = {2090-1224},
mesh = {*DNA Transposable Elements/genetics ; *Oryza/genetics ; DNA Methylation ; Gene Duplication ; Chromatin/genetics ; Transcription, Genetic/genetics ; },
abstract = {INTRODUCTION: Polyploidy is a major force in plant evolution and the domestication of cultivated crops.
OBJECTIVES: The study aimed to explore the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene transcription upon rice genome duplication.
METHODS: The 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice were compared using high-throughput chromosome conformation capture (Hi-C) analysis. The study combined genetics, transcriptomics, whole-genome bisulfite sequencing (WGBS-seq) and 3D genomics approaches to uncover the mechanism for DNA methylation in modulating gene transcription through 3D chromatin architectures upon rice genome duplication.
RESULTS: We found that 4C rice presents weakened intra-chromosomal interactions compared to its 2C progenitor in some chromosomes. In addition, we found that changes of 3D chromatin organizations including chromatin compartments, topologically associating domains (TADs), and loops, are uncorrelated with gene transcription. Moreover, DNA methylations in the regulatory sequences of genes in compartment A/B switched regions and TAD boundaries are unrelated to their expression. Importantly, although there was no significant difference in the methylation levels in transposable elements (TEs) in differentially expressed gene (DEG) and non-DEG promoters between 2C and 4C rice, we found that the hypermethylated TEs across genes in compartment A/B switched regions and TAD boundaries may suppress the expression of these genes.
CONCLUSION: The study proposed that the rice genome doubling might modulate TE methylation to buffer the effects of chromatin architecture on gene transcription in compartment A/B switched regions and TAD boundaries, resulting in the disconnection between 3D chromatin structure alteration and gene transcription upon rice genome duplication.},
}
@article {pmid35932855,
year = {2022},
author = {Zhang, X and Manzanedo, RD and Lv, P and Xu, C and Hou, M and Huang, X and Rademacher, T},
title = {Reduced diurnal temperature range mitigates drought impacts on larch tree growth in North China.},
journal = {The Science of the total environment},
volume = {848},
number = {},
pages = {157808},
doi = {10.1016/j.scitotenv.2022.157808},
pmid = {35932855},
issn = {1879-1026},
mesh = {China ; Climate Change ; Droughts ; Forests ; *Larix ; Temperature ; Trees ; },
abstract = {Forests are facing climate changes such as warmer temperatures, accelerated snowmelt, increased drought, as well as changing diurnal temperature ranges (DTR) and cloud cover regimes. How tree growth is influenced by the changes in daily to monthly temperatures and its associations with droughts has been extensively investigated, however, few studies have focused on how changes in sub-daily temperatures i.e., DTR, influence tree growth during drought events. Here, we used a network of Larix principis-rupprechtii tree-ring data from 1989 to 2018, covering most of the distribution of planted larch across North China, to investigate how DTR, cloud cover and their interactions influence the relationship between drought stress and tree growth. DTR showed a negative correlation with larch growth in 95 % of sites (rmean = -0.30, significant in 42 % of sites). Cloud cover was positively correlated with growth in 87 % of sites (rmean = 0.13, significant in 5 % of sites). Enhanced tree growth was found at lower DTR in the absence of severe drought. Our findings highlight that in the absence of severe droughts, reduced DTR benefits tree growth, while increased cloud cover tended to benefit tree growth only during severe drought periods. Given how DTR influences drought impacts on tree growth, net tree growth was found to be larger in regions with smaller DTR.},
}
@article {pmid35930070,
year = {2022},
author = {Chakraborty, H and Kayal, T and Lianthuamluaia, L and Sarkar, UK and Das, AK and Chakraborty, S and Sahoo, BK and Mondal, K and Mandal, S and Das, BK},
title = {Use of geographical information systems (GIS) in assessing ecological profile, fish community structure and production of a large reservoir of Himachal Pradesh.},
journal = {Environmental monitoring and assessment},
volume = {194},
number = {9},
pages = {643},
doi = {10.1007/s10661-022-10292-5},
pmid = {35930070},
issn = {1573-2959},
mesh = {Animals ; *Biodiversity ; Ecosystem ; Environmental Monitoring ; Fishes ; *Geographic Information Systems ; Water ; },
abstract = {The present study demonstrates the spatial analysis and mapping of fish and different measures of environmental parameters and fish diversity of Pong reservoir, Himachal Pradesh, using Kriging spatial interpolation methods for geographical information system mapping. Seasonal data on environmental parameters, potential fish habitat and fish diversity was collected from lentic (dam), lentic (reservoir), transitional and lotic zone of the reservoir.. Important environmental parameters like water temperature, dissolved oxygen, electrical conductivity, water depth and transparency showed variations across the different zones of the reservoir. The sediment of the reservoir was sandy clay loam in nature as per texture analysis. Fish species richness, Shannon index and evenness index showed a similarity of the lotic and lentic (reservoir) zones of the reservoir. Six potential fish breeding grounds were identified in the reservoir indicating high conservation significance. The analysis of data showed a declining trend in fish production from 456.9 tonnes during the decade 1976-1987 to 347.91 tonnes during 2009-2020. The factors like anthropogenic climate change, predation of a stocked fish juvenile by water birds, undersized fish stocking and unscientific management are the probable reasons for the decreasing fish production. The spatial variation pattern of the water spread area, environmental parameters, fish catch and potential fish breeding grounds depicted in the GIS platform can be used as an important information base by the policy makers for fisheries management. The stocking of large size fish as a stocking material and adequate protection of the potential fish breeding grounds are the key advisories for the sustainable enhancement of fisheries as well as conservation.},
}
@article {pmid35927942,
year = {2022},
author = {Rademacher, T and Fonti, P and LeMoine, JM and Fonti, MV and Bowles, F and Chen, Y and Eckes-Shephard, AH and Friend, AD and Richardson, AD},
title = {Insights into source/sink controls on wood formation and photosynthesis from a stem chilling experiment in mature red maple.},
journal = {The New phytologist},
volume = {236},
number = {4},
pages = {1296-1309},
doi = {10.1111/nph.18421},
pmid = {35927942},
issn = {1469-8137},
mesh = {*Acer ; Wood/physiology ; Photosynthesis ; Trees/physiology ; Carbon/analysis ; Plant Leaves/physiology ; },
abstract = {Whether sources or sinks control wood growth remains debated with a paucity of evidence from mature trees in natural settings. Here, we altered carbon supply rate in stems of mature red maples (Acer rubrum) within the growing season by restricting phloem transport using stem chilling; thereby increasing carbon supply above and decreasing carbon supply below the restrictions, respectively. Chilling successfully altered nonstructural carbon (NSC) concentrations in the phloem without detectable repercussions on bulk NSC in stems and roots. Ring width responded strongly to local variations in carbon supply with up to seven-fold differences along the stem of chilled trees; however, concurrent changes in the structural carbon were inconclusive at high carbon supply due to large local variability of wood growth. Above chilling-induced bottlenecks, we also observed higher leaf NSC concentrations, reduced photosynthetic capacity, and earlier leaf coloration and fall. Our results indicate that the cambial sink is affected by carbon supply, but within-tree feedbacks can downregulate source activity, when carbon supply exceeds demand. Such feedbacks have only been hypothesized in mature trees. Consequently, these findings constitute an important advance in understanding source-sink dynamics, suggesting that mature red maples operate close to both source- and sink-limitation in the early growing season.},
}
@article {pmid35927319,
year = {2022},
author = {Jang, SK and Evans, L and Fialkowski, A and Arnett, DK and Ashley-Koch, AE and Barnes, KC and Becker, DM and Bis, JC and Blangero, J and Bleecker, ER and Boorgula, MP and Bowden, DW and Brody, JA and Cade, BE and Jenkins, BWC and Carson, AP and Chavan, S and Cupples, LA and Custer, B and Damrauer, SM and David, SP and de Andrade, M and Dinardo, CL and Fingerlin, TE and Fornage, M and Freedman, BI and Garrett, ME and Gharib, SA and Glahn, DC and Haessler, J and Heckbert, SR and Hokanson, JE and Hou, L and Hwang, SJ and Hyman, MC and Judy, R and Justice, AE and Kaplan, RC and Kardia, SLR and Kelly, S and Kim, W and Kooperberg, C and Levy, D and Lloyd-Jones, DM and Loos, RJF and Manichaikul, AW and Gladwin, MT and Martin, LW and Nouraie, M and Melander, O and Meyers, DA and Montgomery, CG and North, KE and Oelsner, EC and Palmer, ND and Payton, M and Peljto, AL and Peyser, PA and Preuss, M and Psaty, BM and Qiao, D and Rader, DJ and Rafaels, N and Redline, S and Reed, RM and Reiner, AP and Rich, SS and Rotter, JI and Schwartz, DA and Shadyab, AH and Silverman, EK and Smith, NL and Smith, JG and Smith, AV and Smith, JA and Tang, W and Taylor, KD and Telen, MJ and Vasan, RS and Gordeuk, VR and Wang, Z and Wiggins, KL and Yanek, LR and Yang, IV and Young, KA and Young, KL and Zhang, Y and Liu, DJ and Keller, MC and Vrieze, S},
title = {Rare genetic variants explain missing heritability in smoking.},
journal = {Nature human behaviour},
volume = {6},
number = {11},
pages = {1577-1586},
pmid = {35927319},
issn = {2397-3374},
support = {R01 NS058700/NS/NINDS NIH HHS/United States ; R01 DK071891/DK/NIDDK NIH HHS/United States ; R01 AG058921/AG/NIA NIH HHS/United States ; R01 HL113323/HL/NHLBI NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; U01 HL089897/HL/NHLBI NIH HHS/United States ; R01 NS058700/NS/NINDS NIH HHS/United States ; R01 DK071891/DK/NIDDK NIH HHS/United States ; R01 AG058921/AG/NIA NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; U01 HL089897/HL/NHLBI NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; U01 HL089897/HL/NHLBI NIH HHS/United States ; HHSN268201100007I/HL/NHLBI NIH HHS/United States ; HHSN268201100007I/HL/NHLBI NIH HHS/United States ; HHSN268201100007I/HL/NHLBI NIH HHS/United States ; HHSN268201700001I/HL/NHLBI NIH HHS/United States ; HHSN268201700002I/HL/NHLBI NIH HHS/United States ; HHSN268201700003I/HL/NHLBI NIH HHS/United States ; HHSN268201700004I/HL/NHLBI NIH HHS/United States ; HHSN268201700005I/HL/NHLBI NIH HHS/United States ; HHSN268201500001I/HL/NHLBI NIH HHS/United States ; 75N92019D00031/HL/NHLBI NIH HHS/United States ; HHSN268201100007I/HL/NHLBI NIH HHS/United States ; U01 HL054457/HL/NHLBI NIH HHS/United States ; U01 HL054464/HL/NHLBI NIH HHS/United States ; R01 HL119443/HL/NHLBI NIH HHS/United States ; R01 HL085571/HL/NHLBI NIH HHS/United States ; R01 HL087660/HL/NHLBI NIH HHS/United States ; HHSN268201200036C/HL/NHLBI NIH HHS/United States ; HHSN268200800007C/HL/NHLBI NIH HHS/United States ; HHSN268201800001C/HL/NHLBI NIH HHS/United States ; N01HC55222/HL/NHLBI NIH HHS/United States ; N01HC85079/HL/NHLBI NIH HHS/United States ; N01HC85080/HL/NHLBI NIH HHS/United States ; N01HC85081/HL/NHLBI NIH HHS/United States ; N01HC85082/HL/NHLBI NIH HHS/United States ; N01HC85086/HL/NHLBI NIH HHS/United States ; 75N92021D00006/HL/NHLBI NIH HHS/United States ; F32 HL085989/HL/NHLBI NIH HHS/United States ; F32 HL085989/HL/NHLBI NIH HHS/United States ; HHSN268201800013I/MD/NIMHD NIH HHS/United States ; HHSN268201800013I/MD/NIMHD NIH HHS/United States ; HHSN268201800011I/HB/NHLBI NIH HHS/United States ; HHSN268201800012I/HB/NHLBI NIH HHS/United States ; HHSN268201800010I/HB/NHLBI NIH HHS/United States ; HHSN268201800011I/HB/NHLBI NIH HHS/United States ; HHSN268201800012I/HB/NHLBI NIH HHS/United States ; HHSN268201800005I/HL/NHLBI NIH HHS/United States ; HHSN268201800007I/HL/NHLBI NIH HHS/United States ; HHSN268201800005I/HL/NHLBI NIH HHS/United States ; HHSN268201800007I/HL/NHLBI NIH HHS/United States ; HHSN268201800003I/HL/NHLBI NIH HHS/United States ; HHSN268201800003I/HL/NHLBI NIH HHS/United States ; HHSN268201800006I/HL/NHLBI NIH HHS/United States ; HHSN268201800006I/HL/NHLBI NIH HHS/United States ; HHSN268201800004I/HL/NHLBI NIH HHS/United States ; HHSN268201800004I/HL/NHLBI NIH HHS/United States ; HHSN268201500014C/HL/NHLBI NIH HHS/United States ; },
mesh = {*Genome-Wide Association Study ; Gene Frequency ; *Polymorphism, Single Nucleotide/genetics ; Phenotype ; Smoking/genetics ; },
abstract = {Common genetic variants explain less variation in complex phenotypes than inferred from family-based studies, and there is a debate on the source of this 'missing heritability'. We investigated the contribution of rare genetic variants to tobacco use with whole-genome sequences from up to 26,257 unrelated individuals of European ancestries and 11,743 individuals of African ancestries. Across four smoking traits, single-nucleotide-polymorphism-based heritability ([Formula: see text]) was estimated from 0.13 to 0.28 (s.e., 0.10-0.13) in European ancestries, with 35-74% of it attributable to rare variants with minor allele frequencies between 0.01% and 1%. These heritability estimates are 1.5-4 times higher than past estimates based on common variants alone and accounted for 60% to 100% of our pedigree-based estimates of narrow-sense heritability ([Formula: see text], 0.18-0.34). In the African ancestry samples, [Formula: see text] was estimated from 0.03 to 0.33 (s.e., 0.09-0.14) across the four smoking traits. These results suggest that rare variants are important contributors to the heritability of smoking.},
}
@article {pmid35925968,
year = {2022},
author = {Xu, W and Yi, J and Shuai, J and Yu, Z and Cheng, J},
title = {Dynamic evaluation of the ecological civilization of Jiangxi Province: GIS and AHP approaches.},
journal = {PloS one},
volume = {17},
number = {8},
pages = {e0271768},
pmid = {35925968},
issn = {1932-6203},
mesh = {China ; Cities ; *Civilization ; Conservation of Natural Resources ; Ecosystem ; Environment ; *Geographic Information Systems ; Humans ; },
abstract = {Faced with the increasingly severe ecological environment, China promotes the construction of ecological civilization vigorously. Therefore, it is of great significance to adopt scientific, effective and comprehensive methods to evaluate development status of ecological civilization. Based on the panel data from 2010 to 2014, this paper employs GIS and AHP methods to dynamically examine the level of ecological civilization construction in Jiangxi Province. The results indicate that: (1) The ecological civilization construction in Jiangxi Province is 13.23% higher than the national average, whereas there is an imbalance in the development of different cities within the province; (2) The ecological civilization construction in the whole province rises first and then falls; (3) The performances of the cities vary in different dimensions of the construction of ecological civilization that cities in Jiangxi province perform well in the dimension of ecological environment, but perform poorly in the dimension of social development. Finally, we put forward policy recommendations for improving ecological environment to realize harmonious development between human and nature.},
}
@article {pmid35925662,
year = {2022},
author = {Martinez, GJ and Grover, T and Mattingly, SM and Mark, G and D'Mello, S and Aledavood, T and Akbar, F and Robles-Granda, P and Striegel, A},
title = {Alignment Between Heart Rate Variability From Fitness Trackers and Perceived Stress: Perspectives From a Large-Scale In Situ Longitudinal Study of Information Workers.},
journal = {JMIR human factors},
volume = {9},
number = {3},
pages = {e33754},
pmid = {35925662},
issn = {2292-9495},
abstract = {BACKGROUND: Stress can have adverse effects on health and well-being. Informed by laboratory findings that heart rate variability (HRV) decreases in response to an induced stress response, recent efforts to monitor perceived stress in the wild have focused on HRV measured using wearable devices. However, it is not clear that the well-established association between perceived stress and HRV replicates in naturalistic settings without explicit stress inductions and research-grade sensors.
OBJECTIVE: This study aims to quantify the strength of the associations between HRV and perceived daily stress using wearable devices in real-world settings.
METHODS: In the main study, 657 participants wore a fitness tracker and completed 14,695 ecological momentary assessments (EMAs) assessing perceived stress, anxiety, positive affect, and negative affect across 8 weeks. In the follow-up study, approximately a year later, 49.8% (327/657) of the same participants wore the same fitness tracker and completed 1373 EMAs assessing perceived stress at the most stressful time of the day over a 1-week period. We used mixed-effects generalized linear models to predict EMA responses from HRV features calculated over varying time windows from 5 minutes to 24 hours.
RESULTS: Across all time windows, the models explained an average of 1% (SD 0.5%; marginal R[2]) of the variance. Models using HRV features computed from an 8 AM to 6 PM time window (namely work hours) outperformed other time windows using HRV features calculated closer to the survey response time but still explained a small amount (2.2%) of the variance. HRV features that were associated with perceived stress were the low frequency to high frequency ratio, very low frequency power, triangular index, and SD of the averages of normal-to-normal intervals. In addition, we found that although HRV was also predictive of other related measures, namely, anxiety, negative affect, and positive affect, it was a significant predictor of stress after controlling for these other constructs. In the follow-up study, calculating HRV when participants reported their most stressful time of the day was less predictive and provided a worse fit (R[2]=0.022) than the work hours time window (R[2]=0.032).
CONCLUSIONS: A significant but small relationship between perceived stress and HRV was found. Thus, although HRV is associated with perceived stress in laboratory settings, the strength of that association diminishes in real-life settings. HRV might be more reflective of perceived stress in the presence of specific and isolated stressors and research-grade sensing. Relying on wearable-derived HRV alone might not be sufficient to detect stress in naturalistic settings and should not be considered a proxy for perceived stress but rather a component of a complex phenomenon.},
}
@article {pmid35924138,
year = {2022},
author = {McCall, T and Asuzu, K and Oladele, CR and Leung, TI and Wang, KH},
title = {A Socio-Ecological Approach to Addressing Digital Redlining in the United States: A Call to Action for Health Equity.},
journal = {Frontiers in digital health},
volume = {4},
number = {},
pages = {897250},
pmid = {35924138},
issn = {2673-253X},
abstract = {Physical distancing requirements due to the coronavirus (COVID-19) pandemic has increased the need for broadband internet access. The World Health Organization defines social determinants of health as non-medical factors that impact health outcomes by affecting the conditions in which people are born, grow, work, live, and age. By this definition broadband internet access is a social determinant of health. Digital redlining-the systematic process by which specific groups are deprived of equal access to digital tools such as the internet-creates inequities in access to educational and employment opportunities, as well as healthcare and health information. Although it is known that internet service providers systematically exclude low-income communities from broadband service, little has been done to stop this discriminatory practice. In this paper, we seek to amplify the call to action against the practice of digital redlining in the United States, describe how it contributes to health disparities broadly and within the context of the COVID-19 pandemic, and use a socio-ecological framework to propose short- and long-term actions to address this inequity.},
}
@article {pmid35923402,
year = {2022},
author = {Derx, J and Demeter, K and Linke, R and Cervero-Aragó, S and Lindner, G and Stalder, G and Schijven, J and Sommer, R and Walochnik, J and Kirschner, AKT and Komma, J and Blaschke, AP and Farnleitner, AH},
title = {Corrigendum: Genetic microbial source tracking support QMRA modeling for a riverine wetland drinking water resource.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {973379},
doi = {10.3389/fmicb.2022.973379},
pmid = {35923402},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2021.668778.].},
}
@article {pmid35922501,
year = {2022},
author = {Kreibich, H and Van Loon, AF and Schröter, K and Ward, PJ and Mazzoleni, M and Sairam, N and Abeshu, GW and Agafonova, S and AghaKouchak, A and Aksoy, H and Alvarez-Garreton, C and Aznar, B and Balkhi, L and Barendrecht, MH and Biancamaria, S and Bos-Burgering, L and Bradley, C and Budiyono, Y and Buytaert, W and Capewell, L and Carlson, H and Cavus, Y and Couasnon, A and Coxon, G and Daliakopoulos, I and de Ruiter, MC and Delus, C and Erfurt, M and Esposito, G and François, D and Frappart, F and Freer, J and Frolova, N and Gain, AK and Grillakis, M and Grima, JO and Guzmán, DA and Huning, LS and Ionita, M and Kharlamov, M and Khoi, DN and Kieboom, N and Kireeva, M and Koutroulis, A and Lavado-Casimiro, W and Li, HY and LLasat, MC and Macdonald, D and Mård, J and Mathew-Richards, H and McKenzie, A and Mejia, A and Mendiondo, EM and Mens, M and Mobini, S and Mohor, GS and Nagavciuc, V and Ngo-Duc, T and Thao Nguyen Huynh, T and Nhi, PTT and Petrucci, O and Nguyen, HQ and Quintana-Seguí, P and Razavi, S and Ridolfi, E and Riegel, J and Sadik, MS and Savelli, E and Sazonov, A and Sharma, S and Sörensen, J and Arguello Souza, FA and Stahl, K and Steinhausen, M and Stoelzle, M and Szalińska, W and Tang, Q and Tian, F and Tokarczyk, T and Tovar, C and Tran, TVT and Van Huijgevoort, MHJ and van Vliet, MTH and Vorogushyn, S and Wagener, T and Wang, Y and Wendt, DE and Wickham, E and Yang, L and Zambrano-Bigiarini, M and Blöschl, G and Di Baldassarre, G},
title = {The challenge of unprecedented floods and droughts in risk management.},
journal = {Nature},
volume = {608},
number = {7921},
pages = {80-86},
pmid = {35922501},
issn = {1476-4687},
mesh = {Climate Change/statistics & numerical data ; Datasets as Topic ; *Droughts/prevention & control/statistics & numerical data ; *Extreme Weather ; *Floods/prevention & control/statistics & numerical data ; Humans ; Hydrology ; Internationality ; *Risk Management/methods/statistics & numerical data/trends ; },
abstract = {Risk management has reduced vulnerability to floods and droughts globally[1,2], yet their impacts are still increasing[3]. An improved understanding of the causes of changing impacts is therefore needed, but has been hampered by a lack of empirical data[4,5]. On the basis of a global dataset of 45 pairs of events that occurred within the same area, we show that risk management generally reduces the impacts of floods and droughts but faces difficulties in reducing the impacts of unprecedented events of a magnitude not previously experienced. If the second event was much more hazardous than the first, its impact was almost always higher. This is because management was not designed to deal with such extreme events: for example, they exceeded the design levels of levees and reservoirs. In two success stories, the impact of the second, more hazardous, event was lower, as a result of improved risk management governance and high investment in integrated management. The observed difficulty of managing unprecedented events is alarming, given that more extreme hydrological events are projected owing to climate change[3].},
}
@article {pmid35921404,
year = {2022},
author = {Kass, JM and Guénard, B and Dudley, KL and Jenkins, CN and Azuma, F and Fisher, BL and Parr, CL and Gibb, H and Longino, JT and Ward, PS and Chao, A and Lubertazzi, D and Weiser, M and Jetz, W and Guralnick, R and Blatrix, R and Lauriers, JD and Donoso, DA and Georgiadis, C and Gomez, K and Hawkes, PG and Johnson, RA and Lattke, JE and MacGown, JA and Mackay, W and Robson, S and Sanders, NJ and Dunn, RR and Economo, EP},
title = {The global distribution of known and undiscovered ant biodiversity.},
journal = {Science advances},
volume = {8},
number = {31},
pages = {eabp9908},
pmid = {35921404},
issn = {2375-2548},
mesh = {Animals ; *Ants/physiology ; Biodiversity ; Ecosystem ; Invertebrates ; Phylogeny ; Vertebrates ; },
abstract = {Invertebrates constitute the majority of animal species and are critical for ecosystem functioning and services. Nonetheless, global invertebrate biodiversity patterns and their congruences with vertebrates remain largely unknown. We resolve the first high-resolution (~20-km) global diversity map for a major invertebrate clade, ants, using biodiversity informatics, range modeling, and machine learning to synthesize existing knowledge and predict the distribution of undiscovered diversity. We find that ants and different vertebrate groups have distinct features in their patterns of richness and rarity, underscoring the need to consider a diversity of taxa in conservation. However, despite their phylogenetic and physiological divergence, ant distributions are not highly anomalous relative to variation among vertebrate clades. Furthermore, our models predict that rarity centers largely overlap (78%), suggesting that general forces shape endemism patterns across taxa. This raises confidence that conservation of areas important for small-ranged vertebrates will benefit invertebrates while providing a "treasure map" to guide future discovery.},
}
@article {pmid35915718,
year = {2022},
author = {Aziz, MA and Mattalia, G and Sulaiman, N and Shah, AA and Polesny, Z and Kalle, R and Sõukand, R and Pieroni, A},
title = {The nexus between traditional foraging and its sustainability: a qualitative assessment among a few selected Eurasian case studies.},
journal = {Environment, development and sustainability},
volume = {},
number = {},
pages = {1-26},
pmid = {35915718},
issn = {1573-2975},
abstract = {Plant foraging is an important human ecological phenomenon being studied by a number of contemporary ethnobiologists as well as by a few social anthropologists among rural communities and, more recently, in urban environments. The sustainability dimension of foraging is, however, largely unexplored. We analyse a few case studies from recent field research and qualitatively assess both the environmental and social sustainability of diverse patterns of traditional foraging practices in three distinct human ecological environments (horticulturalism-, forestry-, and pastoralism-driven) located in the Eastern Mediterranean, Eastern Europe, and North Pakistan, i.e. we address the question of when does traditional foraging become unsustainable and what factors may influence this. The main findings are multidimensional. First, in all case studies, we sometimes observed competitive foraging among the gatherers of certain wild food plants potentially causing ecological degradation; such unsustainable practices seem to be linked to the market pressure on certain species. However, also customs and norms promoted by states can be detrimental (former Soviet Union), as well as climate change (Eastern Europe), and marginalisation of some minority groups (Pakistan). Second, in the Mediterranean Syrian context, wild food plant resources are largely represented by widely available weedy "wild" vegetables, normally (but not exclusively) collected by women, and usually easily accessible; only very few wild food plants seem to be threatened due to specific market demands or to disequilibria created by household economic instabilities due to the recent war. We also argue that unsustainable foraging is enhanced by the abandonment of daily practices and continuous interaction with the natural environment and by the increasingly uneven distribution of active practical knowledge on wild food plants among the middle-aged and younger population. Facilitating the transmission of sustainable foraging knowledge and practices could be therefore crucial, also for coping with food insecurity in times of crisis; but for that to occur, holistic environmental and food educational frameworks, appropriate policies for fostering community-based biodiversity conservation and also social cohesion and communal management of lands should be seriously considered as well. Moreover, future gastronomic and eco-tourism initiatives, if organised in a thoughtful manner, could represent a positive turning point not only for the local small-scale economies of the considered rural communities but also for helping them to dynamically preserve the entire socio-ecological system underpinned in plant foraging and ultimately to better adapt to the current global crisis.},
}
@article {pmid35910222,
year = {2022},
author = {Li, L and Lan, LY and Huang, L and Ye, C and Andrade, J and Wilson, PC},
title = {Selecting Representative Samples From Complex Biological Datasets Using K-Medoids Clustering.},
journal = {Frontiers in genetics},
volume = {13},
number = {},
pages = {954024},
pmid = {35910222},
issn = {1664-8021},
abstract = {Rapid growth of single-cell sequencing techniques enables researchers to investigate almost millions of cells with diverse properties in a single experiment. Meanwhile, it also presents great challenges for selecting representative samples from massive single-cell populations for further experimental characterization, which requires a robust and compact sampling with balancing diverse properties of different priority levels. The conventional sampling methods fail to generate representative and generalizable subsets from a massive single-cell population or more complicated ensembles. Here, we present a toolkit called Cookie which can efficiently select out the most representative samples from a massive single-cell population with diverse properties. This method quantifies the relationships/similarities among samples using their Manhattan distances by vectorizing all given properties and then determines an appropriate sample size by evaluating the coverage of key properties from multiple candidate sizes, following by a k-medoids clustering to group samples into several clusters and selects centers from each cluster as the most representatives. Comparison of Cookie with conventional sampling methods using a single-cell atlas dataset, epidemiology surveillance data, and a simulated dataset shows the high efficacy, efficiency, and flexibly of Cookie. The Cookie toolkit is implemented in R and is freely available at https://wilsonimmunologylab.github.io/Cookie/.},
}
@article {pmid35904963,
year = {2022},
author = {Smyth, JM and Zawadzki, MJ and Marcusson-Clavertz, D and Scott, SB and Johnson, JA and Kim, J and Toledo, MJ and Stawski, RS and Sliwinski, MJ and Almeida, DM},
title = {Computing Components of Everyday Stress Responses: Exploring Conceptual Challenges and New Opportunities.},
journal = {Perspectives on psychological science : a journal of the Association for Psychological Science},
volume = {},
number = {},
pages = {17456916221082108},
doi = {10.1177/17456916221082108},
pmid = {35904963},
issn = {1745-6924},
support = {UH2 AG052167/AG/NIA NIH HHS/United States ; },
abstract = {Repeated assessments in everyday life enables collecting ecologically valid data on dynamic, within-persons processes. These methods have widespread utility and application and have been extensively used for the study of stressors and stress responses. Enhanced conceptual sophistication of characterizing intraindividual stress responses in everyday life would help advance the field. This article provides a pragmatic overview of approaches, opportunities, and challenges when intensive ambulatory methods are applied to study everyday stress responses in "real time." We distinguish between three stress-response components (i.e., reactivity, recovery, and pileup) and focus on several fundamental questions: (a) What is the appropriate stress-free resting state (or "baseline") for an individual in everyday life? (b) How does one index the magnitude of the initial response to a stressor (reactivity)? (c) Following a stressor, how can recovery be identified (e.g., when the stress response has completed)? and (d) Because stressors may not occur in isolation, how can one capture the temporal clustering of stressors and/or stress responses (pileup)? We also present initial ideas on applying this approach to intervention research. Although we focus on stress responses, these issues may inform many other dynamic intraindividual constructs and behaviors (e.g., physical activity, physiological processes, other subjective states) captured in ambulatory assessment.},
}
@article {pmid35902858,
year = {2022},
author = {Plekhanova, T and Rowlands, AV and Evans, RA and Edwardson, CL and Bishop, NC and Bolton, CE and Chalmers, JD and Davies, MJ and Daynes, E and Dempsey, PC and Docherty, AB and Elneima, O and Greening, NJ and Greenwood, SA and Hall, AP and Harris, VC and Harrison, EM and Henson, J and Ho, LP and Horsley, A and Houchen-Wolloff, L and Khunti, K and Leavy, OC and Lone, NI and Marks, M and Maylor, B and McAuley, HJC and Nolan, CM and Poinasamy, K and Quint, JK and Raman, B and Richardson, M and Sargeant, JA and Saunders, RM and Sereno, M and Shikotra, A and Singapuri, A and Steiner, M and Stensel, DJ and Wain, LV and Whitney, J and Wootton, DG and Brightling, CE and Man, WD and Singh, SJ and Yates, T and , },
title = {Device-assessed sleep and physical activity in individuals recovering from a hospital admission for COVID-19: a multicentre study.},
journal = {The international journal of behavioral nutrition and physical activity},
volume = {19},
number = {1},
pages = {94},
pmid = {35902858},
issn = {1479-5868},
mesh = {Accelerometry/methods ; Aftercare ; Aged ; *COVID-19 ; *Diabetes Mellitus, Type 2/therapy ; Exercise ; Female ; Hospitalization ; Hospitals ; Humans ; Male ; Patient Discharge ; Sleep ; },
abstract = {BACKGROUND: The number of individuals recovering from severe COVID-19 is increasing rapidly. However, little is known about physical behaviours that make up the 24-h cycle within these individuals. This study aimed to describe physical behaviours following hospital admission for COVID-19 at eight months post-discharge including associations with acute illness severity and ongoing symptoms.
METHODS: One thousand seventy-seven patients with COVID-19 discharged from hospital between March and November 2020 were recruited. Using a 14-day wear protocol, wrist-worn accelerometers were sent to participants after a five-month follow-up assessment. Acute illness severity was assessed by the WHO clinical progression scale, and the severity of ongoing symptoms was assessed using four previously reported data-driven clinical recovery clusters. Two existing control populations of office workers and individuals with type 2 diabetes were comparators.
RESULTS: Valid accelerometer data from 253 women and 462 men were included. Women engaged in a mean ± SD of 14.9 ± 14.7 min/day of moderate-to-vigorous physical activity (MVPA), with 12.1 ± 1.7 h/day spent inactive and 7.2 ± 1.1 h/day asleep. The values for men were 21.0 ± 22.3 and 12.6 ± 1.7 h /day and 6.9 ± 1.1 h/day, respectively. Over 60% of women and men did not have any days containing a 30-min bout of MVPA. Variability in sleep timing was approximately 2 h in men and women. More severe acute illness was associated with lower total activity and MVPA in recovery. The very severe recovery cluster was associated with fewer days/week containing continuous bouts of MVPA, longer total sleep time, and higher variability in sleep timing. Patients post-hospitalisation with COVID-19 had lower levels of physical activity, greater sleep variability, and lower sleep efficiency than a similarly aged cohort of office workers or those with type 2 diabetes.
CONCLUSIONS: Those recovering from a hospital admission for COVID-19 have low levels of physical activity and disrupted patterns of sleep several months after discharge. Our comparative cohorts indicate that the long-term impact of COVID-19 on physical behaviours is significant.},
}
@article {pmid35902604,
year = {2022},
author = {Röhr, S and Pabst, A and Baber, R and Engel, C and Glaesmer, H and Hinz, A and Schroeter, ML and Witte, AV and Zeynalova, S and Villringer, A and Löffler, M and Riedel-Heller, SG},
title = {Social determinants and lifestyle factors for brain health: implications for risk reduction of cognitive decline and dementia.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {12965},
pmid = {35902604},
issn = {2045-2322},
mesh = {Adult ; Aged ; Brain ; *Cognitive Dysfunction/epidemiology/prevention & control/psychology ; *Dementia/epidemiology/prevention & control/psychology ; Female ; Humans ; Life Style ; Male ; Middle Aged ; Risk Factors ; Risk Reduction Behavior ; Social Determinants of Health ; },
abstract = {Substantial evidence indicates a huge potential for risk reduction of cognitive decline and dementia based on modifiable health and lifestyle factors. To maximize the chances for risk reduction, it is useful to investigate associations of social determinants and lifestyle for brain health. We computed the "LIfestyle for BRAin health" (LIBRA) score for baseline participants of the Leipzig Research Centre for Civilization Diseases (LIFE) Adult Study, a population-based urban cohort in Germany. LIBRA predicts dementia in midlife and early late life populations, comprising 12 modifiable risk factors (heart disease, kidney disease, diabetes, obesity, hypertension, hypercholesterolemia, alcohol consumption, smoking, physical inactivity, diet, depression, cognitive inactivity). Associations of social determinants (living situation, marital status, social isolation, education, net equivalence income, occupational status, socioeconomic status/SES, employment) with LIBRA were inspected using age- and sex-adjusted multivariable linear regression analysis. Z-standardization and sampling weights were applied. Participants (n = 6203) were M = 57.4 (SD = 10.6, range 40-79) years old and without dementia, 53.0% were women. Except for marital status, all considered social determinants were significantly associated with LIBRA. Beta coefficients for the association with higher LIBRA scores were most pronounced for low SES (β = 0.80, 95% CI [0.72-0.88]; p < 0.001) and middle SES (β = 0.55, 95% CI [0.47-0.62]; p < 0.001). Social determinants, particularly socioeconomic factors, are associated with lifestyle for brain health, and should thus be addressed in risk reduction strategies for cognitive decline and dementia. A social-ecological public health perspective on risk reduction might be more effective and equitable than focusing on individual lifestyle behaviors alone.},
}
@article {pmid35902586,
year = {2022},
author = {McManamay, RA and George, R and Morrison, RR and Ruddell, BL},
title = {Mapping hydrologic alteration and ecological consequences in stream reaches of the conterminous United States.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {450},
pmid = {35902586},
issn = {2052-4463},
abstract = {Environmental flows are critical for balancing societal water needs with that of riverine ecosystems; however, data limitations often hinder the development of predictive relationships between anthropogenic modifications to streamflow regimes and ecological responses - these relationships are the basis for setting regional water policy standards for rivers. Herein, we present and describe a comprehensive dataset of modeled hydrologic alteration and consequences for native fish biodiversity, both mapped at the stream-reach resolution for the conterminous U.S. Using empirical observations of reference conditions and anthropogenically altered streamflow at over 7000 stream gauges, we developed a predictive model of hydrologic alteration, which was extended to >2.6 million stream reaches. We then used a previous nationwide assessment of ecological responses to hydrologic alteration to predict fish biodiversity loss in stream reaches resulting from streamflow modification. Validation efforts suggested hydrologic alteration models had satisfactory performance, whereas modeled ecological responses were susceptible to compounded errors. The dataset could ameliorate regional data deficits for setting environmental flow standards while providing tools for prioritizing streamflow protection or restoration.},
}
@article {pmid35900894,
year = {2022},
author = {Marino, JL and Tait, RJ and Straker, LM and Schofield, DJ and Doherty, DA and Ivers, RQ and Graham, PL and Steinbeck, K and Lymer, S and Sanci, LA and Patton, GC and Liu, B and Brooks, FM and Kang, MS and Hickey, M and Cunich, M and Bista, S and Skinner, SR},
title = {Health, social and economic implications of adolescent risk behaviours/states: protocol for Raine Study Gen2 cohort data linkage study.},
journal = {Longitudinal and life course studies : international journal},
volume = {13},
number = {4},
pages = {647-666},
doi = {10.1332/175795921X16424353247247},
pmid = {35900894},
issn = {1757-9597},
mesh = {Child ; Humans ; Adolescent ; Female ; Pregnancy ; Young Adult ; Adult ; Prospective Studies ; *Risk-Taking ; *Substance-Related Disorders/epidemiology ; Cohort Studies ; Information Storage and Retrieval ; },
abstract = {BACKGROUND: Risk-taking behaviours are a major contributor to youth morbidity and mortality. Vulnerability to these negative outcomes is constructed from individual behaviour including risk-taking, and from social context, ecological determinants, early life experience, developmental capacity and mental health, contributing to a state of higher risk. However, although risk-taking is part of normal adolescent development, there is no systematic way to distinguish young people with a high probability of serious adverse outcomes, hindering the capacity to screen and intervene. This study aims to explore the association between risk behaviours/states in adolescence and negative health, social and economic outcomes through young adulthood.
METHODS: The Raine Study is a prospective cohort study which recruited pregnant women in 1989-91, in Perth, Western Australia. The offspring cohort (N = 2,868) was followed up at regular intervals from 1 to 27 years of age. These data will be linked to State government health and welfare administrative data. We will empirically examine relationships across multiple domains of risk (for example, substance use, sexual behaviour, driving) with health and social outcomes (for instance, road-crash injury, educational underachievement). Microsimulation models will measure the impact of risk-taking on educational attainment and labour force outcomes.
DISCUSSION: Comprehensive preventive child health programmes and policy prioritise a healthy start to life. This is the first linkage study focusing on adolescence to adopt a multi-domain approach, and to integrate health economic modelling. This approach captures a more complete picture of health and social impacts of risk behaviour/states in adolescence and young adulthood.},
}
@article {pmid35900003,
year = {2022},
author = {Arruda, CL and Ferreira D'Agostini Marin, D and Depieri Michels, B and Martins Rosa, V and Iser, BPM},
title = {Maternal mortality in South region of Brazil: an analysis from 2000 to 2018.},
journal = {Journal of obstetrics and gynaecology : the journal of the Institute of Obstetrics and Gynaecology},
volume = {},
number = {},
pages = {1-7},
doi = {10.1080/01443615.2022.2099737},
pmid = {35900003},
issn = {1364-6893},
abstract = {This study characterises maternal mortality in southern Brazil and verifies its trends between 2000 and 2018. It is an ecological time-series study, analysing secondary data from the Department of Informatics of the Unified Health System. The trend of the maternal mortality ratio (MMR) was calculated using generalised linear regression, and the ratios of the rates according to women's characteristics, with a confidence interval (CI) of 95%. The MMR in the South region went from 53.4 to 36.8 deaths per 100,000 live births from 2000 to 2018, a reduction trend of 1.2 percentage points per year. Mortality was directly related to increasing age (p < .001) and inversely related to schooling (p < .001) and predominated in non-white women (p < .001). The main cause of death was direct causes, including hypertensive disorders. Despite the reduction trend in maternal mortality in southern Brazil, the MMR observed is constantly above the recommended by the World Health Organisation.Impact StatementWhat is already known on this subject? The Maternal Mortality Ratio (MMR) is an indicator that allows an analysis of women's health in relation to the socio-economic and care characteristics of the region where they live. Between 2000 and 2015, Brazil had presented a high MMR, with around 50 deaths per 100,000 live births, while WHO considers a reasonably adequate MMR of fewer than 20 deaths per 100,000 live births.What do the results of this study add? This study updates data about MMR in the Southern Region of Brazil, the one which has the lowest rates in the country, but with variable values between the states. There was a reduction in MMR in southern Brazil between 2000 and 2018 but higher rates for women over 30 years old and in a situation of social vulnerability, as low-income and non-white women. Santa Catarina State presented stable values in the period and remained below the RMM averages of the other states during all years.What are the implications of these findings for clinical practice and/or further research? Comparing previous and current Maternal Mortality Rates in the regional context is important to adapt public health policies for the most affected population. Maternal death is still a reality for single and low-income women, who have greater difficulty in access to health care. Strategies in the Unified Health System are needed to tackle this problem.},
}
@article {pmid35896546,
year = {2022},
author = {Moon, M and Richardson, AD and Milliman, T and Friedl, MA},
title = {A high spatial resolution land surface phenology dataset for AmeriFlux and NEON sites.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {448},
pmid = {35896546},
issn = {2052-4463},
abstract = {Vegetation phenology is a key control on water, energy, and carbon fluxes in terrestrial ecosystems. Because vegetation canopies are heterogeneous, spatially explicit information related to seasonality in vegetation activity provides valuable information for studies that use eddy covariance measurements to study ecosystem function and land-atmosphere interactions. Here we present a land surface phenology (LSP) dataset derived at 3 m spatial resolution from PlanetScope imagery across a range of plant functional types and climates in North America. The dataset provides spatially explicit information related to the timing of phenophase changes such as the start, peak, and end of vegetation activity, along with vegetation index metrics and associated quality assurance flags for the growing seasons of 2017-2021 for 10 × 10 km windows centred over 104 eddy covariance towers at AmeriFlux and National Ecological Observatory Network (NEON) sites. These LSP data can be used to analyse processes controlling the seasonality of ecosystem-scale carbon, water, and energy fluxes, to evaluate predictions from land surface models, and to assess satellite-based LSP products.},
}
@article {pmid35893025,
year = {2022},
author = {Masarovič, R and Zvaríková, M and Zvarík, M and Majzlan, O and Prokop, P and Fedor, P},
title = {Changes in Diversity and Structure of Thrips (Thysanoptera) Assemblages in the Spruce Forest Stands of High Tatra Mts. after a Windthrow Calamity.},
journal = {Insects},
volume = {13},
number = {8},
pages = {},
pmid = {35893025},
issn = {2075-4450},
abstract = {Strong winds, fire, and subsequent forest management impact arthropod communities. We monitored the diversity and changes in the community structure of forest thrips assemblages in the context of secondary succession and anthropogenic impact. There were eight study plots that were affected to varying degrees by the mentioned disturbances that were selected in the Central European spruce (Picea abies (L.) Karst.) forests in Slovakia. The soil photoeclectors were used to obtain thrips in the study plots during two vegetation seasons. The thrips assemblages and their attributes were analyzed by non-metric multidimensional scaling (NMDS). The significant changes in community structure, composition, stratification, species richness, and diversity of thrips assemblages that were caused by natural- (wind) and human-induced disturbance (forestry and fire) were observed in our research. Our analyses revealed a clear relationship between different thrips assemblages and impacted environment. Moreover, our results indicate that silvicolous thrips species may be useful for indicating changes and disturbances in forest ecological systems.},
}
@article {pmid35891501,
year = {2022},
author = {Hufsky, F and Abecasis, A and Agudelo-Romero, P and Bletsa, M and Brown, K and Claus, C and Deinhardt-Emmer, S and Deng, L and Friedel, CC and Gismondi, MI and Kostaki, EG and Kühnert, D and Kulkarni-Kale, U and Metzner, KJ and Meyer, IM and Miozzi, L and Nishimura, L and Paraskevopoulou, S and Pérez-Cataluña, A and Rahlff, J and Thomson, E and Tumescheit, C and van der Hoek, L and Van Espen, L and Vandamme, AM and Zaheri, M and Zuckerman, N and Marz, M},
title = {Women in the European Virus Bioinformatics Center.},
journal = {Viruses},
volume = {14},
number = {7},
pages = {},
pmid = {35891501},
issn = {1999-4915},
support = {220814/WT_/Wellcome Trust/United Kingdom ; 646891/ERC_/European Research Council/International ; 721367/MCCC_/Marie Curie/United Kingdom ; },
mesh = {*Computational Biology ; Europe ; Female ; Humans ; *Research Personnel/statistics & numerical data ; *Viruses/genetics ; },
abstract = {Viruses are the cause of a considerable burden to human, animal and plant health, while on the other hand playing an important role in regulating entire ecosystems. The power of new sequencing technologies combined with new tools for processing "Big Data" offers unprecedented opportunities to answer fundamental questions in virology. Virologists have an urgent need for virus-specific bioinformatics tools. These developments have led to the formation of the European Virus Bioinformatics Center, a network of experts in virology and bioinformatics who are joining forces to enable extensive exchange and collaboration between these research areas. The EVBC strives to provide talented researchers with a supportive environment free of gender bias, but the gender gap in science, especially in math-intensive fields such as computer science, persists. To bring more talented women into research and keep them there, we need to highlight role models to spark their interest, and we need to ensure that female scientists are not kept at lower levels but are given the opportunity to lead the field. Here we showcase the work of the EVBC and highlight the achievements of some outstanding women experts in virology and viral bioinformatics.},
}
@article {pmid35886637,
year = {2022},
author = {Cen, Y and Zhang, B and Luo, J and Deng, Q and Liu, H and Wang, L},
title = {Influence of Topographic Factors on the Characteristics of Gully Systems in Mountainous Areas of Ningnan Dry-Hot Valley, SW China.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {14},
pages = {},
pmid = {35886637},
issn = {1660-4601},
mesh = {China ; *Conservation of Natural Resources/methods ; Ecosystem ; Geographic Information Systems ; *Soil ; },
abstract = {A gully system is an important indicator that reflects the development of regional topography and landforms, and topography is one of the most important factors affecting the development of gullies. However, at present, research on the impact of topography on the development of gully systems in the mountainous area of Ningnan dry-hot valley still needs to be strengthened. In order to study the characteristics of gullies and the influence of topography on the development of gully systems, based on both the visual interpretation of remote sensing images and field investigations, five topographic factors (elevation, slope gradient, aspect, relief, and dissection) were employed and three gully erosion indexes (gully length, density, and frequency) were calculated. The geographical information system was used in this study to carry out the spatial analysis, Ward's hierarchical clustering and correlation analysis. Results showed that the development of gully systems is greatly affected by the degree of relief and dissection, and there is a significant positive correlation (p < 0.01; p < 0.05), while elevation, slope gradient and aspect have little influence on it. Analysis of the gully systems showed that the gully erosion is the most intense in the area with an elevation of 2800-3200 m and slope gradients ≥ 38°. Furthermore, the degree of erosion on shady slopes was greater than that on sunny slopes. These results will help us to understand the spatial distribution and formation of gully systems in mountainous areas.},
}
@article {pmid35886522,
year = {2022},
author = {Chen, M and Zheng, L and Zhang, D and Li, J},
title = {Spatio-Temporal Evolution and Obstacle Factors Analysis of Tourism Ecological Security in Huanggang Dabieshan UNESCO Global Geopark.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {14},
pages = {},
pmid = {35886522},
issn = {1660-4601},
mesh = {China ; *Conservation of Natural Resources/methods ; Ecosystem ; Humans ; Industry ; *Tourism ; UNESCO ; },
abstract = {The United Nations Educational, Scientific and Cultural Organization (UNESCO) Global Geoparks (UGGp) and geotourism activities not only improve people's scientific quality by popularizing geoscience knowledge, but also play important roles in protecting precious geoheritages and promoting the development of regional economies. However, tourism activities also have a negative impact on the local ecological environment, placing the regional ecological system under great pressure. Therefore, this paper constructed a tourism ecological security evaluation indicator system suitable for geoparks by using the "Driving-Pressure-State-Impact-Response" (DPSIR) model. The spatial autocorrelation and obstacle degree model are used to analyze the spatio-temporal characteristics and influencing factors of the tourism ecological security index (TESI) of Huanggang Dabieshan UGGp in 2000, 2005, 2010, 2015 and 2018, respectively. The results indicate that the TESI of the study area has gradually improved from 2000 to 2018. Spatially, the level of TESI presents a gradient distribution from the townships where the main scenic spots are located to the surrounding townships. The main obstacle factors affecting TESI include: per capita tourism income, proportion of comprehensive tourism revenue in GDP, per capita net income of rural residents, proportion of tertiary industry in GDP, coverage of nature reserves, planning integrity of geopark, informatization of geopark, growth rate of tourists, comprehensive utilization rate of solid waste, etc. The influencing factors of TESI varied from time to time. Balancing the conflict between local tourism activities and environmental protection, encouraging the participation of local communities, and strengthening science popularization for the local public will effectively improve the tourism ecological security of geoparks.},
}
@article {pmid35885950,
year = {2022},
author = {Kolobkov, DS and Sviridova, DA and Abilev, SK and Kuzovlev, AN and Salnikova, LE},
title = {Genes and Diseases: Insights from Transcriptomics Studies.},
journal = {Genes},
volume = {13},
number = {7},
pages = {},
pmid = {35885950},
issn = {2073-4425},
mesh = {*Gene Expression Profiling ; Gene Ontology ; Humans ; Phenotype ; *Transcriptome/genetics ; },
abstract = {Results of expression studies can be useful to clarify the genotype-phenotype relationship. However, according to data from recent literature, there is a large group of genes that are revealed as differentially expressed (DE) in many studies, regardless of the biological context. Additional analyses could shed more light on the relationships between genes, their differential expression, and diseases. We generated a set of 9972 disease genes from five gene-phenotype databases (OMIM, ORPHANET, DDG2P, DisGeNet and MalaCards) and a report of the International Union of Immunological Societies. To study transcriptomics of disease and non-disease genes in healthy tissues, we obtained data from the Human Protein Atlas (HPA) website. We analyzed the dependency between expression in healthy tissues and gene occurrence in Gene Expression Omnibus series using tools within the Enrichr libraries. The results of expression studies were annotated with Gene Ontology (GO) and Human Phenotype Ontology (HPO) terms. Using transcriptomics analysis of healthy tissues, we validated the previous findings of higher expression levels of disease genes in pathologically linked tissues compared to other tissues. Preferentially DE genes were generally highly expressed in one or multiple tissues and were enriched for disease genes. According to the results of GO enrichment analyses, both down- and up-regulated DE genes most often took part in immune response, translation and tissue-specific processes. A connection between DE-related pathology and the diversity of HPO terms was found. Investigating a link between expression and phenotype contributes to understanding the mode of development and progression of human diseases.},
}
@article {pmid35883471,
year = {2022},
author = {Zhang, Y and Jin, J and Huang, B and Ying, H and He, J and Jiang, L},
title = {Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective.},
journal = {Biomolecules},
volume = {12},
number = {7},
pages = {},
pmid = {35883471},
issn = {2218-273X},
mesh = {Archaea/genetics/metabolism ; *Computational Biology ; Humans ; Prokaryotic Cells ; *Selenium/metabolism ; Selenoproteins/genetics/metabolism ; },
abstract = {Selenium (Se) is an important trace element that mainly occurs in the form of selenocysteine in selected proteins. In prokaryotes, Se is also required for the synthesis of selenouridine and Se-containing cofactor. A large number of selenoprotein families have been identified in diverse prokaryotic organisms, most of which are thought to be involved in various redox reactions. In the last decade or two, computational prediction of selenoprotein genes and comparative genomics of Se metabolic pathways and selenoproteomes have arisen, providing new insights into the metabolism and function of Se and their evolutionary trends in bacteria and archaea. This review aims to offer an overview of recent advances in bioinformatics analysis of Se utilization in prokaryotes. We describe current computational strategies for the identification of selenoprotein genes and generate the most comprehensive list of prokaryotic selenoproteins reported to date. Furthermore, we highlight the latest research progress in comparative genomics and metagenomics of Se utilization in prokaryotes, which demonstrates the divergent and dynamic evolutionary patterns of different Se metabolic pathways, selenoprotein families, and selenoproteomes in sequenced organisms and environmental samples. Overall, bioinformatics analyses of Se utilization, function, and evolution may contribute to a systematic understanding of how this micronutrient is used in nature.},
}
@article {pmid35882317,
year = {2022},
author = {Chen, X and Jiang, L and Xia, Y and Wang, L and Ye, J and Hou, T and Zhang, Y and Li, M and Li, Z and Song, Z and Li, J and Jiang, Y and Li, P and Zhang, X and Zhang, Y and Rosenfeld, D and Seinfeld, JH and Yu, S},
title = {Quantifying on-road vehicle emissions during traffic congestion using updated emission factors of light-duty gasoline vehicles and real-world traffic monitoring big data.},
journal = {The Science of the total environment},
volume = {847},
number = {},
pages = {157581},
doi = {10.1016/j.scitotenv.2022.157581},
pmid = {35882317},
issn = {1879-1026},
mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; Big Data ; Environmental Monitoring ; Excipients ; Gasoline/analysis ; Humans ; Motor Vehicles ; Vehicle Emissions/analysis ; },
abstract = {Light-duty gasoline vehicles (LDGVs) have made up >90 % of vehicle fleets in China since 2019, moreover, with a high annual growth rate (> 10 %) since 2017. Hence, accurate estimates of air pollutant emissions of these fast-changing LDGVs are vital for air quality management, human healthcare, and ecological protection. However, this issue is poorly quantified due to insufficient reserves of timely updated LDGV emission factors, which are dependent on real-world activity levels. Here we constructed a big dataset of explicit emission profiles (e.g., emission factors and accumulated mileages) for 159,051 LDGVs based on an official I/M database by matching real-time traffic dynamics via real-world traffic monitoring (e.g., traffic volumes and speeds). Consequently, we provide robust evidence that the emission factors of these LDGVs follow a clear heavy-tailed distribution. The top 10 % emitters contributed >60 % to the total fleet emissions, while the bottom 50 % contributed <10 %. Such emission factors were effectively reduced by 75.7-86.2 % as official emission standards upgraded gradually (i.e., from China 2 to China 5) within 13 years from 2004 to 2017. Nevertheless, such achievements would be offset once traffic congestion occurred. In the real world, the typical traffic congestions (i.e., vehicle speed <5 km/h) can lead to emissions 5- 9 times higher than those on non-congested roads (i.e., vehicle speed >50 km/h). These empirical analyses enabled us to propose future traffic scenarios that could harmonize emission standards and traffic congestion. Practical approaches on vehicle emission controls under realistic conditions are proposed, which would provide new insights for future urban vehicle emission management.},
}
@article {pmid35881864,
year = {2022},
author = {Özdemir, V},
title = {Call for Papers: COVID-19 Systems Biology, Multi-Omics Integration, and Digital Technologies in Ecology, Health, and Society.},
journal = {Omics : a journal of integrative biology},
volume = {26},
number = {9},
pages = {471-472},
doi = {10.1089/omi.2022.0094},
pmid = {35881864},
issn = {1557-8100},
mesh = {*COVID-19/epidemiology ; Computational Biology ; Digital Technology ; Genomics ; Humans ; *Systems Biology ; },
}
@article {pmid35881010,
year = {2022},
author = {Worobey, M and Levy, JI and Malpica Serrano, L and Crits-Christoph, A and Pekar, JE and Goldstein, SA and Rasmussen, AL and Kraemer, MUG and Newman, C and Koopmans, MPG and Suchard, MA and Wertheim, JO and Lemey, P and Robertson, DL and Garry, RF and Holmes, EC and Rambaut, A and Andersen, KG},
title = {The Huanan Seafood Wholesale Market in Wuhan was the early epicenter of the COVID-19 pandemic.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6609},
pages = {951-959},
pmid = {35881010},
issn = {1095-9203},
support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI132223/AI/NIAID NIH HHS/United States ; U54 CA260581/CA/NCI NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 AI132244/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; R01 AI136056/AI/NIAID NIH HHS/United States ; U19 AI142790/AI/NIAID NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; F32 AI152341/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; UL1 TR002550/TR/NCATS NIH HHS/United States ; U01 AI151812/AI/NIAID NIH HHS/United States ; U54 HG007480/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; *COVID-19/epidemiology/transmission/virology ; China/epidemiology ; Humans ; *Pandemics ; *SARS-CoV-2/isolation & purification ; *Seafood/virology ; *Viral Zoonoses/epidemiology/transmission/virology ; },
abstract = {Understanding how severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in 2019 is critical to preventing future zoonotic outbreaks before they become the next pandemic. The Huanan Seafood Wholesale Market in Wuhan, China, was identified as a likely source of cases in early reports, but later this conclusion became controversial. We show here that the earliest known COVID-19 cases from December 2019, including those without reported direct links, were geographically centered on this market. We report that live SARS-CoV-2-susceptible mammals were sold at the market in late 2019 and that within the market, SARS-CoV-2-positive environmental samples were spatially associated with vendors selling live mammals. Although there is insufficient evidence to define upstream events, and exact circumstances remain obscure, our analyses indicate that the emergence of SARS-CoV-2 occurred through the live wildlife trade in China and show that the Huanan market was the epicenter of the COVID-19 pandemic.},
}
@article {pmid35881005,
year = {2022},
author = {Pekar, JE and Magee, A and Parker, E and Moshiri, N and Izhikevich, K and Havens, JL and Gangavarapu, K and Malpica Serrano, LM and Crits-Christoph, A and Matteson, NL and Zeller, M and Levy, JI and Wang, JC and Hughes, S and Lee, J and Park, H and Park, MS and Ching Zi Yan, K and Lin, RTP and Mat Isa, MN and Noor, YM and Vasylyeva, TI and Garry, RF and Holmes, EC and Rambaut, A and Suchard, MA and Andersen, KG and Worobey, M and Wertheim, JO},
title = {The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2.},
journal = {Science (New York, N.Y.)},
volume = {377},
number = {6609},
pages = {960-966},
pmid = {35881005},
issn = {1095-9203},
support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; R01 AI132223/AI/NIAID NIH HHS/United States ; U54 CA260581/CA/NCI NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; R01 AI132244/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; R01 AI136056/AI/NIAID NIH HHS/United States ; U19 AI142790/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; UL1 TR002550/TR/NCATS NIH HHS/United States ; U01 AI151812/AI/NIAID NIH HHS/United States ; U54 HG007480/HG/NHGRI NIH HHS/United States ; },
mesh = {Animals ; *COVID-19/epidemiology/transmission/virology ; Computer Simulation ; Genetic Variation ; Genomics/methods ; Humans ; Molecular Epidemiology ; *Pandemics ; Phylogeny ; *SARS-CoV-2/classification/genetics/isolation & purification ; *Viral Zoonoses/epidemiology/virology ; },
abstract = {Understanding the circumstances that lead to pandemics is important for their prevention. We analyzed the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted "A" and "B." Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October to 8 December), and the separate introduction of lineage A likely occurred within weeks of this event. These findings indicate that it is unlikely that SARS-CoV-2 circulated widely in humans before November 2019 and define the narrow window between when SARS-CoV-2 first jumped into humans and when the first cases of COVID-19 were reported. As with other coronaviruses, SARS-CoV-2 emergence likely resulted from multiple zoonotic events.},
}
@article {pmid35880005,
year = {2022},
author = {Macharia, PM and Ray, N and Gitonga, CW and Snow, RW and Giorgi, E},
title = {Combining school-catchment area models with geostatistical models for analysing school survey data from low-resource settings: Inferential benefits and limitations.},
journal = {Spatial statistics},
volume = {51},
number = {},
pages = {100679},
pmid = {35880005},
issn = {2211-6753},
support = {079080/WT_/Wellcome Trust/United Kingdom ; 081829/WT_/Wellcome Trust/United Kingdom ; 203077/WT_/Wellcome Trust/United Kingdom ; 212176/WT_/Wellcome Trust/United Kingdom ; },
abstract = {School-based sampling has been used to inform targeted responses for malaria and neglected tropical diseases. Standard geostatistical methods for mapping disease prevalence use the school location to model spatial correlation, which is questionable since exposure to the disease is more likely to occur in the residential location. In this paper, we propose to overcome the limitations of standard geostatistical methods by introducing a modelling framework that accounts for the uncertainty in the location of the residence of the students. By using cost distance and cost allocation models to define spatial accessibility and in absence of any information on the travel mode of students to school, we consider three school catchment area models that assume walking only, walking and bicycling and, walking and motorized transport. We illustrate the use of this approach using two case studies of malaria in Kenya and compare it with the standard approach that uses the school locations to build geostatistical models. We argue that the proposed modelling framework presents several inferential benefits, such as the ability to combine data from multiple surveys some of which may also record the residence location, and to deal with ecological bias when estimating the effects of malaria risk factors. However, our results show that invalid assumptions on the modes of travel to school can worsen the predictive performance of geostatistical models. Future research in this area should focus on collecting information on the modes of transportation to school which can then be used to better parametrize the catchment area models.},
}
@article {pmid35877609,
year = {2022},
author = {Wangithi, C and Muriithi, BW and Diiro, G and Dubois, T and Mohamed, S and Lattorff, MG and Ngowi, BV and Abdel-Rahman, EM and Adan, M and Kassie, M},
title = {Synergies of integrated pest and pollinator management in avocado farming in East Africa: An ex-ante economic analysis.},
journal = {PloS one},
volume = {17},
number = {7},
pages = {e0271241},
pmid = {35877609},
issn = {1932-6203},
mesh = {Agriculture ; Humans ; *Persea ; Pest Control ; Pollination ; Tanzania ; },
abstract = {Using synthetic pesticides to manage pests can threaten pollination services, affecting the productivity of pollination-dependent crops such as avocado. The need to mitigate this negative externality has led to the emergence of the concept of integrated pest and pollinator management (IPPM) to achieve both pest and pollinator management, leading to complementary or synergistic benefits for yield and quality of the harvest. This paper aims to evaluate the potential economic and welfare impact of IPPM in avocado production systems in Kenya and Tanzania. We utilize both primary and secondary data and employed the economic surplus model. On average the potential economic gain from the adoption of IPPM is US$ 66 million annually in Kenya, with a benefit-cost ratio (BCR) of 13:1, while in Tanzania US$ 1.4 million per year, with a BCR of 34:1. The potential benefits from IPPM intervention gains are expected to reduce the number of poor people in Kenya and Tanzania by 10,464 and 1,255 people per year respectively. The findings conclude that policies that enhance the adoption of IPPM can fast-track economic development and therefore improve the livelihoods of various actors across the avocado value chain.},
}
@article {pmid35875359,
year = {2022},
author = {Constant, A and Clark, A and Kirchhoff, M and Friston, KJ},
title = {Extended active inference: Constructing predictive cognition beyond skulls.},
journal = {Mind & language},
volume = {37},
number = {3},
pages = {373-394},
pmid = {35875359},
issn = {0268-1064},
abstract = {Cognitive niche construction is the process whereby organisms create and maintain cause-effect models of their niche as guides for fitness influencing behavior. Extended mind theory claims that cognitive processes extend beyond the brain to include predictable states of the world. Active inference and predictive processing in cognitive science assume that organisms embody predictive (i.e., generative) models of the world optimized by standard cognitive functions (e.g., perception, action, learning). This paper presents an active inference formulation that views cognitive niche construction as a cognitive function aimed at optimizing organisms' generative models. We call that process of optimization extended active inference.},
}
@article {pmid35874548,
year = {2022},
author = {Czapanskiy, MF and Beltran, RS},
title = {How Reproducibility Will Accelerate Discovery Through Collaboration in Physio-Logging.},
journal = {Frontiers in physiology},
volume = {13},
number = {},
pages = {917976},
pmid = {35874548},
issn = {1664-042X},
abstract = {What new questions could ecophysiologists answer if physio-logging research was fully reproducible? We argue that technical debt (computational hurdles resulting from prioritizing short-term goals over long-term sustainability) stemming from insufficient cyberinfrastructure (field-wide tools, standards, and norms for analyzing and sharing data) trapped physio-logging in a scientific silo. This debt stifles comparative biological analyses and impedes interdisciplinary research. Although physio-loggers (e.g., heart rate monitors and accelerometers) opened new avenues of research, the explosion of complex datasets exceeded ecophysiology's informatics capacity. Like many other scientific fields facing a deluge of complex data, ecophysiologists now struggle to share their data and tools. Adapting to this new era requires a change in mindset, from "data as a noun" (e.g., traits, counts) to "data as a sentence", where measurements (nouns) are associate with transformations (verbs), parameters (adverbs), and metadata (adjectives). Computational reproducibility provides a framework for capturing the entire sentence. Though usually framed in terms of scientific integrity, reproducibility offers immediate benefits by promoting collaboration between individuals, groups, and entire fields. Rather than a tax on our productivity that benefits some nebulous greater good, reproducibility can accelerate the pace of discovery by removing obstacles and inviting a greater diversity of perspectives to advance science and society. In this article, we 1) describe the computational challenges facing physio-logging scientists and connect them to the concepts of technical debt and cyberinfrastructure, 2) demonstrate how other scientific fields overcame similar challenges by embracing computational reproducibility, and 3) present a framework to promote computational reproducibility in physio-logging, and bio-logging more generally.},
}
@article {pmid35873380,
year = {2022},
author = {Lim, T and Lee, K and Kim, RH and Cha, KH and Koo, SY and Moon, EC and Hwang, KT},
title = {Black raspberry extract can lower serum LDL cholesterol via modulation of gut microbial composition and serum bile acid profile in rats fed trimethylamine-N-oxide with a high-fat diet.},
journal = {Food science and biotechnology},
volume = {31},
number = {8},
pages = {1041-1051},
pmid = {35873380},
issn = {2092-6456},
abstract = {UNLABELLED: Blood trimethylamine-N-oxide (TMAO) has been associated with cardiovascular disease. Black raspberry (Rubus occidentalis, BR) has been regarded to be beneficial for cardiovascular health. This study aimed to investigate how BR extract affects serum lipid profile, gut microbial composition, metabolites in rats fed TMAO with a high-fat diet. Dietary TMAO increased serum LDL cholesterol, while BR extract decreased its level. α-Diversity of gut microbiota was not changed; however, in the rats fed TMAO, Macellibacteroides and Mucispirillum were enriched, while Ruminococcaceae was reduced. The BR supplementation could restore Macellibacteroides, Clostridium, and Ruminococcaceae. The BR supplementation increased cecal hippuric acid and serum farnesoid X receptor-antagonistic bile acids, including ursodeoxycholic acid (UDCA), tauro-α-muricholic acid, and tauro-UDCA. The BR supplementation tended to upregulate Cyp7a1 and Abcg5 expressions while downregulating Srebf2 and Hmgcr expressions. BR extract affects the gut bacterial community and microbial metabolites, lowering serum LDL cholesterol in rats with elevated serum TMAO.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-022-01079-y.},
}
@article {pmid35870534,
year = {2022},
author = {Hossain Bhuiyan, MA and Chandra Karmaker, S and Saha, BB},
title = {Nexus between potentially toxic elements' accumulation and seasonal/anthropogenic influences on mangrove sediments and ecological risk in Sundarbans, Bangladesh: An approach from GIS, self-organizing map, conditional inference tree and random forest models.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {309},
number = {},
pages = {119765},
doi = {10.1016/j.envpol.2022.119765},
pmid = {35870534},
issn = {1873-6424},
mesh = {Bangladesh ; Cadmium/analysis ; China ; Ecosystem ; Environmental Monitoring/methods ; Geographic Information Systems ; Geologic Sediments ; Humans ; Lead/analysis ; *Metals, Heavy/analysis ; Risk Assessment/methods ; Seasons ; *Water Pollutants, Chemical/analysis ; },
abstract = {Mangroves play a vital role in protecting the coastal community from the climate change effect and in the restoration of the coastal ecosystem. This research has been designed to determine the spatial and seasonal changes of potentially toxic elements' (PTEs) concentration in sediments and their potential source contribution among the different human-driven processes in Sundarbans, Bangladesh. Different pollution evaluation indices, random forest (RF) model, conditional inference tree (CIT), self-organizing map (SOM), geographical information system (GIS), and principal component analysis (PCA) were used for the interpretation of sources and risk assessment of PTEs. The mean concentration of PTEs both in winter and monsoon seasons has fallen below the threshold effect level but exceeded the rare effect level of marine sediments quality standards. Results showed that the PTEs were significantly enriched (EF > 1.00 < 70.00) in sediments, whereas the Cd enrichment (7.00% samples) was very alarming (EF = 60-70). Except for Zn and Cd, other PTEs were enriched in 30-60% samples. The highest geoaccumulation and contamination factors for Cd were observed in 46-72% of samples. The ecological risk (ER) factors showed similar results where Cd showed strong to very strong factors (ER = 110-2218) in 80% of samples. The CIT explained the natural/geogenic and anthropogenic sources of pollution, where the higher CIT values for Cd indicated industrial, aquaculture, and coal-based thermal powerplant. The RF model provided that shrimp firms, power plants, industry, and seaport were recognized as the influential sources for Zn, Pb, Cr, Cd, and As in sediments. Though Pb and As were found as the most significant pollutants, Cd was identified as a severe threat to ecology and public health. Based on CIT, RF, SOM and PCA the order of PTEs in mangroves sediment were:industrial/urban > aquaculture/shrimpfirm > powerplant > seaportoperation > tourism > geogenic/natural. The present study will help the policymakers for effective and sustainable management of the mangrove ecosystem.},
}
@article {pmid35868837,
year = {2022},
author = {Nishizawa, N and Okawara, M and Mori, M and Fujino, Y and Matsuda, S and Fushimi, K and Tanaka, F},
title = {Postoperative cerebral infarction risk is related to lobectomy site in lung cancer: a retrospective cohort study of nationwide data in Japan.},
journal = {BMJ open respiratory research},
volume = {9},
number = {1},
pages = {},
pmid = {35868837},
issn = {2052-4439},
mesh = {Cerebral Infarction/epidemiology/etiology/surgery ; Humans ; Japan/epidemiology ; *Lung Neoplasms/complications/epidemiology/surgery ; *Pneumonectomy/adverse effects/methods ; Postoperative Complications/epidemiology/etiology ; Retrospective Studies ; },
abstract = {OBJECTIVES: To determine the incidence of cerebral infarction after lobectomy at different sites using inpatient data from a diagnosis procedure combination database.
DESIGN: Retrospective cohort study.
SETTING: Data were retrieved from the Japanese diagnosis procedure combination inpatient database for patients who underwent lobectomies for lung cancer between April 2018 and March 2020.
PARTICIPANTS: The analysis included 37 352 patients from 556 institutions who underwent lobectomies for lung cancer.
MAIN OUTCOMES AND MEASURES: The occurrence of cerebral infarction after lobectomy during hospitalisation was estimated using multilevel logistic regression models adjusted for sex, age, body mass index, smoking history, activity of daily living, surgical approach (thoracotomy or video-assisted), clinical cancer stage, comorbidities and hospital-level factors to describe the association between cerebral infarction and different lobectomy sites.
RESULTS: Overall cerebral infarction after lobectomy occurred in 99 patients (0.27%): 29 with left upper lobectomy (0.39%), 19 with left lower lobectomy (0.34%), 32 with right upper lobectomy (0.24%), 6 with right middle lobectomy (0.21%) and 13 with right lower lobectomy (0.16%). The multilevel multivariate logistic regression analysis revealed high ORs for the left upper lobectomy and left lower lobectomy groups. In both univariate and multivariate analyses, left upper lobectomy had the highest OR for the occurrence of cerebral infarction compared with lobectomies at other sites.
CONCLUSIONS AND RELEVANCE: Left upper lobectomy had the highest OR for the occurrence of cerebral infarction after lung cancer lobectomy during hospitalisation. There is an urgent need to investigate the specific mechanisms underlying postoperative cerebral infarction after left upper lobectomy and to establish preventive measures such as altering surgical methods, using radiological examinations for early detection and better use of anticoagulants.},
}
@article {pmid35866021,
year = {2022},
author = {Singh, P and Irisarri, I and Torres-Dowdall, J and Thallinger, GG and Svardal, H and Lemmon, EM and Lemmon, AR and Koblmüller, S and Meyer, A and Sturmbauer, C},
title = {Phylogenomics of trophically diverse cichlids disentangles processes driving adaptive radiation and repeated trophic transitions.},
journal = {Ecology and evolution},
volume = {12},
number = {7},
pages = {e9077},
pmid = {35866021},
issn = {2045-7758},
abstract = {Cichlid fishes of the tribe Tropheini are a striking case of adaptive radiation, exemplifying multiple trophic transitions between herbivory and carnivory occurring in sympatry with other established cichlid lineages. Tropheini evolved highly specialized eco-morphologies to exploit similar trophic niches in different ways repeatedly and rapidly. To better understand the evolutionary history and trophic adaptations of this lineage, we generated a dataset of 532 targeted loci from 21 out of the 22 described Tropheini species. We resolved the Tropheini into seven monophyletic genera and discovered one to be polyphyletic. The polyphyletic genus, Petrochromis, represents three convergent origins of the algae grazing trophic specialization. This repeated evolution of grazing may have been facilitated by adaptive introgression as we found evidence for gene flow among algae grazing genera. We also found evidence of gene flow among algae browsing genera, but gene flow was restricted between herbivorous and carnivorous genera. Furthermore, we observed no evidence supporting a hybrid origin of this radiation. Our molecular evolutionary analyses suggest that opsin genes likely evolved in response to selection pressures associated with trophic ecology in the Tropheini. We found surprisingly little evidence of positive selection in coding regions of jaw-shaping genes in this trophically diverse lineage. This suggests low degrees of freedom for further change in these genes, and possibly a larger role for regulatory variation in driving jaw adaptations. Our study emphasizes Tropheini cichlids as an important model for studying the evolution of trophic specialization and its role in speciation.},
}
@article {pmid35865637,
year = {2022},
author = {Dwivedi, D and Santos, ALD and Barnard, MA and Crimmins, TM and Malhotra, A and Rod, KA and Aho, KS and Bell, SM and Bomfim, B and Brearley, FQ and Cadillo-Quiroz, H and Chen, J and Gough, CM and Graham, EB and Hakkenberg, CR and Haygood, L and Koren, G and Lilleskov, EA and Meredith, LK and Naeher, S and Nickerson, ZL and Pourret, O and Song, HS and Stahl, M and Taş, N and Vargas, R and Weintraub-Leff, S},
title = {Biogeosciences Perspectives on Integrated, Coordinated, Open, Networked (ICON) Science.},
journal = {Earth and space science (Hoboken, N.J.)},
volume = {9},
number = {3},
pages = {e2021EA002119},
pmid = {35865637},
issn = {2333-5084},
support = {P01 ES028939/ES/NIEHS NIH HHS/United States ; },
abstract = {This article is composed of three independent commentaries about the state of Integrated, Coordinated, Open, Networked (ICON) principles in the American Geophysical Union Biogeosciences section, and discussion on the opportunities and challenges of adopting them. Each commentary focuses on a different topic: (a) Global collaboration, technology transfer, and application (Section 2), (b) Community engagement, community science, education, and stakeholder involvement (Section 3), and (c) Field, experimental, remote sensing, and real-time data research and application (Section 4). We discuss needs and strategies for implementing ICON and outline short- and long-term goals. The inclusion of global data and international community engagement are key to tackling grand challenges in biogeosciences. Although recent technological advances and growing open-access information across the world have enabled global collaborations to some extent, several barriers, ranging from technical to organizational to cultural, have remained in advancing interoperability and tangible scientific progress in biogeosciences. Overcoming these hurdles is necessary to address pressing large-scale research questions and applications in the biogeosciences, where ICON principles are essential. Here, we list several opportunities for ICON, including coordinated experimentation and field observations across global sites, that are ripe for implementation in biogeosciences as a means to scientific advancements and social progress.},
}
@article {pmid35864989,
year = {2022},
author = {Simoes, J and Bulla, J and Neff, P and Pryss, R and Marcrum, SC and Langguth, B and Schlee, W},
title = {Daily Contributors of Tinnitus Loudness and Distress: An Ecological Momentary Assessment Study.},
journal = {Frontiers in neuroscience},
volume = {16},
number = {},
pages = {883665},
pmid = {35864989},
issn = {1662-4548},
abstract = {BACKGROUND: Tinnitus is a heterogeneous condition which may be associated with moderate to severe disability, but the reasons why only a subset of individuals is burdened by the condition are not fully clear. Ecological momentary assessment (EMA) allows a better understanding of tinnitus by capturing the fluctuations of tinnitus symptoms, such as distress and loudness, and psychological processes, such as emotional arousal, overall stress, mood, and concentration and how these variables interact over time. Whether any of those variables have an influence over the next day, that is, whether any of these variables are auto- or cross-correlated, is still unanswered.
OBJECTIVES: Assess whether behavioral and symptom-related data from tinnitus users from the TrackYourTinnitus (TYT) mobile app have an impact on tinnitus loudness and distress on subsequent days.
METHODS: Anonymized data was collected from 278 users of the iOS or Android TYT apps between 2014 and 2020. Tinnitus-related distress, tinnitus loudness, concentration level, mood, emotional arousal, and overall stress level were assessed using either a slider or the Wong-Baker Pain FACES scale via a daily survey. Three modeling strategies were used to investigate whether tinnitus loudness and distress are affected by previous days symptoms or psychological processes: auto- and cross correlations, regressions with elastic net regularization, and subgrouping within group iterative multiple model estimation (S-GIMME).
RESULTS: No autocorrelation or cross-correlation was observed at the group level between the variables assessed. However, application of the regression models with elastic net regularization identified individualized predictors of tinnitus loudness and distress for most participants, with the models including contemporaneous and lagged information from the previous day. S-GIMME corroborated these findings by identifying individualized predictors of tinnitus loudness and distress from the previous day.
DISCUSSION: We showed that tinnitus loudness and tinnitus distress are affected by the contemporaneous and lagged dynamics of behavioral and emotional processes measured through EMA. These effects were seen at the group, and individual levels. The relevance EMA and the implications of the insights derived from it for tinnitus care are discussed, especially considering current trends toward the individualization of tinnitus care.},
}
@article {pmid35864391,
year = {2022},
author = {Zhu, Q and Ruan, M and Hu, Z and Ye, C},
title = {Addition of carbon sources and nutrient salts can inhibit gangue acidification by changing microbial community structure.},
journal = {Environmental science and pollution research international},
volume = {29},
number = {60},
pages = {90046-90057},
pmid = {35864391},
issn = {1614-7499},
mesh = {*Carbon ; Sodium Lactate ; RNA, Ribosomal, 16S ; China ; *Microbiota ; },
abstract = {Acidic pollution from gangue oxidation has become a primary environmental problem in coal mining areas in China. The use of microorganisms to remediate acidic pollution in coal gangue piles has been indicated to be effective, but environmental differences and carbon sources in different mining areas have become important factors restricting microbial activity. Instead of the addition of new functional bacteria to gangue piles, carbon sources and nutrient salts were added to recently discharged gangue to enhance the activity of beneficial bacteria in the indigenous microbial community. The changes in pH and electrical conductivity (EC) of the gangue leachate as well as the composition and abundance of the functional microbial community on the surface of the gangue were analyzed by leaching simulation experiments and 16S rRNA sequencing. The results showed that the addition of a carbon source maintained the pH of the gangue leachate at 6.31~6.65 in 14 d, which was significantly higher than that of the control group, but the pH of the leachate decreased significantly after the addition of the carbon source was stopped. The most effective treatment is adding a low concentration of nutrient salt (20% concentration) and sodium lactate (0.02 g/L) to the gangue first, and then adding sodium lactate (0.1 mg/L) every 7 days. The addition of carbon sources and nutrient salts changed the microbial community composition on the surface of the gangue, and the species diversity index decreased. The dominant genera in the experimental group were Listeria, Arthrobacter, and Enterococcus. The functional gene types in the experimental and control groups were almost the same, but their relative abundance changed. The abundance of functional genes related to the sulfur cycle increased substantially in the experimental group, and the abundance of genes involved in the nitrogen and carbon cycles also increased, albeit to different degrees.},
}
@article {pmid35863666,
year = {2022},
author = {Liao, PJ and Ting, MK and Kuo, CF and Ding, YH and Lin, CM and Hsu, KH},
title = {Kinship analysis of type 2 diabetes mellitus familial aggregation in Taiwan.},
journal = {Biomedical journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bj.2022.07.003},
pmid = {35863666},
issn = {2320-2890},
abstract = {BACKGROUND: Family disease history plays a vital role in type 2 diabetes mellitus (T2DM) risk. However, the familial aggregation of T2DM among different kinship relatives warrants further investigation.
METHODS: This nationwide kinship relationship study collected 2000-2016 data of two to five generations of the Taiwanese population from the National Health Insurance Research Database. Approximately 4 million family trees were constructed from the records of 20, 890, 264 Taiwanese residents during the study period. T2DM was diagnosed on the basis of ICD-9-CM codes 250.x0 or 250.x2, with three consecutive related prescriptions. The Cox proportional hazard model was used for statistical analysis.
RESULTS: Compared with their counterparts, individuals who had first-degree relatives with T2DM were more likely to develop T2DM during the follow-up period (hazard ratio [HR], 2.37-27.75), followed by individuals who had second-degree relatives with T2DM (HR, 1.29-1.88). T2DM relative risk was higher in those with an affected mother than in those with affected father. The HR for T2DM was 20.32 (95%CI = 15.64-26.42) among male individuals with an affected twin brother, whereas among female individuals with an affected twin sister, it was 60.07 (95%CI = 40.83-88.36). The HRs presented a dose-response relationship with the number of affected family members.
CONCLUSION: The study suggests a significant familial aggregation of T2DM occurrence; these findings could aid in identifying the high-risk group for T2DM and designing early intervention strategies and treatment plans.},
}
@article {pmid35859343,
year = {2022},
author = {Treerat, P and McGuire, B and Palmer, E and Dahl, EM and Karstens, L and Merritt, J and Kreth, J},
title = {Oral microbiome diversity: The curious case of Corynebacterium sp. isolation.},
journal = {Molecular oral microbiology},
volume = {37},
number = {5},
pages = {167-179},
pmid = {35859343},
issn = {2041-1014},
support = {R01 DE022083/DE/NIDCR NIH HHS/United States ; R56 DE021726/DE/NIDCR NIH HHS/United States ; R01 DE018893/DE/NIDCR NIH HHS/United States ; R01 DE021726/DE/NIDCR NIH HHS/United States ; },
mesh = {Actinomyces/genetics ; *Corynebacterium/genetics ; DNA, Bacterial/genetics ; Fatty Acids ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Streptococcus sanguis/genetics ; },
abstract = {Oral microbiome sequencing efforts revealed the presence of hundreds of different microbes. Interindividual differences at strain and species resolution suggest that microbiome diversity could lead to mechanistically distinct gene regulation as well as species-related differences in phenotypes. Commonly, gene regulation and related phenotypes are studied in a few selected strains of a particular species with conclusions that are mostly generalized. The aim of this study was to isolate several species of Corynebacterium using an established protocol that led to the previous isolation of C. durum. Characterization of C. durum interspecies interactions revealed a specific mechanism for chain elongation in Streptococcus sanguinis that was the result of corynebacterial fatty acid production and secretion. While the protocol was successfully applied to isolate what we presumed to be additional Corynebacterium based on several phenotypic traits that seem to be identical to C. durum, genome sequencing of the newly isolated strains placed them closer to Actinomyces. Both Corynebacterium and Actinomyces are suborders of the Actinobacteridae and related species. Our study suggests to take several comprehensive strategies into consideration when taxonomically identifying closely related microorganisms. Furthermore, it seems to be important to test common core phenotypes in bacterial ecology to understand the behavior of specific groups of microbes, rather than simply relying upon genome sequence homology to establish relationships in the microbiome.},
}
@article {pmid35858960,
year = {2022},
author = {Raja, NB and Dimitrijević, D and Krause, MC and Kiessling, W},
title = {Ancient Reef Traits, a database of trait information for reef-building organisms over the Phanerozoic.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {425},
pmid = {35858960},
issn = {2052-4463},
mesh = {Animals ; *Anthozoa ; Biological Evolution ; *Coral Reefs ; Databases, Factual ; Fossils ; Phenotype ; },
abstract = {Trait-based approaches are increasingly relevant to understand ecological and evolutionary patterns. A comprehensive trait database for extant reef corals is already available and widely used to reveal vulnerabilities to environmental disturbances including climate change. However, the lack of similar trait compilations for extinct reef builders prevents the derivation of generalities from the fossil record and to address similar questions. Here we present the Ancient Reef Traits Database (ARTD), which aims to compile trait information of various reef-building organisms in one single repository. ARTD contains specimen-level data from both published and unpublished resources. In this first version, we release 15 traits for 505 genera and 1129 species, comprising a dataset of 17,841 trait values of Triassic to mid-Holocene scleractinian corals, the dominant reef-builders in the modern ocean. Other trait data, including for other reef-building organisms, are currently being collated.},
}
@article {pmid35857750,
year = {2022},
author = {Debnath, J and Meraj, G and Das Pan, N and Chand, K and Debbarma, S and Sahariah, D and Gualtieri, C and Kanga, S and Singh, SK and Farooq, M and Sahu, N and Kumar, P},
title = {Integrated remote sensing and field-based approach to assess the temporal evolution and future projection of meanders: A case study on River Manu in North-Eastern India.},
journal = {PloS one},
volume = {17},
number = {7},
pages = {e0271190},
pmid = {35857750},
issn = {1932-6203},
mesh = {Geographic Information Systems ; India ; *Remote Sensing Technology ; *Rivers ; Soil ; },
abstract = {A common phenomenon associated with alluvial rivers is their meander evolution, eventually forming cutoffs. Point bar deposits and ox-bow lakes are the products of lateral bend migration and meander cutoff. The present study focuses on identifying the meanders of River Manu and their cutoffs. Moreover, this study compares the temporal evolution and predicts the progress of selected meanders of River Manu. In the present research, the Survey of India topographical map, satellite imagery, and geographic information system (GIS) technique were used to examine the evolution of the Manu River meander. Subsequently, a field visit was done to the selected cutoffs and meanders of River Manu to ascertain the present status and collect data. It has been observed that many cutoffs have undergone temporal changes, and their sizes have decreased. Some have become dried or converted to agricultural fields. The width of River Manu has decreased in all the selected bends from 1932 to 2017. The sinuosity index has changed from 2.04 (1932) to 1.90 (2017), and the length of the river has decreased by 7 km in 85 years (1932-2017). The decrease in length is evident from lowering the number of meanders. Uniformity coefficient and coefficient of curvature of the bank soil samples were calculated, indicating that the soil is poorly graded and falls under the cohesionless category. Based on cross-section analysis, sediment discharge, grain-size analysis of the bank material, channel planform change, and radius of curvature, it can be stated that almost all the selected bends have the probability of future cutoff. The highest probabilities were observed in bend 3 (Jalai) and bend 4 (Chhontail). This work is aimed to provide planners with decisions regarding the construction of roads and bridges in areas that show the huge dynamicity of river meandering.},
}
@article {pmid35855607,
year = {2022},
author = {Bledsoe, EK and Burant, JB and Higino, GT and Roche, DG and Binning, SA and Finlay, K and Pither, J and Pollock, LS and Sunday, JM and Srivastava, DS},
title = {Data rescue: saving environmental data from extinction.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1979},
pages = {20220938},
pmid = {35855607},
issn = {1471-2954},
abstract = {Historical and long-term environmental datasets are imperative to understanding how natural systems respond to our changing world. Although immensely valuable, these data are at risk of being lost unless actively curated and archived in data repositories. The practice of data rescue, which we define as identifying, preserving, and sharing valuable data and associated metadata at risk of loss, is an important means of ensuring the long-term viability and accessibility of such datasets. Improvements in policies and best practices around data management will hopefully limit future need for data rescue; these changes, however, do not apply retroactively. While rescuing data is not new, the term lacks formal definition, is often conflated with other terms (i.e. data reuse), and lacks general recommendations. Here, we outline seven key guidelines for effective rescue of historically collected and unmanaged datasets. We discuss prioritization of datasets to rescue, forming effective data rescue teams, preparing the data and associated metadata, and archiving and sharing the rescued materials. In an era of rapid environmental change, the best policy solutions will require evidence from both contemporary and historical sources. It is, therefore, imperative that we identify and preserve valuable, at-risk environmental data before they are lost to science.},
}
@article {pmid35855596,
year = {2022},
author = {Sieben, AJ and Mihaljevic, JR and Shoemaker, LG},
title = {Quantifying mechanisms of coexistence in disease ecology.},
journal = {Ecology},
volume = {103},
number = {12},
pages = {e3819},
doi = {10.1002/ecy.3819},
pmid = {35855596},
issn = {1939-9170},
mesh = {*Ecosystem ; *Plants ; Models, Biological ; Ecology ; },
abstract = {Pathogen coexistence depends on ecological processes operating at both within and between-host scales, making it difficult to quantify which processes may promote or prevent coexistence. Here, we propose that adapting modern coexistence theory-traditionally applied in plant communities-to pathogen systems provides an exciting approach for examining mechanisms of coexistence operating across different spatial scales. We first overview modern coexistence theory and its mechanistic decomposition; we subsequently adapt the framework to quantify how spatial variation in pathogen density, host resources and immunity, and their interaction may promote pathogen coexistence. We apply this derivation to an example two pathogen, multiscale model comparing two scenarios with generalist and strain-specific immunity: one with demographic equivalency among pathogens and one with demographic trade-offs among pathogens. We then show how host-pathogen feedbacks generate spatial heterogeneity that promote pathogen coexistence and decompose those mechanisms to quantify how each spatial heterogeneity contributes to that coexistence. Specifically, coexistence of demographically equivalent pathogens occurs due to spatial variation in host resources, immune responses, and pathogen aggregation. With a competition-colonization trade-off, the superior colonizer requires spatial heterogeneity to coexist, whereas the superior competitor does not. Finally, we suggest ways forward for linking theory and empirical tests of coexistence in disease systems.},
}
@article {pmid35854053,
year = {2022},
author = {Schäfer, B and Beck, C and Rhys, H and Soteriou, H and Jennings, P and Beechey, A and Heppell, CM},
title = {Machine learning approach towards explaining water quality dynamics in an urbanised river.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {12346},
pmid = {35854053},
issn = {2045-2322},
support = {Marie-Sklodowska-Curie Grant agreement No 840825/MCCC_/Marie Curie/United Kingdom ; },
mesh = {Ecosystem ; Environmental Monitoring/methods ; Humans ; Machine Learning ; Rivers ; *Water Pollutants, Chemical/analysis ; *Water Quality ; },
abstract = {Human activities alter river water quality and quantity, with consequences for the ecosystems of urbanised rivers. Quantifying the role of human-induced drivers in controlling spatio-temporal patterns in water quality is critical to develop successful strategies for improving the ecological health of urban rivers. Here, we analyse high-frequency electrical conductivity and temperature data collected from the River Chess in South-East England during a Citizen Science project. Utilizing machine learning, we find that boosted trees outperform GAM and accurately describe water quality dynamics with less than 1% error. SHapley Additive exPlanations reveal the importance of and the (inter)dependencies between the individual variables, such as river level and Wastewater Treatment Works (WWTW) outflow. WWTW outflows give rise to diurnal variations in electrical conductivity, which are detectable throughout the year, and to an increase in average water temperature of 1 [Formula: see text] in a 2 km reach downstream of the wastewater treatment works during low flows. Overall, we showcase how high-frequency water quality measurements initiated by a Citizen Science project, together with machine learning techniques, can help untangle key drivers of water quality dynamics in an urbanised chalk stream.},
}
@article {pmid35850342,
year = {2022},
author = {Cao, X and Chen, W and Ge, X and Chen, X and Wang, J and Ding, J},
title = {Multidimensional soil salinity data mining and evaluation from different satellites.},
journal = {The Science of the total environment},
volume = {846},
number = {},
pages = {157416},
doi = {10.1016/j.scitotenv.2022.157416},
pmid = {35850342},
issn = {1879-1026},
mesh = {Data Mining ; Environmental Monitoring/methods ; Remote Sensing Technology ; *Salinity ; *Soil ; },
abstract = {Soil salinization, a common land degradation mode, restricts the ecological environment and is a global issue due to climate change. Accurately, quickly and effectively monitoring soil salinity is critical for governmental institutions that develop hazard prevention and mitigation strategies. Remote sensing (RS) technology provides a viable alternative to traditional field work due to its large area coverage, abundant spectral information and nearly constant observations. Key issues in RS-based soil salinity monitoring include the lack of both data-mining techniques for obtaining spectral band information and comprehensive considerations of synergies among different spectra. The main objective of this study was to provide in-depth explorations of data mining and integration algorithms from different satellites to multidimensionally evaluate soil salinity models. The Ebinur Lake Wetland Reserve (Xinjiang Province, China) was selected as a case study. First, ground-measured visible and near infrared (VIS-NIR) spectral data were combined with the RS band to simulate Landsat 8 (L8) and Sentinel 2 (S2) and 3 (S3) data. Second, one-dimensional RS bands and 15 soil salinity and vegetation indices were selected, and 15 spectral data transformations (reciprocal, differential, absorbance, etc.) were obtained. Two- and three-dimensional spectral indices were constructed, and the response relationships between different spectral indices and soil electrical conductivity (EC) were comprehensively explored. Finally, an integrated multidimensional algorithm was used to estimate soil salinity in high-performance models for the three satellites. The results showed that all data-mining-based model combinations performed well for all satellites (R[2] > 0.80). However, with multidimensional model combinations, S3 presented the highest predictive capability (R[2] = 0.89, RMSE = 2.57 mS·cm[-1], RPD = 2.05), followed by S2 (R[2] = 0.86, RMSE = 2.71 mS·cm[-1], RPD = 1.90) and L8 (R[2] = 0.85, RMSE = 2.84 mS·cm[-1], RPD = 1.87). Therefore, data mining with integration algorithms in model combinations performs significantly better than previous models and could be considered a promising method for obtaining improved results from soil salinity susceptibility models in similar cases.},
}
@article {pmid35845917,
year = {2022},
author = {Hemanand, D and Mishra, N and Premalatha, G and Mavaluru, D and Vajpayee, A and Kushwaha, S and Sahile, K},
title = {Applications of Intelligent Model to Analyze the Green Finance for Environmental Development in the Context of Artificial Intelligence.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {2977824},
pmid = {35845917},
issn = {1687-5273},
mesh = {*Artificial Intelligence ; Carbon ; *Financial Management ; Industry ; Investments ; },
abstract = {Green finance can be referred to as financial investments made on sustainable projects and policies that focus on a sustainable economy. The procedures include promoting renewable energy sources, energy efficiency, water sanitation, industrial pollution control, transportation pollution control, reduction of deforestation, and carbon emissions, etc. Mainly, these green finance initiatives are carried out by private and public agents like business organizations, banks, international organizations, government organizations, etc. Green finance provides a financial solution to create a positive impact on society and leads to environmental development. In the age of artificial intelligence, all industries adopt AI technologies. In this research, we see the applications of the intelligent model to examine the green finance for ecological advancement with regard to artificial intelligence. Feasible transportation and energy proficiency and power transmission are two significant fields to be advanced and focused on minimizing the carbon impression in these industries. Renewable sources like solar energies for power generation and electric vehicles are to be researched and developed. This R&D requires a considerable fund supply, thus comes the green finance. Globally, green finance plays a vital role in creating a sustainable environment. In this research, for performing the green finance analysis, financial maximally filtered graph (FMFG) algorithm is implemented in different domains. The proposed algorithm is compared with the neural model and observed that the proposed model has obtained 98.85% of accuracy which is higher than the neural model.},
}
@article {pmid35841531,
year = {2022},
author = {Agius, PA and Cutts, JC and Song, P and Rudan, I and Rudan, D and Aboyans, V and McDermott, MM and Criqui, MH and Fowkes, FGR and Fowkes, FJI},
title = {The Global Epidemiological Transition in Cardiovascular Diseases: Unrecognised Impact of Endemic Infections on Peripheral Artery Disease.},
journal = {Journal of epidemiology and global health},
volume = {12},
number = {3},
pages = {219-223},
pmid = {35841531},
issn = {2210-6014},
mesh = {*Cardiovascular Diseases/epidemiology ; Humans ; *Noncommunicable Diseases ; *Peripheral Arterial Disease/epidemiology/etiology ; Prevalence ; Risk Factors ; },
abstract = {An epidemiological transition in the prevalence of peripheral artery disease (PAD) is taking place especially in low- and middle-income countries (LMICs) where an ageing population and adoption of western lifestyles are associated with an increase in PAD. We discuss the limited evidence which suggests that infection, potentially mediated by inflammation, may be a risk factor for PAD, and show by means of an ecological analysis that country-level prevalence of the major endemic infections of HIV, tuberculosis and malaria are associated with the prevalence of PAD. While further research is required, we propose that scientists and health authorities pay more attention to the interplay between communicable and non-communicable diseases, and we suggest that limiting the occurrence of endemic infections might have some effect on slowing the epidemiological transition in PAD.},
}
@article {pmid35840893,
year = {2022},
author = {Mack, M and Stojan, R and Bock, O and Voelcker-Rehage, C},
title = {Cognitive-motor multitasking in older adults: a randomized controlled study on the effects of individual differences on training success.},
journal = {BMC geriatrics},
volume = {22},
number = {1},
pages = {581},
pmid = {35840893},
issn = {1471-2318},
mesh = {Aged ; *Cognition ; Exercise ; Exercise Therapy/methods ; Humans ; *Individuality ; Walking ; },
abstract = {BACKGROUND: Multitasking is an essential part of our everyday life, but performance declines typically in older age. Many studies have investigated the beneficial effects of cognitive, motor and combined cognitive-motor training on multitasking performance in older adults. Previous work, however, has not regarded interindividual differences in cognitive functioning and motor fitness that may affect training benefits. The current study aims to identify whether different training programs may have differential effects on multitasking performance depending on the initial level of cognitive functioning and motor fitness.
METHODS: We conduct a 12-week single-blinded randomized controlled trial. A total of N = 150 healthy older adults are assigned to either a single cognitive, a single motor, or a simultaneous cognitive-motor training. Participants are trained twice per week for 45 min. A comprehensive test battery assesses cognitive functions, motor and cardiovascular fitness, and realistic multitasking during walking and driving in two virtual environments. We evaluate how multitasking performance is related not only to the training program, but also to participants' initial levels of cognitive functioning and motor fitness.
DISCUSSION: We expect that multitasking performance in participants with lower initial competence in either one or both domains (cognitive functioning, motor fitness) benefits more from single-task training (cognitive training and/or motor training). In contrast, multitasking performance in participants with higher competence in both domains should benefit more from multitask training (simultaneous cognitive-motor training). The results may help to identify whether tailored training is favorable over standardized one-size-fits all training approaches to improve multitasking in older adults. In addition, our findings will advance the understanding of factors that influence training effects on multitasking.
TRIAL REGISTRATION: DRKS (German Clinical Trials Register), DRKS00022407. Registered 26/08/2020 - Retrospectively registered at https://www.drks.de/drks_web/setLocale_EN.do.},
}
@article {pmid35834176,
year = {2022},
author = {Gokyar, S and Voss, HU and Taracila, V and Robb, FJL and Bernico, M and Kelley, D and Ballon, DJ and Winkler, SA},
title = {A pathway towards a two-dimensional, bore-mounted, volume body coil concept for ultra high-field magnetic resonance imaging.},
journal = {NMR in biomedicine},
volume = {35},
number = {12},
pages = {e4802},
doi = {10.1002/nbm.4802},
pmid = {35834176},
issn = {1099-1492},
support = {R00 EB024341/EB/NIBIB NIH HHS/United States ; },
mesh = {Male ; Humans ; *Magnetic Resonance Imaging/methods ; *Radio Waves ; Phantoms, Imaging ; Head ; Brain/diagnostic imaging ; },
abstract = {Lack of a body-sized, bore-mounted, radiofrequency (RF) body coil for ultrahigh field (UHF) magnetic resonance imaging (MRI) is one of the major drawbacks of UHF, hampering the clinical potential of the technology. Transmit field (B1) nonuniformity and low specific absorption rate (SAR) efficiencies in UHF MRI are two challenges to be overcome. To address these problems, and ultimately provide a pathway for the full clinical potential of the modality, we have designed and simulated two-dimensional cylindrical high-pass ladder (2D c-HPL) architectures for clinical bore-size dimensions, and demonstrated a simplified proof of concept with a head-sized prototype at 7 T. A new dispersion relation has been derived and electromagnetic simulations were used to verify coil modes. The coefficient of variation (CV) for brain, cerebellum, heart, and prostate tissues after B1 [+] shimming in silico is reported and compared with previous works. Three prototypes were designed in simulation: a head-sized, body-sized, and long body-sized coil. The head-sized coil showed a CV of 12.3%, a B1 [+] efficiency of 1.33 μT/√W, and a SAR efficiency of 2.14 μT/√(W/kg) for brain simulations. The body-sized 2D c-HPL coil was compared with same-sized transverse electromagnetic (TEM) and birdcage coils in silico with a four-port circularly polarized mode excitation. Improved B1 [+] uniformity (26.9%) and SAR efficiency (16% and 50% better than birdcage and TEM coils, respectively) in spherical phantoms was observed. We achieved a CV of 12.3%, 4.9%, 16.7%, and 2.8% for the brain, cerebellum, heart, and prostate, respectively. Preliminary imaging results for the head-sized coil show good agreement between simulation and experiment. Extending the 1D birdcage coil concept to 2D c-HPLs provides improved B1 [+] uniformity and SAR efficiency.},
}
@article {pmid35830166,
year = {2022},
author = {Konstantyner, TCRO and Martins, CB and Góis, AFT and Castro, BVC and Konstantyner, T},
title = {Trend in the incidence rates of accidents with venomous animals in children and adolescents in Brazil (2007-2019).},
journal = {Revista paulista de pediatria : orgao oficial da Sociedade de Pediatria de Sao Paulo},
volume = {41},
number = {},
pages = {e2021272},
pmid = {35830166},
issn = {1984-0462},
mesh = {*Accidents ; Animals ; Brazil/epidemiology ; Humans ; Incidence ; Information Systems ; *Venoms ; },
abstract = {OBJECTIVE: To estimate the temporal trend of the incidence rates of accidents with venomous animals in children and adolescents in Brazil.
METHODS: An ecological time-series study was carried out between 2007 and 2019. Data were obtained from the Brazilian Information System on Diseases of Compulsory Declaration (Sistema de Informação de Agravos de Notificação - SINAN). The time series of incidence rates of accidents with venomous animals were stratified by age group (children aged 0 to 9 years and adolescents aged 10 to 19 years), Brazilian macro-regions (North, Northeast, Midwest, Southeast, and South), and type of accident (snake, scorpion, spider, and caterpillar). For trend analysis, the Prais-Winsten model and the Annual Percent Change (APC) were used.
RESULTS: The time series of the incidence rate of accidents with venomous animals in children and adolescents from the North, Northeast, Midwest, and Southeast macro-regions and in children from the South region showed an upward trend. The average annual incidence rates were higher in the age group of 10 to 19 years, except for the South macro-region. Accidents with scorpions, snakes, and spiders, in this order, were the most frequent; the trends in the time series stratified by type of animal varied according to the geographic macro-region.
CONCLUSIONS: There was an upward trend in the incidence rate of accidents with venomous animals in children and adolescents in Brazil, except for adolescents in the South macro-region of the country.},
}
@article {pmid35829803,
year = {2022},
author = {Kapp, JM and Micheas, L and Holmes, S and Stormont, M and Reinke, WM},
title = {Prevalence of Poor Mental Health Days and Adverse Childhood Experience Reporting in U.S. Adults Before and After COVID-19.},
journal = {Community mental health journal},
volume = {},
number = {},
pages = {},
pmid = {35829803},
issn = {1573-2789},
abstract = {This is the first study of US adults to examine change in the prevalence of psychological burden (i.e., self-reported poor mental health days in the past 30 days, and ACEs recollections) before compared to after COVID-19 started. We analyzed the prevalence of self-reported poor mental health days, and ACEs recollections from 17 states using the Behavioral Risk Factor Surveillance System. Adjusted models identified an increase in prevalence from before compared to after COVID-19 onset in those married or partnered reporting 48% more poor mental health days in the past 30 days; persons of color reporting living with anyone with mental illness during childhood by 73% and reporting more ACEs by 35%; those employed or self-employed reporting childhood sexual abuse by 45%. This ecological-level analysis revealed population-level changes in psychological well-being reporting of U.S. adults from before compared to after the pandemic onset.},
}
@article {pmid35817763,
year = {2022},
author = {Brophy, JK and Matthews, GJ},
title = {Reference database of teeth images from the Family Bovidae.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {396},
pmid = {35817763},
issn = {2052-4463},
mesh = {Animals ; *Cattle ; Databases, Factual ; *Fossils ; Paleodontology ; Tooth/diagnostic imaging ; },
abstract = {Researchers typically rely on fossils from the Family Bovidae to generate African paleoenvironmental reconstructions due to their strict ecological tendencies. Bovids have dominated the southern African fauna for the past four million years and, therefore, dominate the fossil faunal assemblages, especially isolated teeth. Traditionally, researchers reference modern and fossil comparative collections to identify teeth. However, researchers are limited by the specific type and number of bovids at each institution. B.O.V.I.D. (Bovidae Occlusal Visual IDentification) is a repository of images of the occlusal surface of bovid teeth. The dataset currently includes extant bovids from 7 tribes and 20 species (~3900). B.O.V.I.D. contains two scaled images per specimen: a color and a black and white (binarized) image. The database is a useful reference for identifying bovid teeth. The large sample size also allows one to observe the natural variation that exists in each taxa. The binarized images can be used in statistical shape analyses, such as taxonomic classification. B.O.V.I.D. is a valuable supplement to other methods for taxonomically identifying bovid teeth.},
}
@article {pmid35817397,
year = {2022},
author = {Gloria-Soria, A and Faraji, A and Hamik, J and White, G and Amsberry, S and Donahue, M and Buss, B and Pless, E and Cosme, LV and Powell, JR},
title = {Origins of high latitude introductions of Aedes aegypti to Nebraska and Utah during 2019.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {103},
number = {},
pages = {105333},
doi = {10.1016/j.meegid.2022.105333},
pmid = {35817397},
issn = {1567-7257},
mesh = {*Aedes/genetics ; Animals ; Humans ; *Mosquito Vectors/genetics ; Nebraska/epidemiology ; Utah/epidemiology ; Yellow Fever ; Zika Virus ; Zika Virus Infection ; },
abstract = {Aedes aegypti (L.), the yellow fever mosquito, is also an important vector of dengue and Zika viruses, and an invasive species in North America. Aedes aegypti inhabits tropical and sub-tropical areas of the world and in North America is primarily distributed throughout the southern US states and Mexico. The northern range of Ae. aegypti is limited by cold winter months and establishment in these areas has been mostly unsuccessful. However, frequent introductions of Ae. aegypti to temperate, non-endemic areas during the warmer months can lead to seasonal activity and disease outbreaks. Two Ae. aegypti incursions were reported in the late summer of 2019 into York, Nebraska and Moab, Utah. These states had no history of established populations of this mosquito and no evidence of previous seasonal activity. We genotyped a subset of individuals from each location at 12 microsatellite loci and ~ 14,000 single nucleotide polymorphic markers to determine their genetic affinities to other populations worldwide and investigate their potential source of introduction. Our results support a single origin for each of the introductions from different sources. Aedes aegypti from Utah likely derived from Tucson, Arizona, or a nearby location. Nebraska specimen results were not as conclusive, but point to an origin from southcentral or southeastern US. In addition to an effective, efficient, and sustainable control of invasive mosquitoes, such as Ae. aegypti, identifying the potential routes of introduction will be key to prevent future incursions and assess their potential health threat based on the ability of the source population to transmit a particular virus and its insecticide resistance profile, which may complicate vector control.},
}
@article {pmid35816807,
year = {2022},
author = {Wu, X and Zhou, Q and Mu, L and Hu, X},
title = {Machine learning in the identification, prediction and exploration of environmental toxicology: Challenges and perspectives.},
journal = {Journal of hazardous materials},
volume = {438},
number = {},
pages = {129487},
doi = {10.1016/j.jhazmat.2022.129487},
pmid = {35816807},
issn = {1873-3336},
mesh = {Algorithms ; Databases, Factual ; *Ecotoxicology ; Hazardous Substances ; *Machine Learning ; },
abstract = {Over the past few decades, data-driven machine learning (ML) has distinguished itself from hypothesis-driven studies and has recently received much attention in environmental toxicology. However, the use of ML in environmental toxicology remains in the early stages, with knowledge gaps, technical bottlenecks in data quality, high-dimensional/heterogeneous/small-sample data analysis and model interpretability, and a lack of an in-depth understanding of environmental toxicology. Given the above problems, we review the recent progress in the literature and highlight state-of-the-art toxicological studies using ML (such as learning and predicting toxicity in complicated biosystems and multiple-factor environmental scenarios of long-term and large-scale pollution). Beyond predicting simple biological endpoints by integrating untargeted omics and adverse outcome pathways, ML development should focus on revealing toxicological mechanisms. The integration of data-driven ML with other methods (e.g., omics analysis and adverse outcome pathway frameworks) endows ML with widely promising application in revealing toxicological mechanisms. High-quality databases and interpretable algorithms are urgently needed for toxicology and environmental science. Addressing the core issues and future challenges for ML in this review may narrow the knowledge gap between environmental toxicity and computational science and facilitate the control of environmental risk in the future.},
}
@article {pmid35810285,
year = {2022},
author = {Borges, G and Garcia, JA and Pirkis, J and Spittal, MJ and Gunnell, D and Sinyor, M and John, A},
title = {A state level analyses of suicide and the COVID-19 pandemic in Mexico.},
journal = {BMC psychiatry},
volume = {22},
number = {1},
pages = {460},
pmid = {35810285},
issn = {1471-244X},
mesh = {*COVID-19/epidemiology ; Humans ; Interrupted Time Series Analysis ; Mexico/epidemiology ; Pandemics ; *Suicide ; },
abstract = {BACKGROUND: While suicide rates in high- and middle-income countries appeared stable in the early stages of the pandemic, we know little about within-country variations. We sought to investigate the impact of COVID-19 on suicide in Mexico's 32 states and to identify factors that may have contributed to observed variations between states.
METHODS: Interrupted time-series analysis to model the trend in monthly suicides before COVID-19 (from Jan 1, 2010, to March 31, 2020), comparing the expected number of suicides derived from the model with the observed number for the remainder of the year (April 1 to December 31, 2020) for each of Mexico's 32 states. Next, we modeled state-level trends using linear regression to study likely contributing factors at ecological level.
RESULTS: Suicide increased slightly across Mexico during the first nine months of the pandemic (RR 1.03; 95%CI 1.01-1.05). Suicides remained stable in 19 states, increase in seven states (RR range: 1.12-2.04) and a decrease in six states (RR range: 0.46-0.88). Suicide RR at the state level was positively associated with population density in 2020 and state level suicide death rate in 2019.
CONCLUSIONS: The COVID-19 pandemic had a differential effect on suicide death within the 32 states of Mexico. Higher population density and higher suicide rates in 2019 were associated with increased suicide. As the country struggles to cope with the ongoing pandemic, efforts to improve access to primary care and mental health care services (including suicide crisis intervention services) in these settings should be given priority.},
}
@article {pmid35808154,
year = {2022},
author = {Han, J and Xu, C and An, Z and Qian, K and Tan, W and Wang, D and Fang, Q},
title = {PRAPNet: A Parallel Residual Atrous Pyramid Network for Polyp Segmentation.},
journal = {Sensors (Basel, Switzerland)},
volume = {22},
number = {13},
pages = {},
pmid = {35808154},
issn = {1424-8220},
mesh = {Colonoscopy ; Deep Learning ; Humans ; *Image Processing, Computer-Assisted/methods ; *Intestinal Polyps/diagnostic imaging ; *Neural Networks, Computer ; },
abstract = {In a colonoscopy, accurate computer-aided polyp detection and segmentation can help endoscopists to remove abnormal tissue. This reduces the chance of polyps developing into cancer, which is of great importance. In this paper, we propose a neural network (parallel residual atrous pyramid network or PRAPNet) based on a parallel residual atrous pyramid module for the segmentation of intestinal polyp detection. We made full use of the global contextual information of the different regions by the proposed parallel residual atrous pyramid module. The experimental results showed that our proposed global prior module could effectively achieve better segmentation results in the intestinal polyp segmentation task compared with the previously published results. The mean intersection over union and dice coefficient of the model in the Kvasir-SEG dataset were 90.4% and 94.2%, respectively. The experimental results outperformed the scores achieved by the seven classical segmentation network models (U-Net, U-Net++, ResUNet++, praNet, CaraNet, SFFormer-L, TransFuse-L).},
}
@article {pmid35805698,
year = {2022},
author = {Eichinger, M and Bechtoldt, M and Bui, ITM and Grund, J and Keller, J and Lau, AG and Liu, S and Neuber, M and Peter, F and Pohle, C and Reese, G and Schäfer, F and Heinzel, S},
title = {Evaluating the Public Climate School-A School-Based Programme to Promote Climate Awareness and Action in Students: Protocol of a Cluster-Controlled Pilot Study.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {13},
pages = {},
pmid = {35805698},
issn = {1660-4601},
mesh = {Adolescent ; Humans ; Peer Group ; Pilot Projects ; Program Evaluation ; Randomized Controlled Trials as Topic ; School Health Services ; *Schools ; *Students ; },
abstract = {Introduction: School-based programmes may promote knowledge and skills required to address climate change and better health and well-being in adolescents, yet evidence of their effectiveness is limited. In preparation for evaluating the Public Climate School, a school-based intervention to promote climate awareness and action in adolescents, we conduct a pilot study intended to assess procedures for participant recruitment, retention, and data collection, data quality issues and to provide preliminary parameter estimates to guide sample size calculations. Methods and analysis: This unblinded, cluster-controlled pilot study targets students in twelve classes from grades seven to thirteen in German public schools. Seven and five classes were allocated to the intervention and waitlist control arms, respectively. The intervention consisted of (1) live lessons on YouTube, (2) climate-related challenges of the day, (3) workshops and (4) peer exchange sessions. Waitlist control classes participated three weeks later. Measures included the proportion of students completing baseline and follow-up surveys, a comparison of baseline characteristics between students in the retained subsample and those lost to follow-up, proportions of students completing online and paper-pencil-based surveys and problems during data collection based on information reported by teachers. Data quality was assessed as proportions of missing data, associations between missingness and sociodemographic measures using logistic regression models and basic psychometric properties of scales including ceiling effects and internal consistency. Intentions to reduce one's ecological footprint, the primary outcome, and all secondary outcomes for effect estimation were assessed one week pre- and post-intervention from November to December 2021 using items adapted from internationally used instruments and will be investigated using generalised linear mixed models and intention-to-treat analyses. Conclusions: The pilot study will lay the methodological groundwork for a large-scale cluster-randomised effectiveness and process evaluation of the Public Climate School. If proven effective and rolled out more broadly, the Public Climate School has the potential to contribute meaningfully to national climate mitigation and adaptation efforts by reaching a substantial share of adolescents in public schools, including those traditionally less involved in climate action.},
}
@article {pmid35795771,
year = {2022},
author = {Zhai, Y and Li, W},
title = {Evaluation and Change Analysis of Ecosystem Service Value of China's Northeast Tiger-Leopard National Park Based on Big Data Land Use Change.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {6270731},
pmid = {35795771},
issn = {1687-5273},
mesh = {Animals ; Big Data ; China ; Conservation of Natural Resources/methods ; Ecosystem ; *Panthera ; Parks, Recreational ; *Tigers ; },
abstract = {The aim of the construction of Northeast Tiger-Leopard National Park is to protect the integrity of endangered wild animals and natural resources. There is a close relationship between land use and ecosystem service value. Improving the quality of ecological environment is the demand of ecological civilization construction. Therefore, this paper aims to evaluate and analyze the ecosystem service value of Tiger and Leopard Park, which is particularly based on big data land use change. Firstly, using ArcGIS software as the support, we have discussed the impact of the dynamic trend of land use change, transfer matrix, and sensitivity coefficient on ecosystem services in different periods of Tiger and Leopard Park. Secondly, we constructed an evaluation model based on the ecological service value method, which is primarily based on geographical conditions and surface coverage. We have completed the value evaluation and change analysis of ecosystem service in Tiger and Leopard Park by analyzing the generation process of ecosystem service data and information characteristics, as well as the ecosystem classification standard of Tiger and Leopard Park and equivalent factor of ecosystem service value per unit area. Simulation experiments show that the method proposed in this paper can reflect the service value of the ecosystem of the Tiger and Leopard Park, lay the foundation for the construction of ecotourism, and promote the green and sustainable development of the regional ecosystem of the Tiger and Leopard Park.},
}
@article {pmid35795770,
year = {2022},
author = {Zhou, Z and Wang, H and Hu, Q and Zhou, M},
title = {GIS Multimedia Technology in Regional Construction Land Suitability Evaluation in Mountainous Villages and Towns.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {8305285},
pmid = {35795770},
issn = {1687-5273},
mesh = {Cities ; Cluster Analysis ; *Geographic Information Systems ; Information Technology ; *Multimedia ; },
abstract = {In order to explore the suitability evaluation of regional construction land in mountainous villages and towns, a method based on GIS technology is proposed. Supported by GIS and RS technology, the Delphi method is used to determine the natural, socioeconomic, and ecological security factors affecting the ecological suitability of regional construction land in mountainous villages and towns, and analytic hierarchy process is used to calculate the weight of relevant influencing factors. Following the principle of giving priority to ecological protection, a set of ecological suitability evaluation model system and method of regional construction land in mountainous villages and towns are established, based on which the basic ecological control areas of mountainous villages and towns in the study area are divided, so as to provide suggestions for rational and effective planning of land resources in mountainous villages and towns. The experimental results show that the K-means clustering method is divided into five categories: the most suitable land, the more suitable land, the basically suitable land, the unsuitable land, and the unavailable land. Finally, according to the suitability grade system of construction land, it is reclassified, the unsuitable land and unavailable land are divided into basic ecological control areas, the most suitable land and more suitable land are divided into construction control areas, and the basically suitable land is listed as ecological buffer areas. It is proved that the basic ecological control area determined by the model method is basically consistent with the current basic ecological control line of a city, which shows that the model is practical and scientific.},
}
@article {pmid35794151,
year = {2022},
author = {Riley, M and Meagher, P and Huveneers, C and Leto, J and Peddemors, VM and Slip, D and West, J and Bradshaw, CJA},
title = {The Australian Shark-Incident Database for quantifying temporal and spatial patterns of shark-human conflict.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {378},
pmid = {35794151},
issn = {2052-4463},
mesh = {Animals ; *Bites and Stings/epidemiology ; Databases, Factual ; Fisheries ; Humans ; Northern Territory ; *Sharks ; },
abstract = {We describe the Australian Shark-Incident Database, formerly known as the Australian Shark-Attack File, which contains comprehensive reports of 1,196 shark bites that have occurred in Australia over 231 years (1791-2022). Data were collated by the Taronga Conservation Society Australia using purpose-designed questionnaires provided to shark-bite victims or witnesses, media reports, and information provided by the department responsible for fisheries in each Australian state (including the Northern Territory). The dataset includes provoked and unprovoked bites from fresh, brackish, and marine waters in Australia. Data span 22 suspected shark species. This dataset will be publicly available, and can be used by analysts to decipher environmental, biological, and social patterns of shark bites in Australia. The information will aid scientists, conservationists, authorities, and members of the public to make informed decisions when implementing or selecting mitigation measures.},
}
@article {pmid35792777,
year = {2022},
author = {Nascimento, MID and Przibilski, ALF and Coelho, CSG and Leite, KFA and Makenze, M and Jesus, SB},
title = {Mortality attributed to sickle cell disease in children and adolescents in Brazil, 2000-2019.},
journal = {Revista de saude publica},
volume = {56},
number = {},
pages = {65},
pmid = {35792777},
issn = {1518-8787},
mesh = {Adolescent ; Adult ; *Anemia, Sickle Cell ; Brazil/epidemiology ; Child ; Child, Preschool ; Data Collection ; Female ; Humans ; Infant, Newborn ; *Information Systems ; Male ; Young Adult ; },
abstract = {OBJECTIVE: Estimate rates and describe mortality trends attributed to sickle cell disease in children and adolescents in Brazil from 2000 to 2019.
METHODS: This is an ecological study of the time-trend of mortality rates that used the autoregressive method, proposed by Prais-Winsten, to evaluate trends in the estimated rates of sickle cell disease deaths in children and adolescents in Brazil. Deaths with code D57 were obtained from the Mortality Information System, considering age groups (0-4, 5-9, 10-14, 15-19 years) and were used to estimate age-specific and standardized rates by gender and age.
RESULTS: From 2000 to 2019, Brazil had 2,422 deaths from sickle cell disease in people under 20 years of age, with higher frequency in the Northeast (40.46%), followed by the Southeast (39.02%), Midwest (9.58%), North (7.84%), and South (3.10%). The main victims were people of Black skin/race (78.73%). In Brazil, the global standardized average rate was 0.20/100,000 people-year, with an elevation trend (annual percentage change - APC = 5.44%; confidence interval - 95%CI: 2.57-8.39). The pattern was repeated in males (APC = 4.38%; 95%CI: 2.17-6.64) and females (APC = 6.96%; 95%CI: 3.05-11.01). Elaborating age-specific rates showed that the range up to four years experienced the highest rates, without distinction by region. The age group of 15 and 19 years was the second most affected in Brazil and in the Northeast, Southeast, and Midwest regions.
CONCLUSION: Deaths due to sickle cell disorders showed an elevation trend in children and adolescents. Considering that the magnitude of deaths was more evident in the first years (0-4) and late adolescence (15-19), the study suggests that age-specific approaches may impact the control of fatal outcomes caused by sickle cell disease in Brazil.},
}
@article {pmid35791567,
year = {2022},
author = {Ma, J and Dong, WX and Zhu, YF and Xiao, D and Chen, F},
title = {[Characteristics and Assembly Process of Reclaimed Soil Microbial Communities in Eastern Plain Mining Areas].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {43},
number = {7},
pages = {3844-3853},
doi = {10.13227/j.hjkx.202110018},
pmid = {35791567},
issn = {0250-3301},
mesh = {Acidobacteria ; Bacteroidetes ; *Microbiota ; RNA, Ribosomal, 16S ; *Soil ; },
abstract = {Understanding how soil microorganisms respond to land reclamation is essential to evaluating the success of ecological restoration actions in disturbed mine soil. However, the microbiological mechanism referred to as productivity reconstruction of the reclaimed soil is still unclear. To shed light on this mechanism, a total of 75 soil samples were collected for 16S rRNA amplicon high-throughput sequencing. The five sampling sites contained four reclamation plots (reclaimed 8 a, 11 a, 14 a, and 17 a) and 1 non-reclaimed plot, which served as the control sampling site. The microbial community composition, potential functions, and assembly mechanisms were also analyzed. The results showed that:①the richness of the microbial community increased with the reclamation time and was higher than that of the control site. However, the community diversity and evenness decreased with the increasing reclamation year (P<0.05). ②Acidobacteria, Chloroflexi, Proteobacteria, and Bacteroidetes dominated in the reclaimed soil, and the relative abundances of the first two phyla were significantly higher than that of the control (P<0.05), whereas the latter two presented the opposite trends (P<0.05). ③ Eight functions, including coenzyme transport and metabolism, translation, ribosomal structure, and biogenesis, showed a positive succession in the reclamation sites and enhanced with increasing reclamation years. ④ The molecular ecological networks of the microbial community in the plain mining area were well modular, whereas the key microbial groups belonged to the Acidobacteria and Bacteroidetes. The microbial communities were dominantly assembled with the deterministic process, and the homogeneous selection contributed the most, which might have been mainly controlled by the local special environment. The results presented herein will undoubtedly aid in the establishment of success indicators of ecological restoration activities in disturbed mining soil. These findings also provide the theoretical basis for improving the productivity and ecological services of reclaimed soil.},
}
@article {pmid35790740,
year = {2022},
author = {Beninde, J and Toffelmier, EM and Andreas, A and Nishioka, C and Slay, M and Soto, A and Bueno, JP and Gonzalez, G and Pham, HV and Posta, M and Pace, JL and Shaffer, HB},
title = {CaliPopGen: A genetic and life history database for the fauna and flora of California.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {380},
pmid = {35790740},
issn = {2052-4463},
mesh = {Animals ; California ; *Databases, Factual ; Ecosystem ; Fishes/genetics ; *Genetics, Population ; Humans ; Microsatellite Repeats ; },
abstract = {CaliPopGen is a database of population genetic data for native and naturalized eukaryotic species in California, USA. It summarizes the published literature (1985-2020) for 5,453 unique populations with genetic data from more than 187,394 individuals and 448 species (513 species plus subspecies) across molecular markers including allozymes, RFLPs, mtDNA, microsatellites, nDNA, and SNPs. Terrestrial habitats accounted for the majority (46.4%) of the genetic data. Taxonomic groups with the greatest representation were Magnoliophyta (20.31%), Insecta (13.4%), and Actinopterygii (12.85%). CaliPopGen also reports life-history data for most included species to enable analyses of the drivers of genetic diversity across the state. The large number of populations and wide taxonomic breadth will facilitate explorations of ecological patterns and processes across the varied geography of California. CaliPopGen covers all terrestrial and marine ecoregions of California and has a greater density of species and georeferenced populations than any previously published population genetic database. It is thus uniquely suited to inform conservation management at the regional and state levels across taxonomic groups.},
}
@article {pmid35789323,
year = {2022},
author = {Baranasic, D and Hörtenhuber, M and Balwierz, PJ and Zehnder, T and Mukarram, AK and Nepal, C and Várnai, C and Hadzhiev, Y and Jimenez-Gonzalez, A and Li, N and Wragg, J and D'Orazio, FM and Relic, D and Pachkov, M and Díaz, N and Hernández-Rodríguez, B and Chen, Z and Stoiber, M and Dong, M and Stevens, I and Ross, SE and Eagle, A and Martin, R and Obasaju, O and Rastegar, S and McGarvey, AC and Kopp, W and Chambers, E and Wang, D and Kim, HR and Acemel, RD and Naranjo, S and Łapiński, M and Chong, V and Mathavan, S and Peers, B and Sauka-Spengler, T and Vingron, M and Carninci, P and Ohler, U and Lacadie, SA and Burgess, SM and Winata, C and van Eeden, F and Vaquerizas, JM and Gómez-Skarmeta, JL and Onichtchouk, D and Brown, BJ and Bogdanovic, O and van Nimwegen, E and Westerfield, M and Wardle, FC and Daub, CO and Lenhard, B and Müller, F},
title = {Multiomic atlas with functional stratification and developmental dynamics of zebrafish cis-regulatory elements.},
journal = {Nature genetics},
volume = {54},
number = {7},
pages = {1037-1050},
pmid = {35789323},
issn = {1546-1718},
support = {U24 HG002659/HG/NHGRI NIH HHS/United States ; BB/R015457/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 106955/WT_/Wellcome Trust/United Kingdom ; P61715/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Chromatin/genetics ; *Databases, Genetic ; *Gene Expression Regulation, Developmental ; *Genome/genetics ; *Genomics ; Humans ; Mice ; Molecular Sequence Annotation ; Organogenesis/genetics ; *Regulatory Sequences, Nucleic Acid/genetics ; *Zebrafish/embryology/genetics ; *Zebrafish Proteins/genetics ; },
abstract = {Zebrafish, a popular organism for studying embryonic development and for modeling human diseases, has so far lacked a systematic functional annotation program akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created a central repository to store and process zebrafish developmental functional genomic data. Our data coordination center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and re-analyzed published genomic data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements throughout development, including classes with distinct features dependent on their activity in time and space. We delineated the distinct distance topology and chromatin features between regulatory elements active during zygotic genome activation and those active during organogenesis. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predicted functional relationships between them beyond sequence similarity, thus extending the utility of zebrafish developmental genomics to mammals.},
}
@article {pmid35788820,
year = {2022},
author = {Li, J and Miao, B and Wang, S and Dong, W and Xu, H and Si, C and Wang, W and Duan, S and Lou, J and Bao, Z and Zeng, H and Yang, Z and Cheng, W and Zhao, F and Zeng, J and Liu, XS and Wu, R and Shen, Y and Chen, Z and Chen, S and Wang, M and , },
title = {Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization.},
journal = {Briefings in bioinformatics},
volume = {23},
number = {4},
pages = {},
doi = {10.1093/bib/bbac261},
pmid = {35788820},
issn = {1477-4054},
mesh = {Computational Biology/methods ; Data Visualization ; Genomics ; Humans ; *Software ; *User-Computer Interface ; },
abstract = {Complex biomedical data generated during clinical, omics and mechanism-based experiments have increasingly been exploited through cloud- and visualization-based data mining techniques. However, the scientific community still lacks an easy-to-use web service for the comprehensive visualization of biomedical data, particularly high-quality and publication-ready graphics that allow easy scaling and updatability according to user demands. Therefore, we propose a community-driven modern web service, Hiplot (https://hiplot.org), with concise and top-quality data visualization applications for the life sciences and biomedical fields. This web service permits users to conveniently and interactively complete a few specialized visualization tasks that previously could only be conducted by senior bioinformatics or biostatistics researchers. It covers most of the daily demands of biomedical researchers with its equipped 240+ biomedical data visualization functions, involving basic statistics, multi-omics, regression, clustering, dimensional reduction, meta-analysis, survival analysis, risk modelling, etc. Moreover, to improve the efficiency in use and development of plugins, we introduced some core advantages on the client-/server-side of the website, such as spreadsheet-based data importing, cross-platform command-line controller (Hctl), multi-user plumber workers, JavaScript Object Notation-based plugin system, easy data/parameters, results and errors reproduction and real-time updates mode. Meanwhile, using demo/real data sets and benchmark tests, we explored statistical parameters, cancer genomic landscapes, disease risk factors and the performance of website based on selected native plugins. The statistics of visits and user numbers could further reflect the potential impact of this web service on relevant fields. Thus, researchers devoted to life and data sciences would benefit from this emerging and free web service.},
}
@article {pmid35787295,
year = {2022},
author = {Zeng, J and Tu, Q and Yu, X and Qian, L and Wang, C and Shu, L and Liu, F and Liu, S and Huang, Z and He, J and Yan, Q and He, Z},
title = {PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes.},
journal = {Microbiome},
volume = {10},
number = {1},
pages = {101},
pmid = {35787295},
issn = {2049-2618},
mesh = {Bacteria/genetics ; Databases, Factual ; Metagenome/genetics ; *Microbiota ; *Phosphorus ; },
abstract = {BACKGROUND: Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database.
RESULTS: In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments.
CONCLUSIONS: We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract.},
}
@article {pmid35785929,
year = {2022},
author = {Nocci, M and Ragazzoni, L and Barone-Adesi, F and Hubloue, I and Romagnoli, S and Peris, A and Bertini, P and Scolletta, S and Cipollini, F and Mechi, MT and Della Corte, F},
title = {Dynamic assessment of surge capacity in a large hospital network during COVID-19 pandemic.},
journal = {Minerva anestesiologica},
volume = {88},
number = {11},
pages = {928-938},
doi = {10.23736/S0375-9393.22.16460-6},
pmid = {35785929},
issn = {1827-1596},
mesh = {Humans ; *Surge Capacity ; *COVID-19 ; Pandemics ; Hospital Bed Capacity ; Intensive Care Units ; Hospitals ; },
abstract = {BACKGROUND: The COVID-19 pandemic has provided an unprecedented scenario to deepen knowledge of surge capacity (SC), assessment of which remains a challenge. This study reports a large-scale experience of a multi-hospital network, with the aim of evaluating the characteristics of different hospitals involved in the response and of measuring a real-time SC based on two complementary modalities (actual, base) referring to the intensive care units (ICU).
METHODS: Data analysis referred to two consecutive pandemic waves (March-December 2020). Regarding SC, two different levels of analysis are considered: single hospital category (referring to a six-level categorization based on the number of hospital beds) and multi-hospital wide (referring to the response of the entire hospital network).
RESULTS: During the period of 114 days, the analysis revealed a key role of the biggest hospitals (>Category-4) in terms of involvement in the pandemic response. In terms of SC, Category-4 hospitals showed the highest mean SC values, irrespective of the calculation method and level of analysis. At the multi-hospital level, the analysis revealed an overall ICU-SC (base) of 84.4% and an ICU-SC (actual) of 106.5%.
CONCLUSIONS: The results provide benchmarks to better understand ICU hospital response capacity, highlighting the need for a more flexible approach to SC definition.},
}
@article {pmid35783389,
year = {2022},
author = {Glaser, K and Van, AT and Pushkareva, E and Barrantes, I and Karsten, U},
title = {Microbial Communities in Biocrusts Are Recruited From the Neighboring Sand at Coastal Dunes Along the Baltic Sea.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {859447},
pmid = {35783389},
issn = {1664-302X},
abstract = {Biological soil crusts occur worldwide as pioneer communities stabilizing the soil surface. In coastal primary sand dunes, vascular plants cannot sustain due to scarce nutrients and the low-water-holding capacity of the sand sediment. Thus, besides planted dune grass, biocrusts are the only vegetation there. Although biocrusts can reach high coverage rates in coastal sand dunes, studies about their biodiversity are rare. Here, we present a comprehensive overview of the biodiversity of microorganisms in such biocrusts and the neighboring sand from sampling sites along the Baltic Sea coast. The biodiversity of Bacteria, Cyanobacteria, Fungi, and other microbial Eukaryota were assessed using high-throughput sequencing (HTS) with a mixture of universal and group-specific primers. The results showed that the biocrusts recruit their microorganisms mainly from the neighboring sand rather than supporting a universal biocrust microbiome. Although in biocrusts the taxa richness was lower than in sand, five times more co-occurrences were identified using network analysis. This study showed that by comparing neighboring bare surface substrates with biocrusts holds the potential to better understand biocrust development. In addition, the target sequencing approach helps outline potential biotic interactions between different microorganisms groups and identify key players during biocrust development.},
}
@article {pmid35779528,
year = {2022},
author = {de Ferran, V and Figueiró, HV and de Jesus Trindade, F and Smith, O and Sinding, MS and Trinca, CS and Lazzari, GZ and Veron, G and Vianna, JA and Barbanera, F and Kliver, S and Serdyukova, N and Bulyonkova, T and Ryder, OA and Gilbert, MTP and Koepfli, KP and Eizirik, E},
title = {Phylogenomics of the world's otters.},
journal = {Current biology : CB},
volume = {32},
number = {16},
pages = {3650-3658.e4},
doi = {10.1016/j.cub.2022.06.036},
pmid = {35779528},
issn = {1879-0445},
mesh = {Animals ; Base Sequence ; *Otters/genetics ; Phylogeny ; },
abstract = {Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,[1-5] a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.},
}
@article {pmid35779167,
year = {2022},
author = {Güneri, FD and Karaarslan, F and Forestıer, FBE and Forestıer, RJ and Odabaşı, E},
title = {Publication activity in water treatments: Web of Science-based bibliometric analysis of the last two decades.},
journal = {International journal of biometeorology},
volume = {66},
number = {9},
pages = {1829-1839},
pmid = {35779167},
issn = {1432-1254},
mesh = {*Bibliometrics ; Databases, Factual ; Efficiency ; *Mineral Waters ; Turkey ; },
abstract = {We evaluated the quantity and quality of scientific publications linked with water treatments using the Web of Science (WoS) database. The WoS was searching by using the following terms "hydrotherapy," "balneotherapy," "spa therapy," "spa treatment," "creno-balneotherapy," "water treatments," and "aqua therapy," on February 10th, 2022. The recorded data were the total number of articles, year of articles, country of articles, journal, document type, index data, and citation data. Also, the studies performed with natural source mineral water were marked to make a further subgroup analysis through quality and quantity. We obtained 816 articles; 667 (81.74%) were original research articles, and 149 (18.26%) were review articles. A statistically significant and increasing trend was shown in the publication about water treatments (p < 0.01). About three-quarters of the trials were sourced from high-income countries. Italy (n = 98; 12.01%); Turkey (n = 75; 9.19%); Australia (n = 65; 7.97%); Brazil (n = 46; 5.64%); and France (n = 38; 4.66%) were the most productive countries. Calculating the number of articles per million population, Hungary (3.38), Australia (2.53), and Italy (1.64) ranked in the top three. According to 100 billion dollars GDP, the top three countries were Brazil (24.41), Hungary (21.15), and Turkey (10.41). In the average citation calculation, the Netherlands (60.84), Israel (29.86), and Australia (29.06) were in the top three. The International Journal of Biometeorology was the leading journal for publication trials about water treatments. In the subgroup analysis, we found the total number of studies performed with natural source mineral water and non-specified source water trials as 430 and 386, respectively. We also presented that the natural source and non-specified water trials had a statistically significant and increasing trend between 2000 and 2021 (p < 0.01 and p < 0.01, respectively). The trials performed with natural source water mainly were sourced from Italy (n = 79; 18.37%), Turkey (n = 61; 14.19%), France (n = 38; 8.84%), Poland (n = 30; 6.98%), and Hungary (n = 29; 6.74%), the trials performed with non-specified water were sourced from Australia (n = 61; 15.80%), Brazil (n = 46; 11.92%), USA (n = 27; 6.99%), Italy (n = 19; 4.92%), and England (n = 18; 4.66%). The top journal of the natural source water trials was the International Journal of Biometeorology (n = 65; 15.12%), and for the non-specified water trials, it was the International Journal of Sports Physiology (n = 12; 3.11%).Our study presented an increasing trend in trial publications regarding water treatments between 2000 and 2021. Most of the trials were from high and upper-middle-income countries. We suggest that by demonstrating global productivity worldwide, our results can create more scientific attention on this topic and may promote the quantity and quality of the trials.},
}
@article {pmid35778947,
year = {2022},
author = {Tercel, MPTG and Cuff, JP},
title = {The complex epistemological challenge of data curation in dietary metabarcoding: Comment on "The precautionary principle and dietary DNA metabarcoding: Commonly used abundance thresholds change ecological interpretation" by Littleford-Colquhoun et al. (2022).},
journal = {Molecular ecology},
volume = {31},
number = {22},
pages = {5653-5659},
doi = {10.1111/mec.16576},
pmid = {35778947},
issn = {1365-294X},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Data Curation ; Diet ; DNA/genetics ; },
abstract = {In their article, Littleford-Colquhoun et al. (2022) advise against using arbitrary relative read abundance (RRA) thresholds (i.e., minimum sequence copy thresholds) for removing low-abundance sequences since they can increase false negative rates in dietary DNA metabarcoding data sets. The main criticisms presented against these widespread methods are that they (i) are arbitrary, often existing as standard values or defined based on researcher-selected delineations, (ii) are subjective, varying between studies and contexts, and, most problematically, (iii) result in the exclusion of true positives, particularly rarely consumed taxa, to the detriment of ecological insight. We commend the authors for presenting a refreshing and timely perspective on this often neglected topic, which is certainly in need of greater discussion following over a decade of significant advances in dietary metabarcoding. In this complex epistemological problem of false positives versus false negatives, we feel that several of the points raised deserve additional discussion. We address these aspects below, including measured approaches to data filtration and consistent representation of RRAs, and we welcome any further discourse to solidify or refute the concepts therein.},
}
@article {pmid35776271,
year = {2022},
author = {Thirumurthy, S and Jayanthi, M and Samynathan, M and Duraisamy, M and Kabiraj, S and Vijayakumar, S and Anbazhahan, N},
title = {Assessment of spatial-temporal changes in water bodies and its influencing factors using remote sensing and GIS - a model study in the southeast coast of India.},
journal = {Environmental monitoring and assessment},
volume = {194},
number = {8},
pages = {548},
pmid = {35776271},
issn = {1573-2959},
mesh = {Environmental Monitoring ; *Geographic Information Systems ; India ; *Remote Sensing Technology ; Water ; },
abstract = {Concerns have been raised about the threat of ecological imbalance due to the loss of water bodies in densely populated areas. The present study explored the changes in water bodies in terms of area, number, and size in northern districts of Tamil Nadu, India, between 1978 and 2018 using satellite data, geographic information system, spatial analysis, ground truth verification, and field validation. The analysis indicated that the water bodies' area has reduced by 3027 ha and 4363 ha in the Kancheepuram and Tiruvallur Districts, respectively. Almost 179 water bodies have entirely disappeared, and 628 water bodies have been partly converted for other purposes. Of the disappeared water bodies, small, medium, and large water bodies account for 53, 93, and 33, respectively. The main reason for the changes in water bodies was the conversion to agriculture and buildings. Overall, the water bodies' area and number have been reduced by 9% and 12%, respectively, while the population has grown by 37%. The water bodies lost due to anthropogenic activities demand the scientific inventory of water bodies and integrated water resources management at a state or national level with strict monitoring regulations to protect them.},
}
@article {pmid35775972,
year = {2022},
author = {Feeney, MA and Newitt, JT and Addington, E and Algora-Gallardo, L and Allan, C and Balis, L and Birke, AS and Castaño-Espriu, L and Charkoudian, LK and Devine, R and Gayrard, D and Hamilton, J and Hennrich, O and Hoskisson, PA and Keith-Baker, M and Klein, JG and Kruasuwan, W and Mark, DR and Mast, Y and McHugh, RE and McLean, TC and Mohit, E and Munnoch, JT and Murray, J and Noble, K and Otani, H and Parra, J and Pereira, CF and Perry, L and Pintor-Escobar, L and Pritchard, L and Prudence, SMM and Russell, AH and Schniete, JK and Seipke, RF and Sélem-Mojica, N and Undabarrena, A and Vind, K and van Wezel, GP and Wilkinson, B and Worsley, SF and Duncan, KR and Fernández-Martínez, LT and Hutchings, MI},
title = {ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria.},
journal = {Microbial genomics},
volume = {8},
number = {7},
pages = {},
pmid = {35775972},
issn = {2057-5858},
support = {BB/T001038/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R022054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T004126/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N023544/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/V000993/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/V017586/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T008075/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T014962/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S016651/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/W000628/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T015446/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S00811X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P005292/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/F009429/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/J/000PR9790/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; G0801721/MRC_/Medical Research Council/United Kingdom ; BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {*Actinobacteria/genetics ; Anti-Bacterial Agents ; *Streptomyces/genetics ; },
abstract = {Actinobacteria is an ancient phylum of Gram-positive bacteria with a characteristic high GC content to their DNA. The ActinoBase Wiki is focused on the filamentous actinobacteria, such as Streptomyces species, and the techniques and growth conditions used to study them. These organisms are studied because of their complex developmental life cycles and diverse specialised metabolism which produces many of the antibiotics currently used in the clinic. ActinoBase is a community effort that provides valuable and freely accessible resources, including protocols and practical information about filamentous actinobacteria. It is aimed at enabling knowledge exchange between members of the international research community working with these fascinating bacteria. ActinoBase is an anchor platform that underpins worldwide efforts to understand the ecology, biology and metabolic potential of these organisms. There are two key differences that set ActinoBase apart from other Wiki-based platforms: [1] ActinoBase is specifically aimed at researchers working on filamentous actinobacteria and is tailored to help users overcome challenges working with these bacteria and [2] it provides a freely accessible resource with global networking opportunities for researchers with a broad range of experience in this field.},
}
@article {pmid35775333,
year = {2022},
author = {Partezani, AD and Duarte-Santos, HO and Amaral, BS and Gomes Barbosa, AR and Apezzato, M and Brunhara, J and Bianco, B and Lemos, GC and Carneiro, A},
title = {Outcomes of nephrectomy for renal cell carcinoma: An ecologic retrospective study in a middle-income country.},
journal = {Archivio italiano di urologia, andrologia : organo ufficiale [di] Societa italiana di ecografia urologica e nefrologica},
volume = {94},
number = {2},
pages = {129-133},
doi = {10.4081/aiua.2022.2.129},
pmid = {35775333},
issn = {2282-4197},
mesh = {Brazil ; *Carcinoma, Renal Cell/surgery ; Humans ; *Kidney Neoplasms/surgery ; Nephrectomy/methods ; Retrospective Studies ; Treatment Outcome ; },
abstract = {OBJECTIVE: The aim of this study was to describe and compare the outcomes and indirect costs of oncological radical (RN) and partial nephrectomies (PN) in hospitals from the São Paulo public health system, Brazil.
MATERIALS AND METHODS: An ecologic retrospective study was performed from 2008 to 2019, using the TabNet Platform of the Brazilian Unified Health System Department of Informatics. Hospitals were classified according to volume of surgeries (low and high-volume, and also into four quartiles according to volume of surgeries), and with or without medical residency program in urology. The results were compared between groups.
RESULTS: In the period analyzed were performed 2.606 RN in 16 hospitals. Data available for PN ranged only from 2013-2019 and included 1.223 surgeries comprising 15 hospitals. Overall mortality rates were 0.41% for PN and 2.87% for RN. The length of hospital stay was significantly higher in low-volume hospitals for both RN and PN (8.97 vs. 5.62 days, p = 0.001, and 7.75 vs. 4.37 days, p = 0.001, respectively), and also for the RN in hospitals without residency program in Urology (9.37 vs. 6.54 days, p = 0.03). When the volume of surgeries was divided into four quartiles, the length of hospital stay and ICU hospitalization days were significantly higher in the first quartile hospitals for RN (p = 0.016) and PN (p = 0.009), respectively. The mortality rates and indirect costs were not different considering PN and RN in the different types of hospitals.
CONCLUSIONS: The length of hospital stay was significantly lower for both PN and RN in high-volume hospitals, and also for RN in hospitals with residency program in Urology.},
}
@article {pmid35773545,
year = {2022},
author = {Sarkar, I and Dey, P and Rathore, SS and Singh, GD and Singh, RP},
title = {Global genomic and proteomic analysis indicates co-evolution of Neisseria species and with their human host.},
journal = {World journal of microbiology & biotechnology},
volume = {38},
number = {9},
pages = {149},
pmid = {35773545},
issn = {1573-0972},
mesh = {Computational Biology ; Genome, Bacterial/genetics ; Genomics ; Humans ; *Neisseria/genetics ; *Proteomics ; },
abstract = {Neisseria, a genus from the beta-proteobacteria class, is of potential clinical importance. This genus contains both pathogenic and commensal strains. Gonorrhea and meningitis are two major diseases caused by pathogens belonging to this genus. With the increased use of antimicrobial agents against these pathogens they have evolved the antimicrobial resistance capacity making these diseases nearly untreatable. The set of anti-bacterial resistance genes (resistome) and genes associated with signal processing (secretomes) are crucial for the host-microbial interaction. With the virtue of whole-genome sequences and computational biology, it is now possible to study the genomic and proteomic riddles of Neisseria along with their comprehensive evolutionary and metabolic profiling. We have studied relative synonymous codon usage, amino acid usage, reverse ecology, comparative genomics, evolutionary analysis and pathogen-host (Neisseria-human) interaction through bioinformatics analysis. Our analysis revealed the co-evolution of Neisseria genomes with the human host. Moreover, the co-occurrence of Neisseria and humans has been supported through reverse ecology analysis. A differential pattern of the evolutionary rate of resistomes and secretomes was evident among the pathogenic and commensal strains. Comparative genomics supported the presence of virulent genes in both pathogenic and commensal strains of the select genus. Our analysis also indicated a transition from commensal to pathogenic Neisseria strains through the long run of evolution.},
}
@article {pmid35773456,
year = {2022},
author = {Nelder, MP and Russell, CB and Johnson, S and Li, Y and Cronin, K and Cawston, T and Patel, SN},
title = {American dog ticks along their expanding range edge in Ontario, Canada.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {11063},
pmid = {35773456},
issn = {2045-2322},
mesh = {Animals ; Data Collection ; Dogs ; *Ixodes ; New Jersey ; Ontario/epidemiology ; *Rhipicephalus sanguineus ; },
abstract = {The American dog tick, Dermacentor variabilis, is a tick of public and veterinary health importance in North America. Using passive tick surveillance data, we document distribution changes for the American dog tick in Ontario, Canada, from 2010 through 2018. Dermacentor variabilis submissions from the public were geocoded and aggregated-from large to small administrative geographies-by health region, public health unit (PHU) and Forward Sortation Area (FSA). PHU hot spots with high rates of D. variabilis submissions were (1) Brant County, Haldimand-Norfolk and Niagara Regional in the Central West region and (2) Lambton and Winsor-Essex County in the South West region. The number of established D. variabilis populations with ≥ 6 submissions per year increased significantly during the study at regional (PHUs: 22 to 31) and local (FSAs: 27 to 91) scales. The range of D. variabilis increased similarly to the positive control (Ixodes scapularis) during the study and in contrast to the static range of the negative control (Ixodes cookei). Submission hot spots were in warmer, low elevation areas with poorly drained soils, compared to the province's low submission areas. Dermacentor variabilis is spreading in Ontario and continued research into their vector ecology is required to assess medicoveterinary health risks.},
}
@article {pmid35770028,
year = {2022},
author = {Xiao, D and He, H and Yan, X and Keita, M and Diaz, ND and Chen, D and Ma, J and Zhang, Y and Li, J and Julien, EO and Yan, X},
title = {Dataset of response characteristics of H2-producing bacteria consortium to β-lactams, aminoglycosides, macrolides, quinolones antibiotics.},
journal = {Data in brief},
volume = {43},
number = {},
pages = {108354},
pmid = {35770028},
issn = {2352-3409},
abstract = {Antibiotics on H2 producing bacteria shall be considered as being one of the critical elements in biological H2 production utilizing livestock manure as raw resources. Despite the fact that the manure stands a significance role in bio-fermentation, the possibility of antibiotics being contained in excreta shall not be eliminated. Findings of whether the above saying might threaten the safety of bio-H2 production needs to be further studied. The experiment subjects include: six single and three combined antibiotics were tested and analyzed by the application of the gradient experiment method. Along with the H2 production rate, CHO content, pH and OD600 were used to analyze the effects of various antibiotics introduction on the hydrolysis, fermentation and H2 production. To a further extent, four typical representative samples were selected for biodiversity analysis from the single antibiotic experiment groups. Amounting more than 6000 pieces of data were obtained in a series of experiments. Data suggested that remarkable measure of antibiotics have various degrees of H2 production inhibition, while some antibiotics, Penicillin G, Streptomycin Sulfate, and their compound antibiotics, could promote the growth of Ethanoligenens sp. and improve H2 yield in the contrary. Correspondent to the transition of key metabolic intermediates and end products, the mechanism of each antibiotic type and dose on H2 production were summarized as follows: the main inhibitory mechanisms were: (1) board-spectrum inhibition, (2) partial inhibition, (3) H2 consumption enhancement; and the enhancement mechanisms were: (1) enhance the growth of H2-producing bacteria, (2) enhanced starch hydrolysis, (3) inhibitory H2 consumption or release of acid inhibition. Meanwhile, data analysis found that the effect of antibiotics on H2 producing was not only related to type, but also to dosage. Even one kind of antibiotic may have completely opposite effects on H2-producing bacteria under different dosage conditions. Inhibition of H2 yield was highest with Levofloxacin at 6.15 mg/L, gas production was reduced by 88.77%; and enhancement of H2 yield was highest with Penicillin G at 7.20 mg/L, the gas production increased by 72.90%.},
}
@article {pmid35767644,
year = {2022},
author = {Tietje, M and Antonelli, A and Baker, WJ and Govaerts, R and Smith, SA and Eiserhardt, WL},
title = {Global variation in diversification rate and species richness are unlinked in plants.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {27},
pages = {e2120662119},
pmid = {35767644},
issn = {1091-6490},
mesh = {Biodiversity ; Climate ; Datasets as Topic ; Ecosystem ; *Extinction, Biological ; *Genetic Speciation ; Phylogeny ; *Plants/classification/genetics ; },
abstract = {Species richness varies immensely around the world. Variation in the rate of diversification (speciation minus extinction) is often hypothesized to explain this pattern, while alternative explanations invoke time or ecological carrying capacities as drivers. Focusing on seed plants, the world's most important engineers of terrestrial ecosystems, we investigated the role of diversification rate as a link between the environment and global species richness patterns. Applying structural equation modeling to a comprehensive distribution dataset and phylogenetic tree covering all circa 332,000 seed plant species and 99.9% of the world's terrestrial surface (excluding Antarctica), we test five broad hypotheses postulating that diversification serves as a mechanistic link between species richness and climate, climatic stability, seasonality, environmental heterogeneity, or the distribution of biomes. Our results show that the global patterns of species richness and diversification rate are entirely independent. Diversification rates were not highest in warm and wet climates, running counter to the Metabolic Theory of Ecology, one of the dominant explanations for global gradients in species richness. Instead, diversification rates were highest in edaphically diverse, dry areas that have experienced climate change during the Neogene. Meanwhile, we confirmed climate and environmental heterogeneity as the main drivers of species richness, but these effects did not involve diversification rates as a mechanistic link, calling for alternative explanations. We conclude that high species richness is likely driven by the antiquity of wet tropical areas (supporting the "tropical conservatism hypothesis") or the high ecological carrying capacity of warm, wet, and/or environmentally heterogeneous environments.},
}
@article {pmid35767535,
year = {2022},
author = {Wild, TA and Koblitz, JC and Dechmann, DKN and Dietz, C and Meboldt, M and Wikelski, M},
title = {Micro-sized open-source and low-cost GPS loggers below 1 g minimise the impact on animals while collecting thousands of fixes.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0267730},
pmid = {35767535},
issn = {1932-6203},
mesh = {Animals ; Animals, Wild ; Dogs ; *Ecology/methods ; *Geographic Information Systems ; Movement ; },
abstract = {GPS-enabled loggers have been proven as valuable tools for monitoring and understanding animal movement, behaviour and ecology. While the importance of recording accurate location estimates is well established, deployment on many, especially small species, has been limited by logger mass and cost. We developed an open-source and low-cost 0.65 g GPS logger with a simple smartphone-compatible user interface, that can record more than 10,000 GPS fixes on a single 30 mAh battery charge (resulting mass including battery: 1.3 g). This low-budget 'TickTag' (currently 32 USD) allows scientists to scale-up studies while becoming a 'wearable' for larger animals and simultaneously enabling high-definition studies on small animals. Tests on two different species (domestic dog, Canis lupus familiaris and greater mouse-eared bats, Myotis myotis) showed that our combination of optimised hardware design and software-based recording strategies increases the number of achievable GPS fixes per g device mass compared to existing micro-sized solutions. We propose that due to the open-source access, as well as low cost and mass, the TickTag fills a technological gap in wildlife ecology and will open up new possibilities for wildlife research and conservation.},
}
@article {pmid35767189,
year = {2022},
author = {Drozdovitch, V and Kukhta, T and Trofimik, S and Melo, DR and Viarenich, K and Podgaiskaya, M and Minenko, V},
title = {Doses from external irradiation and ingestion of [134]Cs, [137]Cs and [90]Sr of the population of Belarus accumulated over 35 years after the Chernobyl accident.},
journal = {Radiation and environmental biophysics},
volume = {61},
number = {3},
pages = {445-464},
pmid = {35767189},
issn = {1432-2099},
mesh = {Animals ; Cattle ; Cesium Radioisotopes ; *Chernobyl Nuclear Accident ; Eating ; Female ; Radiation Dosage ; Republic of Belarus ; Strontium Radioisotopes ; },
abstract = {This study considers the exposure of the population of the most contaminated Gomel and Mogilev Oblasts in Belarus to prolonged sources of irradiation resulting from the Chernobyl accident. Dose reconstruction methods were developed and applied in this study to estimate the red bone-marrow doses (RBMs) from (i) external irradiation from gamma-emitting radionuclides deposited on the ground and (ii) [134]Cs, [137]Cs and [90]Sr ingestion with locally produced foodstuffs. The mean population-weighted RBM doses accumulated during 35 years after the Chernobyl accident were 12 and 5.7 mGy for adult residents in Gomel and Mogilev Oblasts, respectively, while doses for youngest age groups were 20-40% lower. The highest mean area-specific RBM doses for adults accumulated in 1986-2021 were 63, 56 and 46 mGy in Narovlya, Vetka and Korma raions in Gomel Oblast, respectively. For most areas, external irradiation was the predominant pathway of exposure (60-70% from the total dose), except for areas with an extremely high aggregated [137]Cs soil to cow's milk transfer coefficient (≥ 5.0 Bq L[-1] per kBq m[-2]), where the contribution of [134]Cs and [137]Cs ingestion to the total RBM dose was more than 70%. The contribution of [90]Sr intake to the total RBM dose did not exceed 4% for adults and 10% for newborns in most raion in Gomel and Mogilev Oblasts. The validity of the doses estimated in this study was assessed by comparison with doses obtained from measurements by thermoluminescence dosimeters and whole-body counters done in 1987-2015. The methodology developed in this study can be used to calculate doses to target organs other than RBM such as thyroid and breast doses. The age-dependent and population-weighted doses estimated in this study are useful for ecological epidemiological studies, for projection of radiation risk, and for justification of analytical epidemiological studies in populations exposed to Chernobyl fallout.},
}
@article {pmid35766770,
year = {2022},
author = {Caló, RDS and Souza, RAG and Alves, MR and Lima, FCDS and Galvão, ND and Souza, BDSN and Aguilar, LB},
title = {Trends in the incidence of colorectal cancer in Greater Cuiabá, Mato Grosso (Brazil), from 2000 to 2016.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {25},
number = {Supl 1},
pages = {e220013},
doi = {10.1590/1980-549720220013.supl.1},
pmid = {35766770},
issn = {1980-5497},
mesh = {Adult ; Aged ; Brazil/epidemiology ; *Colorectal Neoplasms/epidemiology ; Female ; Humans ; Imidazoles ; Incidence ; *Information Systems ; Male ; Middle Aged ; Sulfonamides ; Thiophenes ; },
abstract = {OBJECTIVE: To analyze the temporal incidence trend of colorectal cancer (CRC), according to sex and age, in the Greater Cuiabá, Mato Grosso, Brazil, from 2000 to 2016.
METHODS: Ecological time series study, with cases of CRC (C18 to C21) diagnosed from 2000 to 2016, of residents of the Greater Cuiabá (Cuiabá and Várzea Grande), in Mato Grosso. The information on the cases was obtained from the Population-Based Cancer Registry and population data from the Brazilian Institute of Geography and Statistics (IBGE). The rates were adjusted by world population. The age groups considered ranged from 30 to 39 years, 40 to 49 years, 50 to 59 years, 60 to 69 years, 70 to 79 years and 80 years and older. Joinpoint regression was used to analyze the trend of incidence.
RESULTS: A total of 1,715 cases of CRC were registered with information on sex and age, with an adjusted rate of 16.4 new cases/100,000 men and 16.1 new cases/100,000 women. Men presented trend of increasing incidence rates in the age group of 70 to 79 years, with increase of 4.0% per year, while women presented trend of increase in the age group 50 to 59 years, with increase of 2.7% per year.
CONCLUSION: Older men showed a more significant trend towards an increase in the incidence of CRC, but in women this occurred in a younger age group, highlighting the importance of considering age related information in the analyzes of occurrence of the disease in this population.},
}
@article {pmid35766767,
year = {2022},
author = {Oliveira, JFP and Lima, FCDS and Galvão, ND and Souza, PCF},
title = {Cancer Incidence in Mato Grosso state, Brazil: analysis of population-based registries (2007 a 2011).},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {25},
number = {Supl 1},
pages = {e220010},
doi = {10.1590/1980-549720220010.supl.1},
pmid = {35766767},
issn = {1980-5497},
mesh = {Brazil/epidemiology ; Female ; Humans ; Incidence ; *Information Systems ; Male ; *Neoplasms/epidemiology ; Registries ; },
abstract = {OBJECTIVE: To analyze five types of cancer health region in the state of Mato Grosso according to sex.
METHODS: A descriptive ecological study of the health regions of Mato Grosso state using two data sets on the incidence of population-based cancer registries in Mato Grosso - inland and Cuiabá. Age-adjusted annual incidence rates were calculated for the world population in 1960, according to sex, for the period comprising 2007 to 2011.
RESULTS: Although we are still facing problems related to data completeness and quality, the most common cancer types were prostate, female breast, cervix, lung, colorectal and stomach cancer in the state of Mato Grosso from 2007 to 2011. The most frequent types among men were prostate and lung cancer. Among women, breast and cervix cancer were the most frequent ones. The highest incidence rates of cancer per 100,000 inhabitants were found in health regions Tangará da Serra, Sinop, Rondonópolis, and Porto Alegre do Norte.
CONCLUSIONS: Identifying the main types of cancer is important for the improvement of cancer prevention and control actions, as well as to understand its magnitude and impact on society. We must continue to improve the quality of information available in population-based cancer records in the state of Mato Grosso, Brazil.},
}
@article {pmid35766764,
year = {2022},
author = {Carvalho, AE and Souza, RAG and Galvão, ND and Melanda, FN and Caló, RDS and Souza, BDSN and Lima, FCDS and Aguilar, LB},
title = {Colorectal cancer mortality trend in Mato Grosso, Brazil, 2000 to 2019.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {25},
number = {Supl 1},
pages = {e220007},
doi = {10.1590/1980-549720220007.supl.1},
pmid = {35766764},
issn = {1980-5497},
mesh = {Brazil/epidemiology ; *Colorectal Neoplasms ; Female ; Geography ; Humans ; Imidazoles ; *Information Systems ; Male ; Sulfonamides ; Thiophenes ; },
abstract = {OBJECTIVE: To analyze the time series of colorectal cancer (CRC) mortality, according to sex and age group, in Mato Grosso, Brazil, from 2000 to 2019.
METHODS: Ecological time series study, with standardized mortality rates from CRC (C18 to C21) among residents of Mato Grosso. Information on deaths was provided by the Mato Grosso State Health Department, comprising the Mortality Information System and demographic information obtained from the Brazilian Institute of Geography and Statistics. The joinpoint regression analysis was used in the analysis of temporal trend.
RESULTS: A total of 2,406 deaths from CRC were identified in Mato Grosso between 2000 and 2019. The highest rates were found among the age group from 60 to 79 years. There was an increasing trend in mortality rates among men due to CRC for almost all age groups, with the exception of those aged 40 to 49 years and 80 years and older. For women, there was a significant increase in the age groups from 50 to 59 years and 80 years and older.
CONCLUSION: The results showed an increase in mortality rates from CRC in the state of Mato Grosso, from 2000 to 2019, in certain age groups for both sexes, but especially for men. Knowledge about the evolution of mortality can provide data on the epidemiological situation of cancer at the local level and, thus, contribute to the development of actions to control and prevent this disease.},
}
@article {pmid35766762,
year = {2022},
author = {Modesto, VC and Evangelista, FM and Soares, MR and Alves, MR and Neves, MABD and Corrêa, MLM and Sousa, NFDSE and Galvão, ND and Andrade, ACS},
title = {Cancer mortality in the State of Mato Grosso from 2000 to 2015: temporal trend and regional differences.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {25},
number = {Supl 1},
pages = {e220005},
doi = {10.1590/1980-549720220005.supl.1},
pmid = {35766762},
issn = {1980-5497},
mesh = {Brazil/epidemiology ; Humans ; *Information Systems ; *Liver Neoplasms ; Male ; Time Factors ; },
abstract = {OBJECTIVE: To analyze the trend of standardized cancer mortality rate in the state of Mato Grosso according to health regions, from 2000 to 2015.
METHODS: Ecological time series study with data on deaths by cancer from the Mortality Information System. The rates were standardized using direct method and calculated by year and health regions. The annual percentage changes (APC) and respective confidence interval (95%CI) were obtained through simple linear regression. Thematic maps were built to show the spatial distribution of rates.
RESULTS: There were 28,525 deaths by cancer registered in Mato Grosso, with the main types being lung, prostate, stomach, breast and liver cancer. The highest mortality rates were found in regions Médio Norte, Baixada Cuiabana and Sul Mato-Grossense. From 2000 to 2015, an upward trend was seen in the mortality rate by cancer in Mato Grosso (APC=0.81%; 95%CI 0.38-1.26), and in four health regions, Garças Araguaia (APC=2.27%; 95%CI 1.46-3.08), Sul Mato-Grossense (APC=1.12%; 95%CI 0.28-1.97), Teles Pires (APC=1.93%; 95%CI 0,11-3,74) and Vale dos Arinos (APC=2.61%; 95%CI 1.10-4.70), while the other regions remained stable.
CONCLUSION: In the state of Mato Grosso and in the four health regions, cancer mortality rate showed a growing trend. The results point to the need to consider regional differences when thinking about actions for cancer prevention, control and assistance.},
}
@article {pmid35766761,
year = {2022},
author = {Aguilar, LB and Gomes, CV and Lima Neto, GS and Montenegro, LHF and Oliveira, JCS and Galvão, ND and Melanda, FN and Alves, MR and Souza, BDSN},
title = {Mortality trend of cancer and main types according to macroregion in the state of Mato Grosso, Brazil, 2000 to 2015.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {25},
number = {Supl 1},
pages = {e220004},
doi = {10.1590/1980-549720220004.supl.1},
pmid = {35766761},
issn = {1980-5497},
mesh = {Brazil/epidemiology ; *Colorectal Neoplasms ; Humans ; *Information Systems ; Male ; Time Factors ; },
abstract = {OBJECTIVE: To describe the mortality trend from all cancers and the five main ones in the state of Mato Grosso, Brazil, from 2000 to 2015.
METHODS: This is a descriptive, ecological, time series study, with data referring to deaths of residents of Mato Grosso due to cancer (ICD-10 codes C00 to C97), from the Mortality Information System (SIM). Time trend analyses of the standardized mortality rate from all cancers and five specific cancers (lung, prostate, breast, colorectal and cervical) for the state and according to macroregion (South, West, North, East and Center-North) were performed using linear regression (p<0.05).
RESULTS: From 2000 to 2015, 28,525 deaths from all cancers in residents of the state of Mato Grosso were recorded. An increasing trend was observed for all cancers, in addition to lung, breast and colorectal cancers. The South and North macroregions showed an increasing trend for all cancers, breast and colorectal, and Center-North for breast and colorectal. East showed an increasing trend for all cancers, prostate and colorectal, and decreasing for cervical.
CONCLUSION: In the state of Mato Grosso, there was an increasing trend in mortality for all cancers and from specific ones, with emphasis on breast and colorectal cancer in most macroregions.},
}
@article {pmid35766760,
year = {2022},
author = {Souza, BDSN and Lima, DV and Caló, RDS and Oliveira, JCS and Andrade, ACS and Oliveira, LR and Galvão, ND},
title = {Trend of incompleteness of cancer death records in the Mortality Information System database, state of Mato Grosso, Brazil, 2000 to 2016.},
journal = {Revista brasileira de epidemiologia = Brazilian journal of epidemiology},
volume = {25},
number = {Supl 1},
pages = {e220003},
doi = {10.1590/1980-549720220003.supl.1},
pmid = {35766760},
issn = {1980-5497},
mesh = {Brazil/epidemiology ; Databases, Factual ; *Death Certificates ; Humans ; Information Systems ; *Neoplasms ; },
abstract = {OBJECTIVE: To describe the trend of incompleteness of cancer death records in the Mortality Information System (SIM, in Portuguese) database, state of Mato Grosso, Brazil, 2000 to 2016.
METHODS: This is a descriptive, ecological, time series study of records of death from cancer of people living in the state of Mato Grosso (codes C00 to C97 of the 10th revision of the International Statistical Classification of Diseases and Related Health Problems - ICD-10), collected from SIM. To asses incompleteness in the filling of the variables of race/skin color, education, marital status, occupation and underlying cause of death, the relative frequency was calculated in the percentage of null values. The time trend analyzes of the incomplete percentage of categories and variables of interest was performed using linear regression (p<0.05).
RESULTS: From 2000 to 2016, there were 31,097 deaths from cancer among residents of the state of Mato Grosso. Race/skin color, marital status and occupation presented a stable trend of incompleteness; education and underlying cause of death were decreasing. An increasing trend was observed in the categories ignored (marital status) and retired (occupation); a decreasing trend was observed for blank (education), unidentified and housewife (occupation), and C76-other and ill-defined sites and C80-without specification of site (underlying cause of death). Incompleteness of occupation was classified as very poor, with emphasis on housewife and retired. For the remaining variables and categories, the classification was excellent or good.
CONCLUSIONS: Although most of the indicators showed satisfactory trend and classification, the marital status and occupation variables stood out for indicating poorer quality in the records.},
}
@article {pmid35764639,
year = {2022},
author = {Dong, B and Liu, Y and Mu, W and Jiang, Z and Pandey, P and Hong, T and Olesen, B and Lawrence, T and O'Neil, Z and Andrews, C and Azar, E and Bandurski, K and Bardhan, R and Bavaresco, M and Berger, C and Burry, J and Carlucci, S and Chvatal, K and De Simone, M and Erba, S and Gao, N and Graham, LT and Grassi, C and Jain, R and Kumar, S and Kjærgaard, M and Korsavi, S and Langevin, J and Li, Z and Lipczynska, A and Mahdavi, A and Malik, J and Marschall, M and Nagy, Z and Neves, L and O'Brien, W and Pan, S and Park, JY and Pigliautile, I and Piselli, C and Pisello, AL and Rafsanjani, HN and Rupp, RF and Salim, F and Schiavon, S and Schwee, J and Sonta, A and Touchie, M and Wagner, A and Walsh, S and Wang, Z and Webber, DM and Yan, D and Zangheri, P and Zhang, J and Zhou, X and Zhou, X},
title = {A Global Building Occupant Behavior Database.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {369},
pmid = {35764639},
issn = {2052-4463},
abstract = {This paper introduces a database of 34 field-measured building occupant behavior datasets collected from 15 countries and 39 institutions across 10 climatic zones covering various building types in both commercial and residential sectors. This is a comprehensive global database about building occupant behavior. The database includes occupancy patterns (i.e., presence and people count) and occupant behaviors (i.e., interactions with devices, equipment, and technical systems in buildings). Brick schema models were developed to represent sensor and room metadata information. The database is publicly available, and a website was created for the public to access, query, and download specific datasets or the whole database interactively. The database can help to advance the knowledge and understanding of realistic occupancy patterns and human-building interactions with building systems (e.g., light switching, set-point changes on thermostats, fans on/off, etc.) and envelopes (e.g., window opening/closing). With these more realistic inputs of occupants' schedules and their interactions with buildings and systems, building designers, energy modelers, and consultants can improve the accuracy of building energy simulation and building load forecasting.},
}
@article {pmid35763352,
year = {2022},
author = {Stuart, KC and Edwards, RJ and Cheng, Y and Warren, WC and Burt, DW and Sherwin, WB and Hofmeister, NR and Werner, SJ and Ball, GF and Bateson, M and Brandley, MC and Buchanan, KL and Cassey, P and Clayton, DF and De Meyer, T and Meddle, SL and Rollins, LA},
title = {Transcript- and annotation-guided genome assembly of the European starling.},
journal = {Molecular ecology resources},
volume = {22},
number = {8},
pages = {3141-3160},
doi = {10.1111/1755-0998.13679},
pmid = {35763352},
issn = {1755-0998},
support = {P013759/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Australia ; Genome/genetics ; Genomics ; Molecular Sequence Annotation ; *Starlings/genetics ; },
abstract = {The European starling, Sturnus vulgaris, is an ecologically significant, globally invasive avian species that is also suffering from a major decline in its native range. Here, we present the genome assembly and long-read transcriptome of an Australian-sourced European starling (S. vulgaris vAU), and a second, North American, short-read genome assembly (S. vulgaris vNA), as complementary reference genomes for population genetic and evolutionary characterization. S. vulgaris vAU combined 10× genomics linked-reads, low-coverage Nanopore sequencing, and PacBio Iso-Seq full-length transcript scaffolding to generate a 1050 Mb assembly on 6222 scaffolds (7.6 Mb scaffold N50, 94.6% busco completeness). Further scaffolding against the high-quality zebra finch (Taeniopygia guttata) genome assigned 98.6% of the assembly to 32 putative nuclear chromosome scaffolds. Species-specific transcript mapping and gene annotation revealed good gene-level assembly and high functional completeness. Using S. vulgaris vAU, we demonstrate how the multifunctional use of PacBio Iso-Seq transcript data and complementary homology-based annotation of sequential assembly steps (assessed using a new tool, saaga) can be used to assess, inform, and validate assembly workflow decisions. We also highlight some counterintuitive behaviour in traditional busco metrics, and present buscomp, a complementary tool for assembly comparison designed to be robust to differences in assembly size and base-calling quality. This work expands our knowledge of avian genomes and the available toolkit for assessing and improving genome quality. The new genomic resources presented will facilitate further global genomic and transcriptomic analysis on this ecologically important species.},
}
@article {pmid35761171,
year = {2022},
author = {Wang, H and Zhang, X and Ding, S and Huang, Y and Wang, S and Chen, H and Chen, Y and Li, Y},
title = {VisProDom: an interactive Shiny/R application for displaying protein domains with transcriptional features.},
journal = {BMC genomics},
volume = {23},
number = {1},
pages = {472},
pmid = {35761171},
issn = {1471-2164},
mesh = {Databases, Factual ; *Genome ; Genomics ; Protein Domains ; *Software ; },
abstract = {BACKGROUND: Both the protein domains and transcript structures influence protein functional variation. The genomic location of both protein domains and transcript structural features can be described using the genomic coordinates of their encoded sequences. However, the coordinates of protein domains and transcriptional features often differ greatly, and it is difficult to view them in combination at the genome-wide level. In this paper, we describe the development of a new tool that allows users to visualize domains and transcript features together, using either built-in or uploaded genome datasets, and export publication-ready figures. RESULTS: We developed a user-friendly, independent R package and Shiny web application named "VisProDom". VisProDom consists of a genome-wide database containing entire annotated transcripts merged with annotated protein domains from the Pfam database. The built-in dataset includes 82 files, which merge genome general feature format (GFF) annotations with rpsblast tabular outputs from protein sequence searches in the Pfam database. Multiple genomes can be simultaneously screened for protein domains or transcript names. VisProDom includes step-by-step introductions and clickable elements for ease of use.
CONCLUSION: VisProDom can display hundreds of transcripts alongside protein domains and export figures in a publication-ready format. This makes it a valuable tool for molecular evolution and comparative genomics.},
}
@article {pmid35759658,
year = {2022},
author = {Abrahms, B and Rafiq, K and Jordan, NR and McNutt, JW},
title = {Long-term, climate-driven phenological shift in a tropical large carnivore.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {27},
pages = {e2121667119},
pmid = {35759658},
issn = {1091-6490},
mesh = {Animals ; *Canidae/physiology ; *Climate Change ; Datasets as Topic ; Ecosystem ; *Endangered Species ; Seasons ; Temperature ; },
abstract = {Understanding the degree to which animals are shifting their phenology to track optimal conditions as the climate changes is essential to predicting ecological responses to global change. Species at low latitudes or high trophic levels are theoretically expected to exhibit weaker phenological responses than other species, but limited research on tropical systems or on top predators impedes insight into the contexts in which these predictions are upheld. Moreover, a lack of phenological studies on top predators limits understanding of how climate change impacts propagate through entire ecosystems. Using a 30-y dataset on endangered African wild dogs (Lycaon pictus), we examined changes in reproductive phenology and temperatures during birthing and denning over time, as well as potential fitness consequences of these changes. We hypothesized that their phenology would shift to track a stable thermal range over time. Data from 60 packs and 141 unique pack-years revealed that wild dogs have delayed parturition by 7 days per decade on average in response to long-term warming. This shift has led to temperatures on birthing dates remaining relatively stable but, contrary to expectation, has led to increased temperatures during denning periods. Increased denning temperatures were associated with reduced reproductive success, suggesting that a continued phenological shift in the species may become maladaptive. Such results indicate that climate-driven shifts could be more widespread in upper trophic levels than previously appreciated, and they extend theoretical understanding of the species traits and environmental contexts in which large phenological shifts can be expected to occur as the climate changes.},
}
@article {pmid35757606,
year = {2022},
author = {Ali, EOM and Babalghith, AO and Bahathig, AOS and Dafalla, OM and Al-Maghamsi, IW and Mustafa, NEAG and Al-Zahrani, AAA and Al-Mahmoudi, SMY and Abdel-Latif, ME},
title = {Detection of Dengue Virus From Aedes aegypti (Diptera, Culicidae) in Field-Caught Samples From Makkah Al-Mokarramah, Kingdom of Saudi Arabia, Using RT-PCR.},
journal = {Frontiers in public health},
volume = {10},
number = {},
pages = {850851},
pmid = {35757606},
issn = {2296-2565},
mesh = {*Aedes ; Animals ; *Dengue/diagnosis/epidemiology ; *Dengue Virus/genetics ; Female ; Mosquito Vectors ; Reverse Transcriptase Polymerase Chain Reaction ; Saudi Arabia ; },
abstract = {Dengue fever (DF) is endemic to Makkah and Jeddah, the Kingdom of Saudi Arabia (KSA). However, until recently, the circulation of dengue virus (DENV) in Aedes mosquitoes in these areas was unknown. Serological surveillance of DENV in Ae aegypti is a powerful tool for early detection of dengue outbreaks and essential for developing effective control strategies. Therefore, this research aimed to examine a sample of adult Ae aegypti mosquitoes from Makkah, KSA, to detect DENV. In total, 1295 Ae aegypti mosquitoes were collected from the field from target areas of Makkah with a high incidence and prevalence of DF. The samples were divided into 259 coded pools (five mosquitoes in each) and preserved in 1.5 mL plastic tubes. The tubes were labeled, capped, and stored at-86°C until use. RT-PCR was used to detect DENV in the samples. All positive pools were confirmed by RT-PCR. The RT-PCR products were analyzed by gel electrophoresis (1.5% agarose in Tris-acetate EDTA buffer), stained with ethidium bromide, and visualized. DENV was isolated from six female Ae Aegypti collected from six pools (out of 259 pools). No other viruses were detected. Only five of the nine target localities had positive pools. Samples from the remaining four localities yielded negative results. Four DENV-positive mosquitoes were collected at the aquatic stages, and two were collected at the adult stage. These results show the circulation of DENV in adult mosquitoes and offspring, indicating vertical transmission of DENV. In conclusion, this study found that, in Makkah, DENV is circulating in dengue vectors with a high significance rate, suggesting the possibility of a dengue outbreak in the future; therefore, a sensitive surveillance system is vital to predict the outbreak and for early intervention and control.},
}
@article {pmid35757168,
year = {2022},
author = {Rosenberg, G and Auffenberg, K and Bank, R and Bieler, R and Bouchet, P and Herbert, D and Köhler, F and Neubauer, TA and Neubert, E and Páll-Gergely, B and Richling, I and Schneider, S},
title = {Adapting mark-recapture methods to estimating accepted species-level diversity: a case study with terrestrial Gastropoda.},
journal = {PeerJ},
volume = {10},
number = {},
pages = {e13139},
pmid = {35757168},
issn = {2167-8359},
abstract = {We introduce a new method of estimating accepted species diversity by adapting mark-recapture methods to comparisons of taxonomic databases. A taxonomic database should become more complete over time, so the error bar on an estimate of its completeness and the known diversity of the taxon it treats will decrease. Independent databases can be correlated, so we use the time course of estimates comparing them to understand the effect of correlation. If a later estimate is significantly larger than an earlier one, the databases are positively correlated, if it is significantly smaller, they are negatively correlated, and if the estimate remains roughly constant, then the correlations have averaged out. We tested this method by estimating how complete MolluscaBase is for accepted names of terrestrial gastropods. Using random samples of names from an independent database, we determined whether each name led to a name accepted in MolluscaBase. A sample tested in August 2020 found that 16.7% of tested names were missing; one in July 2021 found 5.3% missing. MolluscaBase grew by almost 3,000 accepted species during this period, reaching 27,050 species. The estimates ranged from 28,409 ± 365 in 2021 to 29,063 ± 771 in 2020. All estimates had overlapping 95% confidence intervals, indicating that correlations between the databases did not cause significant problems. Uncertainty beyond sampling error added 475 ± 430 species, so our estimate for accepted terrestrial gastropods species at the end of 2021 is 28,895 ± 630 species. This estimate is more than 4,000 species higher than previous ones. The estimate does not account for ongoing flux of species into and out of synonymy, new discoveries, or changing taxonomic methods and concepts. The species naming curve for terrestrial gastropods is still far from reaching an asymptote, and combined with the additional uncertainties, this means that predicting how many more species might ultimately be recognized is presently not feasible. Our methods can be applied to estimate the total number of names of Recent mollusks (as opposed to names currently accepted), the known diversity of fossil mollusks, and known diversity in other phyla.},
}
@article {pmid35755650,
year = {2022},
author = {Li, Y and Miao, Y and Zhang, J and Cammarano, D and Li, S and Liu, X and Tian, Y and Zhu, Y and Cao, W and Cao, Q},
title = {Improving Estimation of Winter Wheat Nitrogen Status Using Random Forest by Integrating Multi-Source Data Across Different Agro-Ecological Zones.},
journal = {Frontiers in plant science},
volume = {13},
number = {},
pages = {890892},
pmid = {35755650},
issn = {1664-462X},
abstract = {Timely and accurate estimation of plant nitrogen (N) status is crucial to the successful implementation of precision N management. It has been a great challenge to non-destructively estimate plant N status across different agro-ecological zones (AZs). The objective of this study was to use random forest regression (RFR) models together with multi-source data to improve the estimation of winter wheat (Triticum aestivum L.) N status across two AZs. Fifteen site-year plot and farmers' field experiments involving different N rates and 19 cultivars were conducted in two AZs from 2015 to 2020. The results indicated that RFR models integrating climatic and management factors with vegetation index (R[2] = 0.72-0.86) outperformed the models by only using the vegetation index (R[2] = 0.36-0.68) and performed well across AZs. The Pearson correlation coefficient-based variables selection strategy worked well to select 6-7 key variables for developing RFR models that could achieve similar performance as models using full variables. The contributions of climatic and management factors to N status estimation varied with AZs and N status indicators. In higher-latitude areas, climatic factors were more important to N status estimation, especially water-related factors. The addition of climatic factors significantly improved the performance of the RFR models for N nutrition index estimation. Climatic factors were important for the estimation of the aboveground biomass, while management variables were more important to N status estimation in lower-latitude areas. It is concluded that integrating multi-source data using RFR models can significantly improve the estimation of winter wheat N status indicators across AZs compared to models only using one vegetation index. However, more studies are needed to develop unmanned aerial vehicles and satellite remote sensing-based machine learning models incorporating multi-source data for more efficient monitoring of crop N status under more diverse soil, climatic, and management conditions across large regions.},
}
@article {pmid35754095,
year = {2022},
author = {Balfour, NJ and Castellanos, MC and Goulson, D and Philippides, A and Johnson, C},
title = {DoPI: The Database of Pollinator Interactions.},
journal = {Ecology},
volume = {103},
number = {11},
pages = {e3801},
pmid = {35754095},
issn = {1939-9170},
mesh = {Animals ; Ecosystem ; Flowers ; *Insecta ; *Plants ; Pollination ; Databases, Factual ; },
abstract = {Despite the importance of pollinating insects to natural environments and agriculture, there have been few attempts to unite the existing plant-pollinator interaction datasets into a single depository using a common format. Accordingly, we have created one of the world's first online, open-access, and searchable pollinator-plant interaction databases. DoPI (The Database of Pollinator Interactions) was built from a systematic review of the scientific literature and unpublished datasets requested from researchers and organizations. We collated records of interactions between British plant and insect flower-visitor species (or genera), together with associated metadata (date, location, habitat, source publication) when available. The dataset currently (December 2021) contains 101,539 records, detailing over 320,000 interactions. The number of interactions (i.e., the number of times a pairwise species interaction was recorded per occasion) varies considerably among records, averaging 3.6. These include records from 1888 pollinator species and 1241 plant species, totaling >17,000 pairwise species interactions. By combining a large volume of information in a single repository, DoPI can be used to answer fundamental ecological questions on the dynamics of pollination interactions in space and time, as well as applied questions in conservation practice. We hope this dynamic database will be a useful tool not only for researchers, but also for conservationists, funding agencies, governmental departments, beekeepers, agronomists, and gardeners. We request that this paper is cited when using the data in publications and individual studies when appropriate. Researchers and organizations are encouraged to add further data in the future. The database can be accessed at: https://www.dopi.org.uk/.},
}
@article {pmid35753285,
year = {2022},
author = {Feng, Y and Cheng, X and Lu, Y and Wang, H and Chen, D and Luo, C and Liu, H and Gao, S and Lei, T and Huang, C and Yu, X},
title = {Gas chromatography-mass spectrometry analysis of floral fragrance-related compounds in scented rose (Rosa hybrida) varieties and a subsequent evaluation on the basis of the analytical hierarchy process.},
journal = {Plant physiology and biochemistry : PPB},
volume = {185},
number = {},
pages = {368-377},
doi = {10.1016/j.plaphy.2022.06.007},
pmid = {35753285},
issn = {1873-2690},
mesh = {Analytic Hierarchy Process ; Flowers ; Gas Chromatography-Mass Spectrometry/methods ; Odorants/analysis ; *Oils, Volatile ; *Rosa/chemistry ; *Volatile Organic Compounds/analysis ; },
abstract = {Scented rose (Rosa hybrida) varieties are valued as ornamentals, but they also contain volatile organic compounds (VOCs) that produce pleasant aromas. In plants, aromas are produced via metabolism during growth, and each aroma compound has a unique function. In this study, the floral aroma compounds of diverse scented rose varieties were analyzed and classified. The VOCs of different rose varieties were qualitatively and quantitatively analyzed via headspace solid-phase microextraction combined with gas chromatography and mass spectrometry. The test materials were the mature flowers of 55 scented rose varieties that were cultivated under identical conditions. Seventeen important aroma compounds were selected and an analytical hierarchy process (AHP)-based method was developed to identify the most suitable essential oil resources, aromatherapy resources, and healthcare resources. A floral fragrance evaluation model was established for the comprehensive evaluation of the scented rose varieties. The 55 varieties were classified into three grades according to their suitability for each use. 'Soeur Emmanuelle', 'Wollerton Old Hall', 'Accademia', and 'Tianmidemeng' were revealed to be suitable essential oil, aromatherapy, and healthcare resources. On the basis of their aroma compound types, the fifty-five rose varieties were divided into eight groups. The results of this study provide the theoretical basis for the classification of rose flower aromas as well as the rational use of diverse rose varieties to further develop the rose industry.},
}
@article {pmid35752802,
year = {2022},
author = {Darcy, JL and Amend, AS and Swift, SOI and Sommers, PS and Lozupone, CA},
title = {specificity: an R package for analysis of feature specificity to environmental and higher dimensional variables, applied to microbiome species data.},
journal = {Environmental microbiome},
volume = {17},
number = {1},
pages = {34},
pmid = {35752802},
issn = {2524-6372},
support = {PG/16/78/32402/BHF_/British Heart Foundation/United Kingdom ; 5 T15 LM009451-12/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Understanding the factors that influence microbes' environmental distributions is important for determining drivers of microbial community composition. These include environmental variables like temperature and pH, and higher-dimensional variables like geographic distance and host species phylogeny. In microbial ecology, "specificity" is often described in the context of symbiotic or host parasitic interactions, but specificity can be more broadly used to describe the extent to which a species occupies a narrower range of an environmental variable than expected by chance. Using a standardization we describe here, Rao's (Theor Popul Biol, 1982. https://doi.org/10.1016/0040-5809(82)90004-1, Sankhya A, 2010. https://doi.org/10.1007/s13171-010-0016-3) Quadratic Entropy can be conveniently applied to calculate specificity of a feature, such as a species, to many different environmental variables.
RESULTS: We present our R package specificity for performing the above analyses, and apply it to four real-life microbial data sets to demonstrate its application. We found that many fungi within the leaves of native Hawaiian plants had strong specificity to rainfall and elevation, even though these variables showed minimal importance in a previous analysis of fungal beta-diversity. In Antarctic cryoconite holes, our tool revealed that many bacteria have specificity to co-occurring algal community composition. Similarly, in the human gut microbiome, many bacteria showed specificity to the composition of bile acids. Finally, our analysis of the Earth Microbiome Project data set showed that most bacteria show strong ontological specificity to sample type. Our software performed as expected on synthetic data as well.
CONCLUSIONS: specificity is well-suited to analysis of microbiome data, both in synthetic test cases, and across multiple environment types and experimental designs. The analysis and software we present here can reveal patterns in microbial taxa that may not be evident from a community-level perspective. These insights can also be visualized and interactively shared among researchers using specificity's companion package, specificity.shiny.},
}
@article {pmid35749381,
year = {2022},
author = {Favila, N and Madrigal-Trejo, D and Legorreta, D and Sánchez-Pérez, J and Espinosa-Asuar, L and Eguiarte, LE and Souza, V},
title = {MicNet toolbox: Visualizing and unraveling a microbial network.},
journal = {PloS one},
volume = {17},
number = {6},
pages = {e0259756},
pmid = {35749381},
issn = {1932-6203},
mesh = {Cluster Analysis ; Computational Biology/methods ; Microbial Consortia ; *Microbiota ; *Software ; },
abstract = {Applications of network theory to microbial ecology are an emerging and promising approach to understanding both global and local patterns in the structure and interplay of these microbial communities. In this paper, we present an open-source python toolbox which consists of two modules: on one hand, we introduce a visualization module that incorporates the use of UMAP, a dimensionality reduction technique that focuses on local patterns, and HDBSCAN, a clustering technique based on density; on the other hand, we have included a module that runs an enhanced version of the SparCC code, sustaining larger datasets than before, and we couple the resulting networks with network theory analyses to describe the resulting co-occurrence networks, including several novel analyses, such as structural balance metrics and a proposal to discover the underlying topology of a co-occurrence network. We validated the proposed toolbox on 1) a simple and well described biological network of kombucha, consisting of 48 ASVs, and 2) we validate the improvements of our new version of SparCC. Finally, we showcase the use of the MicNet toolbox on a large dataset from Archean Domes, consisting of more than 2,000 ASVs. Our toolbox is freely available as a github repository (https://github.com/Labevo/MicNetToolbox), and it is accompanied by a web dashboard (http://micnetapplb-1212130533.us-east-1.elb.amazonaws.com) that can be used in a simple and straightforward manner with relative abundance data. This easy-to-use implementation is aimed to microbial ecologists with little to no experience in programming, while the most experienced bioinformatics will also be able to manipulate the source code's functions with ease.},
}
@article {pmid35748824,
year = {2022},
author = {Mehta, TK and Penso-Dolfin, L and Nash, W and Roy, S and Di-Palma, F and Haerty, W},
title = {Evolution of miRNA-Binding Sites and Regulatory Networks in Cichlids.},
journal = {Molecular biology and evolution},
volume = {39},
number = {7},
pages = {},
pmid = {35748824},
issn = {1537-1719},
support = {BB/J004669//BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P016774/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CSP17270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Animals ; Binding Sites ; *Cichlids/genetics ; Evolution, Molecular ; Gene Regulatory Networks ; *MicroRNAs/genetics ; Phylogeny ; },
abstract = {The divergence of regulatory regions and gene regulatory network (GRN) rewiring is a key driver of cichlid phenotypic diversity. However, the contribution of miRNA-binding site turnover has yet to be linked to GRN evolution across cichlids. Here, we extend our previous studies by analyzing the selective constraints driving evolution of miRNA and transcription factor (TF)-binding sites of target genes, to infer instances of cichlid GRN rewiring associated with regulatory binding site turnover. Comparative analyses identified increased species-specific networks that are functionally associated to traits of cichlid phenotypic diversity. The evolutionary rewiring is associated with differential models of miRNA- and TF-binding site turnover, driven by a high proportion of fast-evolving polymorphic sites in adaptive trait genes compared with subsets of random genes. Positive selection acting upon discrete mutations in these regulatory regions is likely to be an important mechanism in rewiring GRNs in rapidly radiating cichlids. Regulatory variants of functionally associated miRNA- and TF-binding sites of visual opsin genes differentially segregate according to phylogeny and ecology of Lake Malawi species, identifying both rewired, for example, clade-specific and conserved network motifs of adaptive trait associated GRNs. Our approach revealed several novel candidate regulators, regulatory regions, and three-node motifs across cichlid genomes with previously reported associations to known adaptive evolutionary traits.},
}
@article {pmid35748425,
year = {2022},
author = {Pelletier, TA and Parsons, DJ and Decker, SK and Crouch, S and Franz, E and Ohrstrom, J and Carstens, BC},
title = {phylogatR: Phylogeographic data aggregation and repurposing.},
journal = {Molecular ecology resources},
volume = {22},
number = {8},
pages = {2830-2842},
doi = {10.1111/1755-0998.13673},
pmid = {35748425},
issn = {1755-0998},
mesh = {*Data Aggregation ; *Ecology/methods ; Ecosystem ; Humans ; Phylogeography ; Software ; },
abstract = {Patterns of genetic diversity within species contain information the history of that species, including how they have responded to historical climate change and how easily the organism is able to disperse across its habitat. More than 40,000 phylogeographic and population genetic investigations have been published to date, each collecting genetic data from hundreds of samples. Despite these millions of data points, meta-analyses are challenging because the synthesis of results across hundreds of studies, each using different methods and forms of analysis, is a daunting and time-consuming task. It is more efficient to proceed by repurposing existing data and using automated data analysis. To facilitate data repurposing, we created a database (phylogatR) that aggregates data from different sources and conducts automated multiple sequence alignments and data curation to provide users with nearly ready-to-analyse sets of data for thousands of species. Two types of scientific research will be made easier by phylogatR: large meta-analyses of thousands of species that can address classic questions in evolutionary biology and ecology, and student- or citizen- science based investigations that will introduce a broad range of people to the analysis of genetic data. phylogatR enhances the value of existing data via the creation of software and web-based tools that enable these data to be recycled and reanalysed and increase accessibility to big data for research laboratories and classroom instructors with limited computational expertise and resources.},
}
@article {pmid35748219,
year = {2022},
author = {Weyrich, A and Joel, M and Lewin, G and Hofmann, T and Frericks, M},
title = {Review of the state of science and evaluation of currently available in silico prediction models for reproductive and developmental toxicity: A case study on pesticides.},
journal = {Birth defects research},
volume = {114},
number = {14},
pages = {812-842},
pmid = {35748219},
issn = {2472-1727},
mesh = {Computer Simulation ; Databases, Factual ; *Pesticides/toxicity ; Quantitative Structure-Activity Relationship ; Reproduction ; },
abstract = {BACKGROUND: In silico methods for toxicity prediction have increased significantly in recent years due to the 3Rs principle. This also applies to predicting reproductive toxicology, which is one of the most critical factors in pesticide approval. The widely used quantitative structure-activity relationship (QSAR) models use experimental toxicity data to create a model that relates experimentally observed toxicity to molecular structures to predict toxicity. Aim of the study was to evaluate the available prediction models for developmental and reproductive toxicity regarding their strengths and weaknesses in a pesticide database.
METHODS: The reproductive toxicity of 315 pesticides, which have a GHS classification by ECHA, was compared with the prediction of different in silico models: VEGA, OECD (Q)SAR Toolbox, Leadscope Model Applier, and CASE Ultra by MultiCASE.
RESULTS: In all models, a large proportion (up to 77%) of all pesticides were outside the chemical space of the model. Analysis of the prediction of remaining pesticides revealed a balanced accuracy of the models between 0.48 and 0.66.
CONCLUSION: Overall, predictions were only meaningful in rare cases and therefore always require evaluation by an expert. The critical factors were the underlying data and determination of molecular similarity, which offer great potential for improvement.},
}
@article {pmid35747132,
year = {2022},
author = {Li, W and Guo, Y},
title = {A Secure Private Cloud Storage Platform for English Education Resources Based on IoT Technology.},
journal = {Computational and mathematical methods in medicine},
volume = {2022},
number = {},
pages = {8453470},
pmid = {35747132},
issn = {1748-6718},
mesh = {*Big Data ; *Cloud Computing ; Humans ; Technology ; },
abstract = {The contemporary ubiquitous "cloud" network knowledge and information resources, as well as ecological pedagogy theory, have enlarged teaching research's perspective, widened teaching research's innovation area, and created practical options for English classroom reform. Cloud education relies on the Internet of Things, cloud computing, and big data to have a huge impact on the English learning process. The key to the integration of English education resources is the storage of huge amount of English teaching data. Applying the technology and methods of cloud storage to the construction of English education resource integration can effectively save the educational resources of schools, improve the utilization rate of English education resources, and thus enhance the teaching level of English subjects. In this work, we examine the existing state of English education resource building and teaching administration and offer a way for creating a "private cloud" of English education materials. We not only examined the architecture and three-layer modules of cloud computing in depth, but we also analyzed the "private cloud" technology and built the cloud structure of English teaching materials on this foundation. We hope that this paper can help and inspire us to solve the problems of uneven distribution, irregular management, and difficult sharing in the construction of English education resources.},
}
@article {pmid35743915,
year = {2022},
author = {Vargová, B and Majláth, I and Kurimský, J and Cimbala, R and Zbojovský, J and Tryjanowski, P and Majláthová, V},
title = {Locomotor Activity of Ixodes ricinus Females in 900 MHz Electromagnetic Field.},
journal = {Life (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
pmid = {35743915},
issn = {2075-1729},
abstract = {Mobile telecommunications technologies have become an indispensable part of people's lives of all ages around the world. They affect personal life and social interactions and are a work tool in the work routine. Network availability requirements and the quality of the Internet connection are constantly increasing, to which telecommunications providers are responding. Humans and wildlife live in the permanent presence of electromagnetic radiation with just a minor knowledge of the impact this radiation has. The aim of our study was to investigate the effect of a 900 MHz electromagnetic field (EMF) on the locomotor behavior of female Ixodes ricinus ticks under laboratory conditions. Experiments were performed in the radiation-shielded tube (RST) test and radiation-shielded circular open-field arena placed in an anechoic chamber. Altogether, 480 female I. ricinus ticks were tested. In the RST arena, no differences in preference for irradiated and shielded parts of experimental modules were observed; in the open-field arena, the time spent and the trajectory passed was significantly longer in the part exposed to the EMF.},
}
@article {pmid35742413,
year = {2022},
author = {Maturkanič, P and Tomanová Čergeťová, I and Konečná, I and Thurzo, V and Akimjak, A and Hlad, Ľ and Zimny, J and Roubalová, M and Kurilenko, V and Toman, M and Petrikovič, J and Petrikovičová, L},
title = {Well-Being in the Context of COVID-19 and Quality of Life in Czechia.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {12},
pages = {},
pmid = {35742413},
issn = {1660-4601},
mesh = {Adolescent ; *COVID-19/epidemiology ; Czech Republic/epidemiology ; Female ; Humans ; Male ; *Quality of Life ; Religion ; Surveys and Questionnaires ; },
abstract = {The present study focuses on exploring the differences and relationship between well-being and experience of pastoral and psychological service of religious denomination based on religious affiliation during the first wave of the pandemic in Czechia. Our research has been focused on the investigation, comparison, and correlation between the level of well-being and pastoral and psychological service. The research sample (n = 1126) consisted of the Czech health population with age over 16 years, of which 42.4% were men (n = 478) and 57.5% were women (n = 648). From the perspective of religiosity, the study sample was divided in terms of religion into two groups-51.9% participants with religious affiliation (n = 584) and 48.1% participants without religious affiliation (n = 542). The level of well-being was identified by means of The Satisfaction with Life Scale (Diener, Emmons, Larsen, & Griffin, 1985). The level of experience with pastoral and psychological service was measured using our non-standardised questionnaire. The results confirmed the differences between the variables of well-being and positive experience with pastoral and psychological service based on religious affiliation. Moreover, we confirmed the hypothesis of a positive correlation between well-being and positive experience with pastoral and psychological service in Czechia.},
}
@article {pmid35739750,
year = {2022},
author = {Li, S and Shen, W and Lian, S and Wu, Y and Qu, Y and Deng, Y},
title = {DARHD: A sequence database for aromatic ring-hydroxylating dioxygenase analysis and primer evaluation.},
journal = {Journal of hazardous materials},
volume = {436},
number = {},
pages = {129230},
doi = {10.1016/j.jhazmat.2022.129230},
pmid = {35739750},
issn = {1873-3336},
mesh = {Amino Acid Sequence ; Bacteria/metabolism ; Biodegradation, Environmental ; Databases, Nucleic Acid ; *Dioxygenases/genetics/metabolism ; Phylogeny ; *Polycyclic Aromatic Hydrocarbons/metabolism ; },
abstract = {Biodegradation of aromatic compounds is ubiquitous in the environment and important for controlling organic pollutants. Aromatic ring-hydroxylating dioxygenases (ARHDs) are responsible for the first and rate-limiting step of aerobic biodegradation of aromatic compounds. The ARHD α subunit is a good biomarker for studying functional microorganisms in the environment, however their diversity and corresponding primer coverage are unclear, both of which require a comprehensive sequence database for the ARHD α subunit. Here amino acid sequences of the ARHD α subunit were collected, and a total of 103 sequences were selected as seed sequences that were distributed in 72 bacterial genera with 34 gene names. Based on both homolog search and keyword confirmation against the GenBank, a sequence database of ARHD (DARHD) has been established and 6367 highly credible sequences were retrieved. DARHD contained 407 bacterial genera capable of degrading 38 aromatic substrates, and intricate relationships among the gene name, aromatic substrate and microbial taxa were observed. Thereafter, a total of 136 pairs of primers were collected and assessed. Results showed coverages of most published primers were low. Our research provides new insights for understanding the diversity of ARHD α subunit, and gives guidance on the design and application of primers in the future.},
}
@article {pmid35738644,
year = {2022},
author = {Knauer, J and Terhorst, Y and Philippi, P and Kallinger, S and Eiler, S and Kilian, R and Waldmann, T and Moshagen, M and Bader, M and Baumeister, H},
title = {Effectiveness and cost-effectiveness of a web-based routine assessment with integrated recommendations for action for depression and anxiety (RehaCAT+): protocol for a cluster randomised controlled trial for patients with elevated depressive symptoms in rehabilitation facilities.},
journal = {BMJ open},
volume = {12},
number = {6},
pages = {e061259},
pmid = {35738644},
issn = {2044-6055},
mesh = {Anxiety/therapy ; Cost-Benefit Analysis ; *Depression/psychology ; Humans ; Internet ; *Quality of Life ; Randomized Controlled Trials as Topic ; },
abstract = {INTRODUCTION: The integration of a web-based computer-adaptive patient-reported outcome test (CAT) platform with persuasive design optimised features including recommendations for action into routine healthcare could provide a promising way to translate reliable diagnostic results into action. This study aims to evaluate the effectiveness and cost-effectiveness of such a platform for depression and anxiety (RehaCAT+) compared with the standard diagnostic system (RehaCAT) in cardiological and orthopaedic health clinics in routine care.
METHODS AND ANALYSIS: A two-arm, pragmatic, cluster-randomised controlled trial will be conducted. Twelve participating rehabilitation clinics in Germany will be randomly assigned to a control (RehaCAT) or experimental group (RehaCAT+) in a 1:1 design. A total sample of 1848 participants will be recruited across all clinics. The primary outcome, depression severity at 12 months follow-up (T3), will be assessed using the CAT Patient-Reported Outcome Measurement Information System Emotional Distress-Depression Item set. Secondary outcomes are depression at discharge (T1) and 6 months follow-up (T2) as well as anxiety, satisfaction with participation in social roles and activities, pain impairment, fatigue, sleep, health-related quality of life, self-efficacy, physical functioning, alcohol, personality and health economic-specific general quality of life and socioeconomic cost and benefits at T1-3. User behaviour, acceptance, facilitating and hindering factors will be assessed with semistructured qualitative interviews. Additionally, a smart sensing substudy will be conducted, with daily ecological momentary assessments and passive collection of smartphone usage variables. Data analysis will follow the intention-to-treat principle with additional per-protocol analyses. Cost-effectiveness analyses will be conducted from a societal perspective and the perspective of the statutory pension insurance.
ETHICS AND DISSEMINATION: The study will be conducted according to the Declaration of Helsinki. The Ethics Committee of Ulm University, has approved the study (on 24 February 2021 ref. 509/20). Written informed consent will be obtained for all participants. Results will be published via peer-reviewed journals.
TRIAL REGISTRATION NUMBER: DRKS00027447.},
}
@article {pmid35735943,
year = {2022},
author = {Da Costa, HVV and Vieira do Bonfim, C and Fusco, W and Moreira, MM and Maciano de Paula Neto, F},
title = {Impact of the COVID-19 pandemic on the number of births in Pernambuco Brazil.},
journal = {Geospatial health},
volume = {17},
number = {s1},
pages = {},
doi = {10.4081/gh.2022.1069},
pmid = {35735943},
issn = {1970-7096},
mesh = {Brazil/epidemiology ; *COVID-19/epidemiology ; Forecasting ; Humans ; Pandemics ; Time Factors ; },
abstract = {This study aimed at analysing the potential effects of the COVID-19 pandemic on the time series and spatial patterns of live births in the state of Pernambuco, Brazil, from 2010 to 2021. This is an ecological study that applied intervention analysis in time series, with the goal to identify how projected data behaved in relation to observed data in the months December 2020 to November 2021, i.e. months representing conceptions from March2020 to April 2021. For the state of Pernambuco, a discrepancy up to +5.7% was found between the observed and projected data, while the respective difference for the São Francisco mesoregion showed the opposite trend with maximum discrepancy of -9%. The results did not indicate a clear change in the number of live births but supported the expected continuation of the downward trend of the previous years. Considering the importance of the number of live births in the context of demography, economy and public health, monitoring must be maintained to analyse the possible future impact of the COVID-19 pandemic on live birth projections.},
}
@article {pmid35733262,
year = {2022},
author = {Qiu, Z and Espinoza, B and Vasconcelos, VV and Chen, C and Constantino, SM and Crabtree, SA and Yang, L and Vullikanti, A and Chen, J and Weibull, J and Basu, K and Dixit, A and Levin, SA and Marathe, MV},
title = {Understanding the coevolution of mask wearing and epidemics: A network perspective.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {119},
number = {26},
pages = {e2123355119},
pmid = {35733262},
issn = {1091-6490},
mesh = {*Epidemics/prevention & control ; Humans ; *Masks ; },
abstract = {Nonpharmaceutical interventions (NPIs) such as mask wearing can be effective in mitigating the spread of infectious diseases. Therefore, understanding the behavioral dynamics of NPIs is critical for characterizing the dynamics of disease spread. Nevertheless, standard infection models tend to focus only on disease states, overlooking the dynamics of "beneficial contagions," e.g., compliance with NPIs. In this work, we investigate the concurrent spread of disease and mask-wearing behavior over multiplex networks. Our proposed framework captures both the competing and complementary relationships between the dueling contagion processes. Further, the model accounts for various behavioral mechanisms that influence mask wearing, such as peer pressure and fear of infection. Our results reveal that under the coupled disease-behavior dynamics, the attack rate of a disease-as a function of transition probability-exhibits a critical transition. Specifically, as the transmission probability exceeds a critical threshold, the attack rate decreases abruptly due to sustained mask-wearing responses. We empirically explore the causes of the critical transition and demonstrate the robustness of the observed phenomena. Our results highlight that without proper enforcement of NPIs, reductions in the disease transmission probability via other interventions may not be sufficient to reduce the final epidemic size.},
}
@article {pmid35733118,
year = {2022},
author = {Sawires, R and Kuldorff, M and Fahey, M and Clothier, H and Buttery, J},
title = {Snotwatch: an ecological analysis of the relationship between febrile seizures and respiratory virus activity.},
journal = {BMC pediatrics},
volume = {22},
number = {1},
pages = {359},
pmid = {35733118},
issn = {1471-2431},
mesh = {Child ; Humans ; Infant ; *Influenza, Human/complications/diagnosis/epidemiology ; *Seizures, Febrile/epidemiology/etiology ; Victoria/epidemiology ; *Virus Diseases/complications ; *Viruses ; },
abstract = {BACKGROUND: Febrile seizures are the commonest type of seizure in occurring in the first few years of life, mostly affecting children aged six months to five years old. While largely benign, the incidence of each febrile seizure increases the risk of recurrence, afebrile seizures and epilepsy. Viruses are the most frequent cause of febrile illnesses in which a febrile seizure occurs. Febrile seizure presentation patterns appear to follow a seasonal trend.
AIMS: To identify patterns of febrile seizure incidence across different seasons with specific viral activity, and to establish a framework for analysing virus circulation data with common illnesses within a shared region and population.
SETTING: Our study was a study of febrile seizure presentations in Victoria, Australia and respiratory virus detection.
PARTICIPANTS: We obtained independent datasets of emergency department febrile seizure presentations at Monash Health and all respiratory multiplex PCR tests performed at Monash Health from January 2010-December 2019 to observe common trends in virus circulation and febrile seizure incidence.
STUDY DESIGN: Trends were studied temporally through mixed effects Poisson regression analysis of the monthly incidence of febrile seizures and the rate of positive PCR tests. Peak viral seasons (95th centile incidence) were compared to median viral circulation (50th centile incidence) to calculate peak season risk ratios.
RESULTS: We found a 1.75-2.06 annual risk ratio of febrile seizure incidence in June-September. Temporal analysis of our data showed this peak in febrile seizures was attributable to circulating viruses in this season, and virus modelling showed correlation with increased rates of positive Influenza A (1.48 peak season risk ratio), Influenza B (1.31 peak season risk ratio), Human metapneumovirus (1.19 peak season risk ratio) and Respiratory Syncytial Virus (1.53 peak season risk ratio) on PCR testing.
CONCLUSION: Our ecological study statistically demonstrates the recognised winter peak in febrile seizure incidence and ascribes the seasonal relationship to several viral infections which affect the community, including a novel association with Human metapneumovirus.},
}
@article {pmid35732838,
year = {2022},
author = {Zhao, Y and Niu, Z and Zhong, Q and Wang, L and He, S and Xu, M and Wang, J},
title = {Preparation and Characterization of Red Mud/Fly Ash Composite Material (RFCM) for Phosphate Removal.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {109},
number = {1},
pages = {169-179},
pmid = {35732838},
issn = {1432-0800},
mesh = {Adsorption ; Aluminum Oxide ; *Coal Ash ; Industrial Waste/analysis ; *Phosphates/chemistry ; },
abstract = {In this study, a new red mud/fly ash composite material (RFCM) for phosphate removal was prepared by granulation and activation methods, using bauxite residue (red mud, RM) as the main raw material, adding with some fly ash and a few adhesives. The effects of different types of RM and adhesives on RFCM for phosphate removal were discussed. It was found that RFCM prepared from sintering red mud and cement waste performed better on phosphate removal than that prepared from Bayer red mud and common industrial adhesives. After calcination activated at appropriate temperature around 800-900℃, the specific surface area of RFCM increased, and new substances with hydroxyl (-OH) appeared on the surface of RFCM, which were the functional groups for phosphate removal. Mechanism of RFCM for phosphate removal was speculated as a combination of physical adsorption, chemical adsorption and chemical precipitation, which mainly depended on ligand exchange and chemical reaction. This research will provide a potential application of bauxite residue in environmental remediation.},
}
@article {pmid35732736,
year = {2022},
author = {Paoli, L and Ruscheweyh, HJ and Forneris, CC and Hubrich, F and Kautsar, S and Bhushan, A and Lotti, A and Clayssen, Q and Salazar, G and Milanese, A and Carlström, CI and Papadopoulou, C and Gehrig, D and Karasikov, M and Mustafa, H and Larralde, M and Carroll, LM and Sánchez, P and Zayed, AA and Cronin, DR and Acinas, SG and Bork, P and Bowler, C and Delmont, TO and Gasol, JM and Gossert, AD and Kahles, A and Sullivan, MB and Wincker, P and Zeller, G and Robinson, SL and Piel, J and Sunagawa, S},
title = {Biosynthetic potential of the global ocean microbiome.},
journal = {Nature},
volume = {607},
number = {7917},
pages = {111-118},
pmid = {35732736},
issn = {1476-4687},
support = {835067/ERC_/European Research Council/International ; },
mesh = {Bacteria/classification/genetics ; *Biosynthetic Pathways/genetics ; Genomics ; *Microbiota/genetics ; Multigene Family/genetics ; *Oceans and Seas ; Phylogeny ; },
abstract = {Natural microbial communities are phylogenetically and metabolically diverse. In addition to underexplored organismal groups[1], this diversity encompasses a rich discovery potential for ecologically and biotechnologically relevant enzymes and biochemical compounds[2,3]. However, studying this diversity to identify genomic pathways for the synthesis of such compounds[4] and assigning them to their respective hosts remains challenging. The biosynthetic potential of microorganisms in the open ocean remains largely uncharted owing to limitations in the analysis of genome-resolved data at the global scale. Here we investigated the diversity and novelty of biosynthetic gene clusters in the ocean by integrating around 10,000 microbial genomes from cultivated and single cells with more than 25,000 newly reconstructed draft genomes from more than 1,000 seawater samples. These efforts revealed approximately 40,000 putative mostly new biosynthetic gene clusters, several of which were found in previously unsuspected phylogenetic groups. Among these groups, we identified a lineage rich in biosynthetic gene clusters ('Candidatus Eudoremicrobiaceae') that belongs to an uncultivated bacterial phylum and includes some of the most biosynthetically diverse microorganisms in this environment. From these, we characterized the phospeptin and pythonamide pathways, revealing cases of unusual bioactive compound structure and enzymology, respectively. Together, this research demonstrates how microbiomics-driven strategies can enable the investigation of previously undescribed enzymes and natural products in underexplored microbial groups and environments.},
}
@article {pmid35730806,
year = {2022},
author = {Barbosa, ÁRG and Takemura, LS and Amaral, BS and Wroclawski, ML and Alfer, W and Gil, AO and Monteiro, J and Lourenço, DB and Cha, JD and Apezzato, M and Barbosa, JABA and Bianco, B and Lemos, GC and Carneiro, A},
title = {Benign prostatic hyperplasia surgical treatment trends in the Public Health System in São Paulo, Brazil.},
journal = {Einstein (Sao Paulo, Brazil)},
volume = {20},
number = {},
pages = {eAO6880},
pmid = {35730806},
issn = {2317-6385},
mesh = {Brazil/epidemiology ; Humans ; *Laser Therapy/methods ; Male ; Prostatectomy ; *Prostatic Hyperplasia/surgery ; Public Health ; Retrospective Studies ; *Transurethral Resection of Prostate/methods ; Treatment Outcome ; },
abstract = {OBJECTIVE: To describe and compare the number of surgeries, mortality rate, length of hospital stay, and costs of transurethral resection of the prostate and open prostatectomy for the treatment of benign prostatic hyperplasia, between 2008 and 2018, in the Public Health System in São Paulo, Brazil.
METHODS: Ecological and retrospective study using data from the informatics department of the Brazilian Public Health System database. Procedure codes were "open prostatectomy" and "transurethral resection of the prostate." The outcomes analyzed were compared between transurethral resection of the prostate and open prostatectomy according to the hospital surgical volume and presence or absence of a residency program.
RESULTS: A total of 18,874 surgeries were analyzed (77% transurethral resection of the prostate) and overall mortality was not statistically different between procedures. Intermediate and high-volume centers had shorter length of hospital stay than low-volume centers for transurethral resection of the prostate (3.28, 3.02, and 6.58 days, respectively, p=0.01 and p=0.004). Length of hospital stay was also shorter for open prostatectomy in high-volume compared to low-volume centers (4.86 versus 10.76 days, p=0.036). Intrahospital mortality was inversely associated with surgical volume for transurethral resection of the prostate. Centers with residency program had shorter length of hospital stay considering open prostatectomy and less mortality regarding transurethral resection of the prostate. Open prostatectomy was 64% more expensive than transurethral resection of the prostate.
CONCLUSION: The findings suggest the importance of investing in specialized centers, which could be potential referral centers for surgical cases.},
}
@article {pmid35727537,
year = {2022},
author = {Terraneo, TI and Mariappan, KG and Forsman, Z and Arrigoni, R},
title = {Mitochondrial Genome of Nonmodel Marine Metazoans by Next-Generation Sequencing (NGS).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2498},
number = {},
pages = {1-18},
pmid = {35727537},
issn = {1940-6029},
mesh = {Animals ; Computational Biology ; DNA ; Gene Library ; *Genome, Mitochondrial ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; },
abstract = {Mitochondrial genomes (mtgenome) represent an important source of information for addressing fundamental evolutionary, phylogeographic, systematic, and ecological questions in marine organisms. In the last two decades the advent of high-throughput next-generation sequencing (NGS) has provided an unprecedented possibility to access large amount of genomic data and, as such, there has been a rapid growth in mtgenome resources and studies. In particular, NGS strategies represent a great advantage for investigating nonmodel marine organisms for which no or limited genomic resources are available. Here, we describe a routinely used standardized protocol to obtain mtgenome of nonmodel marine organisms by NGS. The protocol is composed of five main steps, including DNA extraction, DNA fragmentation, library preparation, high-throughput sequencing, and bioinformatic analyses. Each of the first three steps is followed by size/quality and concentration validations. The advantages of the described protocol rely on the assumption that no a priori information on mtgenome of the studied organism is needed and on its versatility as researchers may choose several kits for DNA extraction and library preparation and adopt different methods for DNA fragmentation depending on their needs, experience, and suppliers.},
}
@article {pmid35724975,
year = {2022},
author = {Prajapati, J and Singh, A and Patil, K and Bhowmick, AR and Mukherjee, A and Huang, Y and Banerjee, AK},
title = {An occurrence data set for invasive and naturalized alien plants in India.},
journal = {Ecology},
volume = {103},
number = {11},
pages = {e3794},
doi = {10.1002/ecy.3794},
pmid = {35724975},
issn = {1939-9170},
mesh = {*Introduced Species ; *Ecosystem ; Plants ; Biodiversity ; Databases, Factual ; },
abstract = {India has numerous invasive alien plant species (IAPSs), which seriously impact biodiversity, ecosystem services, and economic development. The availability of reliable occurrence records of IAPSs is of great importance for their successful management, prediction of distribution across time and space, and other research and development efforts. Global databases of occurrence data, like the Global Biodiversity Information Facility (GBIF), are often not exhaustive, especially for India, and poorly represent the actual distribution of IAPSs in the country. Our objective in creating this data set was threefold: (1) to compile occurrence data for the invasive and naturalized alien plant species of India, (2) to collect spatial and temporal information associated with occurrence records, and (3) to share the data in an accessible format so every record is traceable to its sources and allow users to submit data to increase the resolution of the data set. To achieve these objectives, we extracted data from 3137 literature records and 357 herbarium sheets. For each occurrence record, we curated information for 20 variables, which were arranged in a table with the Darwin Core (DwC) terms as column names. All data were subjected to technical validation before being included in the database. A total of 12,347 occurrence records were obtained for 362 species (195 invasive aliens and 167 naturalized aliens). The number of collected occurrence records was much higher for the invasive aliens (73.7%) than for the naturalized alien species (26.3%). Our data set will supplement the GBIF data by 60.39%, and occurrence records will be added for 64 invasive and naturalized alien plant species. The data set, as a part of the larger database of the Indian Alien Flora Information (ILORA) database, is made available without any restrictions on use as long as this data paper is properly cited. We have also made provisions for users to submit occurrence-related data following a data standard. The users are encouraged to cite the original reference when using a specific data record. The data set is expected to assist a wide range of stakeholders involved in India's scientific research, policy formulation, and decision-making related to IAPSs.},
}
@article {pmid35716808,
year = {2022},
author = {Thomas, AC and Wintemute, G and Nathens, AB and Subacius, H and Stey, AM and Bilimoria, KY and Campbell, BT},
title = {The association between gun shows and firearm injuries: An analysis of 259 gun shows across 23 US cities.},
journal = {Preventive medicine},
volume = {161},
number = {},
pages = {107110},
doi = {10.1016/j.ypmed.2022.107110},
pmid = {35716808},
issn = {1096-0260},
mesh = {Cities ; Commerce ; Databases, Factual ; *Firearms ; Humans ; *Wounds, Gunshot/epidemiology ; },
abstract = {Guns shows are estimated to account for 4-9% of firearm sales in the US. Increased regulation of firearm sales at gun shows has been proposed as one approach to reducing firearm injury rates. This study evaluated the association between gun shows and local firearm injury rates. Data regarding the date and location of gun shows from 2017 to 2019 were abstracted from the Big Show Journal. Firearm injury rates were estimated using discharges from trauma centers serving counties within a 25-mile radius of each gun show. Clinical data were derived from the National Trauma Databank (NTDB). We used Poisson regression modeling to adjust for potential confounders including seasonality. We evaluated injury rates before and after 259 gun shows in 23 US locations using firearm injury data from 36 trauma centers. There were 1513 hospitalizations for firearm injuries pre-gun show and 1526 post-gun show. The adjusted mean 2-week rate of all-cause firearm injury per 1,000,000 person-years was 1.79 (1.16-2.76) before and 1.82 (1.18-2.83) after a gun show, with an incident rate ratio of 1.02 (0.94, 1.08). The adjusted mean 2-week rate did not vary significantly by intent after a gun show, (p = 0.24). Within two weeks after a gun show, rates of hospitalization for all-cause firearm injury do not increase significantly within the surrounding communities. The relatively small increase in available firearms after a show and the short time horizon evaluated may account for the absence of an association between gun show firearm sales and local firearm injury rates.},
}
@article {pmid35715815,
year = {2022},
author = {Belichenko, O and Kolosova, V and Kalle, R and Sõukand, R},
title = {Green pharmacy at the tips of your toes: medicinal plants used by Setos and Russians of Pechorsky District, Pskov Oblast (NW Russia).},
journal = {Journal of ethnobiology and ethnomedicine},
volume = {18},
number = {1},
pages = {46},
pmid = {35715815},
issn = {1746-4269},
mesh = {Ethnobotany ; Humans ; Medicine, Traditional ; *Pharmacy ; *Plants, Medicinal ; Russia ; Toes ; },
abstract = {BACKGROUND: While the hybridization of ecological knowledge has attracted substantial attention from researchers, the coexistence of local and allopathic medicinal traditions in literate societies widely exposed to centralized schooling and medical services has not yet been investigated. To this end, we studied the current and remembered local ethnomedical practices of Setos and neighboring Russians at the border with Estonia.
METHODS: During 2018-2019, we carried out 62 semi-structured interviews in the Pechorsky District of Pskov Oblast, NW Russia. For cross-border comparison, we utilized the data from 71 interviews carried out at the same time among Setos in Estonia. The Jaccard Similarity Index and qualitative comparison were used to analyze the data.
RESULTS: The study participants mentioned 819 uses of 112 taxa belonging to 54 families. More than two-thirds of the uses (565) were quoted by 36 Russian interviewees, while the remaining third (254) were quoted by 26 Seto interviewees, with the top 3 in both groups being Viburnum opulus, Rubus idaeus, and Plantago major. The Seto intraethnic similarity index was lower (0.43) than the interethnic similarity in Estonia (0.52) and comparable to the interethnic similarity in Russia (0.43). Setos in Russia and local Russians rely more on wild plants (86% and 80% of medicinal plants, respectively), while Setos in Estonia and Estonians show less preference to them (63% and 61%, respectively). Nevertheless, Setos tend to source wild plants available in their gardens (33% of plants for Setos in Estonia and 38% in Russia), while Russians prefer to source them in the wild (38%).
CONCLUSIONS: The preference of both groups in Russia for wild plants over cultivated and purchased plants was inspired by the overall plant literacy, access to nature, and one-to-many knowledge transfer favoring wild plants. Setos in Russia reported a narrower and more homogenous set of plants transferred vertically. However, due to atomization and the erosion of horizontal connections, there are singular plant uses among Setos that overlap with the local Russian set of medicinal plants and differ qualitatively from that of Setos in Estonia.},
}
@article {pmid35715445,
year = {2022},
author = {Donaldson, DR and Koepke, JW},
title = {A focus groups study on data sharing and research data management.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {345},
pmid = {35715445},
issn = {2052-4463},
mesh = {*Data Management ; Focus Groups ; Humans ; *Information Dissemination ; Metadata ; Research Personnel ; },
abstract = {Data sharing can accelerate scientific discovery while increasing return on investment beyond the researcher or group that produced them. Data repositories enable data sharing and preservation over the long term, but little is known about scientists' perceptions of them and their perspectives on data management and sharing practices. Using focus groups with scientists from five disciplines (atmospheric and earth science, computer science, chemistry, ecology, and neuroscience), we asked questions about data management to lead into a discussion of what features they think are necessary to include in data repository systems and services to help them implement the data sharing and preservation parts of their data management plans. Participants identified metadata quality control and training as problem areas in data management. Additionally, participants discussed several desired repository features, including: metadata control, data traceability, security, stable infrastructure, and data use restrictions. We present their desired repository features as a rubric for the research community to encourage repository utilization. Future directions for research are discussed.},
}
@article {pmid35708657,
year = {2022},
author = {Wang, T and Smith, DA and Campbell, C and Freeman, O and Moysova, Z and Noble, T and Várnai, KA and Harris, S and Salih, H and Roadknight, G and Little, S and Glampson, B and Mercuri, L and Papadimitriou, D and Jones, CR and Taylor, V and Chaudhry, A and Phan, H and Borca, F and Olza, J and Warricker, F and Romão, L and Ramlakhan, D and English, L and Klenerman, P and Andersson, M and Collier, J and Stockdale, AJ and Todd, S and McIntyre, K and Frankland, A and Nastouli, E and Khakoo, SI and Gelson, W and Cooke, GS and Woods, K and Davies, J and Barnes, E and Matthews, PC},
title = {Cohort Profile: The National Institute for Health Research Health Informatics Collaborative: Hepatitis B Virus (NIHR HIC HBV) research dataset.},
journal = {International journal of epidemiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ije/dyac127},
pmid = {35708657},
issn = {1464-3685},
support = {/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; },
}
@article {pmid35708643,
year = {2022},
author = {Perry, A and McGaugh, SE and Keene, AC and Blackmon, H},
title = {CaveCrawler: an interactive analysis suite for cavefish bioinformatics.},
journal = {G3 (Bethesda, Md.)},
volume = {12},
number = {8},
pages = {},
pmid = {35708643},
issn = {2160-1836},
support = {R35 GM138098/GM/NIGMS NIH HHS/United States ; R21 NS122166/NS/NINDS NIH HHS/United States ; R01 CA127872/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Biological Evolution ; Caves ; *Characidae/genetics ; *Computational Biology ; Genome ; },
abstract = {The growing use of genomics in diverse organisms provides the basis for identifying genomic and transcriptional differences across species and experimental conditions. Databases containing genomic and functional data have played critical roles in the development of numerous genetic models but most emerging models lack such databases. The Mexican tetra, Astyanax mexicanus exists as 2 morphs: surface-dwelling and cave-dwelling. There exist at least 30 cave populations, providing a system to study convergent evolution. We have generated a web-based analysis suite that integrates datasets from different studies to identify how gene transcription and genetic markers of selection differ between populations and across experimental contexts. Results of diverse studies can be analyzed in conjunction with other genetic data (e.g. Gene Ontology information), to enable biological inference from cross-study patterns and identify future avenues of research. Furthermore, the framework that we have built for A. mexicanus can be adapted for other emerging model systems.},
}
@article {pmid35708073,
year = {2022},
author = {Weinstein, BG and Garner, L and Saccomanno, VR and Steinkraus, A and Ortega, A and Brush, K and Yenni, G and McKellar, AE and Converse, R and Lippitt, CD and Wegmann, A and Holmes, ND and Edney, AJ and Hart, T and Jessopp, MJ and Clarke, RH and Marchowski, D and Senyondo, H and Dotson, R and White, EP and Frederick, P and Ernest, SKM},
title = {A general deep learning model for bird detection in high-resolution airborne imagery.},
journal = {Ecological applications : a publication of the Ecological Society of America},
volume = {32},
number = {8},
pages = {e2694},
doi = {10.1002/eap.2694},
pmid = {35708073},
issn = {1051-0761},
mesh = {Humans ; Animals ; *Deep Learning ; Ecosystem ; Artificial Intelligence ; Neural Networks, Computer ; Birds ; },
abstract = {Advances in artificial intelligence for computer vision hold great promise for increasing the scales at which ecological systems can be studied. The distribution and behavior of individuals is central to ecology, and computer vision using deep neural networks can learn to detect individual objects in imagery. However, developing supervised models for ecological monitoring is challenging because it requires large amounts of human-labeled training data, requires advanced technical expertise and computational infrastructure, and is prone to overfitting. This limits application across space and time. One solution is developing generalized models that can be applied across species and ecosystems. Using over 250,000 annotations from 13 projects from around the world, we develop a general bird detection model that achieves over 65% recall and 50% precision on novel aerial data without any local training despite differences in species, habitat, and imaging methodology. Fine-tuning this model with only 1000 local annotations increases these values to an average of 84% recall and 69% precision by building on the general features learned from other data sources. Retraining from the general model improves local predictions even when moderately large annotation sets are available and makes model training faster and more stable. Our results demonstrate that general models for detecting broad classes of organisms using airborne imagery are achievable. These models can reduce the effort, expertise, and computational resources necessary for automating the detection of individual organisms across large scales, helping to transform the scale of data collection in ecology and the questions that can be addressed.},
}
@article {pmid35707246,
year = {2022},
author = {Xiao, D and Keita, M and Zhang, C and Wang, E and Diaz, ND and Wu, J and He, H and Ma, J and Julien, EO},
title = {Dataset of coal bio-gasification and coalbed methane stimulation by single well nutrition injection in Qinshui anthracite coalbed methane wells.},
journal = {Data in brief},
volume = {43},
number = {},
pages = {108353},
pmid = {35707246},
issn = {2352-3409},
abstract = {In-situ coal bio-gasification can be defined as one of the coal bio-mining methodology that fully utilizes the methanogenic bacteria in coal to review the current findings, namely anaerobic digestion of organic components. The following experiment has been done in regards, one vertical well and one multi-branch horizontal well were used as experiment wells and two vertical wells were used as control wells, the pilot test was carried out with single well nutrition injection method. By applying the above mentioned method, the concentration of Cl[-] ion and number altered in Methanogen spp. were used to trace nutrition diffusion. Furthermore, technical implementation results analysis has been made with the observation of CH4 production changes and coal bed biome evolution. Gas production rates in each well were monitored by using the FLLQ gas roots flow mete. The concentration of CH4 and CO2 were evaluated by using the Agilent 7890A gas chromatograph, on the other hand, concentrations of Cl[-] were determined by the application of ICS-1100 ion chromatography system. The F420 fluorescence method was adopted to test for the presence of methanogenic bacteria. In the interim of the completion stage, the study stated that the bacterial diversity of underground water of Z-7H well has a high pass sequence with the experimental period of 814 days. Gas production data in Z-159 and Z-7H wells showed the gasification of coal lasted 635 and 799 days, yielded 74817 m[3] and 251754 m[3] coalbed methane, respectively. Furthermore, experimental data presented that one time nutrition injection in anthracite coalbed methane wells achieved an average of 717 days of continuous gas production among all experimental wells. The above fore-said study dedicated the significance of native bacterial fermentation, as it proven the fact that anthracite can be applied to accomplish coal bio-gasification and coalbed methane production stimulation in-situ.},
}
@article {pmid35707189,
year = {2022},
author = {Chen, G and Tang, P and Wang, H},
title = {Boundary Determination of Lake-Type Wetland Park Based on GIS Multifactor Analysis.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {6161491},
pmid = {35707189},
issn = {1687-5273},
mesh = {China ; Conservation of Natural Resources ; *Ecosystem ; Environmental Monitoring ; Geographic Information Systems ; Humans ; Remote Sensing Technology ; *Wetlands ; },
abstract = {One key carrier for wetland resource protection is wetland park, the main form of which includes lake-type wetland park. To determine the management and control boundary of lake-type wetland parks scientifically and reasonably is of great significance to the sustainable protection and utilization of wetland resources. From the perspective of landscape architecture, and landscape ecology, this paper studies the boundary determination of Changdang Lake National Wetland Park (the Park) based on satellite remote sensing information technology and GIS technology and in virtue of Analytic Hierarchy Process (AHP). In this study, 12 subindicators were selected from three levels including visual control, human geography, and ecological control. The weight of each indicator was determined by AHP, and then the influencing factors were transformed into graphic data by using GIS technology. Finally, the Park's boundary was determined by factor superposition analysis based on the weight. The research shows that the newly defined management and control boundary are about 340 sq.km, which effectively integrates the human and natural ecological resources around the lake area, makes the development of the surrounding areas harmonious, ensures the integrity of the lake area ecosystem, and facilitates the sustainable development of wetland resources.},
}
@article {pmid35705152,
year = {2022},
author = {Chen, Y and Su, J and Zhao, H and Li, JY and Wang, J and Wang, Q and Yin, J and Jin, L},
title = {In-situ biochar amendment mitigates dietary risks of heavy metals and PAHs in aquaculture products.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {308},
number = {},
pages = {119615},
doi = {10.1016/j.envpol.2022.119615},
pmid = {35705152},
issn = {1873-6424},
mesh = {Animals ; Aquaculture ; Charcoal ; Environmental Monitoring ; Geologic Sediments/chemistry ; *Metals, Heavy/analysis ; *Polycyclic Aromatic Hydrocarbons/analysis ; Water ; *Water Pollutants, Chemical/analysis ; },
abstract = {Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) are two common contaminant groups of concern in aquaculture products. While biochar amendment can be one of the solutions to immobilize these contaminant in pond sediment, its in situ effectiveness in mitigating the bioavailability, tissue residue, and dietary risk of these contaminants is yet to be tested. In this study, we added wheat straw biochar in sediments of three aquaculture ponds with polyculture of fish and shrimps and employed passive sampling techniques (i.e., diffusive gradient in thin film for HMs and polydimethylsiloxane for PAHs) to assess the diffusion flux and bioavailability throughout the culturing cycle. Reduction in HM concentrations in organisms by biochar after 28 weeks ranged from 17% to 65% for benthic organisms and from 6.0% to 47% for fish. ΣTHQs values of HMs dropped from 2.5 to 2.1 and 1.2 to 0.91 for the two organisms with the initial ΣTHQs value above 1.0. The decrease rates of both the concentrations and ΣTHQs values followed the order of Cu > Cr > Pb > Cd, which was closely correlated with the speciation of HMs in the sediments. ΣPAHs values dropped significantly at the growth stage (20[th] week) and the mature stage (28[th] week), and, on average, by 34% across all the organisms. Carcinogenic PAHs in aquaculture products decreased dramatically at the seedling stage (12[th] week), while there was no significant change observed for the Incremental Lifetime Cancer Risk values. By comparing the freely-dissolved concentrations in pore water of sediments and the overlying water, consistently enhanced diffusion fluxes of HMs and PAHs from water to sediment over the whole culturing cycle were obtained. Our results demonstrated the in situ applicability of biochar amendment to remediating chemical pollution in aquaculture environment and safeguarding quality of aquatic products.},
}
@article {pmid35699571,
year = {2022},
author = {Mangal, S and Park, L and Reading Turchioe, M and Choi, J and Niño de Rivera, S and Myers, A and Goyal, P and Dugdale, L and Masterson Creber, R},
title = {Building trust in research through information and intent transparency with health information: representative cross-sectional survey of 502 US adults.},
journal = {Journal of the American Medical Informatics Association : JAMIA},
volume = {29},
number = {9},
pages = {1535-1545},
pmid = {35699571},
issn = {1527-974X},
support = {/NR/NINR NIH HHS/United States ; R00 NR016275/NR/NINR NIH HHS/United States ; },
mesh = {Adult ; Cross-Sectional Studies ; Female ; Health Services Research ; Humans ; *Physicians ; Surveys and Questionnaires ; *Trust ; },
abstract = {OBJECTIVE: Participation in healthcare research shapes health policy and practice; however, low trust is a barrier to participation. We evaluated whether returning health information (information transparency) and disclosing intent of data use (intent transparency) impacts trust in research.
MATERIALS AND METHODS: We conducted an online survey with a representative sample of 502 US adults. We assessed baseline trust and change in trust using 6 use cases representing the Social-Ecological Model. We assessed descriptive statistics and associations between trust and sociodemographic variables using logistic and multinomial regression.
RESULTS: Most participants (84%) want their health research information returned. Black/African American participants were more likely to increase trust in research with individual information transparency (odds ratio (OR) 2.06 [95% confidence interval (CI): 1.06-4.34]) and with intent transparency when sharing with chosen friends and family (3.66 [1.98-6.77]), doctors and nurses (1.96 [1.10-3.65]), or health tech companies (1.87 [1.02-3.40]). Asian, Native American or Alaska Native, Native Hawaiian or Pacific Islander, Multirace, and individuals with a race not listed, were more likely to increase trust when sharing with health policy makers (1.88 [1.09-3.30]). Women were less likely to increase trust when sharing with friends and family (0.55 [0.35-0.87]) or health tech companies (0.46 [0.31-0.70]).
DISCUSSION: Participants wanted their health information returned and would increase their trust in research with transparency when sharing health information.
CONCLUSION: Trust in research is influenced by interrelated factors. Future research should recruit diverse samples with lower baseline trust levels to explore changes in trust, with variation on the type of information shared.},
}
@article {pmid35695566,
year = {2022},
author = {Sajid, M and Srivastava, S and Yadav, RK and Singh, H and Singh, S and Bharadwaj, M},
title = {Composition and Ecological Functionality of Fungal Communities Associated with Smokeless Tobacco Products Mainly Consumed in India.},
journal = {Microbiology spectrum},
volume = {10},
number = {4},
pages = {e0227321},
pmid = {35695566},
issn = {2165-0497},
mesh = {Bacteria/genetics ; Carcinogens/analysis ; India ; *Mycobiome ; *Nitrosamines/analysis ; *Tobacco, Smokeless/analysis ; },
abstract = {The microbial communities present in smokeless tobacco products (STPs) perform critical steps in the synthesis of carcinogens, mainly tobacco-specific nitrosamines (TSNAs). Most studies emphasize the bacterial component, and the mycobiome of STPs has not been well characterized. In this study, we investigated the fungal communities in the different categories of STPs by sequencing the internal transcribed spacer (ITS) rRNA region of the fungal genome. The ecological character of the fungal community associated with STPs was determined by using FUNGuild. Our results indicated that Ascomycota and Basidiomycota were the most abundant fungal phyla across all STPs. The predominant fungal genera in STPs were Pichia, Sterigmatomyces, and Mortierella. The α-diversity varied significantly across the STPs based on observed, Fisher, and Shannon indices. Using SparCC cooccurrence network analysis, significant positive correlations of 58.5% and negative connections of 41.5% were obtained among fungal genera identified in STPs. Furthermore, the functional predictions by FUNGuild determined that STPs possessed high abundances of saprotroph and pathotroph-saprotroph-symbiotroph fungal trophic groups. At the functional guild level, the qiwam samples contained high abundances of soil saprotrophs, while plant pathogens were prevalent in pan-masala samples. These results suggest that various fungal populations reside in STPs and interrelate with each other and can contribute to the synthesis of TSNAs. This study has established the basis for future large-scale investigations of STP-associated mycobiota and the impact of such mycobiota in oral carcinogenesis in STP users via inflammation and carcinogens (TSNAs and mycotoxins). IMPORTANCE Smokeless tobacco products (STPs) contain complex microbial communities that influence the synthesis of carcinogens, such as tobacco-specific nitrosamines (TSNAs). Research on STP-associated bacterial populations revealed connections between bacterial metabolism and TSNA synthesis. The abundance of the fungal population may also have an impact on the production of TSNAs. This study examined STPs popularly used in India, and diverse fungal communities were identified in these STPs. Pichia, Sterigmatomyces, and Mortierella were the predominant fungal genera in the STPs. High abundances of saprotroph and pathotroph-saprotroph-symbiotroph trophic groups in STPs could affect the degradation of tobacco products and the synthesis of TSNAs.},
}
@article {pmid35694197,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Lewin, T and , },
title = {The genome sequence of the pebble prominent, Notodonta ziczac (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {111},
pmid = {35694197},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Notodonta ziczac (the pebble prominent; Arthropoda; Insecta; Lepidoptera; Notodontidae). The genome sequence is 352 megabases in span. The majority of the assembly (99.66%) is scaffolded into 31 chromosomal pseudomolecules, with the Z sex chromosome assembled. The mitochondrial genome was also assembled, and is 18.3 kilobases in length.},
}
@article {pmid35693972,
year = {2022},
author = {van Doorn, M and Nijhuis, LA and Monsanto, A and van Amelsvoort, T and Popma, A and Jaspers, MWM and Noordzij, ML and Öry, FG and Alvarez-Jimenez, M and Nieman, DH},
title = {Usability, Feasibility, and Effect of a Biocueing Intervention in Addition to a Moderated Digital Social Therapy-Platform in Young People With Emerging Mental Health Problems: A Mixed-Method Approach.},
journal = {Frontiers in psychiatry},
volume = {13},
number = {},
pages = {871813},
pmid = {35693972},
issn = {1664-0640},
abstract = {INTRODUCTION: To optimize treatment, it is of utmost importance to take into account the myriad of biological, social, and psychological changes that young people go through during adolescence which make them more vulnerable for developing mental health problems. Biocueing, a non-invasive method to transform physiological parameters into an observable signal, could strengthen stress- and emotion regulation by cueing physiologically unusual values in daily life. The aim of this study is to investigate the usability, feasibility, and exploratory effect of biocueing in addition to ENgage YOung people earlY (ENYOY), a moderated digital social therapy-platform, in young people with emerging mental health complaints.
METHODS: A user-centered mixed-method design was used. A focus group was conducted to optimize the ENYOY-platform and biocueing intervention. Biocueing was operationalized by a smartwatch and the Sense-IT app. A within-subjects design was used; 10 days for all participants 'biofeedback off' (control), followed by 10 days 'biofeedback on' (experimental). Emotional awareness and perceived stress were measured using ecological momentary assessment. Eight individuals participated. User-friendliness, usability, and acceptance were assessed using a qualitative design.
RESULTS: Findings from the focus group resulted in several adaptations of the biocueing intervention to the ENYOY-platform and vice versa. The average measurement compliance rate was 78.8%. Level-one findings showed different individual effects on perceived stress and emotional awareness. Level-two analyses showed no overall effects on perceived stress (B = -0.020, p = 0.562) and overall positive effects on emotional awareness (B = 0.030, p = 0.048) with small effect sizes (Improvement Rate Difference = 0.05-0.35). The intervention was found to be acceptable and showed moderate usability. Participants indicated they experienced improvements in reflection on feelings and changes in behavior, such as pausing and evaluating the situation.
CONCLUSION: These preliminary results show that biocueing could be a promising addition to digital treatment platforms and help young people become more emotionally aware. Improvements should be made regarding the usability and acceptability of the smartwatch, as well as more extensive integration of the biocueing intervention with a digital treatment platform. It would be relevant to gain a better understanding of which individuals would benefit most from an additional biocueing intervention.},
}
@article {pmid35690703,
year = {2022},
author = {Satrovic, E and Adedoyin, FF},
title = {An empirical assessment of electricity consumption and environmental degradation in the presence of economic complexities.},
journal = {Environmental science and pollution research international},
volume = {29},
number = {52},
pages = {78330-78344},
pmid = {35690703},
issn = {1614-7499},
mesh = {*Carbon Dioxide ; *Economic Development ; Carbon Footprint ; Electricity ; },
abstract = {To a large extent, the theories and concepts behind the effect of ecological footprint have been the paramount concern of the recent literature. Since the rising and falling of environmental degradation have been a continuous issue since the first phase of development, determinants such as economic complexity may play a critical role in achieving long-term sustainable development in the framework of environmental Kuznets curve (EKC) paradigm. Therefore, this research expands on the notion of an EKC paradigm for the world's top ten most complex economies by considering four variables, such as real GDP per capita, electricity consumption, trade openness, and a new putative factor of environmental obstacle, the economic complexity index (ECI). This is one of the first studies to look at the impact of ECI on the ecological footprint of a specific sample from 1998 to 2017. The findings demonstrate a continuous inverted U-shaped link between real GDP per capita, the square of real GDP per capita, and ecological footprint. The EKC hypothesis is found to be valid in the long term in the examined complex economies. The findings of the panel autoregressive distributed lag (ARDL) of the pooled mean group (PMG) and fully modified ordinary least squares (FMOLS) estimations demonstrate that in the long term, electric power usage contributed to the carbon footprints. Furthermore, the economic complexity index and trade openness increase environmental performance over time. To determine if there is causation between the variables, we employ the panel vector error correction model (VECM) framework. Particularly, the results show unidirectional causality running from electric power consumption to ecological footprint and bidirectional causal relationship between (1) economic growth and ecological footprint; (2) square of economic growth and ecological footprint; (3) economic complexity index and ecological footprint; and (4) trade openness and ecological footprint.},
}
@article {pmid35686764,
year = {2022},
author = {Yan, YY and Yin, SS and He, Q and Qin, K and Zhang, RQ},
title = {[Trend Changes in Ozone Pollution and Sensitivity Analysis of Ozone in Henan Province].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {43},
number = {6},
pages = {2947-2956},
doi = {10.13227/j.hjkx.202108287},
pmid = {35686764},
issn = {0250-3301},
mesh = {*Air Pollutants/analysis ; *Air Pollution/analysis ; China ; Cities ; Environmental Monitoring/methods ; *Ozone/analysis ; Seasons ; },
abstract = {Based on air quality station data and satellite remote sensing data, the interannual variation characteristics and seasonal variation trends of near-surface ozone (O3) in Henan province were studied, and the variation in O3 sensitivity was analyzed. The results showed that the O3 concentration near the surface of Henan province increased first and then decreased from 2015 to 2020. The highest O3 concentration was found in 2018, and the annual mean of the maximum daily 8 h moving mean (MDA8) of O3 was 110.70 μg·m[-3]. The difference in MDA8 values among different stations gradually decreased. From 2015 to 2020, the average monthly MDA8 in Henan province showed an upward trend, with a growth rate of 2.46 μg·(m[3]·a)[-1]. According to the MK trend test, except for in Luohe, Nanyang, and Pingdingshan, the rising trend in other cities was significant (P<0.05). The concentration of MDA8 in the four seasons also showed an increasing trend during the 6 years as follows:autumn (19.31%)>winter (17.09%)>spring (16.82%)>summer (7.24%). From 2015 to 2019, the high value of tropospheric NO2 was concentrated in the northwest of Henan province, and the concentration showed a decreasing trend with a decreasing rate of 0.34×10[15] molecules·(cm[2]·a)[-1], whereas the tropospheric HCHO showed a slow rising trend with an annual growth rate of 0.19×10[15] molecules·(cm[2]·a)[-1], with a higher concentration in the northern urban area. The O3 sensitivity control area from 2015 to 2019 showed that most of the eastern part of Henan province belonged to the VOCs limited category.},
}
@article {pmid35684257,
year = {2022},
author = {Gašparovičová, P and Ševčík, M and David, S},
title = {The Prediction of Distribution of the Invasive Fallopia Taxa in Slovakia.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
pmid = {35684257},
issn = {2223-7747},
abstract = {Invasive species are now considered the second biggest threat for biodiversity and have adverse environmental, economic and social impacts. Understanding its spatial distribution and dynamics is crucial for the development of tools for large-scale mapping, monitoring and management. The aim of this study was to predict the distribution of invasive Fallopia taxa in Slovakia and to identify the most important predictors of spreading of these species. We designed models of species distribution for invasive species of Fallopia-Fallopia japonica-Japanese knotweed, Fallopia sachalinensis-Sakhalin knotweed and their hybrid Fallopia × bohemica-Czech knotweed. We designed 12 models-generalized linear model (GLM), generalized additive model (GAM), classification and regression trees (CART), boosted regression trees (BRT), multivariate adaptive regression spline (MARS), random forests (RF), support vector machine (SVM), artificial neural networks (ANN), maximum entropy (Maxent), penalized maximum likelihood GLM (GLMNET), domain, and radial basis function network (RBF). The accuracy of the models was evaluated using occurrence data for the presence and absence of species. The final simplified logistic regression model showed the three most important prediction variables lead by distances from roads and rails, then type of soil and distances from water bodies. The probability of invasive Fallopia species occurrence was evaluated using Pearson's chi-squared test (χ21). It significantly decreases with increasing distance from transport lines (χ21 = 118.85, p < 0.001) and depends on soil type (χ21 = 49.56, p < 0.001) and the distance from the water, where increasing the distance decrease the probability (χ21 = 8.95, p = 0.003).},
}
@article {pmid35684255,
year = {2022},
author = {Chao, L and Pan, Z and Wang, J and Wu, Y and Shui, G and Aini, N and Tang, B and Guo, C and Han, P and Shao, P and Tian, X and Chang, X and An, Q and Ma, C and You, C and Zhu, L and Nie, X},
title = {Genetic Mapping and Analysis of a Compact Plant Architecture and Precocious Mutant in Upland Cotton.},
journal = {Plants (Basel, Switzerland)},
volume = {11},
number = {11},
pages = {},
pmid = {35684255},
issn = {2223-7747},
abstract = {With the promotion and popularization of machine cotton-picking, more and more attention has been paid to the selection of early-maturity varieties with compact plant architecture. The type of fruit branch is one of the most important factors affecting plant architecture and early maturity of cotton. Heredity analysis of the cotton fruit branch is beneficial to the breeding of machine-picked cotton. Phenotype analysis showed that the types of fruit branches in cotton are controlled by a single recessive gene. Using an F2 population crossed with Huaxin102 (normal branch) and 04N-11 (nulliplex branch), BSA (Bulked Segregant Analysis) resequencing analysis and GhNB gene cloning in 04N-11, and allelic testing, showed that fruit branch type was controlled by the GhNB gene, located on chromosome D07. Ghnb5, a new recessive genotype of GhNB, was found in 04N-11. Through candidate gene association analysis, SNP 20_15811516_SNV was found to be associated with plant architecture and early maturity in the Xinjiang natural population. The GhNB gene, which is related to early maturity and the plant architecture of cotton, is a branch-type gene of cotton. The 20_15811516_SNV marker, obtained from the Xinjiang natural population, was used for the assisted breeding of machine-picked cotton varieties.},
}
@article {pmid35682045,
year = {2022},
author = {Ma, L and Hong, Y and Chen, X},
title = {Can Green Economy and Ecological Welfare Achieve Synergistic Development? The Perspective of the "Two Mountains" Theory.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {11},
pages = {},
pmid = {35682045},
issn = {1660-4601},
mesh = {China ; Cities ; *Conservation of Energy Resources ; Economic Development ; *Efficiency ; Sustainable Development ; Urbanization ; },
abstract = {China's high-speed economic growth and severe environmental problems have resulted in a poor Environmental Performance Index and have affected China's sustainable development and ecological welfare improvement. Therefore, exploring whether there is a certain relationship between the two and their influencing factors is an important way and a breakthrough to solve the problems regarding green economic progress and ecological welfare enhancement. To this end, by using the undesirable slack-based measure (SBM) model, this paper measures the ecological welfare performance and the green economic efficiency of 11 cities in Zhejiang Province, China, from 2000 to 2019. Through the methods of spatiotemporal evolution, coefficient of variation, coupling coordination degree, and the Tobit model, we found that: (1) The development trend of urban green economic efficiency and ecological welfare performance were both in a "U" shape that first fell and then rose; (2) The coupling coordination degree between green economic efficiency and ecological welfare performance showed a wave-like upward trend as a whole and most cities have entered a more advanced coupling coordination stage during the study period. The coefficient of variation revealed a downward trend; (3) The urbanization level, industrial structure, and government investment can promote the regional coordinated development, while the industrialization degree and the opening level had a negative impact on it; (4) The "Two Mountains" theory was beneficial to the improvement of regional urban green economic efficiency and ecological welfare performance and their coordinated development both in theory and practice. Finally, according to the findings, we offer relevant suggestions on making good use of the country's preferential policies and informatization means from the perspective of the regional coordinated development.},
}
@article {pmid35678830,
year = {2022},
author = {Zhao, Y and Wang, J and Yang, B and Zhong, Q and Wang, L and Niu, Z and Xin, H and Zhang, W},
title = {Performance of Red Mud/Biochar Composite Material (RMBC) as Heavy Metal Passivator in Pb-Contaminated Soil.},
journal = {Bulletin of environmental contamination and toxicology},
volume = {109},
number = {1},
pages = {30-43},
pmid = {35678830},
issn = {1432-0800},
mesh = {Charcoal/chemistry ; Lead ; *Metals, Heavy/analysis ; Soil/chemistry ; *Soil Pollutants/analysis ; },
abstract = {Red mud/biochar composite material (RMBC), which was applied as heavy metal passivator in this research, was prepared with red mud (the bauxite residue) and cornstalk under anoxic sintering condition. Based on the batch experiments in Pb contaminated soil, the passivating properties of several materials, including red mud (RM), biochar (BC), RMBC and phosphate-containing RMBC (PRMBC), were investigated in comparison with each other. Some interesting results are as follows: through anoxic thermal activation, a rough and porous structure of RMBC was obtained. Substances such as Fe3O4 and metal-organic complexes generated in RMBC provided effective sites for Pb passivation; and the mechanisms were speculated as the precipitation between Pb[2+] and the carbonate (or hydroxide), as well as the complexation reaction between Pb and metal organic complexes through ligand bonding. The pot experiments showed the promotion effects of four passivators on the growth of red onion were in the following order: PRMBC > RMBC > BC > RM. PRMBC stabilized Pb content in soil significantly due to the formation of insoluble substances, with the minimum transfer factor and bioconcentration factor for plant growth. The evidences above implied the composite materials (PRMBC and RMBC) would be potential passivators for heavy metal-contaminated soil.},
}
@article {pmid35676946,
year = {2022},
author = {Fan, L},
title = {Big Data Technology Oriented to Wetland Resource Ecosystem Value Evaluation.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {6815102},
pmid = {35676946},
issn = {1687-5273},
mesh = {Big Data ; China ; Conservation of Natural Resources/methods ; *Ecosystem ; Technology ; *Wetlands ; },
abstract = {In order to study a big data technology research for the evaluation of wetland resource ecosystem value. This paper proposes a wetland dimension oriented to the evaluation of wetland ecosystem services space attribute through big data coupling analysis framework. The framework used China's coastal wetlands as a case for empirical research and summarized the future direction of the research on the value evaluation of wetland ecosystem services in the era of big data. The result shows: Wetland Ecosystem Observation Network can obtain long-term series of dynamic data, remote sensing Earth observation can realize the integrated observation of space, space, and Earth, the combination of the two will help to build a wetland ecological big data observation system. The service value of China's coastal wetland ecosystem is 5010.32 × 108 yuan. The research results can effectively solve the problem of geographical heterogeneity and have reference value for the protection and management of the wetland ecosystem.},
}
@article {pmid35672133,
year = {2022},
author = {Arif, S and MacNeil, MA},
title = {Predictive models aren't for causal inference.},
journal = {Ecology letters},
volume = {25},
number = {8},
pages = {1741-1745},
doi = {10.1111/ele.14033},
pmid = {35672133},
issn = {1461-0248},
mesh = {Causality ; *Confounding Factors, Epidemiologic ; Data Interpretation, Statistical ; },
abstract = {Ecologists often rely on observational data to understand causal relationships. Although observational causal inference methodologies exist, predictive techniques such as model selection based on information criterion (e.g. AIC) remains a common approach used to understand ecological relationships. However, predictive approaches are not appropriate for drawing causal conclusions. Here, we highlight the distinction between predictive and causal inference and show how predictive techniques can lead to biased causal estimates. Instead, we encourage ecologists to valid causal inference methods such as the backdoor criterion, a graphical rule that can be used to determine causal relationships across observational studies.},
}
@article {pmid35669667,
year = {2022},
author = {Wang, Y},
title = {Research on Performance Optimization Algorithm of Resource and Environment Audit Based on Computer Technology.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {4288729},
doi = {10.1155/2022/4288729},
pmid = {35669667},
issn = {1687-5273},
mesh = {*Algorithms ; *Artificial Intelligence ; Big Data ; Computers ; Humans ; Technology ; },
abstract = {With the rapid development of the economy and society, the sustainable development of resources and environment has been paid more and more attention. As an important part of the national environmental supervision system, resources and environmental audits have attracted great attention from the society. In order to explore the application effect of intelligent networking technology in resource and environment audit, this study carries out monitoring sampling, information collection, and later data processing optimization in resource and environment audit projects through the reference of artificial intelligence technology and method and combined with Internet of things big data analysis, which brings new Turks to the development of natural resource and environment audit and helps to improve the efficiency of audit work. Through the application of new technology in the sampling process of environmental information, the staff use new technology to collect, analyze, and mine data and explore how the new technology can promote the efficiency of resource and environmental audit and better promote the construction of ecological civilization.},
}
@article {pmid35668508,
year = {2022},
author = {Hickson, J and Athayde, LFA and Miranda, TG and Junior, PAS and Dos Santos, AC and da Cunha Galvão, LM and da Câmara, ACJ and Bartholomeu, DC and de Souza, RCM and Murta, SMF and Nahum, LA},
title = {Trypanosoma cruzi iron superoxide dismutases: insights from phylogenetics to chemotherapeutic target assessment.},
journal = {Parasites & vectors},
volume = {15},
number = {1},
pages = {194},
pmid = {35668508},
issn = {1756-3305},
mesh = {Antioxidants ; Bayes Theorem ; *Chagas Disease/parasitology ; Humans ; Phylogeny ; Superoxide Dismutase/genetics ; Superoxides ; *Trypanosoma cruzi/genetics ; },
abstract = {BACKGROUND: Components of the antioxidant defense system in Trypanosoma cruzi are potential targets for new drug development. Superoxide dismutases (SODs) constitute key components of antioxidant defense systems, removing excess superoxide anions by converting them into oxygen and hydrogen peroxide. The main goal of the present study was to investigate the genes coding for iron superoxide dismutase (FeSOD) in T. cruzi strains from an evolutionary perspective.
METHODS: In this study, molecular biology methods and phylogenetic studies were combined with drug assays. The FeSOD-A and FeSOD-B genes of 35 T. cruzi strains, belonging to six discrete typing units (Tcl-TcVI), from different hosts and geographical regions were amplified by PCR and sequenced using the Sanger method. Evolutionary trees were reconstructed based on Bayesian inference and maximum likelihood methods. Drugs that potentially interacted with T. cruzi FeSODs were identified and tested against the parasites.
RESULTS: Our results suggest that T. cruzi FeSOD types are members of distinct families. Gene copies of FeSOD-A (n = 2), FeSOD-B (n = 4) and FeSOD-C (n = 4) were identified in the genome of the T. cruzi reference clone CL Brener. Phylogenetic inference supported the presence of two functional variants of each FeSOD type across the T. cruzi strains. Phylogenetic trees revealed a monophyletic group of FeSOD genes of T. cruzi TcIV strains in both distinct genes. Altogether, our results support the hypothesis that gene duplication followed by divergence shaped the evolution of T. cruzi FeSODs. Two drugs, mangafodipir and polaprezinc, that potentially interact with T. cruzi FeSODs were identified and tested in vitro against amastigotes and trypomastigotes: mangafodipir had a low trypanocidal effect and polaprezinc was inactive.
CONCLUSIONS: Our study contributes to a better understanding of the molecular biodiversity of T. cruzi FeSODs. Herein we provide a successful approach to the study of gene/protein families as potential drug targets.},
}
@article {pmid35665284,
year = {2022},
author = {Wu, H and Cheng, M},
title = {Trust of Information during the Dissemination of Popular Science Web Videos in the New Media Era.},
journal = {Computational intelligence and neuroscience},
volume = {2022},
number = {},
pages = {1746472},
pmid = {35665284},
issn = {1687-5273},
mesh = {Information Dissemination ; *Social Media ; *Trust ; Video Recording ; },
abstract = {Web videos have gradually replaced text, voice, pictures, and other information carriers to become an important way of information dissemination in the new media era. As digital technology brings a new dissemination ecology, the original dissemination trust theory and its framework are facing the crisis of explanatory power failure. This paper considers the popular science web video as an object of study. It analyses and interprets the development of popular science web videos based on the evolution of dissemination form and the basic principle of social trust, from perspectives such as mediology, informatics, and sociology. To maintain or improve the trust relationship in web videos, it's necessary to find positive incentive and reverse punishment, and establish a trust certification and regulation mechanism. In this way, active dissemination and sharing of information can be promoted for a more vigorous society and culture. Moreover, this paper explores a new way of web video development from the perspective of trust.},
}
@article {pmid35658270,
year = {2022},
author = {Plaza, A and Castillo, M and Naulin, PI},
title = {Seed and seedling interactions in three tree species from Mediterranean forests as a knowledge base for ecological restoration.},
journal = {Journal of environmental management},
volume = {316},
number = {},
pages = {115241},
doi = {10.1016/j.jenvman.2022.115241},
pmid = {35658270},
issn = {1095-8630},
mesh = {Ecosystem ; Forests ; Germination/physiology ; Humans ; Knowledge Bases ; Plant Extracts ; *Seedlings ; Seeds ; *Trees ; },
abstract = {The ecosystems of the Mediterranean regions are severely threatened by human activity, and although we have made progress in physical restoration measures, little is known about the interactions between the plants of these biomes. The objective of this study is to contribute to document interactions between seeds and seedlings of three woody species native to Chile (P. chilensis, Q. saponaria and A. caven), which could be used for restoration actions (e.g., after forest fires). In a first experiment, we evaluated the germination response, the initial elongation and the interactions between the seedlings that germinate exposed to the chemical compounds of the other species. In a second experiment, we compared the survival and growth of seedlings in monospecific versus bispecific mixtures, using a substrate similar to that which is present after a wildfire. Seed extracts of teguments promoted germination of P. chilensis, but cotyledons and whole seed extracts inhibited germination of only one species, Q. saponaria, with very high intensity. The effects of the extracts on initial seedling elongation were more variable, including five inhibitions and one facilitation. Negative effects on germination and elongation included two cases of autotoxicity. The survival of seedlings grown in mixtures showed only two differences between monospecific and bispecific mixtures, both positive, constituting a reciprocal effect between two species. Only in one case was there a significant difference in seedling growth, which was root growth inhibition. Indeed, these results reveal an interaction between species, the type and intensity of which varies according to the condition of the seed or seedling. The negative effect found in seedling root growth reflects an allelopathic interaction that conditions a vital aspect for the establishment of these species, so this information is an opportunity to improve the establishment conditions in future reforestation projects, by avoiding particular species or promoting their proportion in plantation mixtures, either by planting or direct seeding.},
}
@article {pmid35656925,
year = {2023},
author = {Figus, C and Stephens, NB and Sorrentino, R and Bortolini, E and Arrighi, S and Higgins, OA and Lugli, F and Marciani, G and Oxilia, G and Romandini, M and Silvestrini, S and Baruffaldi, F and Belcastro, MG and Bernardini, F and Festa, A and Hajdu, T and Mateovics-László, O and Pap, I and Szeniczey, T and Tuniz, C and Ryan, TM and Benazzi, S},
title = {Morphologies in-between: The impact of the first steps on the human talus.},
journal = {Anatomical record (Hoboken, N.J. : 2007)},
volume = {306},
number = {1},
pages = {124-142},
doi = {10.1002/ar.25010},
pmid = {35656925},
issn = {1932-8494},
mesh = {Humans ; *Walking ; X-Ray Microtomography ; },
abstract = {OBJECTIVE: The development of bipedalism is a very complex activity that contributes to shaping the anatomy of the foot. The talus, which starts ossifying in utero, may account for the developing stages from the late gestational phase onwards. Here, we explore the early development of the talus in both its internal and external morphology to broaden the knowledge of the anatomical changes that occur during early development.
MATERIALS AND METHODS: The sample consists of high-resolution microCT scans of 28 modern juvenile tali (from 36 prenatal weeks to 2 years), from a broad chronological range from the Late Roman period to the 20th century. We applied geometric morphometric and whole-bone trabecular analysis to investigate the early talar morphological changes.
RESULTS: In the youngest group (<6 postnatal months), the immature external shell is accompanied by an isotropic internal structure, with thin and densely packed trabeculae. After the initial attempts of locomotion, bone volume fraction decreases, while anisotropy and trabecular thickness increase. These internal changes correspond to the maturation of the external shell, which is now more defined and shows the development of the articular surfaces.
DISCUSSION: The internal and external morphology of the human talus reflects the diverse load on the foot during the initial phases of the bipedal locomotion, with the youngest group potentially reflecting the lack of readiness of the human talus to bear forces and perform bipedal walking. These results highlight the link between mechanical loading and bone development in the human talus during the acquisition of bipedalism, providing new insight into the early phases of talar development.},
}
@article {pmid35654905,
year = {2022},
author = {Herberstein, ME and McLean, DJ and Lowe, E and Wolff, JO and Khan, MK and Smith, K and Allen, AP and Bulbert, M and Buzatto, BA and Eldridge, MDB and Falster, D and Fernandez Winzer, L and Griffith, SC and Madin, JS and Narendra, A and Westoby, M and Whiting, MJ and Wright, IJ and Carthey, AJR},
title = {AnimalTraits - a curated animal trait database for body mass, metabolic rate and brain size.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {265},
pmid = {35654905},
issn = {2052-4463},
mesh = {Animals ; *Basal Metabolism ; *Body Weight ; *Brain ; *Databases, Factual ; Ecology ; Organ Size ; Phenotype ; },
abstract = {Trait databases have become important resources for large-scale comparative studies in ecology and evolution. Here we introduce the AnimalTraits database, a curated database of body mass, metabolic rate and brain size, in standardised units, for terrestrial animals. The database has broad taxonomic breadth, including tetrapods, arthropods, molluscs and annelids from almost 2000 species and 1000 genera. All data recorded in the database are sourced from their original empirical publication, and the original metrics and measurements are included with each record. This allows for subsequent data transformations as required. We have included rich metadata to allow users to filter the dataset. The additional R scripts we provide will assist researchers with aggregating standardised observations into species-level trait values. Our goals are to provide this resource without restrictions, to keep the AnimalTraits database current, and to grow the number of relevant traits in the future.},
}
@article {pmid35644269,
year = {2022},
author = {Grover, E and Paull, S and Kechris, K and Buchwald, A and James, K and Liu, Y and Carlton, EJ},
title = {Predictors of bovine Schistosoma japonicum infection in rural Sichuan, China.},
journal = {International journal for parasitology},
volume = {52},
number = {8},
pages = {485-496},
pmid = {35644269},
issn = {1879-0135},
support = {R01 AI068854/AI/NIAID NIH HHS/United States ; R01 AI134673/AI/NIAID NIH HHS/United States ; R21 AI115288/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Cattle ; China/epidemiology ; Cross-Sectional Studies ; Humans ; Prevalence ; Schistosoma ; *Schistosoma japonicum ; *Schistosomiasis/epidemiology ; *Schistosomiasis japonica/epidemiology/veterinary ; Snails ; Swine ; Water ; },
abstract = {In China, bovines are believed to be the most common animal source of human schistosomiasis infections, though little is known about what factors promote bovine infections. The current body of literature features inconsistent, and sometimes contradictory results, and to date, few studies have looked beyond physical characteristics to identify the broader environmental conditions that predict bovine schistosomiasis. Because schistosomiasis is a sanitation-related, water-borne disease transmitted by many animals, we hypothesised that several environmental factors - such as the lack of improved sanitation systems, or participation in agricultural production that is water-intensive - could promote schistosomiasis infection in bovines. Using data collected as part of a repeat cross-sectional study conducted in rural villages in Sichuan, China from 2007 to 2016, we used a Random Forests, machine learning approach to identify the best physical and environmental predictors of bovine Schistosoma japonicum infection. Candidate predictors included: (i) physical/biological characteristics of bovines, (ii) human sources of environmental schistosomes, (iii) socio-economic indicators, (iv) animal reservoirs, and (v) agricultural practices. The density of bovines in a village and agricultural practices such as the area of rice and dry summer crops planted, and the use of night soil as an agricultural fertilizer, were among the top predictors of bovine S. japonicum infection in all collection years. Additionally, human infection prevalence, pig ownership and bovine age were found to be strong predictors of bovine infection in at least 1 year. Our findings highlight that presumptively treating bovines in villages with high bovine density or human infection prevalence may help to interrupt transmission. Furthermore, village-level predictors were stronger predictors of bovine infection than household-level predictors, suggesting future investigations may need to apply a broad ecological lens to identify potential underlying sources of persistent transmission.},
}
@article {pmid35643307,
year = {2022},
author = {Inoue, K and Muramatsu, K and Nishimura, T and Fujino, Y and Matsuda, S and Fushimi, K and Kamochi, M},
title = {Association between early diagnosis of and inpatient mortality from invasive pulmonary aspergillosis among patients without immunocompromised host factors: a nationwide observational study.},
journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
volume = {122},
number = {},
pages = {279-284},
doi = {10.1016/j.ijid.2022.05.048},
pmid = {35643307},
issn = {1878-3511},
mesh = {Aged ; Antifungal Agents/therapeutic use ; Cross-Sectional Studies ; Early Diagnosis ; Humans ; Immunocompromised Host ; Inpatients ; *Invasive Pulmonary Aspergillosis/complications/diagnosis/drug therapy ; Retrospective Studies ; },
abstract = {OBJECTIVES: The incidence of invasive pulmonary aspergillosis (IPA) among patients without immunocompromised host factors (ICHF) has been described extensively. However, its diagnosis remains challenging. To date, no study has statistically confirmed the efficacy of early IPA diagnosis in patients without ICHF.
METHODS: We conducted a cross-sectional study on mortality from IPA among patients without ICHF, using the Japanese Diagnosis Procedure Combination National Inpatient Database (April 2014-March 2018). The early diagnosis group was defined according to antifungal therapy initiation within 7 days of hospital admission. The delayed diagnosis group was defined according to antifungal therapy initiation between 8 and 28 days of the hospitalization. Associations were estimated using multivariate logistic regression.
RESULTS: A total of 423 patients were registered (early diagnosis group, n = 262, 62%). The early diagnosis group had a lower mortality rate (30%) than the delayed diagnosis group (42%). The early diagnosis group that was treated with voriconazole was associated with lower odds of mortality (odds ratio 0.55, 95% confidence interval 0.31-0.99, P = 0.047). An age of ≥65 years and mechanical ventilation were associated with a higher mortality rate.
CONCLUSION: Early diagnosis along with optimal antifungal treatment are crucial for achieving favorable outcomes among patients with IPA without ICHF.},
}
@article {pmid35643184,
year = {2022},
author = {Suresh, KP and Sengupta, PP and Jacob, SS and Sathyanarayana, MKG and Patil, SS and Swarnkar, CP and Singh, D},
title = {Exploration of machine learning models to predict the environmental and remote sensing risk factors of haemonchosis in sheep flocks of Rajasthan, India.},
journal = {Acta tropica},
volume = {233},
number = {},
pages = {106542},
doi = {10.1016/j.actatropica.2022.106542},
pmid = {35643184},
issn = {1873-6254},
mesh = {Animals ; *Haemonchiasis ; India/epidemiology ; Machine Learning ; *Nematode Infections ; Remote Sensing Technology ; Risk Factors ; Seasons ; Sheep ; *Sheep Diseases/epidemiology ; },
abstract = {Globally haemonchosis in sheep is a known devastating disease imposing considerable economic loss. Understanding the environmental risk factors and their role is essentially required to manage the disease successfully. In this study, 14 years' disease data was analysed to predict the risk factors responsible for the occurrence of the disease. Season-wise analysis revealed high incidence during monsoon and post-monsoon and least in winter and summer seasons. The linear discriminant analysis (LDA) revealed the significant environmental and remote sensing risk factors contributing to haemonchosis incidence as enhanced vegetation index, leaf area index, potential evapotranspiration and specific humidity. Further, significant ecological and environmental risk factors identified using LDA were subjected to the climate-disease modelling and risk maps were generated. Basic reproduction number (R0) was estimated and was ranged from 0.76 to 2.08 for >1000 egg per gram of faeces (EPG) in four districts whereas R0 values of 1.09-1.69 for >2000 EPG in three districts indicating the severity of the infection. The random forest and adaptive boosting models emerged out as best fitted models for both the EPG groups. The results of the study will help to focus on high-risk areas of haemonchosis in sheep to implement the available control strategies and better animal production globally.},
}
@article {pmid35642818,
year = {2022},
author = {Chen, A and Yang, X and Guo, J and Zhang, M and Xing, X and Yang, D and Xu, B and Jiang, L},
title = {Dynamic of land use, landscape, and their impact on ecological quality in the northern sand-prevention belt of China.},
journal = {Journal of environmental management},
volume = {317},
number = {},
pages = {115351},
doi = {10.1016/j.jenvman.2022.115351},
pmid = {35642818},
issn = {1095-8630},
mesh = {China ; *Conservation of Natural Resources ; *Ecosystem ; Forests ; Poaceae ; Sand ; },
abstract = {Changes in land use and landscapes have a direct impact on the regional eco-environment. It is of great importance to understand the change pattern of land use, landscapes, and their mechanism on the ecological quality, especially ecologically fragile areas. The northern sand-prevention belt (NSPB) is an important ecologically fragile area in China, which has a large influence on the ecological security of the entire country. Based on the land use data of the NSPB in 2000, 2010, and 2018, we studied the spatio-temporal characteristics of land-use change and change in landscape patterns. The ecological quality represented by the remote sensing-based desertification index (RSDI) was calculated using satellite images. The effects of land use and landscape patterns on RSDI were analyzed by geographic detector and geographically weighted regression. Important results include the following: (1) Land-use change in the study area was high during 2000-2010 but slower in 2010-2018. Grassland was the largest land-use type in the NSPB, and varied greatly in terms of total change and spatial location. The major change was the conversion between dense and moderate grass, with 64,860 km[2] of dense grass turning into moderate grass, and 48,505 km[2] changing the other way. (2) Among the four landscape metrics, patch density, area-weighted mean fractal dimension, and edge density increased, whereas the aggregation index decreased, which indicated that the landscape was developing towards heterogeneity, fragmentation, complexity, and aggregation. Spatially, the landscape metrics presented a strip distribution in the east of the NSPB. (3) The effects of various land-use types on ecological quality, from high to low, were unused land, woodland, dense grass, cropland, moderate grass, built-up land, sparse grass, and waterbody. The areas where the ecological quality was greatly affected by the landscape patterns were concentrated in the agro-pastoral ecotone and the forest-steppe ecotone. The results of this study reveal the trends of land use and landscape patterns in the NSPB over 18 years and can help to understand their mechanism on ecological quality, which is of significance for the management of this area.},
}
@article {pmid35641949,
year = {2022},
author = {Botero-Mesa, S and Coelho, FC and Nwosu, K and Wicht, B and Venkatasubramanian, A and Wagner, O and Valera, C and Nguimbis, B and Câmara, D and Reis, I and Bianchi, L and Mahdiani, M and Onsimbie, PA and Diallo, PAN and Jacques, L and Muloliwa, AM and Bougma, M and Mukavhi, L and Kaneria, A and Peruvemba, R and Gupta, A and Triulzi, I and James, A and Carrara, V and Ngambi, W and Habibi, Z and Adhanom, MT and Rodriguez Velásquez, S and Sestito, P and Kousil, T and Biru, L and Vivacqua, D and Dalal, J and Mian, A and Roelens, M and Orel, E and Hofer, CB and Wangara, F and Mboussou, F and Mlanda, T and Bukhari, A and Lee, TM and Ngom, R and Stoll, B and Chimbetete, C and Abbate, J and Impouma, B and Keiser, O},
title = {Leveraging human resources for outbreak analysis: lessons from an international collaboration to support the sub-Saharan African COVID-19 response.},
journal = {BMC public health},
volume = {22},
number = {1},
pages = {1073},
pmid = {35641949},
issn = {1471-2458},
support = {001/WHO_/World Health Organization/International ; },
mesh = {Africa South of the Sahara/epidemiology ; *COVID-19/epidemiology ; Disease Outbreaks/prevention & control ; Humans ; Public Health ; Workforce ; },
abstract = {Emerging infectious diseases are a growing threat in sub-Saharan African countries, but the human and technical capacity to quickly respond to outbreaks remains limited. Here, we describe the experience and lessons learned from a joint project with the WHO Regional Office for Africa (WHO AFRO) to support the sub-Saharan African COVID-19 response.In June 2020, WHO AFRO contracted a number of consultants to reinforce the COVID-19 response in member states by providing actionable epidemiological analysis. Given the urgency of the situation and the magnitude of work required, we recruited a worldwide network of field experts, academics and students in the areas of public health, data science and social science to support the effort. Most analyses were performed on a merged line list of COVID-19 cases using a reverse engineering model (line listing built using data extracted from national situation reports shared by countries with the Regional Office for Africa as per the IHR (2005) obligations). The data analysis platform The Renku Project (https://renkulab.io) provided secure data storage and permitted collaborative coding.Over a period of 6 months, 63 contributors from 32 nations (including 17 African countries) participated in the project. A total of 45 in-depth country-specific epidemiological reports and data quality reports were prepared for 28 countries. Spatial transmission and mortality risk indices were developed for 23 countries. Text and video-based training modules were developed to integrate and mentor new members. The team also began to develop EpiGraph Hub, a web application that automates the generation of reports similar to those we created, and includes more advanced data analyses features (e.g. mathematical models, geospatial analyses) to deliver real-time, actionable results to decision-makers.Within a short period, we implemented a global collaborative approach to health data management and analyses to advance national responses to health emergencies and outbreaks. The interdisciplinary team, the hands-on training and mentoring, and the participation of local researchers were key to the success of this initiative.},
}
@article {pmid35641668,
year = {2022},
author = {Esen, F},
title = {Determining the effects of geomorphological factors on the distribution of land use and plant cover by different statistical methods.},
journal = {Environmental monitoring and assessment},
volume = {194},
number = {7},
pages = {465},
pmid = {35641668},
issn = {1573-2959},
mesh = {Agriculture ; *Environmental Monitoring/methods ; Geographic Information Systems ; *Plants ; },
abstract = {The aim of this study is to determine the role of geomorphological factors in land use and plant cover organization. For this purpose, the relationship between geomorphological factors such as geomorphological unit, elevation, slope, aspect, and curvature with land use and plant cover was analyzed using GIS (Geographical Information Systems) techniques and statistical methods (zonal analysis, correlation analysis, regression analysis). Using zonal analysis, the boundaries of both land use patterns and plant species are clearly drawn according to geomorphological factors. Using correlation analysis, the direction and intensity of the relationship between each geomorphological factor with land use patterns and plant species were determined. Finally, regression analysis method was used to determine the impact rate of geomorphological factors on land use patterns and plant cover. Thus, the effects of geomorphological factors on the distribution of both land use patterns and the each plant species were explained in detail. When the results of all three analyses are evaluated in general, the elevation is very strong, the slope strong, the aspect medium, the geomorphological unit weak, and the curvature has a very weak effect on the distribution of land use patterns and the plant species in the research area. The data obtained from the study will contribute to the planning and implementation of activities such as forest, agriculture, land use, water management to be carried out by local administrations and decision-makers. In addition, it will form a scientific basis for the sustainability of forest existence in harmony with the ecological conditions of Göksun Plain and its surroundings.},
}
@article {pmid35639883,
year = {2022},
author = {Dong, X and Penrice-Randal, R and Goldswain, H and Prince, T and Randle, N and Donovan-Banfield, I and Salguero, FJ and Tree, J and Vamos, E and Nelson, C and Clark, J and Ryan, Y and Stewart, JP and Semple, MG and Baillie, JK and Openshaw, PJM and Turtle, L and Matthews, DA and Carroll, MW and Darby, AC and Hiscox, JA},
title = {Analysis of SARS-CoV-2 known and novel subgenomic mRNAs in cell culture, animal model, and clinical samples using LeTRS, a bioinformatic tool to identify unique sequence identifiers.},
journal = {GigaScience},
volume = {11},
number = {},
pages = {},
pmid = {35639883},
issn = {2047-217X},
support = {75F40120C00085/FD/FDA HHS/United States ; MR/W005611/1/MRC_/Medical Research Council/United Kingdom ; 215091/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; *COVID-19 ; Cell Culture Techniques ; Computational Biology ; Humans ; Mammals/genetics ; Models, Animal ; RNA, Messenger/genetics ; *SARS-CoV-2/genetics ; },
abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a complex strategy for the transcription of viral subgenomic mRNAs (sgmRNAs), which are targets for nucleic acid diagnostics. Each of these sgmRNAs has a unique 5' sequence, the leader-transcriptional regulatory sequence gene junction (leader-TRS junction), that can be identified using sequencing. High-resolution sequencing has been used to investigate the biology of SARS-CoV-2 and the host response in cell culture and animal models and from clinical samples. LeTRS, a bioinformatics tool, was developed to identify leader-TRS junctions and can be used as a proxy to quantify sgmRNAs for understanding virus biology. LeTRS is readily adaptable for other coronaviruses such as Middle East respiratory syndrome coronavirus or a future newly discovered coronavirus. LeTRS was tested on published data sets and novel clinical samples from patients and longitudinal samples from animal models with coronavirus disease 2019. LeTRS identified known leader-TRS junctions and identified putative novel sgmRNAs that were common across different mammalian species. This may be indicative of an evolutionary mechanism where plasticity in transcription generates novel open reading frames, which can then subject to selection pressure. The data indicated multiphasic abundance of sgmRNAs in two different animal models. This recapitulates the relative sgmRNA abundance observed in cells at early points in infection but not at late points. This pattern is reflected in some human nasopharyngeal samples and therefore has implications for transmission models and nucleic acid-based diagnostics. LeTRS provides a quantitative measure of sgmRNA abundance from sequencing data. This can be used to assess the biology of SARS-CoV-2 (or other coronaviruses) in clinical and nonclinical samples, especially to evaluate different variants and medical countermeasures that may influence viral RNA synthesis.},
}
@article {pmid35639882,
year = {2022},
author = {Salim, JA and Saraiva, AM and Zermoglio, PF and Agostini, K and Wolowski, M and Drucker, DP and Soares, FM and Bergamo, PJ and Varassin, IG and Freitas, L and Maués, MM and Rech, AR and Veiga, AK and Acosta, AL and Araujo, AC and Nogueira, A and Blochtein, B and Freitas, BM and Albertini, BC and Maia-Silva, C and Nunes, CEP and Pires, CSS and Dos Santos, CF and Queiroz, EP and Cartolano, EA and de Oliveira, FF and Amorim, FW and Fontúrbel, FE and da Silva, GV and Consolaro, H and Alves-Dos-Santos, I and Machado, IC and Silva, JS and Aleixo, KP and Carvalheiro, LG and Rocca, MA and Pinheiro, M and Hrncir, M and Streher, NS and Ferreira, PA and de Albuquerque, PMC and Maruyama, PK and Borges, RC and Giannini, TC and Brito, VLG},
title = {Data standardization of plant-pollinator interactions.},
journal = {GigaScience},
volume = {11},
number = {},
pages = {},
pmid = {35639882},
issn = {2047-217X},
mesh = {Animals ; Biodiversity ; *Ecosystem ; Phylogeny ; *Pollination ; Reference Standards ; },
abstract = {BACKGROUND: Animal pollination is an important ecosystem function and service, ensuring both the integrity of natural systems and human well-being. Although many knowledge shortfalls remain, some high-quality data sets on biological interactions are now available. The development and adoption of standards for biodiversity data and metadata has promoted great advances in biological data sharing and aggregation, supporting large-scale studies and science-based public policies. However, these standards are currently not suitable to fully support interaction data sharing.
RESULTS: Here we present a vocabulary of terms and a data model for sharing plant-pollinator interactions data based on the Darwin Core standard. The vocabulary introduces 48 new terms targeting several aspects of plant-pollinator interactions and can be used to capture information from different approaches and scales. Additionally, we provide solutions for data serialization using RDF, XML, and DwC-Archives and recommendations of existing controlled vocabularies for some of the terms. Our contribution supports open access to standardized data on plant-pollinator interactions.
CONCLUSIONS: The adoption of the vocabulary would facilitate data sharing to support studies ranging from the spatial and temporal distribution of interactions to the taxonomic, phenological, functional, and phylogenetic aspects of plant-pollinator interactions. We expect to fill data and knowledge gaps, thus further enabling scientific research on the ecology and evolution of plant-pollinator communities, biodiversity conservation, ecosystem services, and the development of public policies. The proposed data model is flexible and can be adapted for sharing other types of interactions data by developing discipline-specific vocabularies of terms.},
}
@article {pmid35633848,
year = {2022},
author = {McDonald, PJ and Brown, RM and Kraus, F and Bowles, P and Arifin, U and Eliades, SJ and Fisher, RN and Gaulke, M and Grismer, LL and Ineich, I and Karin, BR and Meneses, CG and Richards, SJ and Sanguila, MB and Siler, CD and Oliver, PM},
title = {Cryptic extinction risk in a western Pacific lizard radiation.},
journal = {Biodiversity and conservation},
volume = {31},
number = {8-9},
pages = {2045-2062},
pmid = {35633848},
issn = {0960-3115},
abstract = {UNLABELLED: Cryptic ecologies, the Wallacean Shortfall of undocumented species' geographical ranges and the Linnaean Shortfall of undescribed diversity, are all major barriers to conservation assessment. When these factors overlap with drivers of extinction risk, such as insular distributions, the number of threatened species in a region or clade may be underestimated, a situation we term 'cryptic extinction risk'. The genus Lepidodactylus is a diverse radiation of insular and arboreal geckos that occurs across the western Pacific. Previous work on Lepidodactylus showed evidence of evolutionary displacement around continental fringes, suggesting an inherent vulnerability to extinction from factors such as competition and predation. We sought to (1) comprehensively review status and threats, (2) estimate the number of undescribed species, and (3) estimate extinction risk in data deficient and candidate species, in Lepidodactylus. From our updated IUCN Red List assessment, 60% of the 58 recognized species are threatened (n = 15) or Data Deficient (n = 21), which is higher than reported for most other lizard groups. Species from the smaller and isolated Pacific islands are of greatest conservation concern, with most either threatened or Data Deficient, and all particularly vulnerable to invasive species. We estimated 32 undescribed candidate species and linear modelling predicted that an additional 18 species, among these and the data deficient species, are threatened with extinction. Focusing efforts to resolve the taxonomy and conservation status of key taxa, especially on small islands in the Pacific, is a high priority for conserving this remarkably diverse, yet poorly understood, lizard fauna. Our data highlight how cryptic ecologies and cryptic diversity combine and lead to significant underestimation of extinction risk.
SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10531-022-02412-x.},
}
@article {pmid35633719,
year = {2022},
author = {Gevi, F and Leo, P and Cassaro, A and Pacelli, C and de Vera, JP and Rabbow, E and Timperio, AM and Onofri, S},
title = {Metabolomic Profile of the Fungus Cryomyces antarcticus Under Simulated Martian and Space Conditions as Support for Life-Detection Missions on Mars.},
journal = {Frontiers in microbiology},
volume = {13},
number = {},
pages = {749396},
pmid = {35633719},
issn = {1664-302X},
abstract = {The identification of traces of life beyond Earth (e.g., Mars, icy moons) is a challenging task because terrestrial chemical-based molecules may be destroyed by the harsh conditions experienced on extraterrestrial planetary surfaces. For this reason, studying the effects on biomolecules of extremophilic microorganisms through astrobiological ground-based space simulation experiments is significant to support the interpretation of the data that will be gained and collected during the ongoing and future space exploration missions. Here, the stability of the biomolecules of the cryptoendolithic black fungus Cryomyces antarcticus, grown on two Martian regolith analogues and on Antarctic sandstone, were analysed through a metabolomic approach, after its exposure to Science Verification Tests (SVTs) performed in the frame of the European Space Agency (ESA) Biology and Mars Experiment (BIOMEX) project. These tests are building a set of ground-based experiments performed before the space exposure aboard the International Space Station (ISS). The analysis aimed to investigate the effects of different mineral mixtures on fungal colonies and the stability of the biomolecules synthetised by the fungus under simulated Martian and space conditions. The identification of a specific group of molecules showing good stability after the treatments allow the creation of a molecular database that should support the analysis of future data sets that will be collected in the ongoing and next space exploration missions.},
}
@article {pmid35630464,
year = {2022},
author = {Papale, M and Rizzo, C and Giannarelli, S and Caruso, G and Amalfitano, S and Aspholm, PE and Maimone, G and Miserocchi, S and Rappazzo, AC and Lo Giudice, A and Azzaro, M},
title = {Benthic Microbial Communities in a Seasonally Ice-Covered Sub-Arctic River (Pasvik River, Norway) Are Shaped by Site-Specific Environmental Conditions.},
journal = {Microorganisms},
volume = {10},
number = {5},
pages = {},
pmid = {35630464},
issn = {2076-2607},
abstract = {The Pasvik River experiences chemical, physical, and biological stressors due to the direct discharges of domestic sewage from settlements located within the catchment and runoff from smelter and mine wastes. Sediments, as a natural repository of organic matter and associated contaminants, are of global concern for the possible release of pollutants in the water column, with detrimental effects on aquatic organisms. The present study was aimed at characterizing the riverine benthic microbial community and evaluating its ecological role in relation to the contamination level. Sediments were sampled along the river during two contrasting environmental periods (i.e., beginning and ongoing phases of ice melting). Microbial enzymatic activities, cell abundance, and morphological traits were evaluated, along with the phylogenetic community composition. Amplified 16S rRNA genes from bacteria were sequenced using a next-generation approach. Sediments were also analyzed for a variety of chemical features, namely particulate material characteristics and concentration of polychlorobiphenyls, polycyclic aromatic hydrocarbons, and pesticides. Riverine and brackish sites did not affect the microbial community in terms of main phylogenetic diversity (at phylum level), morphometry, enzymatic activities, and abundance. Instead, bacterial diversity in the river sediments appeared to be influenced by the micro-niche conditions, with differences in the relative abundance of selected taxa. In particular, our results highlighted the occurrence of bacterial taxa directly involved in the C, Fe, and N cycles, as well as in the degradation of organic pollutants and toxic compounds.},
}
@article {pmid35628215,
year = {2022},
author = {Kozicki, M and Pawlaczyk, A and Adamska, A and Szynkowska-Jóźwik, MI and Sąsiadek-Andrzejczak, E},
title = {Golden and Silver-Golden Chitosan Hydrogels and Fabrics Modified with Golden Chitosan Hydrogels.},
journal = {International journal of molecular sciences},
volume = {23},
number = {10},
pages = {},
pmid = {35628215},
issn = {1422-0067},
mesh = {*Chitosan/chemistry ; Hydrogels/chemistry ; Microscopy, Electron, Scanning ; *Silver/chemistry ; Textiles ; },
abstract = {Golden and silver-golden chitosan hydrogels and hydrogel-modified textiles of potential biomedical applications are investigated in this work. The hydrogels are formed by reactions of chitosan with HAuCl4·xH2O. For above the critical concentration of chitosan (c*), chitosan-Au hydrogels were prepared. For chitosan concentrations lower than c*, chitosan-Au nano- and microgels were formed. To characterise chitosan-Au structures, sol-gel analysis, UV-Vis spectrophotometry and dynamic light scattering were performed. Au concentration in the hydrogels was determined by the flame atomic absorption spectrophotometry. Colloidal chitosan-Au solutions were used for the modification of fabrics. The Au content in the modified fabrics was quantified by inductively coupled plasma mass spectrometry technique. Scanning electron microscopy with energy dispersion X-ray spectrometer was used to analyse the samples. Reflectance spectrophotometry was applied to examine the colour of the fabrics. The formation of chitosan-Au-Ag hydrogels by the competitive reaction of Au and Ag ions with the chitosan macromolecules is reported.},
}
@article {pmid35627689,
year = {2022},
author = {Xu, D and Lin, W and Gao, J and Jiang, Y and Li, L and Gao, F},
title = {PM2.5 Exposure and Health Risk Assessment Using Remote Sensing Data and GIS.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {10},
pages = {},
pmid = {35627689},
issn = {1660-4601},
mesh = {China ; *Geographic Information Systems ; Particulate Matter/analysis ; *Remote Sensing Technology ; Risk Assessment ; },
abstract = {Assessing personal exposure risk from PM2.5 air pollution poses challenges due to the limited availability of high spatial resolution data for PM2.5 and population density. This study introduced a seasonal spatial-temporal method of modeling PM2.5 distribution characteristics at a 1-km grid level based on remote sensing data and Geographic Information Systems (GIS). The high-accuracy population density data and the relative exposure risk model were used to assess the relationship between exposure to PM2.5 air pollution and public health. The results indicated that the spatial-temporal PM2.5 concentration could be simulated by MODIS images and GIS method and could provide high spatial resolution data sources for exposure risk assessment. PM2.5 air pollution risks were most serious in spring and winter, and high risks of environmental health hazards were mostly concentrated in densely populated areas in Shanghai-Hangzhou Bay, China. Policies to control the total population and pollution discharge need follow the principle of adaptation to local conditions in high-risk areas. Air quality maintenance and ecological maintenance should be carried out in low-risk areas to reduce exposure risk and improve environmental health.},
}
@article {pmid35624681,
year = {2022},
author = {Baszyński, J and Kamiński, P and Bogdzińska, M and Mroczkowski, S and Szymański, M and Wasilow, K and Stanek, E and Hołderna-Bona, K and Brodzka, S and Bilski, R and Tkachenko, H and Kurhaluk, N and Stuczyński, T and Lorek, M and Woźniak, A},
title = {Enzymatic Antioxidant Defense and Polymorphic Changes in Male Infertility.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {11},
number = {5},
pages = {},
pmid = {35624681},
issn = {2076-3921},
abstract = {The intensification of oxidative stress and destabilization of the antioxidative defenses of an organism is a consequence of many environmental factors. We considered aspects conditioning male reproductive potential and the functionality of enzymatic antioxidative mechanisms, i.e., superoxide dismutase (SOD), catalase (CAT), glutathione peroxidase (GPx) and glutathione reductase (GR), and their correlations with Li, Be, B, Na, Mg, Al, P, K, Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Sr, Mo, Ag, Cd, Sn, Sb, Ba, Hg, Tl, Pb, and malondialdehyde (MDA), as well as genetic polymorphism IL-4v.C589T (rs2243250) in men with infertility (n = 76). A healthy normozoospermic control (n = 87) was also used. We assessed the impact of negative changes driven by oxidative stress on enzymatic antioxidative mechanisms as well as the role of MDA in the overall process. On this basis, we infer connections between disturbances in enzymatic antioxidative defense and reproductive potential. Based on a molecular analysis of the polymorphism of gene IL-4v.C589T (rs2243250) (chromosome 5) (PCR-RFLP), we considered the relationships among particular genotypes with the possibility of occurrence of male infertility. Concentrations of chemical elements were measured in the blood. The activity of antioxidants and MDA levels were measured in serum. In the infertile group, higher GPx activity was noted (6.56 nmoL·min[-1]·mL[-1], control: 4.31 nmoL·min[-1]·mL[-1]; p = 0.004), while GR achieved a greater level in the control (17.74 nmoL·min[-1]·mL[-1], infertile: 15.97 nmoL·min[-1]·mL[-1], p = 0.043), which implies diversified efficiency of the first and second lines of defense. The polymorphism of IL-4v.C589T (rs2243250) was not directly connected with infertility because there were not any differences in the frequency of genotypes between the infertile and control group (p = 0.578). An analysis of genotypes CC and TT (polymorphism IL-4v.C589T (rs2243250)) indicated numerous correlations between antioxidants, chemical elements and MDA. Therefore, chemical economy, antioxidative defense and genetic conditions are connected and jointly shape male reproductive potential. Chemical elements influence antioxidative defense and male fertility; the most important modulators appeared to be Na, Ba, Al and B. The polymorphism of gene IL-4v.C589T (rs2243250) has a limited influence on antioxidative defense and the metabolism of chemical elements.},
}
@article {pmid35622850,
year = {2022},
author = {Madzík, P and Falát, L},
title = {State-of-the-art on analytic hierarchy process in the last 40 years: Literature review based on Latent Dirichlet Allocation topic modelling.},
journal = {PloS one},
volume = {17},
number = {5},
pages = {e0268777},
pmid = {35622850},
issn = {1932-6203},
mesh = {Algorithms ; *Analytic Hierarchy Process ; Databases, Factual ; *Ecosystem ; Fuzzy Logic ; },
abstract = {Although there are several articles that have carried out a systematic literature review of the analytical hierarchy process (AHP), many of them work with a limited number of analyzed documents. This article presents a computer-aided systematic literature review of articles related to AHP. The objectives are: (i) to identify AHP usage and research impact in different subject areas; (ii) to identify trends in the popularity of the AHP from the first introduction of the method in 1980 to the present; (iii) to identify the most common topics related to AHP and topic development over time. We process 35,430 documents related to AHP, published between 1980 and 2021, retrieved from the Scopus database. We provide detailed statistics about research interest, research impact in particular subject areas over the analyzed time period. We use Latent Dirichlet Allocation (LDA) using Gibbs sampling to perform topic modeling based on the corpus of abstracts. We identify nine topics related to AHP: Ecology & Ecosystems; Multi-criteria decision-making; Production and performance management; Sustainable development; Computer network, optimization and algorithms; Service quality; Fuzzy logic; Systematic evaluation; Risk assessment. We also present the individual topics trends over time and point out the possible future direction of AHP.},
}
@article {pmid35620757,
year = {2022},
author = {Kraemer, R and Remmler, P and Bumberger, J and Kabisch, N},
title = {Running a dense air temperature measurement field campaign at the urban neighbourhood level: Protocol and lessons learned.},
journal = {MethodsX},
volume = {9},
number = {},
pages = {101719},
pmid = {35620757},
issn = {2215-0161},
abstract = {The cooling capacity of urban green spaces constitutes a key measure for cities to mitigate heat events, which is gaining importance in climate change adaptation and mitigation. In this protocol article, we present details on two field campaigns aiming at collecting dense air temperature data in two urban inner city parks in Leipzig, Germany, under unprecedented heat and drought conditions. We introduce all the steps required to plan and conduct qualified fieldwork in environmental research, including study design, technical and logistical preparations, on-site work and data management steps from data acquisition, transfer into research outcomes to dissemination. We further share valuable lessons learned before, during and after fieldwork that helped us improve our work and that could support and improve similar future project campaigns.},
}
@article {pmid35618868,
year = {2022},
author = {Mammola, S and Pavlek, M and Huber, BA and Isaia, M and Ballarin, F and Tolve, M and Čupić, I and Hesselberg, T and Lunghi, E and Mouron, S and Graco-Roza, C and Cardoso, P},
title = {A trait database and updated checklist for European subterranean spiders.},
journal = {Scientific data},
volume = {9},
number = {1},
pages = {236},
pmid = {35618868},
issn = {2052-4463},
mesh = {Animals ; *Databases, Factual ; Ecosystem ; Europe ; *Spiders ; },
abstract = {Species traits are an essential currency in ecology, evolution, biogeography, and conservation biology. However, trait databases are unavailable for most organisms, especially those living in difficult-to-access habitats such as caves and other subterranean ecosystems. We compiled an expert-curated trait database for subterranean spiders in Europe using both literature data (including grey literature published in many different languages) and direct morphological measurements whenever specimens were available to us. We started by updating the checklist of European subterranean spiders, now including 512 species across 20 families, of which at least 192 have been found uniquely in subterranean habitats. For each of these species, we compiled 64 traits. The trait database encompasses morphological measures, including several traits related to subterranean adaptation, and ecological traits referring to habitat preference, dispersal, and feeding strategies. By making these data freely available, we open up opportunities for exploring different research questions, from the quantification of functional dimensions of subterranean adaptation to the study of spatial patterns in functional diversity across European caves.},
}
@article {pmid35618416,
year = {2022},
author = {Krieger, G and Lupo, O and Wittkopp, P and Barkai, N},
title = {Evolution of transcription factor binding through sequence variations and turnover of binding sites.},
journal = {Genome research},
volume = {32},
number = {6},
pages = {1099-1111},
pmid = {35618416},
issn = {1549-5469},
mesh = {Binding Sites ; Chromatin Immunoprecipitation ; *Computational Biology/methods ; Protein Binding ; Saccharomyces cerevisiae/genetics/metabolism ; *Transcription Factors/genetics/metabolism ; },
abstract = {Variations in noncoding regulatory sequences play a central role in evolution. Interpreting such variations, however, remains difficult even in the context of defined attributes such as transcription factor (TF) binding sites. Here, we systematically link variations in cis-regulatory sequences to TF binding by profiling the allele-specific binding of 27 TFs expressed in a yeast hybrid, in which two related genomes are present within the same nucleus. TFs localize preferentially to sites containing their known consensus motifs but occupy only a small fraction of the motif-containing sites available within the genomes. Differential binding of TFs to the orthologous alleles was well explained by variations that alter motif sequence, whereas differences in chromatin accessibility between alleles were of little apparent effect. Motif variations that abolished binding when present in only one allele were still bound when present in both alleles, suggesting evolutionary compensation, with a potential role for sequence conservation at the motif's vicinity. At the level of the full promoter, we identify cases of binding-site turnover, in which binding sites are reciprocally gained and lost, yet most interspecific differences remained uncompensated. Our results show the flexibility of TFs to bind imprecise motifs and the fast evolution of TF binding sites between related species.},
}
@article {pmid35617745,
year = {2022},
author = {Antony, S and Unnikrishnan, K and Aswin, S and Dev, VV and Arun, V and Krishnan, KA},
title = {Heavy metals in coral reef sediments of Kavaratti Island, India: An integrated quality assessment using GIS and pollution indicators.},
journal = {Marine pollution bulletin},
volume = {180},
number = {},
pages = {113721},
doi = {10.1016/j.marpolbul.2022.113721},
pmid = {35617745},
issn = {1879-3363},
mesh = {Cadmium/analysis ; China ; Coral Reefs ; Environmental Monitoring/methods ; Geographic Information Systems ; Geologic Sediments ; Lead/analysis ; *Metals, Heavy/analysis ; Risk Assessment ; *Water Pollutants, Chemical/analysis ; },
abstract = {The present study aims to document the contamination levels and ecological risks of heavy metals in the sediments of Kavaratti lagoon, India. A total of 15 sediment samples were collected for the analysis of Al, Pb, Cd, Cu, Cr, Mn, Ni and Zn. The decreasing trend of heavy metals was observed in the lagoon sediment as Pb > Zn > Al > Mn > Ni > Cr > Cd > Cu. The Geo-accumulation index (Igeo) results indicate that Cu, Cr, Mn, Ni and Zn were uncontaminated, while Cd was strong to extremely contaminated and Al and Pb were moderately contaminated. The enrichment factors (EF) of Cd and Pb range from moderate to extremely high (EF > 1) indicating that they have anthropogenic origin on Kavaratti Island. The Contamination factor (Cf) indicated that Cd, Pb and Al belong to a high risk of contamination (Cf > 6). The pollution load index (PLI) value near one suggested that a moderate level of pollution occurs in the study area. The modified degree of contamination (mCd) shows that Al, Cd and Pb have an ultra- higher degree of contamination (mCd ≤ 32). The potential ecological risk (RI) index confirmed that Pb and Cd have considerable to the serious thread of ecological risk (RI > 600). Additionally, multivariate statistical analysis and pollution indexes showed that the Kavaratti lagoon is moderate to considerably polluted by heavy metals. Diesel-based power generation, activities related to shipping, untreated sewage, fishing and tourism activities are the main anthropogenic sources of heavy metal pollution on Kavaratti Island.},
}
@article {pmid35617403,
year = {2022},
author = {Bonnet, T and Morrissey, MB and de Villemereuil, P and Alberts, SC and Arcese, P and Bailey, LD and Boutin, S and Brekke, P and Brent, LJN and Camenisch, G and Charmantier, A and Clutton-Brock, TH and Cockburn, A and Coltman, DW and Courtiol, A and Davidian, E and Evans, SR and Ewen, JG and Festa-Bianchet, M and de Franceschi, C and Gustafsson, L and Höner, OP and Houslay, TM and Keller, LF and Manser, M and McAdam, AG and McLean, E and Nietlisbach, P and Osmond, HL and Pemberton, JM and Postma, E and Reid, JM and Rutschmann, A and Santure, AW and Sheldon, BC and Slate, J and Teplitsky, C and Visser, ME and Wachter, B and Kruuk, LEB},
title = {Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals.},
journal = {Science (New York, N.Y.)},
volume = {376},
number = {6596},
pages = {1012-1016},
doi = {10.1126/science.abk0853},
pmid = {35617403},
issn = {1095-9203},
mesh = {*Adaptation, Biological/genetics ; Animals ; *Animals, Wild/genetics ; *Biological Evolution ; Birds/genetics ; Datasets as Topic ; *Genetic Fitness ; Genetic Variation ; Mammals/genetics ; Population Dynamics ; Selection, Genetic ; },
abstract = {The rate of adaptive evolution, the contribution of selection to genetic changes that increase mean fitness, is determined by the additive genetic variance in individual relative fitness. To date, there are few robust estimates of this parameter for natural populations, and it is therefore unclear whether adaptive evolution can play a meaningful role in short-term population dynamics. We developed and applied quantitative genetic methods to long-term datasets from 19 wild bird and mammal populations and found that, while estimates vary between populations, additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates. We show that these rates of contemporary adaptive evolution can affect population dynamics and hence that natural selection has the potential to partly mitigate effects of current environmental change.},
}
@article {pmid35616633,
year = {2022},
author = {Rutz, A and Sorokina, M and Galgonek, J and Mietchen, D and Willighagen, E and Gaudry, A and Graham, JG and Stephan, R and Page, R and Vondrášek, J and Steinbeck, C and Pauli, GF and Wolfender, JL and Bisson, J and Allard, PM},
title = {The LOTUS initiative for open knowledge management in natural products research.},
journal = {eLife},
volume = {11},
number = {},
pages = {},
pmid = {35616633},
issn = {2050-084X},
support = {P50 AT000155/AT/NCCIH NIH HHS/United States ; U41 AT008706/AT/NCCIH NIH HHS/United States ; },
mesh = {*Biological Products ; Computational Biology ; Databases, Factual ; Knowledge ; *Knowledge Management ; },
abstract = {Contemporary bioinformatic and chemoinformatic capabilities hold promise to reshape knowledge management, analysis and interpretation of data in natural products research. Currently, reliance on a disparate set of non-standardized, insular, and specialized databases presents a series of challenges for data access, both within the discipline and for integration and interoperability between related fields. The fundamental elements of exchange are referenced structure-organism pairs that establish relationships between distinct molecular structures and the living organisms from which they were identified. Consolidating and sharing such information via an open platform has strong transformative potential for natural products research and beyond. This is the ultimate goal of the newly established LOTUS initiative, which has now completed the first steps toward the harmonization, curation, validation and open dissemination of 750,000+ referenced structure-organism pairs. LOTUS data is hosted on Wikidata and regularly mirrored on https://lotus.naturalproducts.net. Data sharing within the Wikidata framework broadens data access and interoperability, opening new possibilities for community curation and evolving publication models. Furthermore, embedding LOTUS data into the vast Wikidata knowledge graph will facilitate new biological and chemical insights. The LOTUS initiative represents an important advancement in the design and deployment of a comprehensive and collaborative natural products knowledge base.},
}
@article {pmid35614412,
year = {2022},
author = {Kim, MS and Yu, J},
title = {Text mining for identifying the nature of online questions about non-suicidal self-injury.},
journal = {BMC public health},
volume = {22},
number = {1},
pages = {1041},
pmid = {35614412},
issn = {1471-2458},
mesh = {Data Mining ; Humans ; Risk Factors ; *Self-Injurious Behavior/epidemiology ; Suicidal Ideation ; },
abstract = {OBJECTIVE: The internet provides convenient access to information about non-suicidal self-injury (NSSI) owing to its accessibility and anonymity. This study aimed to explore the distribution of topics regarding NSSI posted on the internet and yearly trends in the derived topics using text mining.
METHODS: We searched for the keyword "non-suicidal self-injury" (Ja-Hae in Korean) in the Naver Q&A using the statistical package R. We analyzed 7893 NSSI-related questions posted between 2009 and 2018. Text mining was performed using latent Dirichlet allocation (LDA) on the dataset to determine associations between phrases and thus identify common themes in posts about NSSI.
RESULTS: In the LDA, we selected the following 10 most common topics: anger, family troubles, collecting information on NSSI, stress, concerns regarding NSSI scarring, ways to help a non-suicidal self-injurious friend, depression, medical advice, ways to perform or stop NSSI, and prejudices and thoughts regarding non-suicidal self-injurious people.
CONCLUSIONS: This study provides valuable information on the nature of NSSI questions posted online. In future research, developing websites that provide NSSI information and support or guidance on effectively communicating with NSSI is necessary.},
}
@article {pmid35605833,
year = {2022},
author = {Bernardini, I and Fabrello, J and Vecchiato, M and Ferraresso, S and Babbucci, M and Peruzza, L and Rovere, GD and Masiero, L and Marin, MG and Bargelloni, L and Gambaro, A and Patarnello, T and Matozzo, V and Milan, M},
title = {Effects of environmental concentrations of the fragrance amyl salicylate on the mediterranean mussel Mytilus galloprovincialis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {307},
number = {},
pages = {119502},
doi = {10.1016/j.envpol.2022.119502},
pmid = {35605833},
issn = {1873-6424},
mesh = {Animals ; *Microbiota ; *Mytilus/metabolism ; Odorants/analysis ; Salicylates/toxicity ; Water/metabolism ; *Water Pollutants, Chemical/analysis ; },
abstract = {Amyl salicylate (AS) is a fragrance massively used as a personal care product and following the discharged in wastewaters may end up in the aquatic environment representing a potential threat for the ecosystem and living organisms. AS was recently detected in water of the Venice Lagoon, a vulnerable area continuously subjected to the income of anthropogenic chemicals. The lagoon is a relevant area for mollusc farming, including the Mediterranean mussels (Mytilus galloprovincialis) having an important economic and ecological role. Despite high levels of AS occurred in water of the Lagoon of Venice, no studies investigated the possible consequences of AS exposures on species inhabiting this ecosystem to date. For the first time, we applied a multidisciplinary approach to investigate the potential effects of the fragrance AS on Mediterranean mussels. To reach such a goal, bioaccumulation, cellular, biochemical, and molecular analyses (RNA-seq and microbiota characterization) were measured in mussels treated for 7 and 14 days with different AS Venice lagoon environmental levels (0.1 and 0.5 μg L[-1]). Despite chemical investigations suggested low AS bioaccumulation capability, cellular and molecular analyses highlighted the disruption of several key cellular processes after the prolonged exposures to the high AS concentration. Among them, potential immunotoxicity and changes in transcriptional regulation of pathways involved in energy metabolism, stress response, apoptosis and cell death regulations have been observed. Conversely, exposure to the low AS concentration demonstrated weak transcriptional changes and transient increased representation of opportunistic pathogens, as Arcobacter genus and Vibrio aestuarianus. Summarizing, this study provides the first overview on the effects of AS on one of the most widely farmed mollusk species.},
}
@article {pmid35605726,
year = {2022},
author = {Ma, J and Chen, F and Zhu, Y and Li, X and Yu, H and Sun, Y},
title = {Joint effects of microplastics and ciprofloxacin on their toxicity and fates in wheat: A hydroponic study.},
journal = {Chemosphere},
volume = {303},
number = {Pt 2},
pages = {135023},
doi = {10.1016/j.chemosphere.2022.135023},
pmid = {35605726},
issn = {1879-1298},
mesh = {Anti-Bacterial Agents ; Chlorophyll A/analysis ; Ciprofloxacin/analysis/toxicity ; Hydroponics ; *Microplastics ; Plastics/toxicity ; Polystyrenes/analysis ; Triticum ; *Water Pollutants, Chemical/analysis/toxicity ; },
abstract = {The toxicological impacts of microplastics (MPs) and antibiotics in the soil environment have gradually drawn widespread attention, while little research has focused on the combined pollution of MPs and antibiotics on plants. In this work, a 21-day hydroponic study was conducted to test the hypothesis that polystyrene MPs (0.1, 1 and 10 μm particle sizes, 50 mg/L) and ciprofloxacin (CIP) (1.0 and 5.0 mg/L) had a joint toxicity to wheat seedlings and they could be absorbed by wheat. Plant samples were taken for analyses after 21 days of exposure. The results showed that 0.1 and 1 μm MP could enter wheat roots but only the former could translocate to aerial parts. Moreover, 0.1 μm MP showed a greater toxicity effect than 1 μm MP, whereas 10 μm MP exhibited little toxicity on wheat. The dosing of 0.1 μm MP significantly increased the toxic effects of CIP to wheat. Compared to the control treatment (without MPs and CIP), 0.1 μm MPs-5.0 mg/L CIP treatment resulted in inhibition of root length and weight by 60.1% and 44.3%, respectively, while the contents of chlorophyll a and chlorophyll b decreased by 36.3% and 44.6%, respectively. The presence of CIP (5.0 mg/L) potentially aggravated the combined toxicity. The exposure of 0.1 μm MP significantly reduced root superoxide distumase activity but increased root malondialdehyde content. The amount of CIP in wheat tissues carried by MPs was negligible compared with the uptake quantity of CIP by wheat.},
}
@article {pmid35605195,
year = {2022},
author = {Zhao, F and Tian, S and Wu, Q and Li, Z and Ye, L and Zhuang, Y and Wang, M and Xie, Y and Zou, S and Teng, W and Tong, Y and Tang, D and Mahato, AK and Benhamed, M and Liu, Z and Zhang, Y},
title = {Utility of Triti-Map for bulk-segregated mapping of causal genes and regulatory elements in Triticeae.},
journal = {Plant communications},
volume = {3},
number = {4},
pages = {100304},
pmid = {35605195},
issn = {2590-3462},
mesh = {*Evolution, Molecular ; *Genome, Plant ; Plant Breeding ; Poaceae/genetics ; Triticum/genetics ; },
abstract = {Triticeae species, including wheat, barley, and rye, are critical for global food security. Mapping agronomically important genes is crucial for elucidating molecular mechanisms and improving crops. However, Triticeae includes many wild relatives with desirable agronomic traits, and frequent introgressions occurred during Triticeae evolution and domestication. Thus, Triticeae genomes are generally large and complex, making the localization of genes or functional elements that control agronomic traits challenging. Here, we developed Triti-Map, which contains a suite of user-friendly computational packages specifically designed and optimized to overcome the obstacles of gene mapping in Triticeae, as well as a web interface integrating multi-omics data from Triticeae for the efficient mining of genes or functional elements that control particular traits. The Triti-Map pipeline accepts both DNA and RNA bulk-segregated sequencing data as well as traditional QTL data as inputs for locating genes and elucidating their functions. We illustrate the usage of Triti-Map with a combination of bulk-segregated ChIP-seq data to detect a wheat disease-resistance gene with its promoter sequence that is absent from the reference genome and clarify its evolutionary process. We hope that Triti-Map will facilitate gene isolation and accelerate Triticeae breeding.},
}
@article {pmid35601625,
year = {2022},
author = {Asci, F and Scardapane, S and Zampogna, A and D'Onofrio, V and Testa, L and Patera, M and Falletti, M and Marsili, L and Suppa, A},
title = {Handwriting Declines With Human Aging: A Machine Learning Study.},
journal = {Frontiers in aging neuroscience},
volume = {14},
number = {},
pages = {889930},
pmid = {35601625},
issn = {1663-4365},
abstract = {BACKGROUND: Handwriting is an acquired complex cognitive and motor skill resulting from the activation of a widespread brain network. Handwriting therefore may provide biologically relevant information on health status. Also, handwriting can be collected easily in an ecological scenario, through safe, cheap, and largely available tools. Hence, objective handwriting analysis through artificial intelligence would represent an innovative strategy for telemedicine purposes in healthy subjects and people affected by neurological disorders.
MATERIALS AND METHODS: One-hundred and fifty-six healthy subjects (61 males; 49.6 ± 20.4 years) were enrolled and divided according to age into three subgroups: Younger adults (YA), middle-aged adults (MA), and older adults (OA). Participants performed an ecological handwriting task that was digitalized through smartphones. Data underwent the DBNet algorithm for measuring and comparing the average stroke sizes in the three groups. A convolutional neural network (CNN) was also used to classify handwriting samples. Lastly, receiver operating characteristic (ROC) curves and sensitivity, specificity, positive, negative predictive values (PPV, NPV), accuracy and area under the curve (AUC) were calculated to report the performance of the algorithm.
RESULTS: Stroke sizes were significantly smaller in OA than in MA and YA. The CNN classifier objectively discriminated YA vs. OA (sensitivity = 82%, specificity = 80%, PPV = 78%, NPV = 79%, accuracy = 77%, and AUC = 0.84), MA vs. OA (sensitivity = 84%, specificity = 56%, PPV = 78%, NPV = 73%, accuracy = 74%, and AUC = 0.7), and YA vs. MA (sensitivity = 75%, specificity = 82%, PPV = 79%, NPV = 83%, accuracy = 79%, and AUC = 0.83).
DISCUSSION: Handwriting progressively declines with human aging. The effect of physiological aging on handwriting abilities can be detected remotely and objectively by using machine learning algorithms.},
}
@article {pmid35594026,
year = {2022},
author = {Ren, S and Shen, B},
title = {5G, Big Data, and AI for Smart City and Prevention of Virus Infection.},
journal = {Advances in experimental medicine and biology},
volume = {1368},
number = {},
pages = {189-214},
pmid = {35594026},
issn = {0065-2598},
mesh = {Artificial Intelligence ; *Big Data ; *COVID-19/prevention & control ; Cities ; Humans ; Technology ; },
abstract = {With the development of urbanization, artificial intelligence, communication technology, and the Internet of Things, cities have evolved a new ecology from traditional city structures, that is, smart city. Combining 5G and big data, the applications of smart cities have been extended to every aspect of residents' lives. Based on the popularization of communication equipment and sensors, the great improvement in data transmission and processing technology, the production efficiency in medical field, industrial field, and security field has been improved. This chapter introduces the current research related to smart cities, including its architecture, technologies, and equipment involved. Then it discussed the challenges and opportunities of explainable artificial intelligence (XAI), which is the next important development direction of AI, especially in the medical field, where patients and medical personnel have non-negligible needs for the interpretability of AI models. Then, taking COVID-19 as an example, it discussed how smart cities play a role during virus infection and introduced the specific applications designed so far. Finally, it discussed the shortcomings of the current situation and the aspects that can be improved in the future.},
}
@article {pmid35590257,
year = {2022},
author = {Zhu, Y and Chen, L and Hong, X and Shi, H and Li, X},
title = {Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species.},
journal = {BMC genomics},
volume = {23},
number = {Suppl 4},
pages = {381},
pmid = {35590257},
issn = {1471-2164},
mesh = {Computational Biology/methods ; DNA Transposable Elements ; *RNA, Long Noncoding/genetics ; RNA, Messenger ; RNA, Plant/genetics ; Sequence Analysis, RNA ; Transcriptome ; Exome Sequencing ; },
abstract = {BACKGROUND: Previous studies on plant long noncoding RNAs (lncRNAs) lacked consistency and suffered from many factors like heterogeneous data sources and experimental protocols, different plant tissues, inconsistent bioinformatics pipelines, etc. For example, the sequencing of RNAs with poly(A) tails excluded a large portion of lncRNAs without poly(A), and use of regular RNA-sequencing technique did not distinguish transcripts' direction for lncRNAs. The current study was designed to systematically discover and analyze lncRNAs across eight evolutionarily representative plant species, using strand-specific (directional) and whole transcriptome sequencing (RiboMinus) technique.
RESULTS: A total of 39,945 lncRNAs (25,350 lincRNAs and 14,595 lncNATs) were identified, which showed molecular features of lncRNAs that are consistent across divergent plant species but different from those of mRNA. Further, transposable elements (TEs) were found to play key roles in the origination of lncRNA, as significantly large number of lncRNAs were found to contain TEs in gene body and promoter region, and transcription of many lncRNAs was driven by TE promoters. The lncRNA sequences were divergent even in closely related species, and most plant lncRNAs were genus/species-specific, amid rapid turnover in evolution. Evaluated with PhastCons scores, plant lncRNAs showed similar conservation level to that of intergenic sequences, suggesting that most lincRNAs were young and with short evolutionary age. INDUCED BY PHOSPHATE STARVATION (IPS) was found so far to be the only plant lncRNA group with conserved motifs, which may play important roles in the adaptation of terrestrial life during migration from aquatic to terrestrial. Most highly and specially expressed lncRNAs formed co-expression network with coding genes, and their functions were believed to be closely related to their co-expression genes.
CONCLUSION: The study revealed novel features and complexity of lncRNAs in plants through systematic analysis, providing important insights into the origination and evolution of plant lncRNAs.},
}
@article {pmid35587983,
year = {2022},
author = {Feng, Y and Schmid, B and Loreau, M and Forrester, DI and Fei, S and Zhu, J and Tang, Z and Zhu, J and Hong, P and Ji, C and Shi, Y and Su, H and Xiong, X and Xiao, J and Wang, S and Fang, J},
title = {Multispecies forest plantations outyield monocultures across a broad range of conditions.},
journal = {Science (New York, N.Y.)},
volume = {376},
number = {6595},
pages = {865-868},
doi = {10.1126/science.abm6363},
pmid = {35587983},
issn = {1095-9203},
mesh = {Biodiversity ; *Datasets as Topic ; *Environmental Restoration and Remediation ; *Forestry ; *Forests ; *Trees ; },
abstract = {Multispecies tree planting has long been applied in forestry and landscape restoration in the hope of providing better timber production and ecosystem services; however, a systematic assessment of its effectiveness is lacking. We compiled a global dataset of matched single-species and multispecies plantations to evaluate the impact of multispecies planting on stand growth. Average tree height, diameter at breast height, and aboveground biomass were 5.4, 6.8, and 25.5% higher, respectively, in multispecies stands compared with single-species stands. These positive effects were mainly the result of interspecific complementarity and were modulated by differences in leaf morphology and leaf life span, stand age, planting density, and temperature. Our results have implications for designing afforestation and reforestation strategies and bridging experimental studies of biodiversity-ecosystem functioning relationships with real-world practices.},
}
@article {pmid35587493,
year = {2022},
author = {Tadmor-Levi, R and Borovski, T and Marcos-Hadad, E and Shapiro, J and Hulata, G and Golani, D and David, L},
title = {Establishing and using a genetic database for resolving identification of fish species in the Sea of Galilee, Israel.},
journal = {PloS one},
volume = {17},
number = {5},
pages = {e0267021},
pmid = {35587493},
issn = {1932-6203},
mesh = {Animals ; DNA ; *DNA Barcoding, Taxonomic ; Databases, Genetic ; Fishes/genetics ; *Fresh Water ; Israel ; Phylogeny ; },
abstract = {Freshwaters are a very valuable resource in arid areas, such as Mediterranean countries. Freshwater systems are vulnerable ecological habitats, significantly disturbed globally and especially in arid areas. The Sea of Galilee is the largest surface freshwater body in the Middle East. It is an isolated habitat supporting unique fish populations, including endemic species and populations on the edge of their distribution range. Using the Sea of Galilee for water supply, fishing and recreation has been placing pressure on these fish populations. Therefore, efficient monitoring and effective actions can make a difference in the conservation of these unique fish populations. To set a baseline and develop molecular tools to do so, in this study, DNA barcoding was used to establish a database of molecular species identification based on sequences of Cytochrome C Oxidase subunit I gene. DNA barcodes for 22 species were obtained and deposited in Barcode of Life Database. Among these, 12 barcodes for 10 species were new to the database and different from those already there. Barcode sequences were queried against the database and similar barcodes from the same and closely related species were obtained. Disagreements between morphological and molecular species identification were identified for five species, which were further studied by phylogenetic and genetic distances analyses. These analyses suggested the Sea of Galilee contained hybrid fish of some species and other species for which the species definition should be reconsidered. Notably, the cyprinid fish defined as Garra rufa, should be considered as Garra jordanica. Taken together, along with data supporting reconsideration of species definition, this study sets the basis for further using molecular tools for monitoring fish populations, understanding their ecology, and effectively managing their conservation in this unique and important habitat and in the region.},
}
@article {pmid35585229,
year = {2022},
author = {Łopucki, R and Klich, D and Kociuba, P},
title = {Detection of spatial avoidance between sousliks and moles by combining field observations, remote sensing and deep learning techniques.},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {8264},
pmid = {35585229},
issn = {2045-2322},
mesh = {Animals ; *Deep Learning ; Ecosystem ; *Moles ; Remote Sensing Technology ; Sciuridae ; },
abstract = {Nowadays, remote sensing is being increasingly applied in ecology and conservation, and even underground animals can successfully be studied if they leave clear signs of their presence in the environment. In this work, by combining a field study, analysis of high-resolution aerial images, and machine learning techniques, we investigated the interspecies relationships of two small burrowing mammals: the spotted souslik Spermophilus suslicus and the European mole Talpa europaea. The study was conducted for 3 years (2018-2020) at a 105-ha grass airfield where both species coexist (Poland). Both field studies and the analysis of aerial imagery showed that, in the period of low population numbers, the souslik avoided coexistence with the European mole, and the presence of the mole was found to reduce the area of the habitat suitable for the souslik. The presence of other burrowing species may be an important element in the habitat selectivity of the souslik, but this has not yet been included in the conservation guidelines for this species. We discuss the contribution of our results to the knowledge of the ecology of burrowing mammals and their interspecies relationships. We also assess the possibility of using remote sensing and deep learning methods in ecology and conservation of small burrowing mammals.},
}
@article {pmid35584207,
year = {2022},
author = {Xue, W and Chen, B and Hong, D and Yu, J and Liu, G},
title = {Research on the Comprehensive Evaluation Method for the Automatic Recognition of Raman Spectrum under Multidimensional Constraint.},
journal = {Analytical chemistry},
volume = {94},
number = {21},
pages = {7628-7636},
doi = {10.1021/acs.analchem.2c00852},
pmid = {35584207},
issn = {1520-6882},
mesh = {*Algorithms ; Databases, Factual ; *Spectrum Analysis, Raman/methods ; },
abstract = {Raman spectrum contains abundant substance information with fingerprint characteristics. However, due to the huge variety of substances and their complex characteristic information, it is difficult to recognize the Raman spectrum accurately. Starting from dimensions like the Raman shift, the relative peak intensity, and the overall hit ratio of characteristic peaks, we extracted and recognized the characteristics in the Raman spectrum and analyzed these characteristics from local and global perspectives and then proposed a comprehensive evaluation method for the recognition of Raman spectrum on the basis of the data fusion of the recognition results under multidimensional constraint. Based on the common spectrum database of the normal Raman and surface-enhanced Raman of thousands of substances, we analyzed the performance of the evaluation method. It shows that even for the identification of spectra from instruments of low technical specifications, the automatic recognition rate of the sample can reach 98% and above, a great improvement compared with that of the common identification algorithms, which proves the effectiveness of the comprehensive evaluation method under multidimensional constraint.},
}
@article {pmid35582905,
year = {2022},
author = {Rodino, KG and Peaper, DR and Kelly, BJ and Bushman, F and Marques, A and Adhikari, H and Tu, ZJ and Marrero Rolon, R and Westblade, LF and Green, DA and Berry, GJ and Wu, F and Annavajhala, MK and Uhlemann, AC and Parikh, BA and McMillen, T and Jani, K and Babady, NE and Hahn, AM and Koch, RT and Grubaugh, ND and , and Rhoads, DD},
title = {Partial ORF1ab Gene Target Failure with Omicron BA.2.12.1.},
journal = {Journal of clinical microbiology},
volume = {60},
number = {6},
pages = {e0060022},
pmid = {35582905},
issn = {1098-660X},
support = {K23 AI121485/AI/NIAID NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R61 HL137063/HL/NHLBI NIH HHS/United States ; R01 AI140442/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; L30 AI120149/AI/NIAID NIH HHS/United States ; R33 HL137063/HL/NHLBI NIH HHS/United States ; U01 DA053949/DA/NIDA NIH HHS/United States ; P30 AI045008/AI/NIAID NIH HHS/United States ; },
mesh = {Base Sequence ; *COVID-19 ; Humans ; Mutation ; *SARS-CoV-2/genetics ; },
abstract = {Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene. We demonstrate that pOGTF is 98.6% sensitive and 99.9% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may affect transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly, increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.},
}
@article {pmid35582795,
year = {2022},
author = {Farrell, MJ and Brierley, L and Willoughby, A and Yates, A and Mideo, N},
title = {Past and future uses of text mining in ecology and evolution.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1975},
pages = {20212721},
pmid = {35582795},
issn = {1471-2954},
support = {MR/T027355/1/MRC_/Medical Research Council/United Kingdom ; },
mesh = {*Data Mining ; Language ; Machine Learning ; *Natural Language Processing ; Reproducibility of Results ; },
abstract = {Ecology and evolutionary biology, like other scientific fields, are experiencing an exponential growth of academic manuscripts. As domain knowledge accumulates, scientists will need new computational approaches for identifying relevant literature to read and include in formal literature reviews and meta-analyses. Importantly, these approaches can also facilitate automated, large-scale data synthesis tasks and build structured databases from the information in the texts of primary journal articles, books, grey literature, and websites. The increasing availability of digital text, computational resources, and machine-learning based language models have led to a revolution in text analysis and natural language processing (NLP) in recent years. NLP has been widely adopted across the biomedical sciences but is rarely used in ecology and evolutionary biology. Applying computational tools from text mining and NLP will increase the efficiency of data synthesis, improve the reproducibility of literature reviews, formalize analyses of research biases and knowledge gaps, and promote data-driven discovery of patterns across ecology and evolutionary biology. Here we present recent use cases from ecology and evolution, and discuss future applications, limitations and ethical issues.},
}
@article {pmid35582791,
year = {2022},
author = {Roche, DG and Berberi, I and Dhane, F and Lauzon, F and Soeharjono, S and Dakin, R and Binning, SA},
title = {Slow improvement to the archiving quality of open datasets shared by researchers in ecology and evolution.},
journal = {Proceedings. Biological sciences},
volume = {289},
number = {1975},
pages = {20212780},
pmid = {35582791},
issn = {1471-2954},
mesh = {Data Accuracy ; Data Collection ; *Ecology ; Humans ; *Information Dissemination ; },
abstract = {Many leading journals in ecology and evolution now mandate open data upon publication. Yet, there is very little oversight to ensure the completeness and reusability of archived datasets, and we currently have a poor understanding of the factors associated with high-quality data sharing. We assessed 362 open datasets linked to first- or senior-authored papers published by 100 principal investigators (PIs) in the fields of ecology and evolution over a period of 7 years to identify predictors of data completeness and reusability (data archiving quality). Datasets scored low on these metrics: 56.4% were complete and 45.9% were reusable. Data reusability, but not completeness, was slightly higher for more recently archived datasets and PIs with less seniority. Journal open data policy, PI gender and PI corresponding author status were unrelated to data archiving quality. However, PI identity explained a large proportion of the variance in data completeness (27.8%) and reusability (22.0%), indicating consistent inter-individual differences in data sharing practices by PIs across time and contexts. Several PIs consistently shared data of either high or low archiving quality, but most PIs were inconsistent in how well they shared. One explanation for the high intra-individual variation we observed is that PIs often conduct research through students and postdoctoral researchers, who may be responsible for the data collection, curation and archiving. Levels of data literacy vary among trainees and PIs may not regularly perform quality control over archived files. Our findings suggest that research data management training and culture within a PI's group are likely to be more important determinants of data archiving quality than other factors such as a journal's open data policy. Greater incentives and training for individual researchers at all career stages could improve data sharing practices and enhance data transparency and reusability.},
}
@article {pmid35576571,
year = {2022},
author = {Wonkam, A and Munung, NS and Dandara, C and Esoh, KK and Hanchard, NA and Landoure, G},
title = {Five Priorities of African Genomics Research: The Next Frontier.},
journal = {Annual review of genomics and human genetics},
volume = {23},
number = {},
pages = {499-521},
doi = {10.1146/annurev-genom-111521-102452},
pmid = {35576571},
issn = {1545-293X},
support = {U01 HG009716/HG/NHGRI NIH HHS/United States ; U24 HL135600/HL/NHLBI NIH HHS/United States ; U01 MH127692/MH/NIMH NIH HHS/United States ; U54 HG009790/HG/NHGRI NIH HHS/United States ; U01 HG007044/HG/NHGRI NIH HHS/United States ; H3A/18/001/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Biological Evolution ; *Black People ; Computational Biology ; *Genomics ; Humans ; Pharmacogenetics ; },
abstract = {To embrace the prospects of accurately diagnosing thousands of monogenic conditions, predicting disease risks for complex traits or diseases, tailoring treatment to individuals' pharmacogenetic profiles, and potentially curing some diseases, research into African genomic variation is a scientific imperative. African genomes harbor millions of uncaptured variants accumulated over 300,000 years of modern humans' evolutionary history, with successive waves of admixture, migration, and natural selection combining with extensive ecological diversity to create a broad and exceptional genomic complexity. Harnessing African genomic complexity, therefore, will require sustained commitment and equitable collaboration from the scientific community and funding agencies. African governments must support academic public research and industrial partnerships that build the necessary genetic medicine workforce, utilize the emerging genomic big data to develop expertise in computer science and bioinformatics, and evolve national and globalgovernance frameworks that recognize the ethical implications of data-driven genomic research and empower its application in African social, cultural, economic, and religious contexts.},
}
@article {pmid35576088,
year = {2022},
author = {Schulz, S and Möllerke, A},
title = {MACE - An Open Access Data Repository of Mass Spectra for Chemical Ecology.},
journal = {Journal of chemical ecology},
volume = {48},
number = {7-8},
pages = {589-597},
pmid = {35576088},
issn = {1573-1561},
mesh = {*Access to Information ; Databases, Factual ; Gas Chromatography-Mass Spectrometry/methods ; Mass Spectrometry ; },
abstract = {MACE is an open access collection of electron impact (EI) mass spectra for coupled gas chromatography-mass spectrometry (GC/MS) that serves as an add-on database, comprising curated spectra not present in widely available commercial mass spectral libraries, such as the NIST or WILEY databases. The spectra are stored as text files that allow easy integration into individual GC/MS systems. The article describes the concept of MACE, the data structure, how to contribute, and its usage. MACE is designed as a community effort and will require contributions from the community to be successful.},
}
@article {pmid35573805,
year = {2022},
author = {Record, S and Jarzyna, MA and Hardiman, B and Richardson, AD},
title = {Open data facilitate resilience in science during the COVID-19 pandemic.},
journal = {Frontiers in ecology and the environment},
volume = {20},
number = {2},
pages = {76-77},
pmid = {35573805},
issn = {1540-9295},
}
@article {pmid35569357,
year = {2022},
author = {Proskuryakova, L},
title = {The interaction of environmental systems and human development in a time of wild cards. A big data enhanced foresight study.},
journal = {Journal of environmental management},
volume = {316},
number = {},
pages = {115169},
doi = {10.1016/j.jenvman.2022.115169},
pmid = {35569357},
issn = {1095-8630},
mesh = {*Big Data ; Climate Change ; Conservation of Natural Resources ; Economic Development ; *Ecosystem ; Humans ; },
abstract = {The article contributes to the research discussion around the human-natural and social-ecological systems by identification of a comprehensive list of global trends related to integrated interaction between environmental systems and human development, including climate change, pollution, new quality of economic growth, and challenges for education and healthcare. The foresight study behind it encompasses a combination of quantitative (big data) and qualitative (expert) methods. This approach allows for a systemic vision of structural shifts, assessing their probability and impact. The outcomes of the study include the list of global environmental and human development trends and factors classified by STEEPV categories, their effects that split into opportunities and threats, and an assessment of their inter-relation and mutual impact. Policy implications focus on possible areas of intervention for sustainable growth.},
}
@article {pmid35568273,
year = {2022},
author = {Ruz, GA and Ashlock, D and Allmendinger, R and Fogel, GB},
title = {Editorial: 2020 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (IEEE CIBCB 2020).},
journal = {Bio Systems},
volume = {218},
number = {},
pages = {104698},
doi = {10.1016/j.biosystems.2022.104698},
pmid = {35568273},
issn = {1872-8324},
mesh = {*Artificial Intelligence ; *Computational Biology ; },
}
@article {pmid35565046,
year = {2022},
author = {da Silva Paiva, L and de Alcantara Sousa, LV and Oliveira, FR and de Carvalho, LEW and Raimundo, RD and Correa, JA and de Abreu, LC and Adami, F},
title = {Temporal Trend of the Prevalence of Modifiable Risk Factors of Stroke: An Ecological Study of Brazilians between 2006 and 2012.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {9},
pages = {},
pmid = {35565046},
issn = {1660-4601},
mesh = {Brazil/epidemiology ; *Diabetes Mellitus/epidemiology ; Humans ; *Hypertension/epidemiology ; Obesity/epidemiology ; Overweight/epidemiology ; Prevalence ; Risk Factors ; *Stroke/epidemiology ; },
abstract = {Stroke is one of the leading causes of death worldwide, including in Brazil. This study aimed to analyze the temporal trend of the prevalence of modifiable risk factors of stroke from 2006 to 2012. This ecological study was conducted by secondary analysis in May 2018, using data from the surveillance of risk factors and protection for chronic diseases by telephone inquiry (VIGITEL) available in the Department of Informatics of the Unified Health System (DATASUS). The modifiable risk factors of stroke in Brazilians were systemic arterial hypertension, diabetes mellitus, abusive alcohol consumption, overweight, and obesity. Overall, there was a significant increase in the risk factors of diabetes (β = 0.30, P = 0.001, r[2] = 0.99), overweight (β = 0.50, P = 0.002, r[2] = 0.98), and obesity (β = 0.88, P < 0.001, r[2] = 0.96). However, there was a stability in the prevalence of hypertension (β = 0.25, P = 0.320, r[2] = 0.88) and alcohol abuse (β = 0.32, P = 0.116, r[2] = 0.49). There was an increase in the prevalence of diabetes mellitus, overweight, and obesity, but stability in systemic arterial hypertension and abusive alcohol consumption in the Brazilian population.},
}
@article {pmid35564957,
year = {2022},
author = {Wang, T and Yang, Z and Chen, X and Han, F},
title = {Bibliometric Analysis and Literature Review of Tourism Destination Resilience Research.},
journal = {International journal of environmental research and public health},
volume = {19},
number = {9},
pages = {},
pmid = {35564957},
issn = {1660-4601},
mesh = {*Bibliometrics ; Databases, Factual ; Forecasting ; Publications ; *Tourism ; United States ; },
abstract = {The application of resilience thinking to tourism destination research is a new perspective on sustainable tourism and has gradually become a popular research topic. Some literature has been conducted on tourism destination resilience, but there has not been a comprehensive review and analysis of the whole field. This study was based on the literature from 2000 to 2021 in the Web of Science core collection database. The collaboration analysis, literature co-citation analysis, keyword co-occurrence, burst detection analysis in CiteSpace, and qualitative analysis were adopted to conduct a holistic tourism destination resilience research review. The results indicated that the United States, Australia, China, and the United Kingdom were the primary countries involved in tourism destination resilience research. Five hot research themes were obtained. (1) concept and connotation of tourism destination resilience, (2) drivers of tourism destination resilience, (3) sustainable management framework and practices, (4) perception of tourism destination resilience, and (5) the resilience of the tourism community. Furthermore, four research gaps and future directions were proposed in this study, including the theoretical framework of tourism destination resilience, assessment of tourism destination resilience, sustainable management and resilience, and application of advanced technology in tourism destination resilience. This study assists researchers in understanding the development and future research directions in tourism destination resilience research.},
}
@article {pmid35564261,
year = {2022},
author = {Nozdrenko, D and Prylutska, S and Bogutska, K and Cherepanov, V and Senenko, A and Vygovska, O and Khrapatyi, S and Ritter, U and Prylutskyy, Y and Piosik, J},
title = {Analysis of Biomechanical and Biochemical Markers of Rat Muscle Soleus Fatigue Processes Development during Long-Term Use of C60 Fullerene and N-Acetylcysteine.},
journal = {Nanomaterials (Basel, Switzerland)},
volume = {12},
number = {9},
pages = {},
pmid = {35564261},
issn = {2079-4991},
abstract = {The development of an effective therapy aimed at restoring muscle dysfunctions in clinical and sports medicine, as well as optimizing working activity in general remains an urgent task today. Modern nanobiotechnologies are able to solve many clinical and social health problems, in particular, they offer new therapeutic approaches using biocompatible and bioavailable nanostructures with specific bioactivity. Therefore, the nanosized carbon molecule, C60 fullerene, as a powerful antioxidant, is very attractive. In this study, a comparative analysis of the dynamic of muscle soleus fatigue processes in rats was conducted using 50 Hz stimulation for 5 s with three consistent pools after intraperitoneal administration of the following antioxidants: C60 fullerene (a daily dose of 1 mg/kg one hour prior to the start of the experiment) and N-acetylcysteine (NAC; a daily dose of 150 mg/kg one hour prior to the start of the experiment) during five days. Changes in the integrated power of muscle contraction, levels of the maximum and minimum contraction force generation, time of reduction of the contraction force by 50% of its maximum value, achievement of the maximum force response, and delay of the beginning of a single contraction force response were analyzed as biomechanical markers of fatigue processes. Levels of creatinine, creatine phosphokinase, lactate, and lactate dehydrogenase, as well as pro- and antioxidant balance (thiobarbituric acid reactive substances, hydrogen peroxide, reduced glutathione, and catalase activity) in the blood of rats were analyzed as biochemical markers of fatigue processes. The obtained data indicate that applied therapeutic drugs have the most significant effects on the 2nd and especially the 3rd stimulation pools. Thus, the application of C60 fullerene has a (50-80)% stronger effect on the resumption of muscle biomechanics after the beginning of fatigue than NAC on the first day of the experiment. There is a clear trend toward a positive change in all studied biochemical parameters by about (12-15)% after therapeutic administration of NAC and by (20-25)% after using C60 fullerene throughout the experiment. These findings demonstrate the promise of using C60 fullerenes as potential therapeutic nanoagents that can reduce or adjust the pathological conditions of the muscular system that occur during fatigue processes in skeletal muscles.},
}
@article {pmid35560159,
year = {2022},
author = {Reijnders, MJMF and Waterhouse, RM},
title = {CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation.},
journal = {PLoS computational biology},
volume = {18},
number = {5},
pages = {e1010075},
pmid = {35560159},
issn = {1553-7358},
mesh = {*Computational Biology/methods ; Consensus ; Gene Ontology ; Machine Learning ; Molecular Sequence Annotation ; *Semantics ; },
abstract = {Characterising gene function for the ever-increasing number and diversity of species with annotated genomes relies almost entirely on computational prediction methods. These software are also numerous and diverse, each with different strengths and weaknesses as revealed through community benchmarking efforts. Meta-predictors that assess consensus and conflict from individual algorithms should deliver enhanced functional annotations. To exploit the benefits of meta-approaches, we developed CrowdGO, an open-source consensus-based Gene Ontology (GO) term meta-predictor that employs machine learning models with GO term semantic similarities and information contents. By re-evaluating each gene-term annotation, a consensus dataset is produced with high-scoring confident annotations and low-scoring rejected annotations. Applying CrowdGO to results from a deep learning-based, a sequence similarity-based, and two protein domain-based methods, delivers consensus annotations with improved precision and recall. Furthermore, using standard evaluation measures CrowdGO performance matches that of the community's best performing individual methods. CrowdGO therefore offers a model-informed approach to leverage strengths of individual predictors and produce comprehensive and accurate gene functional annotations.},
}
@article {pmid35554909,
year = {2022},
author = {Khan, MS and Yousafi, Q and Bibi, S and Azhar, M and Ihsan, A},
title = {Bioinformatics-Based Approaches to Study Virus-Host Interactions During SARS-CoV-2 Infection.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2452},
number = {},
pages = {197-212},
pmid = {35554909},
issn = {1940-6029},
mesh = {*COVID-19 ; Computational Biology ; Host Microbial Interactions ; Host-Pathogen Interactions/genetics ; Humans ; Proteins ; SARS-CoV-2/genetics ; },
abstract = {As the knowledge of biomolecules is increasing from the last decades, it is helping the researchers to understand the unsolved issues regarding virology. Recent technologies in high-throughput sequencing are providing the swift generation of SARS-CoV-2 genomic data with the basic inside of viral infection. Owing to various virus-host protein interactions, high-throughput technologies are unable to provide complete details of viral pathogenesis. Identifying the virus-host protein interactions using bioinformatics approaches can assist in understanding the mechanism of SARS-CoV-2 infection and pathogenesis. In this chapter, recent integrative bioinformatics approaches are discussed to help the virologists and computational biologists in the identification of structurally similar proteins of human and SARS-CoV-2 virus, and to predict the potential of virus-host interactions. Considering experimental and time limitations for effective viral drug development, computational aided drug design (CADD) can reduce the gap between drug prediction and development. More research with respect to evolutionary solutions could be helpful to make a new pipeline for virus-host protein-protein interactions and provide more understanding to disclose the cases of host switch, and also expand the virulence of the pathogen and host range in developing viral infections.},
}
@article {pmid35552640,
year = {2022},
author = {Qin, D and Bo, W and Zheng, X and Hao, Y and Li, B and Zheng, J and Liang, G},
title = {DFBP: a comprehensive database of food-derived bioactive peptides for peptidomics research.},
journal = {Bioinformatics (Oxford, England)},
volume = {38},
number = {12},
pages = {3275-3280},
doi = {10.1093/bioinformatics/btac323},
pmid = {35552640},
issn = {1367-4811},
mesh = {*Peptides/chemistry ; Databases, Factual ; Structure-Activity Relationship ; },
abstract = {MOTIVATION: Food-derived bioactive peptides (FBPs) have demonstrated their significance in pharmaceuticals, diets and nutraceuticals, benefiting public health and global ecology. While significant efforts have been made to discover FBPs and to elucidate the underlying bioactivity mechanisms, there is lack of a systemic study of sequence-structure-activity relationship of FBPs in a large dataset.
RESULTS: Here, we construct a database of food-derived bioactive peptides (DFBP), containing a total of 6276 peptide entries in 31 types from different sources. Further, we develop a series of analysis tools for function discovery/repurposing, traceability, multifunctional bioactive exploration and physiochemical property assessment of peptides. Finally, we apply this database and data-mining techniques to discover new FBPs as potential drugs for cardiovascular diseases. The DFBP serves as a useful platform for not only the fundamental understanding of sequence-structure-activity of FBPs but also the design, discovery, and repurposing of peptide-based drugs, vaccines, materials and food ingredients.
DFBP service can be accessed freely via http://www.cqudfbp.net/. All data are incorporated into the article and its online supplementary material.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}
@article {pmid35544870,
year = {2022},
author = {Aragão, CMC and Mascarenhas, MDM},
title = {Temporal trend of adolescent intentional self-harm notifications in the school environment, Brazil, 2011-2018.},
journal = {Epidemiologia e servicos de saude : revista do Sistema Unico de Saude do Brasil},
volume = {31},
number = {1},
pages = {e2021820},
doi = {10.1590/S1679-49742022000100028},
pmid = {35544870},
issn = {2237-9622},
mesh = {Adolescent ; Brazil/epidemiology ; Female ; Humans ; Information Systems ; Linear Models ; Male ; Schools ; *Self-Injurious Behavior/epidemiology ; },
abstract = {OBJECTIVE: To analyze the trend of adolescent intentional self-harm notifications in the school environment, Brazil, 2011 to 2018.
METHODS: This was an ecological time series study, with data from the Notifiable Health Conditions Information System, using the Prais-Winsten linear regression model.
RESULTS: A total of 1,989 cases were notified. Notification rates ranged from 0.09 to 2.75/100,000 inhabitants, with an increasing trend, both in females (APC= 66.0%; 95%CI 39.0;98.3) and male (APC = 55.2%; 95%CI 29.9;85.4). The North region showed a stationary trend, while the Southeast and South regions showed an increasing trend, especially Rio de Janeiro (APC = 85.5%; 95%CI 58.0;117.8) and Paraná (APC = 73.6%; 95%CI 41.9;112.3). In the Midwest region, only the state of Mato Grosso do Sul showed a rising trend (APC = 54.5%; 95%CI 16.9;104.2).
CONCLUSION: There was an increasing trend in adolescent intentional self-harm notifications in the school environment in Brazil, during the study period.},
}
@article {pmid35544285,
year = {2022},
author = {Kieft, K and Adams, A and Salamzade, R and Kalan, L and Anantharaman, K},
title = {vRhyme enables binning of viral genomes from metagenomes.},
journal = {Nucleic acids research},
volume = {50},
number = {14},
pages = {e83},
pmid = {35544285},
issn = {1362-4962},
support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; R35 GM137828/GM/NIGMS NIH HHS/United States ; },
mesh = {*Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Metagenomics ; Sequence Analysis, DNA ; Software ; },
abstract = {Genome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed vRhyme, a fast and precise software for construction of viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds and employs supervised machine learning to identify nucleotide feature similarities, which are compiled into iterations of weighted networks and refined bins. To refine bins, vRhyme utilizes unique features of viral genomes, namely a protein redundancy scoring mechanism based on the observation that viruses seldom encode redundant genes. Using simulated viromes, we displayed superior performance of vRhyme compared to available binning tools in constructing more complete and uncontaminated vMAGs. When applied to 10,601 viral scaffolds from human skin, vRhyme advanced our understanding of resident viruses, highlighted by identification of a Herelleviridae vMAG comprised of 22 scaffolds, and another vMAG encoding a nitrate reductase metabolic gene, representing near-complete genomes post-binning. vRhyme will enable a convention of binning uncultivated viral genomes and has the potential to transform metagenome-based viral ecology.},
}
@article {pmid35537509,
year = {2022},
author = {Xu, N and Zhang, Z and Shen, Y and Zhang, Q and Liu, Z and Yu, Y and Wang, Y and Lei, C and Ke, M and Qiu, D and Lu, T and Chen, Y and Xiong, J and Qian, H},
title = {Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets.},
journal = {The Science of the total environment},
volume = {837},
number = {},
pages = {155807},
doi = {10.1016/j.scitotenv.2022.155807},
pmid = {35537509},
issn = {1879-1026},
mesh = {Algorithms ; *Artificial Intelligence ; High-Throughput Nucleotide Sequencing ; Machine Learning ; *Neural Networks, Computer ; Support Vector Machine ; },
abstract = {The development of machine learning and deep learning provided solutions for predicting microbiota response on environmental change based on microbial high-throughput sequencing. However, there were few studies specifically clarifying the performance and practical of two types of binary classification models to find a better algorithm for the microbiota data analysis. Here, for the first time, we evaluated the performance, accuracy and running time of the binary classification models built by three machine learning methods - random forest (RF), support vector machine (SVM), logistic regression (LR), and one deep learning method - back propagation neural network (BPNN). The built models were based on the microbiota datasets that removed low-quality variables and solved the class imbalance problem. Additionally, we optimized the models by tuning. Our study demonstrated that dataset pre-processing was a necessary process for model construction. Among these 4 binary classification models, BPNN and RF were the most suitable methods for constructing microbiota binary classification models. Using these 4 models to predict multiple microbial datasets, BPNN showed the highest accuracy and the most robust performance, while the RF method was ranked second. We also constructed the optimal models by adjusting the epochs of BPNN and the n_estimators of RF for six times. The evaluation related to performances of models provided a road map for the application of artificial intelligence to assess microbial ecology.},
}
@article {pmid35535680,
year = {2022},
author = {Engelhardt, EK and Biber, MF and Dolek, M and Fartmann, T and Hochkirch, A and Leidinger, J and Löffler, F and Pinkert, S and Poniatowski, D and Voith, J and Winterholler, M and Zeuss, D and Bowler, DE and Hof, C},
title = {Consistent signals of a warming climate in occupancy changes of three insect taxa over 40 years in central Europe.},
journal = {Global change biology},
volume = {28},
number = {13},
pages = {3998-4012},
doi = {10.1111/gcb.16200},
pmid = {35535680},
issn = {1365-2486},
mesh = {Animals ; Biodiversity ; *Butterflies ; Climate ; Climate Change ; Ecosystem ; Europe ; *Odonata ; },
abstract = {Recent climate and land-use changes are having substantial impacts on biodiversity, including population declines, range shifts, and changes in community composition. However, few studies have compared these impacts among multiple taxa, particularly because of a lack of standardized time series data over long periods. Existing data sets are typically of low resolution or poor coverage, both spatially and temporally, thereby limiting the inferences that can be drawn from such studies. Here, we compare climate and land-use driven occupancy changes in butterflies, grasshoppers, and dragonflies using an extensive data set of highly heterogeneous observation data collected in the central European region of Bavaria (Germany) over a 40-year period. Using occupancy models, we find occupancies (the proportion of sites occupied by a species in each year) of 37% of species have decreased, 30% have increased and 33% showed no significant trend. Butterflies and grasshoppers show strongest declines with 41% of species each. By contrast, 52% of dragonfly species increased. Temperature preference and habitat specificity appear as significant drivers of species trends. We show that cold-adapted species across all taxa have declined, whereas warm-adapted species have increased. In butterflies, habitat specialists have decreased, while generalists increased or remained stable. The trends of habitat generalists and specialists both in grasshoppers and semi-aquatic dragonflies, however did not differ. Our findings indicate strong and consistent effects of climate warming across insect taxa. The decrease of butterfly specialists could hint towards a threat from land-use change, as especially butterfly specialists' occurrence depends mostly on habitat quality and area. Our study not only illustrates how these taxa showed differing trends in the past but also provides hints on how we might mitigate the detrimental effects of human development on their diversity in the future.},
}
@article {pmid35534559,
year = {2022},
author = {Howe, LJ and Nivard, MG and Morris, TT and Hansen, AF and Rasheed, H and Cho, Y and Chittoor, G and Ahlskog, R and Lind, PA and Palviainen, T and van der Zee, MD and Cheesman, R and Mangino, M and Wang, Y and Li, S and Klaric, L and Ratliff, SM and Bielak, LF and Nygaard, M and Giannelis, A and Willoughby, EA and Reynolds, CA and Balbona, JV and Andreassen, OA and Ask, H and Baras, A and Bauer, CR and Boomsma, DI and Campbell, A and Campbell, H and Chen, Z and Christofidou, P and Corfield, E and Dahm, CC and Dokuru, DR and Evans, LM and de Geus, EJC and Giddaluru, S and Gordon, SD and Harden, KP and Hill, WD and Hughes, A and Kerr, SM and Kim, Y and Kweon, H and Latvala, A and Lawlor, DA and Li, L and Lin, K and Magnus, P and Magnusson, PKE and Mallard, TT and Martikainen, P and Mills, MC and Njølstad, PR and Overton, JD and Pedersen, NL and Porteous, DJ and Reid, J and Silventoinen, K and Southey, MC and Stoltenberg, C and Tucker-Drob, EM and Wright, MJ and , and , and Hewitt, JK and Keller, MC and Stallings, MC and Lee, JJ and Christensen, K and Kardia, SLR and Peyser, PA and Smith, JA and Wilson, JF and Hopper, JL and Hägg, S and Spector, TD and Pingault, JB and Plomin, R and Havdahl, A and Bartels, M and Martin, NG and Oskarsson, S and Justice, AE and Millwood, IY and Hveem, K and Naess, Ø and Willer, CJ and Åsvold, BO and Koellinger, PD and Kaprio, J and Medland, SE and Walters, RG and Benjamin, DJ and Turley, P and Evans, DM and Davey Smith, G and Hayward, C and Brumpton, B and Hemani, G and Davies, NM},
title = {Within-sibship genome-wide association analyses decrease bias in estimates of direct genetic effects.},
journal = {Nature genetics},
volume = {54},
number = {5},
pages = {581-592},
pmid = {35534559},
issn = {1546-1718},
support = {R01 HL109946/HL/NHLBI NIH HHS/United States ; MC_UU_00011/1//Medical Research Council/United Kingdom ; MC_UU_00011/6//Medical Research Council/United Kingdom ; MC_UU_00007/10//Medical Research Council/United Kingdom ; //Wellcome Trust/United Kingdom ; 208806/Z/17/Z//Wellcome Trust/United Kingdom ; },
mesh = {*Genome-Wide Association Study ; Humans ; Mendelian Randomization Analysis ; Multifactorial Inheritance/genetics ; Phenotype ; *Polymorphism, Single Nucleotide/genetics ; },
abstract = {Estimates from genome-wide association studies (GWAS) of unrelated individuals capture effects of inherited variation (direct effects), demography (population stratification, assortative mating) and relatives (indirect genetic effects). Family-based GWAS designs can control for demographic and indirect genetic effects, but large-scale family datasets have been lacking. We combined data from 178,086 siblings from 19 cohorts to generate population (between-family) and within-sibship (within-family) GWAS estimates for 25 phenotypes. Within-sibship GWAS estimates were smaller than population estimates for height, educational attainment, age at first birth, number of children, cognitive ability, depressive symptoms and smoking. Some differences were observed in downstream SNP heritability, genetic correlations and Mendelian randomization analyses. For example, the within-sibship genetic correlation between educational attainment and body mass index attenuated towards zero. In contrast, analyses of most molecular phenotypes (for example, low-density lipoprotein-cholesterol) were generally consistent. We also found within-sibship evidence of polygenic adaptation on taller height. Here, we illustrate the importance of family-based GWAS data for phenotypes influenced by demographic and indirect genetic effects.},
}
@article {pmid35533868,
year = {2022},
author = {Lencioni, V and Stella, E and Zanoni, MG and Bellin, A},
title = {On the delay between water temperature and invertebrate community response to warming climate.},
journal = {The Science of the total environment},
volume = {837},
number = {},
pages = {155759},
doi = {10.1016/j.scitotenv.2022.155759},
pmid = {35533868},
issn = {1879-1026},
mesh = {Animals ; Climate ; Climate Change ; Ecosystem ; Ice Cover ; *Invertebrates ; Rivers ; Temperature ; *Water ; },
abstract = {We evaluated the effect of global warming on invertebrate communities at high altitudes using data from the Careser system. We procured data on air temperature, which was obtained over 50 years at altitudes above 2600 m a.s.l., and data on water temperature, which was available for approximately 30 years. We sampled thrice in the past 20 years (2001, 2014, 2018) at three sampling sites (CR0-metakryal, CR1-hypokryal, CR2-glacio-rhithral) of the Careser glacier-fed stream and its main non-glacial tributary (CR1bis-krenal). Warmer climates were observed in the last decade compared to the 1980s, with a mean maximum summer air temperature (mTmax) increase of 1.7 °C at 2642 m a.s.l. and 1.8 °C at 2858 m a.s.l. Compared to air temperatures, the rise in water temperature was delayed by approximately 20 years; water mTmax started to increase in 2003, reaching 8.1 °C at 2642 m a.s.l. and 2.4 °C at 2858 m a.s.l in the year 2020. The invertebrate community exhibited a delayed response approximately 13 years from the water warming; there was a sequential increase in the number of taxa, Shannon diversity, and after 17 years, functional diversity. In the kryal sites, taxonomical and functional diversity changed more consistently than in the glacio-rhithral site in the same period, due to the arrival of taxa that were previously absent upstream and bearers of entirely new traits. Progressive taxonomical homogenisation was evident with decreasing glacial influence, mainly between glacio-rhithral and krenal sites. The numbers of Diamesa steinboecki, an insect that was adapted to the cold, declined in summer (water mTmax >6 °C and air mTmax >12 °C). This study highlights the mode and time of response of stream invertebrate communities to global warming in alpine streams and provides guidelines for analysing changes in the stream invertebrate communities of other glacial systems in alpine regions.},
}
@article {pmid35531376,
year = {2022},
author = {Relph, KA and Russell, CD and Fairfield, CJ and Turtle, L and de Silva, TI and Siggins, MK and Drake, TM and Thwaites, RS and Abrams, S and Moore, SC and Hardwick, HE and Oosthuyzen, W and Harrison, EM and Docherty, AB and Openshaw, PJM and Baillie, JK and Semple, MG and Ho, A and , },
title = {Procalcitonin Is Not a Reliable Biomarker of Bacterial Coinfection in People With Coronavirus Disease 2019 Undergoing Microbiological Investigation at the Time of Hospital Admission.},
journal = {Open forum infectious diseases},
volume = {9},
number = {5},
pages = {ofac179},
pmid = {35531376},
issn = {2328-8957},
support = {205228/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MC_PC_19059/MRC_/Medical Research Council/United Kingdom ; },
abstract = {Admission procalcitonin measurements and microbiology results were available for 1040 hospitalized adults with coronavirus disease 2019 (from 48 902 included in the International Severe Acute Respiratory and Emerging Infections Consortium World Health Organization Clinical Characterisation Protocol UK study). Although procalcitonin was higher in bacterial coinfection, this was neither clinically significant (median [IQR], 0.33 [0.11-1.70] ng/mL vs 0.24 [0.10-0.90] ng/mL) nor diagnostically useful (area under the receiver operating characteristic curve, 0.56 [95% confidence interval, .51-.60]).},
}
@article {pmid35526396,
year = {2022},
author = {Coolen, JWP and Vanaverbeke, J and Dannheim, J and Garcia, C and Birchenough, SNR and Krone, R and Beermann, J},
title = {Generalized changes of benthic communities after construction of wind farms in the southern North Sea.},
journal = {Journal of environmental management},
volume = {315},
number = {},
pages = {115173},
doi = {10.1016/j.jenvman.2022.115173},
pmid = {35526396},
issn = {1095-8630},
mesh = {Biodiversity ; *Energy-Generating Resources ; Farms ; Humans ; North Sea ; *Wind ; },
abstract = {Over the last years, the development of offshore renewable energy installations such as offshore wind farms led to an increasing number of man-made structures in marine environments. Since 2009, benthic impact monitoring programs were carried out in wind farms installed in the southern North Sea. We collated and analyzed data sets from three major monitoring programs. Our analysis considered a total of 2849 sampling points converted to a set of biodiversity response metrics. We analyzed biodiversity changes related to the implementation of offshore wind farms and generalized the correlation of these changes with spatial and temporal patterns. Our results demonstrate that depth, season and distance to structure (soft-bottom community) consistently determined diversity indicators and abundance parameters, whereas the age and the country affiliation were significantly related to some but not all indices. The water depth was the most important structuring factor for fouling communities while seasonal effects were driving most of the observed changes in soft-sediment communities. We demonstrate that a meta-analysis can provide an improved level of understanding of ecological patterns on large-scale effects of anthropogenic structures on marine biodiversity, which were not visible in single monitoring studies. We believe that meta-analyses should become an indispensable tool for management of offshore wind farm effects in the future, particularly in the view of the foreseen development of offshore renewable energies. This might lead to a better picture and more comprehensive view on potential alterations. However, this requires a modern open-source data policy and data management, across institutions and across national borders.},
}
@article {pmid35525040,
year = {2022},
author = {Luo, J and Sun, Z and Lu, L and Xiong, Z and Cui, L and Mao, Z},
title = {Rapid expansion of coastal aquaculture ponds in Southeast Asia: Patterns, drivers and impacts.},
journal = {Journal of environmental management},
volume = {315},
number = {},
pages = {115100},
doi = {10.1016/j.jenvman.2022.115100},
pmid = {35525040},
issn = {1095-8630},
mesh = {Aquaculture ; Asia, Southeastern ; *Ecosystem ; Geographic Information Systems ; *Ponds ; },
abstract = {Aquaculture pond is one of the most important land use types and a main income source in coastal zones in Southeast Asia. However, the fast expansion of aquaculture ponds threatens coastal ecosystems - an issue that Sustainable Development Goals (SDGs)14 seeks to address. Investigating expansion patterns is essential for exploring the drivers and understanding its impacts, and thus the focus of the sustainable management of aquaculture. This study aims to assess the spatio-temporal expansion patterns of aquaculture ponds with multitemporal remote sensing images and geographic information system in the coastal zone of Southeast Asia over a 25-year period (1990-2015), to understanding how globalization and economic policies may have contributed to such changes. The results show that, in 2015, total area of coastal aquaculture ponds was about 23,245 km[2], and 79% of coastal aquaculture ponds distributed within 15 km from the coastline. And the amount has expanded about 2.6 times in the past 25 years. Vietnam has the largest area of aquaculture in 2015 and the highest annual increasing rate, accounting for 40.28% and 298.5 km[2]/y, followed by Indonesia (31.50% and 156.8 km[2]/y), Thailand (10.79% and 64.8 km[2]/y), Myanmar (8.76% and 61.1 km[2]/y). The expansion pattern of aquaculture ponds in the region altered from outlying to edge-expansion from the year of 2000. The main drivers of rapid expansion lie to the intensified local fisher policies as a result of economic globalization. While development of aquaculture has enhanced family income, it has also led to significant reduction of mangrove and coastal water pollution (eutrophication). With the prevailing antagonism between aquaculture expansion and ecosystem conversion, our research call for the local government's attention to sustainable management of aquaculture. This will be the key to reduce food safety risk and simultaneously prevent inevitable damages to coastal ecosystems, as stipulated by SDGs 2 and 14.},
}
@article {pmid35523985,
year = {2022},
author = {Martínez-García, PJ and Mas-Gómez, J and Wegrzyn, J and Botía, JA},
title = {Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.).},
journal = {Scientific reports},
volume = {12},
number = {1},
pages = {7481},
pmid = {35523985},
issn = {2045-2322},
mesh = {Computational Biology ; Fruit/metabolism ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Indoleacetic Acids/metabolism ; *Vitis/metabolism ; },
abstract = {Expression quantitative trait loci (eQTLs) are associations between genetic variants, such as Single Nucleotide Polymorphisms (SNPs), and gene expression. eQTLs are an important tool to understand the genetic variance of gene expression of complex phenotypes. eQTLs analyses are common in biomedical models but are scarce in woody crop species such as fruit trees or grapes. In this study, a comprehensive bioinformatic analysis was conducted leveraging with expression data from two different growth stages, around ripening onset, of 10 genotypes of grape (Vitis vinifera L.). A total of 2170 cis-eQTL were identified in 212 gene modulated at ripening onset. The 48% of these DEGs have a known function. Among the annotated protein-coding genes, terpene synthase, auxin-regulatory factors, GRFS, ANK_REP_REGION domain-containing protein, Kinesin motor domain-containing protein and flavonol synthase were noted. This new inventory of cis-eQTLs influencing gene expression during fruit ripening will be an important resource to examine variation for this trait and will help to elucidate the complex genetic architecture underlying this process in grape.},
}
@article {pmid35511143,
year = {2022},
author = {Shoemaker, WR and Polezhaeva, E and Givens, KB and Lennon, JT},
title = {Seed banks alter the molecular evolutionary dynamics of Bacillus subtilis.},
journal = {Genetics},
volume = {221},
number = {2},
pages = {},
pmid = {35511143},
issn = {1943-2631},
mesh = {*Bacillus subtilis/genetics ; Evolution, Molecular ; Humans ; *Seed Bank ; },
abstract = {Fluctuations in the availability of resources constrain the growth and reproduction of individuals, which subsequently affects the evolution of their respective populations. Many organisms contend with such fluctuations by entering a reversible state of reduced metabolic activity, a phenomenon known as dormancy. This pool of dormant individuals (i.e. a seed bank) does not reproduce and is expected to act as an evolutionary buffer, though it is difficult to observe this effect directly over an extended evolutionary timescale. Through genetic manipulation, we analyze the molecular evolutionary dynamics of Bacillus subtilis populations in the presence and absence of a seed bank over 700 days. The ability of these bacteria to enter a dormant state increased the accumulation of genetic diversity over time and altered the trajectory of mutations, findings that were recapitulated using simulations based on a mathematical model of evolutionary dynamics. While the ability to form a seed bank did not alter the degree of negative selection, we found that it consistently altered the direction of molecular evolution across genes. Together, these results show that the ability to form a seed bank can affect the direction and rate of molecular evolution over an extended evolutionary timescale.},
}
@article {pmid35510784,
year = {2022},
author = {Jasper, RJ and McDonald, TK and Singh, P and Lu, M and Rougeux, C and Lind, BM and Yeaman, S},
title = {Evaluating the accuracy of variant calling methods using the frequency of parent-offspring genotype mismatch.},
journal = {Molecular ecology resources},
volume = {22},
number = {7},
pages = {2524-2533},
pmid = {35510784},
issn = {1755-0998},
mesh = {Computational Biology ; Genotype ; *High-Throughput Nucleotide Sequencing/methods ; Mutation ; *Polymorphism, Single Nucleotide ; Software ; },
abstract = {The use of next-generation sequencing (NGS) data sets has increased dramatically over the last decade, but there have been few systematic analyses quantifying the accuracy of the commonly used variant caller programs. Here we used a familial design consisting of diploid tissue from a single lodgepole pine (Pinus contorta) parent and the maternally derived haploid tissue from 106 full-sibling offspring, where mismatches could only arise due to mutation or bioinformatic error. Given the rarity of mutation, we used the rate of mismatches between parent and offspring genotype calls to infer the single nucleotide polymorphism (SNP) genotyping error rates of FreeBayes, HaplotypeCaller, SAMtools, UnifiedGenotyper, and VarScan. With baseline filtering HaplotypeCaller and UnifiedGenotyper yielded more SNPs and higher error rates by one to two orders of magnitude, whereas FreeBayes, SAMtools and VarScan yielded lower numbers of SNPs and more modest error rates. To facilitate comparison between variant callers we standardized each SNP set to the same number of SNPs using additional filtering, where UnifiedGenotyper consistently produced the smallest proportion of genotype errors, followed by HaplotypeCaller, VarScan, SAMtools, and FreeBayes. Additionally, we found that error rates were minimized for SNPs called by more than one variant caller. Finally, we evaluated the performance of various commonly used filtering metrics on SNP calling. Our analysis provides a quantitative assessment of the accuracy of five widely used variant calling programs and offers valuable insights into both the choice of variant caller program and the choice of filtering metrics, especially for researchers using non-model study systems.},
}
@article {pmid35510429,
year = {2022},
author = {Cheng, X and Xie, H and Zhang, K and Wen, J},
title = {Enabling Medicago truncatula forward genetics: identification of genetic crossing partner for R108 and development of mapping resources for Tnt1 mutants.},
journal = {The Plant journal : for cell and molecular biology},
volume = {111},
number = {2},
pages = {608-616},
doi = {10.1111/tpj.15797},
pmid = {35510429},
issn = {1365-313X},
mesh = {Databases, Nucleic Acid ; Genes, Plant ; Genetic Testing ; *Medicago truncatula/genetics ; Mutagenesis, Insertional ; },
abstract = {Though Medicago truncatula Tnt1 mutants are widely used by researchers in the legume community, they are mainly used for reverse genetics because of the availability of the BLAST-searchable large-scale flanking sequence tags database. However, these mutants should have also been used extensively for forward genetic screens, an effort that has been hindered due to the lack of a compatible genetic crossing partner for the M. truncatula genotype R108, from which Tnt1 mutants were generated. In this study, we selected three Medicago HapMap lines (HM017, HM018 and HM022) and performed reciprocal genetic crosses with R108. After phenotypic analyses in F1 and F2 progenies, HM017 was identified as a compatible crossing partner with R108. By comparing the assembled genomic sequences of HM017 and R108, we developed and confirmed 318 Indel markers evenly distributed across the eight chromosomes of the M. truncatula genome. To validate the effectiveness of these markers, by employing the map-based cloning approach, we cloned the causative gene in the dwarf mutant crs isolated from the Tnt1 mutant population, identifying it as gibberellin 3-β-dioxygenase 1, using some of the confirmed Indel markers. The primer sequences and the size difference of each marker were made available for users in the web-based database. The identification of the crossing partner for R108 and the generation of Indel markers will enhance the forward genetics and the overall usage of the Tnt1 mutants.},
}
@article {pmid35505773,
year = {2022},
author = {Boyes, D and , and , and , and , and , and Sivess, L and , },
title = {The genome sequence of the small elephant hawk moth, Deilephila porcellus (Linnaeus, 1758).},
journal = {Wellcome open research},
volume = {7},
number = {},
pages = {80},
pmid = {35505773},
issn = {2398-502X},
abstract = {We present a genome assembly from an individual male Deilephila porcellus (the small elephant hawk moth; Arthropoda; Insecta; Lepidoptera; Sphingidae). The genome sequence is 402 megabases in span. The majority of the assembly (99.99%) is scaffolded into 29 chromosomal pseudomolecules, with the Z sex chromosome assembled.},
}
@article {pmid35504469,
year = {2022},
author = {Zhu, Y and Wang, L and You, Y and Cheng, Y and Ma, J and Chen, F},
title = {Enhancing network complexity and function of soil bacteria by thiourea-modified biochar under cadmium stress in post-mining area.},
journal = {Chemosphere},
volume = {302},
number = {},
pages = {134811},
doi = {10.1016/j.chemosphere.2022.134811},
pmid = {35504469},
issn = {1879-1298},
mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; *Cadmium/analysis ; Charcoal/chemistry ; Soil/chemistry ; *Soil Pollutants/analysis ; Thiourea ; },
abstract = {Cadmium (Cd) pollution cause severe stress to soil microorganisms and biochar utilized for its ability to immobilize Cd in the soil effectively. However, the influence of biochar on the structure and function of the bacterial network under Cd stress is unclear. This research reports a pot experiment conducted to investigate the impact of 2.0% Italian poplar bark biochar (PB), 2.0% thiourea-modified biochar (TP), and control treatment (CK) on the complexity, stability and functional properties of the bacterial community under Cd stress. The results showed that: (1) Biochar increased the diversity of soil bacterial consortia under Cd stress (p < 0.05), and the diversity index demonstrated as order of CK < PB < TP; (2) Compared with CK network, the nodes number of PB and TP treatments networks were much higher, while the modularity and transitivity increased by 0.04% and 37.6%, 2.45% and 1.12%, respectively. The biochar amendment increased the stability and complexity of the network; (3) PICRUSt2 prediction results show that Xenobiotics biodegradation and metabolism membrane transport of TP treatment increased 62.52% and 53.62% compared with CK, respectively, which could be related to the decrease in Cd content according to principal component analysis. (4) The reduction of leaching Cd content caused network complexity and bacterial function changes by biochar amendment. TP amendment enhanced the complexity and stability of soil bacterial community under Cd stress, which will provide a scientific basis for in situ remediations of Cd-contaminated soils.},
}
@article {pmid35504313,
year = {2022},
author = {Carvalho, GML and Silva, DF and Xavier, LDA and Soares, JVR and Ramos, VDV and Madureira, AP and Lima, MA and Tonelli, GB and Paz, GF and Rêgo, FD and Andrade-Filho, JD and Margonari, C},
title = {Sand fly bioecological aspects and risk mapping of leishmaniasis by geographical information systems approach in a mineral exploration area of Brazil.},
journal = {Acta tropica},
volume = {232},
number = {},
pages = {106491},
doi = {10.1016/j.actatropica.2022.106491},
pmid = {35504313},
issn = {1873-6254},
mesh = {Animals ; Brazil/epidemiology ; DNA ; Dogs ; Female ; Geographic Information Systems ; Insect Vectors/genetics ; *Leishmaniasis/epidemiology ; Male ; Minerals ; *Phlebotomus/genetics ; *Psychodidae/genetics ; },
abstract = {Epidemiological studies of leishmaniasis in areas of great human influence and environmental change serve as important tools for the implementation of effective control plans. Mining is currently a major economic activity in Brazil with the municipality of Pains, in the state of Minas Gerais, being one of the main lime producing municipalities in the country. This study aimed to map areas of potential transmission risks within the municipality of Pains using an epidemiological approach in association with the ecological study of sand flies. Twelve samplings carried out between May 2015 and April 2016 collected a total of 12,728 sandflies, comprising 2,854 females (22.42%) and 9,874 males (77.58%), of 20 species belonging to ten genera. The most abundant species was Lutzomyia longipalpis (80%). Leishmania DNA was detected in seven pools of female sand flies with an infection rate of 0.37%. Geoprocessing and the use of maps revealed that vector sand flies are distributed throughout the urban area, as are cases of canine and human leishmaniasis. However, the greatest abundances of sand flies were at sampling points at the border of the urban area. Higher densities of sand flies and the presence of Leishmania DNA may be correlated with extensive degradation by limestone mining. Integrated and multidisciplinary research approaches are necessary to better understand how the impacts of environmental change influence these insect vectors of leishmaniasis.},
}
@article {pmid35502341,
year = {2022},
author = {Qing, J and Song, W and Tian, L and Samuel, SB and Li, Y},
title = {Potential Small Molecules for Therapy of Lupus Nephritis Based on Genetic Effect and Immune Infiltration.},
journal = {BioMed research international},
volume = {2022},
number = {},
pages = {2259164},
pmid = {35502341},
issn = {2314-6141},
mesh = {Computational Biology ; Female ; Gene Expression ; Genes, Regulator ; Humans ; *Lupus Erythematosus, Systemic/genetics ; *Lupus Nephritis/drug therapy/genetics ; Male ; Membrane Proteins/genetics ; RNA-Binding Proteins/genetics ; },
abstract = {Lupus nephritis (LN) is the most common and significant complication of systemic lupus erythematosus (SLE) due to its poor prognosis and mortality rates in SLE patients. There is a critical need for new drugs as the pathogenesis of LN remains to be elucidated and immunosuppressive therapy comes with many deficiencies. In this study, 23 hub genes (IFI6, PLSCR1, XAF1, IFI16, IFI44, MX1, IFI44L, IFIT3, IFIT2, IFI27, DDX58, EIF2AK2, IFITM1, RTP4, IFITM3, TRIM22, PARP12, IFIH1, OAS1, HERC6, RSAD2, DDX60, and MX2) were identified through bioinformatics and network analysis and are closely related to interferon production and function. Interestingly, immune cell infiltration analysis and correlation analysis demonstrate a positive correlation between the expression of 23 hub genes and monocyte infiltration in glomeruli and M2 macrophage infiltration in the tubulointerstitium of LN patients. Additionally, the CTD database, DsigDB database, and DREIMT database were used to explore the bridging role of genes in chemicals and LN as well as the potential influence of these chemicals on immune cells. After comparison and discussion, six small molecules (Acetohexamide, Suloctidil, Terfenadine, Prochlorperazine, Mefloquine, and Triprolidine) were selected for their potential ability in treating lupus nephritis.},
}
@article {pmid35501433,
year = {2022},
author = {Wilk, BK and Szopińska, M and Sobaszek, M and Pierpaoli, M and Błaszczyk, A and Luczkiewicz, A and Fudala-Ksiazek, S},
title = {Electrochemical oxidation of landfill leachate using boron-doped diamond anodes: pollution degradation rate, energy efficiency and toxicity assessment.},
journal = {Environmental science and pollution research international},
volume = {29},
number = {43},
pages = {65625-65641},
pmid = {35501433},
issn = {1614-7499},
mesh = {Ammonia/analysis ; *Boron/analysis ; Chlorine/analysis ; Conservation of Energy Resources ; Electrodes ; Oxidants ; Oxidation-Reduction ; Sulfates/analysis ; Wastewater/analysis ; *Water Pollutants, Chemical/analysis ; },
abstract = {Electrochemical oxidation (EO), due to high efficiency and small carbon footprint, is regarded as an attractive option for on-site treatment of highly contaminated wastewater. This work shows the effectiveness of EO using three boron-doped diamond electrodes (BDDs) in sustainable management of landfill leachate (LL). The effect of the applied current density (25-100 mA cm[-2]) and boron doping concentration (B/C ratio: 500 ppm, 10,000 ppm and 15,000 ppm) on the performance of EO was investigated. It was found that, of the electrodes used, the one most effective at COD, BOD20 and ammonia removal (97.1%, 98.8% and 62%, respectively) was the electrode with the lowest boron doping. Then, to better elucidate the ecological role of LLs, before and after EO, cultivation of faecal bacteria and microscopic analysis of total (prokaryotic) cell number, together with ecotoxicity assay (Daphnia magna, Thamnocephalus platyurus and Artemia salina) were combined for the two better-performing electrodes. The EO process was very effective at bacterial cell inactivation using each of the two anodes, even within 2 h of contact time. In a complex matrix of LLs, this is probably a combined effect of electrogenerated oxidants (hydroxyl radicals, active chlorine and sulphate radicals), which may penetrate into the bacterial cells and/or react with cellular components. The toxicity of EO-treated LLs proved to be lower than that of raw ones. Since toxicity drops with increased boron doping, it is believed that appropriate electrolysis parameters can diminish the toxicity effect without compromising the nutrient-removal and disinfection capability, although salinity of LLs and related multistep-oxidation pathways needs to be further elucidated.},
}
@article {pmid35488501,
year = {2022},
author = {Chen, Y and Rademacher, T and Fonti, P and Eckes-Shephard, AH and LeMoine, JM and Fonti, MV and Richardson, AD and Friend, AD},
title = {Inter-annual and inter-species tree growth explained by phenology of xylogenesis.},
journal = {The New phytologist},
volume = {235},
number = {3},
pages = {939-952},
pmid = {35488501},
issn = {1469-8137},
mesh = {Carbohydrates ; Ecosystem ; *Pinus ; *Quercus ; Seasons ; *Tracheophyta ; Wood ; Xylem ; },
abstract = {Wood formation determines major long-term carbon (C) accumulation in trees and therefore provides a crucial ecosystem service in mitigating climate change. Nevertheless, we lack understanding of how species with contrasting wood anatomical types differ with respect to phenology and environmental controls on wood formation. In this study, we investigated the seasonality and rates of radial growth and their relationships with climatic factors, and the seasonal variations of stem nonstructural carbohydrates (NSC) in three species with contrasting wood anatomical types (red oak: ring-porous; red maple: diffuse-porous; white pine: coniferous) in a temperate mixed forest during 2017-2019. We found that the high ring width variability observed in both red oak and red maple was caused more by changes in growth duration than growth rate. Seasonal radial growth patterns did not vary following transient environmental factors for all three species. Both angiosperm species showed higher concentrations and lower inter-annual fluctuations of NSC than the coniferous species. Inter-annual variability of ring width varied by species with contrasting wood anatomical types. Due to the high dependence of annual ring width on growth duration, our study highlights the critical importance of xylem formation phenology for understanding and modelling the dynamics of wood formation.},
}
@article {pmid35483251,
year = {2022},
author = {Xiao, D and He, H and Yan, X and Díaz, ND and Chen, D and Ma, J and Zhang, Y and Li, J and Keita, M and Julien, EO and Yan, X},
title = {The response regularity of biohydrogen production by anthracite H2-producing bacteria consortium to six conventional veterinary antibiotics.},
journal = {Journal of environmental management},
volume = {315},
number = {},
pages = {115088},
doi = {10.1016/j.jenvman.2022.115088},
pmid = {35483251},
issn = {1095-8630},
mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria ; Bioreactors/microbiology ; *Coal ; Fermentation ; *Hydrogen/analysis ; },
abstract = {The impact of antibiotics on H2-producing bacteria must be considered in the industrialization of biological H2 production using livestock manure as raw resources. However, whether antibiotics that may be contained in excreta will threaten the saf