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arXiv 2020年

作者： Liu, Meijun Bu, Yi Chen, Chongyan Xu, Jian Li, Daifeng Leng, Yan Freeman, Richard Barry Meyer, Eric Yoon, Wonjin Sung, Mujeen Jeong, Minbyul Lee, Jinhyuk Kang, Jaewoo Min, Chao Song, Min Zhai, Yujia Ding, Ying Institute for Global Public Policy Fudan University Shanghai China Department of Information Management Peking University Beijing China School of Information University of Texas at Austin AustinTX United States School of Information Management Sun Yat-Sen University Guangzhou China McCombs School of Business University of Texas at Austin AustinTX United States Department of Economics Harvard University CambridgeMA United States CambridgeMA United States Department of Computer Science and Engineering Korea University Seoul Korea Republic of Interdisciplinary Graduate Program in Bioinformatics Korea University Seoul Korea Republic of School of Information Management Nanjing University Nanjing China Department of Library and Information Science Yonsei University Seoul Korea Republic of Department of Information Resource Management School of Management Tianjin Normal University Tianjin China School of Information Management Wuhan University Wuhan China Dell Medical School University of Texas at Austin AustinTX United States

Scientific novelty drives the efforts to invent new vaccines and solutions during the pandemic. First-time collaboration and international collaboration are two pivotal channels to expand teams' search activities for a broader scope of resources required to address the global challenge, which might facilitate the generation of novel ideas. Our analysis of 98,981 coronavirus papers suggests that scientific novelty measured by the BioBERT model that is pre-trained on 29 million PubMed articles, and first-time collaboration increased after the outbreak of COVID-19, and international collaboration witnessed a sudden decrease. During COVID-19, papers with more first-time collaboration were found to be more novel and international collaboration did not hamper novelty as it had done in the normal periods. The findings suggest the necessity of reaching out for distant resources and the importance of maintaining a collaborative scientific community beyond nationalism during a pandemic. Copyright © 2020, The Authors. All rights reserved.

关键词： Coronavirus

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Multi-stream deep learning framework to predict mild cognitive impairment with Rey Complex Figure Test

arXiv

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arXiv 2024年

作者： Park, Junyoung Seo, Eun Hyun Kim, Sunjun Yi, SangHak Lee, Kun Ho Won, Sungho Department of Neurology and Neurological Sciences Stanford University School of Medicine StanfordCA94305 United States RexSoft Inc Seoul08826 Korea Republic of Gwangju Alzheimer's & Related Dementia Cohort Research Center Chosun University Gwangju61452 Korea Republic of Premedical Science College of Medicine Chosun University Gwangju61452 Korea Republic of Neurozen Inc. Seoul06160 Korea Republic of Department of Neurology Wonkwang University Hospital Wonkwang University School of Medicine Iksan15865 Korea Republic of Department of Biomedical Science Chosun University Gwangju61452 Korea Republic of Korea Brain Research Institute Daegu41068 Korea Republic of Department of Public Health Sciences Graduate School of Public Health Seoul National University Seoul08826 Korea Republic of Interdisciplinary Program in Bioinformatics Seoul National University Seoul08826 Korea Republic of Institute of Health and Environment Seoul National University Seoul08826 Korea Republic of

Drawing tests like the Rey Complex Figure Test (RCFT) are widely used to assess cognitive functions such as visuospatial skills and memory, making them valuable tools for detecting mild cognitive impairment (MCI). Despite their utility, existing predictive models based on these tests often suffer from limitations like small sample sizes and lack of external validation, which undermine their reliability. We developed a multi-stream deep learning framework that integrates two distinct processing streams: a multi-head self-attention based spatial stream using raw RCFT images and a scoring stream employing a previously developed automated scoring system. Our model was trained on data from 1,740 subjects in the Korean cohort and validated on an external hospital dataset of 222 subjects from Korea. The proposed multi-stream model demonstrated superior performance over baseline models (AUC = 0.872, Accuracy = 0.781) in external validation. The integration of both spatial and scoring streams enables the model to capture intricate visual details from the raw images while also incorporating structured scoring data, which together enhance its ability to detect subtle cognitive impairments. This dual approach not only improves predictive accuracy but also increases the robustness of the model, making it more reliable in diverse clinical settings. Our model has practical implications for clinical settings, where it could serve as a cost-effective tool for early MCI screening. © 2024, CC BY.

关键词： Convolutional neural networks

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Author Correction: Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis

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Nature communications 2023年第1期14卷 6540页

作者： Hitomi Takada Yohei Sasagawa Mika Yoshimura Kaori Tanaka Yoshimi Iwayama Tetsutaro Hayashi Ayako Isomura-Matoba Itoshi Nikaido Akira Kurisaki Laboratory of Stem Cell Technologies Graduate School of Science and Technology Nara Institute of Science and Technology Takayama-cho Ikoma Nara Japan. Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research Wako Saitama Japan. Department of Functional Genome Informatics Biological Data Science Medical Research Institute Tokyo Medical and Dental University Bunkyo Tokyo Japan. Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research Wako Saitama Japan. itoshi.nikaido@riken.jp. Department of Functional Genome Informatics Biological Data Science Medical Research Institute Tokyo Medical and Dental University Bunkyo Tokyo Japan. itoshi.nikaido@riken.jp. Master's/Doctoral Program in Life Science Innovation (Bioinformatics) Degree Programs in Systems and Information Engineering Graduate School of Science and Technology University of Tsukuba Tsukuba Ibaraki Japan. itoshi.nikaido@riken.jp. Laboratory of Stem Cell Technologies Graduate School of Science and Technology Nara Institute of Science and Technology Takayama-cho Ikoma Nara Japan. akikuri@bs.naist.jp.

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Author Correction: Type-2 Diabetics Reduces Spatial Variation of Microbiome Based on Extracellular Vesicles from Gut Microbes across Human Body

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Scientific reports 2020年第1期10卷 5368页

作者： Geumkyung Nah Sang-Cheol Park Kangjin Kim Sungmin Kim Jaehyun Park Sanghun Lee Sungho Won Interdisciplinary Program in Bioinformatics Seoul National University Seoul South Korea. Department of public health sciences Seoul National university Seoul South Korea. Inje University College of Medicine and Haeundae Paik Hospital Busan South Korea. Department of medical consilience Graduate school Dankook university Yongin-si South Korea. integrative@***. Interdisciplinary Program in Bioinformatics Seoul National University Seoul South Korea. won1@snu.ac.kr. Department of public health sciences Seoul National university Seoul South Korea. won1@snu.ac.kr. Institute of Health and Environment Seoul National University Seoul South Korea. won1@snu.ac.kr.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

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Sex Differences of Co-Exposures to Melamine and Phthalates and Early Renal Injury in Children

SSRN

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SSRN 2024年

作者： Wu, Ming-Tsang Tsai, Hui-Ju Wu, Chia-Fang Li, Sih-Syuan Chen, Jia-Jen Hsieh, Chia-Jung Chen, Chu-Chih Wang, Shu-Li Chen, Mei-Lien Graduate Institute of Clinical Medicine Taiwan Department of Family Medicine Kaohsiung Municipal Ta-Tung Hospital Kaohsiung Medical University Kaohsiung Taiwan Department of Family Medicine Kaohsiung Medical University Hospital Kaohsiung Medical University Kaohsiung Taiwan Department of Family Medicine School of Medicine College of Medicine Kaohsiung Medical University Kaohsiung Taiwan Research Center for Precision Environmental Medicine Kaohsiung Medical University Kaohsiung Taiwan Taipei Taiwan Ph.D. Program in Environmental and Occupational Medicine Kaohsiung Medical University Kaohsiung Taiwan Department of Public Health Tzu Chi University Hualien Taiwan Division of Biostatistics and Bioinformatics Institute of Population Health Sciences National Health Research Institutes Taiwan Institute of Environmental and Occupational Health Sciences School of Medicine National Yang Ming Chiao Tung University Taipei Taiwan National Institute of Environmental Health Sciences National Health Research Institutes Miaoli Taiwan

Studies concerning the effect of co-exposure to melamine and phthalates, two common environmental chemicals and potential nephrotoxins, on kidney function in children are rare. Thus, this study aims to examine the above-mentioned relationship, and their sex-different effect is also explored. Study children (3-7 years old) were recruited from one cohort of the Taiwan Maternal and Infant Cohort Study (TMICS) between 2016 and 2020. One-spot urine specimens were collected to simultaneously measure melamine, 11 phthalate metabolites, and two markers of renal injury, microalbumin and N-acetyl-beta-D-glucosaminidas (NAG). Daily intakes of melamine and six phthalates, including DEHP (di-2-ethylhexylphthalate), DiBP (Dibutyl phthalate), DnBP (Di-n-butyl phthalate), BBzP (Butyl benzyl phthalate), and DEP (Diethyl phthalate), were estimated using a creatinine excretion-based model. A total of 552 children (319 boys and 213 girls) were studied, with a mean age of 4 years. Although the individual effect of study chemicals on early renal injury was not significant, we did find that boys in the highest quartile of estimated melamine intake (≥ 0.68 µg/kg/day) had significantly higher urine ACR levels and in the highest quartile of estimated phthalate intake of DEHP (≥ 5.36 µg/kg/day), DEP (≥ 0.89 µg/kg/day), and DiBP (≥ 1.19 µg/kg/day) had significantly higher urine NAG levels when compared to the combined three lowest quartile ones as comparison groups. Categorizing the highest quartile of the above four significant chemicals as "1" score and summed, the higher the score of the joint effect of melamine, DEHP, DEP, or DiBP, the higher the urine ACR and NAG levels noted in study children, particularly in boys. We conclude that children with high co-exposure of melamine and certain phthalate chemicals have increased markers of early kidney injury particularly in boys. © 2024, The Authors. All rights reserved.

关键词： Metabolites

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Rainfall forecasting using PSPline and rice production with ocean-atmosphere interaction

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IOP Conference Series: Earth and Environmental Science 2018年第1期195卷

作者： Rezzy Eko Caraka Budi Darmawan Supatmanto Muhammad Tahmid Joko Soebagyo M Ali Mauludin Akbar Iskandar Bens Pardamean Bioinformatics and Data Science Research Center (BDSRC) Bina Nusantara University Jakarta Indonesia 11480 Weather Modification Technology Center Agency for the Assessment and Application of Technology (BPPT Indonesia Agency for Meteorology Climatology and Geophysics Indonesia College of Technology Wastukancana Purwakarta Laboratory of Sociology and Extension Padjadjaran University Informatics Engineering STMIK AKBA Makassar Computer Science Department BINUS Graduate Program – Master of Computer Science Bina Nusantara University Jakarta Indonesia 11480

The role of climate can be affected by plants. The weather can accelerate and multiply the existence of various plant pests and diseases, accelerate the growth and development of grass among plants, and encourage the emergence of infection and significant damage to plants. The elements of climate that affect the growth of plants are one of them is rainfall. In this paper, we performed the simulation using the non-parametric penalized spline (PSPLINE) method and studied the effect on rice production in Lampung. It can be concluded that the increasing fluctuation, frequency, and intensity of climate anomalies in the last decade caused by the ENSO phenomenon have an impact on changes in distribution patterns, intensity, and period of the wet season so that the start of the rainy season and the dry season becomes too late. As a result, there is a seasonal shift from normal average conditions that can ultimately have severe implications for food crops. In a nutshell penalized spline gives high accuracy with R 2 = 96.227% and MAPE = 1.62%.

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Random-effects substitution models for phylogenetics via scalable gradient approximations

arXiv

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arXiv 2023年

作者： Magee, Andrew F. Holbrook, Andrew J. Pekar, Jonathan E. Caviedes-Solis, Itzue W. Matsen, Fredrick A. Baele, Guy Wertheim, Joel O. Ji, Xiang Lemey, Philippe Suchard, Marc A. Department of Biostatistics Jonathan and Karin Fielding School of Public Health University of California Los Angeles Los AngelesCA United States Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA United States Department of Biomedical Informatics University of California San Diega La Jolla CA United States Department of Biology Swarthmore College SwarthmorePA United States Howard Hughes Medical Institute SeattleWA United States Computational Biology Program Fred Hutchinson Cancer Research Center SeattleWA United States Department of Genome Sciences University of Washington SeattleWA United States Department of Statistics University of Washington SeattleWA United States Department of Microbiology Immunology and Transplantation Rega Institute KU Leuven Leuven Belgium Department of Medicine University of California San Diego La Jolla CA United States Department of Mathematics Tulane University New OrleansLA United States Department of Biomathematics David Geffen School of Medicine at UCLA University of California Los Angeles Los AngelesCA United States Department of Human Genetics David Geffen School of Medicine at UCLA Universtiy of California Los Angeles Los AngelesCA United States

Phylogenetic and discrete-trait evolutionary inference depend heavily on an appropriate characterization of the underlying character substitution process. In this paper, we present random-effects substitution models that extend common continuous-time Markov chain models into a richer class of processes capable of capturing a wider variety of substitution dynamics. As these random-effects substitution models often require many more parameters than their usual counterparts, inference can be both statistically and computationally challenging. Thus, we also propose an efficient approach to compute an approximation to the gradient of the data likelihood with respect to all unknown substitution model parameters. We demonstrate that this approximate gradient enables scaling of sampling-based inference, namely Bayesian inference via Hamiltonian Monte Carlo, under random-effects substitution models across large trees and state-spaces. Applied to a dataset of 583 SARS-CoV-2 sequences, an HKY model with random-effects shows strong signals of nonreversibility in the substitution process, and posterior predictive model checks clearly show that it is a more adequate model than a reversible model. When analyzing the pattern of phylogeographic spread of 1441 influenza A virus (H3N2) sequences between 14 regions, a random-effects phylogeographic substitution model infers that air travel volume adequately predicts almost all dispersal rates. A random-effects state-dependent substitution model reveals no evidence for an effect of arboreality on the swimming mode in the tree frog subfamily Hylinae. Simulations reveal that random-effects substitution models can accommodate both negligible and radical departures from the underlying base substitution model. We show that our gradient-based inference approach is over an order of magnitude more time efficient than conventional approaches. Copyright © 2023, The Authors. All rights reserved.

关键词： Phylogenetic

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Expression of concern: Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy

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Nanoscale 2024年第9期16卷 4919页

作者： Michael A Casasanta G M Jonaid Liam Kaylor William Y Luqiu Maria J Solares Mariah L Schroen William J Dearnaley Jarad Wilson Madeline J Dukes Deborah F Kelly Department of Biomedical Engineering Pennsylvania State University University Park PA 16802 USA. Debkelly@psu.edu. Materials Research Institute Pennsylvania State University University Park PA 16802 USA. Bioinformatics and Genomics Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park PA 16802 USA. Molecular Cellular and Integrative Biosciences Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park PA 16802 USA. Department of Electrical and Computer Engineering Duke University Durham NC 27708 USA. RayBiotech Life Peachtree Corners GA 30092 USA. Applications Science Protochips Inc. Morrisville NC 27560 USA.

Expression of concern for 'Microchip-based structure determination of low-molecular weight proteins using cryo-electron microscopy' by Michael A. Casasanta , , 2021, , 7285-7293, https://***/10.1039/D1NR00388G.

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Using species ranges and macroeconomic data to fill the gap in costs of biological invasions

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Nature ecology & evolution 2025年 2025 May 26页

作者： Ismael Soto Pierre Courtois Arman Pili Enrico Tordoni Eléna Manfrini Elena Angulo Céline Bellard Elizabeta Briski Miloš Buřič Ross N Cuthbert Antonín Kouba Melina Kourantidou Rafael L Macêdo Boris Leroy Phillip J Haubrock Franck Courchamp Brian Leung Faculty of Fisheries and Protection of Waters South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses University of South Bohemia in České Budějovice Vodňany Czech Republic. isma-sa@***. CEE-M University of Montpellier CNRS INRAE Instit Agro Montpellier France. School of Biological Sciences Faculty of Science Monash University Clayton Victoria Australia. Institute for Biochemistry and Biology University of Potsdam Potsdam Germany. Department of Botany Institute of Ecology and Earth Science University of Tartu Tartu Estonia. Université Paris-Saclay CNRS AgroParisTech Ecologie Société Evolution Gif sur Yvette France. Unité Biologie des Organismes et Ecosystèmes Aquatiques (BOREA UMR 8067) Muséum national d'Histoire naturelle Sorbonne Université Université de Caen Normandie CNRS IRD Université des Antilles Paris France. Estación Biológica de Doñana CSIC Seville Spain. GEOMAR Helmholtz-Zentrum für Ozeanforschung Kiel Kiel Germany. Faculty of Fisheries and Protection of Waters South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses University of South Bohemia in České Budějovice Vodňany Czech Republic. Institute for Global Food Security School of Biological Sciences Queen's University Belfast Belfast UK. AMURE University of Western Brittany Plouzané France. Department of Sociology Environmental and Business Economics University of Southern Denmark Esbjerg Denmark. Woods Hole Oceanographic Institution Falmouth MA USA. Marine Policy Center Woods Hole MA USA. Graduate Program in Conservation and Ecotourism Federal University of Rio de Janeiro State Rio de Janeiro Brazil. Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany. Institute of Biology Freie Universität Berlin Berlin Germany. Department of River Ecology and Conservation Senckenberg Research Institute and Natural History Museum Frankfurt Gelnhausen Germany. CAMB Center for Applied Mathematics and Bioinformatics Gulf

Biological invasions threaten global biodiversity, human well-being and economies. Many regional and taxonomic syntheses of monetary costs have been produced recently but with important knowledge gaps owing to uneven geographic and taxonomic research intensity. Here we combine species distribution models, macroeconomic data and the InvaCost database to produce the highest resolution spatio-temporal cost estimates currently available to bridge these gaps. From a subset of 162 invasive species with 'highly reliable' documented costs at the national level, our interpolation focuses on countries that have not reported any costs despite the known presence of invasive species. This analysis demonstrates a substantial underestimation, with global costs potentially estimated to be 1,646% higher for these species than previously recorded. This discrepancy was uneven geographically and taxonomically, respectively peaking in Europe and for plants. Our results showed that damage costs were primarily driven by gross domestic product, human population size, agricultural area and environmental suitability, whereas management expenditure correlated with gross domestic product and agriculture areas. We also found a lag time for damage costs of 46 years, but management spending was not delayed. The methodological predictive approach of this study provides a more complete view of the economic dimensions of biological invasions and narrows the global disparity in invasion cost reporting.

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High-Resolution Imaging of Human Viruses in Liquid Droplets

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Advanced materials (Deerfield Beach, Fla.) 2021年第37期33卷 e2103221页

作者： G M Jonaid William J Dearnaley Michael A Casasanta Liam Kaylor Samantha Berry Madeline J Dukes Michael S Spilman Jennifer L Gray Deborah F Kelly Bioinformatics and Genomics Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park PA 16802 USA. Department of Biomedical Engineering Pennsylvania State University University Park PA 16802 USA. Materials Research Institute Pennsylvania State University University Park PA 16802 USA. Center for Structural Oncology Pennsylvania State University University Park PA 16802 USA. Molecular Cellular and Integrative Biosciences Graduate Program Huck Institutes of the Life Sciences Pennsylvania State University University Park PA 16802 USA. Protochips Inc. Morrisville NC 27560 USA. Direct Electron LP. San Diego CA 92128 USA.

Liquid-phase electron microscopy (LP-EM) is an exciting new area in the materials imaging field, providing unprecedented views of molecular processes. Time-resolved insights from LP-EM studies are a strong complement to the remarkable results achievable with other high-resolution techniques. Here, the opportunities to expand LP-EM technology beyond 2D temporal assessments and into the 3D regime are described. The results show new structures and dynamic insights of human viruses contained in minute volumes of liquid while acquired in a rapid timeframe. To develop this strategy, adeno-associated virus (AAV) is used as a model system. AAV is a well-known gene therapy vehicle with current applications involving drug delivery and vaccine development for COVID-19. Improving the understanding of the physical properties of biological entities in a liquid state, as maintained in the human body, has broad societal implications for human health and disease.

关键词： COVID-19 SARS-CoV-2 adeno-associated virus direct electron detector liquid-phase electron microscopy silicon nitride

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