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Global burden of 369 diseases and injuries in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019

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The Lancet 2020年第10258期396卷 1204-1222页

作者： Abbafati, Cristiana Abbas, Kaja M. Abbasi, Mohammad Abbasifard, Mitra Abbasi-Kangevari, Mohsen Abbastabar, Hedayat Abd-Allah, Foad Abdelalim, Ahmed Abdollahi, Mohammad Abdollahpour, Ibrahim Abedi, Aidin Abedi, Parisa Abegaz, Kedir Hussein Abolhassani, Hassan Abosetugn, Akine Eshete Aboyans, Victor Abrams, Elissa M. Abreu, Lucas Guimarães Abrigo, Michael R.M. Abu Haimed, Abdulaziz Khalid Abualhasan, Ahmed Abu-Gharbieh, Eman Abu-Raddad, Laith Jamal Abushouk, Abdelrahman I. Acebedo, Alyssa Ackerman, Ilana N. Adabi, Maryam Adair, Tim Adamu, Abdu A. Adebayo, Oladimeji M. Adedeji, Isaac Akinkunmi Adekanmbi, Victor Adelson, Jaimie D. Adeoye, Abiodun Moshood Adetokunboh, Olatunji O. Adham, Davoud Advani, Shailesh M. Afarideh, Mohsen Afshari, Mahdi Afshin, Ashkan Agardh, Emilie E. Agarwal, Gina Agasthi, Pradyumna Agesa, Kareha M. Aghaali, Mohammad Aghamir, Seyed Mohammad Kazem Agrawal, Anurag Ahmad, Tauseef Ahmadi, Alireza Ahmadi, Keivan Ahmadi, Mehdi Ahmadieh, Hamid Ahmadpour, Ehsan Ahmed, Muktar Beshir Aji, Budi Akalu, Temesgen Yihunie Akinyemi, Rufus Olusola Akinyemiju, Tomi Akombi, Blessing Akunna, Chisom Joyqueenet Alahdab, Fares Al-Aly, Ziyad Alam, Khurshid Alam, Noore Alam, Samiah Alam, Tahiya Alanezi, Fahad Mashhour Alanzi, Turki M. Albertson, Samuel B. Alcalde-Rabanal, Jacqueline Elizabeth Alema, Niguse Meles Alemu, Biresaw Wassihun Alemu, Yihun Mulugeta Alhabib, Khalid F. Alhassan, Robert Kaba Ali, Muhammad Ali, Saqib Alicandro, Gianfranco Alijanzadeh, Mehran Alinia, Cyrus Alipour, Vahid Alizade, Hesam Aljunid, Syed Mohamed Alla, François Allebeck, Peter Almadi, Majid Abdulrahman Hamad Almasi, Ali Almasi-Hashiani, Amir Almasri, Nihad A. Al-Mekhlafi, Hesham M. Almulhim, Abdulaziz M. Alonso, Jordi Al-Raddadi, Rajaa M. Altirkawi, Khalid A. Alumran, Arwa Khalid Alvis-Guzman, Nelson Alvis-Zakzuk, Nelson J. Amare, Azmeraw T. Amare, Bekalu Amini, Saeed Amini-Rarani, Mostafa Aminorroaya, Arya Amiri, Fatemeh Amit, Arianna Maever L. Amugsi, Dickson A. Amul, Gianna Gayle Herrera Anbesu, Etsay Woldu Ancuceanu, Robert Anderl Department of Juridical and Economic Studies La Sapienza University Rome Italy Department of Infectious Disease Epidemiology London School of Hygiene and Tropical Medicine London United Kingdom Social Determinants of Health Research Center Tehran Iran Department of Neurology Cairo University Cairo Egypt School of Pharmacy Tehran Iran The Institute of Pharmaceutical Sciences (TIPS) Tehran Iran Neuroscience Research Center Isfahan University of Medical Sciences Isfahan Iran Biostatistics Department Near East University Nicosia Cyprus Biostatistics and Health Informatics Madda Walabu University Bale Robe Ethiopia Research Center for Immunodeficiencies Tehran Iran Karolinska University Hospital Huddinge Sweden Department of Cardiology Dupuytren University Hospital Limoges France University of Limoges Limoges France Department of Pediatric Dentistry Federal University of Minas Gerais Belo Horizonte Brazil Department of Research Philippine Institute for Development Studies Quezon City Philippines Department of Healthcare Policy and Research Weill Cornell Medical College in Qatar Doha Qatar Harvard Medical School Boston MA United States Department of Medicine Ain Shams University Cairo Egypt Hamadan University of Medical Sciences Hamadan Iran School of Medicine Cardiff University Cardiff United Kingdom School of Laboratory Medicine and Science University College Hospital Ibadan Ibadan Nigeria Institute of Cardiovascular Diseases University of Ibadan Ibadan Nigeria Centre of Excellence for Epidemiological Modelling and Analysis Stellenbosch University Cape Town South Africa Department of Global Health Stellenbosch University Cape Town South Africa School of Health Ardabil University of Medical Science Ardabil Iran Social Behavioral Research Branch National Institute of Health Bethesda MD United States Department of Oncology Georgetown University Washington DC DC United States Department of Health Metrics Sciences School of Medicine Seattle WA

Background: In an era of shifting global agendas and expanded emphasis on non-communicable diseases and injuries along with communicable diseases, sound evidence on trends by cause at the national level is essential. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) provides a systematic scientific assessment of published, publicly available, and contributed data on incidence, prevalence, and mortality for a mutually exclusive and collectively exhaustive list of diseases and injuries. Methods: GBD estimates incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to 369 diseases and injuries, for two sexes, and for 204 countries and territories. Input data were extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service use, air pollution monitors, satellite imaging, disease notifications, and other sources. Cause-specific death rates and cause fractions were calculated using the Cause of Death Ensemble model and spatiotemporal Gaussian process regression. Cause-specific deaths were adjusted to match the total all-cause deaths calculated as part of the GBD population, fertility, and mortality estimates. Deaths were multiplied by standard life expectancy at each age to calculate YLLs. A Bayesian meta-regression modelling tool, DisMod-MR 2.1, was used to ensure consistency between incidence, prevalence, remission, excess mortality, and cause-specific mortality for most causes. Prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases and injuries to calculate YLDs. We considered results in the context of the Socio-demographic Index (SDI), a composite indicator of income per capita, years of schooling, and fertility rate in females younger than 25 years. Uncertainty intervals (UIs) were generated for every metric using the 25th and 975th ordered 1000 draw value

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Correction: Acetyl-CoA metabolism drives epigenome change and contributes to carcinogenesis risk in fatty liver disease

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Genome medicine 2023年第1期15卷 38页

作者： Gabriella Assante Sriram Chandrasekaran Stanley Ng Aikaterini Tourna Carolina H Chung Kowsar A Isse Jasmine L Banks Ugo Soffientini Celine Filippi Anil Dhawan Mo Liu Steven G Rozen Matthew Hoare Peter Campbell J William O Ballard Nigel Turner Margaret J Morris Shilpa Chokshi Neil A Youngson Institute of Hepatology Foundation for Liver Research 111 Coldharbour Lane London SE5 9NT UK. Faculty of Life Sciences and Medicine King's College London London UK. Program in Chemical Biology University of Michigan Ann Arbor MI 48109 USA. Center for Bioinformatics and Computational Medicine Ann Arbor MI 48109 USA. Department of Biomedical Engineering University of Michigan Ann Arbor MI 48109 USA. Rogel Cancer Center University of Michigan Medical School Ann Arbor MI 48109 USA. Wellcome Trust Sanger Institute Cambridge UK. UNSW Sydney Sydney Australia. Cellular Bioenergetics Laboratory Victor Chang Cardiac Research Institute Darlinghurst NSW Australia. Institute of Liver Studies King's College Hospital London UK. Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore. CRUK Cambridge Institute Cambridge UK. Department of Medicine University of Cambridge Addenbrooke's Hospital Cambridge UK. Department of Ecology Environment and Evolution La Trobe University Bundoora Melbourne VIC 3086 Australia. Institute of Hepatology Foundation for Liver Research 111 Coldharbour Lane London SE5 9NT UK. n.youngson@researchinliver.org.uk. Faculty of Life Sciences and Medicine King's College London London UK. n.youngson@researchinliver.org.uk. UNSW Sydney Sydney Australia. n.youngson@researchinliver.org.uk.

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Self-Awareness for Autonomous Systems

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PROCEEDINGS OF THE IEEE 2020年第7期108卷 971-975页

作者： Dutt, Nikil Regazzoni, Carlo S. Rinner, Bernhard Yao, Xin Nikil Dutt (Fellow IEEE) received the Ph.D. degree from the University of Illinois at Urbana–Champaign Champaign IL USA in 1989.""He is currently a Distinguished Professor of computer science (CS) cognitive sciences and electrical engineering and computer sciences (EECS) with the University of California at Irvine Irvine CA USA. He is a coauthor of seven books. His research interests include embedded systems electronic design automation (EDA) computer architecture distributed systems healthcare Internet of Things (IoT) and brain-inspired architectures and computing.""Dr. Dutt is a Fellow of ACM. He was a recipient of the IFIP Silver Core Award. He has received numerous best paper awards. He serves as the Steering Committee Chair of the IEEE/ACM Embedded Systems Week (ESWEEK). He is also on the steering organizing and program committees of several premier EDA and embedded system design conferences and workshops. He has served on the Editorial Boards for the IEEE Transactions on Very Large Scale Integration (VLSI) Systems and the ACM Transactions on Embedded Computing Systems and also previously served as the Editor-in-Chief (EiC) for the ACM Transactions on Design Automation of Electronic Systems. He served on the Advisory Boards of the IEEE Embedded Systems Letters the ACM Special Interest Group on Embedded Systems the ACM Special Interest Group on Design Automationt and the ACM Transactions on Embedded Computing Systems. Carlo S. Regazzoni (Senior Member IEEE) received the M.S. and Ph.D. degrees in electronic and telecommunications engineering from the University of Genoa Genoa Italy in 1987 and 1992 respectively.""He is currently a Full Professor of cognitive telecommunications systems with the Department of Electrical Electronics and Telecommunication Engineering and Naval Architecture (DITEN) University of Genoa and a Co-Ordinator of the Joint Doctorate on Interactive and Cognitive Environments (JDICE) international Ph.D. course started initially as EU Erasmus Mundus Project and

Autonomous systems are able to make decisions and potentially take actions without direct human intervention, which requires some knowledge about the system and its environment as well as goal-oriented reasoning. In computer systems, one can derive such behavior from the concept of a rational agent with autonomy (“control over its own actions”), reactivity (“react to events from the environment”), proactivity (“act on its own initiative”), and sociality (“interact with other agents”) as fundamental properties \n[1]\n. Autonomous systems will undoubtedly pervade into our everyday lives, and we will find them in a variety of domains and applications including robotics, transportation, health care, communications, and entertainment to name a few. \nThe articles in this month’s special issue cover concepts and fundamentals, architectures and techniques, and applications and case studies in the exciting area of self-awareness in autonomous systems.

关键词： Special issues and sections Autonomous systems Self-aware Robot sensing systems computational modeling

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High-depth African genomes inform human migration and health (vol 586, pg 741, 2020)

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NATURE 2021年第7856期592卷 E26-E26页

作者： Choudhury, Ananyo Aron, Shaun Botigue, Laura R. Sengupta, Dhriti Botha, Gerrit Bensellak, Taoufik Wells, Gordon Kumuthini, Judit Shriner, Daniel Fakim, Yasmina J. Ghoorah, Anisah W. Dareng, Eileen Odia, Trust Falola, Oluwadamilare Adebiyi, Ezekiel Hazelhurst, Scott Mazandu, Gaston Nyangiri, Oscar A. Mbiyavanga, Mamana Benkahla, Alia Kassim, Samar K. Mulder, Nicola Adebamowo, Sally N. Chimusa, Emile R. Muzny, Donna Metcalf, Ginger Gibbs, Richard A. Matovu, Enock Bucheton, Bruno Hertz-Fowler, Christiane Koffi, Mathurin Macleod, Annette Mumba-Ngoyi, Dieudonne Noyes, Harry Nyangiri, Oscar A. Simo, Gustave Simuunza, Martin Rotimi, Charles Ramsay, Michele Choudhury, Ananyo Choudhury, Ananyo Aron, Shaun Botigue, Laura Sengupta, Dhriti Botha, Gerrit Bensellak, Taoufik Wells, Gordon Kumuthini, Judit Shriner, Daniel Fakim, Yasmina J. Ghoorah, Anisah W. Dareng, Eileen Odia, Trust Falola, Oluwadamilare Adebiyi, Ezekiel Hazelhurst, Scott Mazandu, Gaston Nyangiri, Oscar A. Mbiyavanga, Mamana Benkahla, Alia Kassim, Samar K. Mulder, Nicola Adebamowo, Sally N. Chimusa, Emile R. Rotimi, Charles Ramsay, Michele Adeyemo, Adebowale A. Lombard, Zane Hanchard, Neil A. Adebamowo, Clement Agongo, Godfred Boua, Romuald P. Oduro, Abraham Sorgho, Hermann Landoure, Guida Cisse, Lassana Diarra, Salimata Samassekou, Oumar Anabwani, Gabriel Matshaba, Mogomotsi Joloba, Moses Kekitiinwa, Adeodata Mardon, Graeme Mpoloka, Sununguko W. Kyobe, Samuel Mlotshwa, Busisiwe Mwesigwa, Savannah Retshabile, Gaone Williams, Lesedi Wonkam, Ambroise Moussa, Ahmed Adu, Dwomoa Ojo, Akinlolu Burke, David Salako, Babatunde O. Matovu, Enock Bucheton, Bruno Hertz-Fowler, Christiane Koffi, Mathurin Macleod, Annette Mumba-Ngoyi, Dieudonne Noyes, Harry Nyangiri, Oscar A. Simo, Gustave Simuunza, Martin Awadalla, Philip Bruat, Vanessa Gbeha, Elias Adeyemo, Adebowale A. Lombard, Zane Hanchard, Neil A. Sydney Brenner Institute for Molecular Bioscience Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa School of Electrical and Information Engineering University of the Witwatersrand Johannesburg South Africa Division of Human Genetics National Health Laboratory Service and School of Pathology Faculty of Health Sciences University of the Witwatersrand Johannesburg South Africa Navrongo Health Research Centre Navrongo Ghana Clinical Research Unit of Nanoro Institut de Recherche en Sciences de la Sante Bobo-Dioulasso Burkina Faso Center for Research in Agricultural Genomics (CRAG) Plant and Animal Genomics Program CSIC-IRTA-UAB-UB Barcelona Spain Computational Biology Division and H3ABioNet Department of Integrative Biomedical Sciences IDM University of Cape Town Cape Town South Africa System and Data Engineering Team Abdelmalek Essaadi University ENSA Tangier Morocco Centre for Proteomic and Genomic Research (CPGR) Cape Town South Africa South African National Bioinformatics Institute University of the Western Cape Bellville South Africa Africa Health Research Institute Durban South Africa Center for Research on Genomics and Global Health National Human Genome Research Institute National Institutes of Health Bethesda MD USA Department of Agriculture and Food Science Faculty of Agriculture University of Mauritius Reduit Mauritius Department of Digital Technologies Faculty of Information Communication & Digital Technologies University of Mauritius Reduit Mauritius Department of Public Health and Primary Care University of Cambridge Cambridge UK Institute of Human Virology Nigeria Abuja Nigeria Department of Epidemiology and Public Health University of Maryland School of Medicine University of Maryland Baltimore Baltimore MD USA University of Maryland Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine University of Maryland Baltimore Baltimore MD USA Institute of Human Virology and Greeneba

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Author Correction: Pathway and network analysis of more than 2500 whole cancer genomes

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Nature communications 2022年第1期13卷 7566页

作者： Matthew A Reyna David Haan Marta Paczkowska Lieven P C Verbeke Miguel Vazquez Abdullah Kahraman Sergio Pulido-Tamayo Jonathan Barenboim Lina Wadi Priyanka Dhingra Raunak Shrestha Gad Getz Michael S Lawrence Jakob Skou Pedersen Mark A Rubin David A Wheeler Søren Brunak Jose M G Izarzugaza Ekta Khurana Kathleen Marchal Christian von Mering S Cenk Sahinalp Alfonso Valencia Jüri Reimand Joshua M Stuart Benjamin J Raphael Department of Computer Science Princeton University Princeton NJ 08540 USA. Department of Biomedical Informatics Emory University Atlanta GA 30322 USA. Department of Biomolecular Engineering and UC Santa Cruz Genomics Institute University of California Santa Cruz Santa Cruz CA 95060 USA. Computational Biology Program Ontario Institute for Cancer Research Toronto Ontario Canada. Department of Information Technology IDLab Ghent University IMEC Ghent the Netherlands. Department of Plant Biotechnology and Bioinformatics Ghent University Ghent the Netherlands. Barcelona Supercomputing Center (BSC) Barcelona 08034 Spain. Department of Clinical and Molecular Medicine Faculty of Medicine and Health Sciences Norwegian University of Science and Technology Trondheim Norway. Institute of Molecular Life Sciences and Swiss Institute of Bioinformatics University of Zurich CH-8057 Zurich Switzerland. Department of Pathology and Molecular Pathology University Hospital Zurich CH-8091 Zurich Switzerland. Department of Physiology and Biophysics Weill Cornell Medicine New York NY 10065 USA. Vancouver Prostate Centre 2660 Oak Street Vancouver BC V6H 3Z6 Canada. The Broad Institute of MIT and Harvard Cambridge MA 02124 USA. Massachusetts General Hospital Center for Cancer Research Charlestown MA 02129 USA. Harvard Medical School 250 Longwood Avenue Boston MA 02115 USA. Massachusetts General Hospital Department of Pathology Boston MA 02114 USA. Department of Molecular Medicine (MOMA) Aarhus University Hospital Aarhus Denmark. Bioinformatics Research Centre (BiRC) Aarhus University Aarhus Denmark. Human Genome Sequencing Center Baylor College of Medicine Houston TX 77030 USA. DTU Bioinformatics Department of Bio and Health Informatics Technical University of Denmark Kemitorvet 2800 Kongens Lyngby Denmark. Novo Nordisk Foundation Center for Protein Research Faculty of Health and Medical Sciences University of Copenhagen 2200 Copenhagen Denmark. De

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Genetic drivers of heterogeneity in type 2 diabetes pathophysiology

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Nature 2024年第8003期627卷 347-357页

作者： Ken Suzuki Konstantinos Hatzikotoulas Lorraine Southam Henry J Taylor Xianyong Yin Kim M Lorenz Ravi Mandla Alicia Huerta-Chagoya Giorgio E M Melloni Stavroula Kanoni Nigel W Rayner Ozvan Bocher Ana Luiza Arruda Kyuto Sonehara Shinichi Namba Simon S K Lee Michael H Preuss Lauren E Petty Philip Schroeder Brett Vanderwerff Mart Kals Fiona Bragg Kuang Lin Xiuqing Guo Weihua Zhang Jie Yao Young Jin Kim Mariaelisa Graff Fumihiko Takeuchi Jana Nano Amel Lamri Masahiro Nakatochi Sanghoon Moon Robert A Scott James P Cook Jung-Jin Lee Ian Pan Daniel Taliun Esteban J Parra Jin-Fang Chai Lawrence F Bielak Yasuharu Tabara Yang Hai Gudmar Thorleifsson Niels Grarup Tamar Sofer Matthias Wuttke Chloé Sarnowski Christian Gieger Darryl Nousome Stella Trompet Soo-Heon Kwak Jirong Long Meng Sun Lin Tong Wei-Min Chen Suraj S Nongmaithem Raymond Noordam Victor J Y Lim Claudia H T Tam Yoonjung Yoonie Joo Chien-Hsiun Chen Laura M Raffield Bram Peter Prins Aude Nicolas Lisa R Yanek Guanjie Chen Jennifer A Brody Edmond Kabagambe Ping An Anny H Xiang Hyeok Sun Choi Brian E Cade Jingyi Tan K Alaine Broadaway Alice Williamson Zoha Kamali Jinrui Cui Manonanthini Thangam Linda S Adair Adebowale Adeyemo Carlos A Aguilar-Salinas Tarunveer S Ahluwalia Sonia S Anand Alain Bertoni Jette Bork-Jensen Ivan Brandslund Thomas A Buchanan Charles F Burant Adam S Butterworth Mickaël Canouil Juliana C N Chan Li-Ching Chang Miao-Li Chee Ji Chen Shyh-Huei Chen Yuan-Tsong Chen Zhengming Chen Lee-Ming Chuang Mary Cushman John Danesh Swapan K Das H Janaka de Silva George Dedoussis Latchezar Dimitrov Ayo P Doumatey Shufa Du Qing Duan Kai-Uwe Eckardt Leslie S Emery Daniel S Evans Michele K Evans Krista Fischer James S Floyd Ian Ford Oscar H Franco Timothy M Frayling Barry I Freedman Pauline Genter Hertzel C Gerstein Vilmantas Giedraitis Clicerio González-Villalpando Maria Elena González-Villalpando Penny Gordon-Larsen Myron Gross Lindsay A Guare Sophie Hackinger Liisa Hakaste Sohee Han Andrew T Hattersley Christian Herder Momoko Horikoshi Annie-Green Howard Willa Centre for Genetics and Genomics Versus Arthritis Centre for Musculoskeletal Research Division of Musculoskeletal and Dermatological Sciences University of Manchester Manchester UK. Department of Diabetes and Metabolic Diseases Graduate School of Medicine University of Tokyo Tokyo Japan. Department of Statistical Genetics Osaka University Graduate School of Medicine Suita Japan. Institute of Translational Genomics Helmholtz Zentrum München German Research Center for Environmental Health Neuherberg Germany. konstantinos.hatzikotoulas@helmholtz-munich.de. Institute of Translational Genomics Helmholtz Zentrum München German Research Center for Environmental Health Neuherberg Germany. Center for Precision Health Research National Human Genome Research Institute National Institutes of Health Bethesda MD USA. British Heart Foundation Cardiovascular Epidemiology Unit Department of Public Health and Primary Care University of Cambridge Cambridge UK. Heart and Lung Research Institute University of Cambridge Cambridge UK. Department of Epidemiology School of Public Health Nanjing Medical University Nanjing China. Department of Biostatistics and Center for Statistical Genetics University of Michigan Ann Arbor MI USA. Corporal Michael J. Crescenz VA Medical Center Philadelphia PA USA. Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania Perelman School of Medicine Philadelphia PA USA. Department of Genetics University of Pennsylvania Perelman School of Medicine Philadelphia PA USA. Programs in Metabolism and Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA. Diabetes Unit and Center for Genomic Medicine Massachusetts General Hospital Boston MA USA. TIMI Study Group Division of Cardiovascular Medicine Brigham and Women's Hospital Harvard Medical School Boston MA USA. William Harvey Research Institute Barts and the London School of Medicine and Dentistry Queen Mary University of London L

Type 2 diabetes (T2D) is a heterogeneous disease that develops through diverse pathophysiological processes and molecular mechanisms that are often specific to cell type. Here, to characterize the genetic contribution to these processes across ancestry groups, we aggregate genome-wide association study data from 2,535,601 individuals (39.7% not of European ancestry), including 428,452 cases of T2D. We identify 1,289 independent association signals at genome-wide significance (P < 5 × 10) that map to 611 loci, of which 145 loci are, to our knowledge, previously unreported. We define eight non-overlapping clusters of T2D signals that are characterized by distinct profiles of cardiometabolic trait associations. These clusters are differentially enriched for cell-type-specific regions of open chromatin, including pancreatic islets, adipocytes, endothelial cells and enteroendocrine cells. We build cluster-specific partitioned polygenic scores in a further 279,552 individuals of diverse ancestry, including 30,288 cases of T2D, and test their association with T2D-related vascular outcomes. Cluster-specific partitioned polygenic scores are associated with coronary artery disease, peripheral artery disease and end-stage diabetic nephropathy across ancestry groups, highlighting the importance of obesity-related processes in the development of vascular outcomes. Our findings show the value of integrating multi-ancestry genome-wide association study data with single-cell epigenomics to disentangle the aetiological heterogeneity that drives the development and progression of T2D. This might offer a route to optimize global access to genetically informed diabetes care.

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Toward the integration of speciation research

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Evolutionary Journal of the Linnean Society 2024年第1期3卷

作者： Stankowski, Sean Cutter, Asher D Satokangas, Ina Lerch, Brian A Rolland, Jonathan Smadja, Carole M Segami Marzal, J Carolina Cooney, Christopher R Feulner, Philine G D Domingos, Fabricius Maia Chaves Bicalho North, Henry L Yamaguchi, Ryo Butlin, Roger K Wolf, Jochen B W Coughlan, Jenn Heidbreder, Patrick Hernández-Gutiérrez, Rebeca Barnard-Kubow, Karen B Peede, David Rancilhac, Loïs Salvador, Rodrigo Brincalepe Thompson, Ken A Stacy, Elizabeth A Moyle, Leonie C Garlovsky, Martin D Maulana, Arif Kantelinen, Annina Cacho, N Ivalú Schneemann, Hilde Domínguez, Marisol Dopman, Erik B Lohse, Konrad Rometsch, Sina J Comeault, Aaron A Merrill, Richard M Scordato, Elizabeth S C Singhal, Sonal Pärssinen, Varpu Lackey, Alycia C R Kumar, Sanghamitra Meier, Joana I Barton, Nicholas Fraïsse, Christelle Ravinet, Mark Kulmuni, Jonna Institute of Science and Technology Austria (ISTA) Klosterneuburg Austria Department of Ecology and Evolution University of Sussex Brighton United Kingdom Ecology & Evolutionary Biology University of Toronto Toronto Canada Organismal and Evolutionary Biology Research Programme University of Helsinki Helsinki Finland Department of Biology University of North Carolina at Chapel Hill Chapel Hill NC United States Centre de Recherche sur la Biodiversité et l’Environnement (CRBE) Université de Toulouse CNRS IRD Toulouse INP Université Toulouse 3 – Paul Sabatier (UT3) Toulouse France Institut des Sciences de l’Evolution de Montpellier ISEM Univ. Montpellier CNRS IRD Montpellier France Department of Biology Duke University Durham NC United States Ecology and Evolutionary Biology School of Biosciences University of Sheffield Sheffield United Kingdom Department of Fish Ecology and Evolution Centre of Ecology Evolution and Biogeochemistry EAWAG Swiss Federal Institute of Aquatic Science and Technology Kastanienbaum Switzerland Division of Aquatic Ecology and Evolution Institute of Ecology and Evolution University of Bern Bern Switzerland Departamento de Zoologia Universidade Federal do Paraná Curitiba PR Brazil Department of Zoology University of Cambridge Cambridge United Kingdom Department of Advanced Transdisciplinary Sciences Hokkaido University Sapporo Japan Department of Zoology & Biodiversity Research Centre University of British Columbia Vancouver Canada Department of Marine Sciences University of Gothenburg Gothenburg Sweden Division of Evolutionary Biology LMU Munich Munich Germany Department of Ecology & Evolutionary Biology Yale University New Haven CT United States Department of Evolution Ecology and Organismal Biology University of California Riverside Riverside CA United States Department of Biology James Madison University Harrisonburg VA United States Department of Ecology Evolution and Organismal Biology Brown University Provi

Speciation research—the scientific field focused on understanding the origin and diversity of species—has a long and complex history. While relevant to one another, the specific goals and activities of speciation researchers are highly diverse, and scattered across a collection of different perspectives. Thus, our understanding of speciation will benefit from efforts to bridge scientific findings and the diverse people who do the work. In this paper, we outline two ways of integrating speciation research: (i) scientific integration, through the bringing together of ideas, data, and approaches; and (ii) social integration, by creating ways for a diversity of researchers to participate in the scientific process. We then discuss five challenges to integration: (i) the multidisciplinary nature of speciation research, (ii) the complex language of speciation; (iii) a bias toward certain study systems; (iv) the challenges of working across scales; and (v) inconsistent measures and reporting standards. We provide practical steps that individuals and groups can take to help overcome these challenges, and argue that integration is a team effort in which we all have a role to play.

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The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2

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Cell 2025年第12期188卷 3167-3183.e18页

作者： Pekar, Jonathan E. Lytras, Spyros Ghafari, Mahan Magee, Andrew F. Parker, Edyth Wang, Yu Ji, Xiang Havens, Jennifer L. Katzourakis, Aris Vasylyeva, Tetyana I. Suchard, Marc A. Hughes, Alice C. Hughes, Joseph Rambaut, Andrew Robertson, David L. Dellicour, Simon Worobey, Michael Wertheim, Joel O. Lemey, Philippe Institute of Ecology and Evolution University of Edinburgh Edinburgh United Kingdom Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla 92093 CA United States Department of Biomedical Informatics University of California San Diego La Jolla 92093 CA United States Department of Medicine University of California San Diego La Jolla 92093 CA United States Division of Systems Virology Department of Microbiology and Immunology The Institute of Medical Science The University of Tokyo Tokyo Japan Medical Research Council University of Glasgow Centre for Virus Research Glasgow United Kingdom Department of Biology University of Oxford Oxford United Kingdom Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles 90095 CA United States Department of Immunology and Microbiology The Scripps Research Institute La Jolla 92037 CA United States Institute of Genomics and Global Health Redeemer's University Osun State Ede Nigeria Department of Computer Science and Engineering University of California San Diego La Jolla 92093 CA United States Department of Mathematics School of Science and Engineering Tulane University New Orleans LA United States Department of Population Health and Disease Prevention University of California Irvine Irvine 92617 CA United States Department of Biostatistics Fielding School of Public Health University of California Los Angeles Los Angeles 90095 CA United States Department of Computational Medicine David Geffen School of Medicine University of California Los Angeles Los Angeles 90095 CA United States School of Biological Sciences University of Hong Kong Hong Kong Hong Kong China Biodiversity Green Development Foundation Beijing China Spatial Epidemiology Lab (SpELL) Université Libre de Bruxelles CP160/12 50 av. FD Roosevelt Bruxelles 1050 Belgium Department of Microbiology Immunology and Transplantation Rega Institute

The emergence of SARS-CoV in 2002 and SARS-CoV-2 in 2019 led to increased sampling of sarbecoviruses circulating in horseshoe bats. Employing phylogenetic inference while accounting for recombination of bat sarbecoviruses, we find that the closest-inferred bat virus ancestors of SARS-CoV and SARS-CoV-2 existed less than a decade prior to their emergence in humans. Phylogeographic analyses show bat sarbecoviruses traveled at rates approximating their horseshoe bat hosts and circulated in Asia for millennia. We find that the direct ancestors of SARS-CoV and SARS-CoV-2 are unlikely to have reached their respective sites of emergence via dispersal in the bat reservoir alone, supporting interactions with intermediate hosts through wildlife trade playing a role in zoonotic spillover. These results can guide future sampling efforts and demonstrate that viral genomic regions extremely closely related to SARS-CoV and SARS-CoV-2 were circulating in horseshoe bats, confirming their importance as the reservoir species for SARS viruses. © 2025 The Authors

关键词： molecular epidemiology phylogeography sarbecoviruses virus evolution

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Jamming of Deformable Polygons

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Physical Review Letters 2018年第24期121卷 248003-248003页

作者： Arman Boromand Alexandra Signoriello Fangfu Ye Corey S. O’Hern Mark D. Shattuck Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics Institute of Physics Chinese Academy of Sciences Beijing China Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut 06520 USA Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut 06520 USA School of Physical Sciences University of Chinese Academy of Sciences Beijing China Department of Physics Yale University New Haven Connecticut 06520 USA Department of Applied Physics Yale University New Haven Connecticut 06520 USA Benjamin Levich Institute and Physics Department The City College of the City University of New York New York New York 10031 USA

We introduce the deformable particle (DP) model for cells, foams, emulsions, and other soft particulate materials, which adds to the benefits and eliminates deficiencies of existing models. The DP model combines the ability to model individual soft particles with the shape-energy function of the vertex model, and adds arbitrary particle deformations. We focus on 2D deformable polygons with a shape-energy function that is minimized for area a0 and perimeter p0 and repulsive interparticle forces. We study the onset of jamming versus particle asphericity, A=p02/4πa0, and find that the packing fraction grows with A until reaching A*=1.16 of the underlying Voronoi cells at confluence. We find that DP packings above and below A* are solidlike, which helps explain the solid-to-fluid transition at A* in the vertex model as a transition from tension- to compression-dominated regimes.

关键词： Jamming Monolayer films Molecular dynamics

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In vitro vascularized tumor platform for modeling breast tumor stromal interactions and characterizing the subsequent response

arXiv

引用

arXiv 2018年

作者： Gadde, Manasa Sorace, Anna G. Wong, Enoch Syed, Anum Phillips, Caleb Rahal, Omar Yankeelov, Thomas E. Woodward, Wendy A. Rylander, Marissa Nichole Department of Biomedical Engineering Austin TX United States Departments of Diagnostic Medicine Austin TX United States Department of Oncology Austin TX United States Livestrong Cancer Institutes Austin TX United States Institute for Computational and Engineering Sciences Austin TX United States M. D. Anderson Morgan Welch Inflammatory Breast Cancer Research Program and Clinic HoustonTX United States Department of Experimental Radiation Oncology HoustonTX United States Department of Mechanical Engineering Austin TX United States

Background: Tumor stromal interactions have been shown to be the driving force behind the poor prognosis associated with aggressive breast tumors. These interactions, specifically between tumor and the surrounding extracellular matrix (ECM), and between tumor and vascular endothelial cells, promote tumor formation, angiogenesis, and metastasis to distant tissues. In this study, we develop an in vitro vascularized breast tumor platform that allows for investigation of tumor-stromal interactions in three aggressive breast tumor derived cell lines: MDA-IBC3, SUM149, and MDA-MB-231. Methods: The in vitro breast tumor platform consists of a cylindrical endothelial vessel, surrounded by a tumor cell-seeded collagen matrix allowing for direct interactions between endothelial and cancer cells. The platform recapitulates key characteristics of breast tumors, including increased vascular permeability, vessel sprouting, and ECM remodeling. Morphological and quantitative analysis reveals differential effects from each tumor cell type on endothelial coverage, permeability, expression of vascular endothelial growth factor (VEGF), and collagen remodeling. Results: The triple negative tumors, SUM149 and MDA-MB-321, resulted in a significantly (p Copyright © 2018, The Authors. All rights reserved.

关键词： Collagen

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