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Reproducible brain-wide association studies require thousands of individuals (Mar, 10.1038/s41586-022-04492-9, 2022)

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NATURE 2022年第7911期605卷 E11-E11页

作者： Marek, Scott Tervo-Clemmens, Brenden Calabro, Finnegan J. Montez, David F. Kay, Benjamin P. Hatoum, Alexander S. Donohue, Meghan Rose Foran, William Miller, Ryland L. Hendrickson, Timothy J. Malone, Stephen M. Kandala, Sridhar Feczko, Eric Miranda-Dominguez, Oscar Graham, Alice M. Earl, Eric A. Perrone, Anders J. Cordova, Michaela Doyle, Olivia Moore, Lucille A. Conan, Gregory M. Uriarte, Johnny Snider, Kathy Lynch, Benjamin J. Wilgenbusch, James C. Pengo, Thomas Tam, Angela Chen, Jianzhong Newbold, Dillan J. Zheng, Annie Seider, Nicole A. Van, Andrew N. Metoki, Athanasia Chauvin, Roselyne J. Laumann, Timothy O. Greene, Deanna J. Petersen, Steven E. Garavan, Hugh Thompson, Wesley K. Nichols, Thomas E. Yeo, B. T. Thomas Barch, Deanna M. Luna, Beatriz Fair, Damien A. Dosenbach, Nico U. F. Department of Psychiatry Washington University School of Medicine St Louis MO USA Department of Neurology Washington University School of Medicine St Louis MO USA Department of Psychological and Brain Sciences Washington University in St Louis St Louis MO USA Department of Psychiatry Massachusetts General Hospital Harvard Medical School Boston MA USA Department of Psychology University of Pittsburgh Pittsburgh PA USA Department of Psychiatry University of Pittsburgh Pittsburgh PA USA Department of Bioengineering University of Pittsburgh Pittsburgh PA USA Department of Biomedical Engineering Washington University in St Louis St Louis MO USA Department of Radiology Washington University School of Medicine St Louis MO USA Department of Neurological Surgery Washington University School of Medicine St Louis MO USA Program in Occupational Therapy Washington University School of Medicine St Louis MO USA Department of Pediatrics Washington University School of Medicine St Louis MO USA University of Minnesota Informatics Institute University of Minnesota Minneapolis MN USA Department of Psychology University of Minnesota Minneapolis MN USA Masonic Institute for the Developing Brain University of Minnesota Medical School Minneapolis MN USA Department of Pediatrics University of Minnesota Medical School Minneapolis MN USA Department of Psychiatry Oregon Health and Science University Portland OR USA Minnesota Supercomputing Institute University of Minnesota Minneapolis MN USA Institute of Child Development University of Minnesota Medical School Minneapolis MN USA Department of Electrical and Computer Engineering National University of Singapore Singapore Singapore Centre for Sleep and Cognition National University of Singapore Singapore Singapore Centre for Translational MR Research National University of Singapore Singapore Singapore N.1 Institute for Health Institute for Digital Medicine National University of Singapore Singapore Sing

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The Power of High Precision Broadband Photometry: Tracing the Milky Way Density Profile with Blue Horizontal Branch Stars in the Dark Energy Survey

arXiv

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arXiv 2024年

作者： Yu, Fengqing Li, Ting S. Speagle, Joshua S. Medina, Gustavo E. Koposov, Sergey E. Bland-Hawthorn, Joss Cullinane, Lara R. Eadie, Gwendolyn M. Erkal, Denis Lewis, Geraint F. Limberg, Guilherme Zucker, Daniel B. Department of Computer Science University of Toronto 40 St. George Street Canada Data Sciences Institute University of Toronto 17th Floor Ontario Power Building 700 University Ave TorontoONM5G 1Z5 Canada David A. Dunlap Department of Astronomy & Astrophysics University of Toronto 50 St George Street TorontoONM5S 3H4 Canada Dunlap Institute for Astronomy & Astrophysics University of Toronto 50 St George Street TorontoONM5S 3H4 Canada Department of Statistical Sciences University of Toronto 9th Floor Ontario Power Building 700 University Ave TorontoONM5G 1Z5 Canada Institute for Astronomy University of Edinburgh Royal Observatory Blackford Hill EdinburghEH9 3HJ United Kingdom Institute of Astronomy University of Cambridge Madingley Road CambridgeCB3 0HA United Kingdom Kavli Institute for Cosmology University of Cambridge Madingley Road CambridgeCB3 0HA United Kingdom Sydney Institute for Astronomy School of Physics A28 The University of Sydney NSW2006 Australia Australia Department of Physics and Astronomy Johns Hopkins University 3400 N. Charles St BaltimoreMD21218 United States Department of Physics University of Surrey GuildfordGU2 7XH United Kingdom Universidade de São Paulo IAG Departamento de Astronomia São PauloSP 05508-090 Brazil School of Mathematical and Physical Sciences Macquarie University SydneyNSW2109 Australia Macquarie University Research Centre for Astrophysics and Space Technologies SydneyNSW2109 Australia

Blue Horizontal Branch (BHB) stars, excellent distant tracers for probing the Milky Way’s halo density profile, are distinguished in the (g−r)0 vs (i−z)0 color space from another class of stars, blue straggler stars (BSs). We develop a Bayesian mixture model to classify BHB stars using high-precision photometry data from the Dark Energy Survey data Release 2 (DES DR2). We select ∼ 2100 highly-probable BHBs based on their griz photometry and the associated uncertainties, and use these stars to map the stellar halo over the Galactocentric radial range 20 R 70 kpc. After excluding known stellar overdensities, we find that the number density n* of BHBs can be represented by a power law density profile n* ∝ R−α with an index of α = 4.28+0.13−012, consistent with existing literature values. In addition, we examine the impact of systematic errors and the spatial inhomogeneity on the fitted density profile. Our work demonstrates the effectiveness of high-precision griz photometry in selecting BHB stars. The upcoming photometric survey from the Rubin Observatory, expected to reach depths 2-3 magnitudes greater than DES during its 10-year mission, will enable us to investigate the density profile of the Milky Way’s halo out to the virial radius, unravelling the complex processes of formation and evolution in our Galaxy. Copyright © 2024, The Authors. All rights reserved.

关键词： Systematic errors

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Beyond Low Earth Orbit: Biomonitoring, Artificial Intelligence, and Precision Space Health

arXiv

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arXiv 2021年

作者： Scott, Ryan T. Antonsen, Erik L. Sanders, Lauren M. Hastings, Jaden J.A. Park, Seung-Min Mackintosh, Graham Reynolds, Robert J. Hoarfrost, Adrienne L. Sawyer, Aenor Greene, Casey S. Glicksberg, Benjamin S. Theriot, Corey A. Berrios, Daniel C. Miller, Jack Babdor, Joel Barker, Richard Baranzini, Sergio E. Beheshti, Afshin Chalk, Stuart Delgado-Aparicio, Guillermo M. Haendel, Melissa Hamid, Arif A. Heller, Philip Jamieson, Daniel Jarvis, Katelyn J. Kalantari, John Khezeli, Kia Komarova, Svetlana V. Komorowski, Matthieu Kothiyal, Prachi Mahabal, Ashish Manor, Uri Martin, Hector Garcia Mason, Christopher E. Matar, Mona Mias, George I. Myers, Jerry G. Nelson, Charlotte Oribello, Jonathan Parsons-Wingerter, Patricia Prabhu, R.K. Qutub, Amina Ann Rask, Jon Saravia-Butler, Amanda Saria, Suchi Singh, Nitin Kumar Soboczenski, Frank Snyder, Michael Soman, Karthik van Valen, David Venkateswaran, Kasthuri Warren, Liz Worthey, Liz Yang, Jason H. Zitnik, Marinka Costes, Sylvain V. KBR Space Biosciences Division NASA Ames Research Center Moffett FieldCA94035 United States Department of Emergency Medicine Center for Space Medicine Baylor College of Medicine HoustonTX77030 United States Blue Marble Space Institute of Science Space Biosciences Division NASA Ames Research Center Moffett FieldCA94035 United States Department of Physiology and Biophysics Weill Cornell Medicine New YorkNY10065 United States Department of Urology Department of Radiology Stanford University School of Medicine StanfordCA94305 United States Bay Area Environmental Research Institute NASA Ames Research Center Moffett FieldCA94035 United States Mortality Research & Consulting Inc. HoustonTX77058 United States Space Biosciences Division NASA Ames Research Center Moffett FieldCA94035 United States UC Space Health Department of Orthopaedic Surgery University of California San Francisco San FranciscoCA94143 United States Center for Health AI Department of Biochemistry and Molecular Genetics University of Colorado School of Medicine Anschutz Medical Campus AuroraCO80045 United States Hasso Plattner Institute for Digital Health at Mount Sinai Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New YorkNY10065 United States Department of Preventive Medicine and Community Health UTMB GalvestonTX77551 United States Human Health and Performance Directorate NASA Johnson Space Center HoustonTX77058 United States Department of Microbiology and Immunology Department of Otolaryngology Head and Neck Surgery University of California San Francisco San FranciscoCA94143 United States The Gilroy AstroBiology Research Group The University of Wisconsin Madison MadisonWI53706 United States Weill Institute for Neurosciences Department of Neurology University of California San Francisco San FranciscoCA94158 United States Department of Chemistry University of North Florida JacksonvilleFL32224 United States Data Scienc

Human space exploration beyond low Earth orbit will involve missions of significant distance and duration. To effectively mitigate myriad space health hazards, paradigm shifts in data and space health systems are necessary to enable Earth-independence, rather than Earth-reliance. Promising developments in the fields of artificial intelligence and machine learning for biology and health can address these needs. We propose an appropriately autonomous and intelligent Precision Space Health system that will monitor, aggregate, and assess biomedical statuses;analyze and predict personalized adverse health outcomes;adapt and respond to newly accumulated data;and provide preventive, actionable, and timely insights to individual deep space crew members and iterative decision support to their crew medical officer. Here we present a summary of recommendations from a workshop organized by the National Aeronautics and Space Administration, on future applications of artificial intelligence in space biology and health. In the next decade, biomonitoring technology, biomarker science, spacecraft hardware, intelligent software, and streamlined data management must mature and be woven together into a Precision Space Health system to enable humanity to thrive in deep space. © 2021, CC BY.

关键词： Earth (planet)

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Beyond Low Earth Orbit: Biological Research, Artificial Intelligence, and Self-Driving Labs

arXiv

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arXiv 2021年

作者： Sanders, Lauren M. Yang, Jason H. Scott, Ryan T. Qutub, Amina Ann Martin, Hector Garcia Berrios, Daniel C. Hastings, Jaden J.A. Rask, Jon Mackintosh, Graham Hoarfrost, Adrienne L. Chalk, Stuart Kalantari, John Khezeli, Kia Antonsen, Erik L. Babdor, Joel Barker, Richard Baranzini, Sergio E. Beheshti, Afshin Delgado-Aparicio, Guillermo M. Glicksberg, Benjamin S. Greene, Casey S. Haendel, Melissa Hamid, Arif A. Heller, Philip Jamieson, Daniel Jarvis, Katelyn J. Komarova, Svetlana V. Komorowski, Matthieu Kothiyal, Prachi Mahabal, Ashish Manor, Uri Mason, Christopher E. Matar, Mona Mias, George I. Miller, Jack Myers, Jerry G. Nelson, Charlotte Oribello, Jonathan Park, Seung-Min Parsons-Wingerter, Patricia Prabhu, R.K. Reynolds, Robert J. Saravia-Butler, Amanda Saria, Suchi Sawyer, Aenor Singh, Nitin Kumar Soboczenski, Frank Snyder, Michael Soman, Karthik Theriot, Corey A. van Valen, David Venkateswaran, Kasthuri Warren, Liz Worthey, Liz Zitnik, Marinka Costes, Sylvain V. Blue Marble Space Institute of Science Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States Center for Emerging and Re-Emerging Pathogens Department of Microbiology Biochemistry and Molecular Genetics Rutgers New Jersey Medical School NewarkNJ07103 United States KBR Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States AI MATRIX Consortium Department of Biomedical Engineering University of Texas San Antonio and UT Health Sciences San AntonioTX78249 United States Biological Systems and Engineering Division Lawrence Berkeley National Lab. BerkeleyCA94608 United States DOE Agile BioFoundry EmeryvilleCA94608 United States Joint BioEnergy Institute EmeryvilleCA94608 United States Department of Physiology and Biophysics Weill Cornell Medicine New YorkNY10065 United States Office of the Center Director NASA Ames Research Center Moffett Field CA94035 United States Bay Area Environmental Research Institute NASA Ames Research Center Moffett Field CA94035 United States Space Biosciences Division NASA Ames Research Center Moffett Field CA94035 United States Department of Chemistry University of North Florida JacksonvilleFL32224 United States Center for Individualized Medicine Department of Surgery Department of Quantitative Health Sciences Mayo Clinic RochesterMN55905 United States Department of Emergency Medicine Center for Space Medicine Baylor College of Medicine HoustonTX77030 United States Department of Microbiology and Immunology Department of Otolaryngology Head and Neck Surgery University of California San Francisco San FranciscoCA94143 United States The Gilroy AstroBiology Research Group The University of Wisconsin - Madison MadisonWI53706 United States Weill Institute for Neurosciences Department of Neurology University of California San Francisco San FranciscoCA94158 United States Data Science Analytics Georgia Institute of Technology Lima15024

Space biology research aims to understand fundamental effects of spaceflight on organisms, develop foundational knowledge to support deep space exploration, and ultimately bioengineer spacecraft and habitats to stabilize the ecosystem of plants, crops, microbes, animals, and humans for sustained multi-planetary life. To advance these aims, the field leverages experiments, platforms, data, and model organisms from both spaceborne and ground-analog studies. As research is extended beyond low Earth orbit, experiments and platforms must be maximally autonomous, light, agile, and intelligent to expedite knowledge discovery. Here we present a summary of recommendations from a workshop organized by the National Aeronautics and Space Administration on artificial intelligence, machine learning, and modeling applications which offer key solutions toward these space biology challenges. In the next decade, the synthesis of artificial intelligence into the field of space biology will deepen the biological understanding of spaceflight effects, facilitate predictive modeling and analytics, support maximally autonomous and reproducible experiments, and efficiently manage spaceborne data and metadata, all with the goal to enable life to thrive in deep space. © 2021, CC BY.

关键词： Predictive analytics

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OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

arXiv

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arXiv 2023年

作者： Eastman, Peter Galvelis, Raimondas Peláez, Raúl P. Abreu, Charlles R.A. Farr, Stephen E. Gallicchio, Emilio Gorenko, Anton Henry, Michael M. Hu, Frank Huang, Jing Krämer, Andreas Michel, Julien Mitchell, Joshua A. Pande, Vijay S. Rodrigues, João P.G.L.M. Rodriguez-Guerra, Jaime Simmonett, Andrew C. Singh, Sukrit Swails, Jason Turner, Philip Wang, Yuanqing Zhang, Ivy Chodera, John D. De Fabritiis, Gianni Markland, Thomas E. Department of Chemistry Stanford University StanfordCA94305 United States Acellera Labs C Dr Trueta 183 Barcelona08005 Spain C Dr. Aiguader 88 Barcelona08003 Spain Chemical Engineering Department School of Chemistry Federal University of Rio de Janeiro Rio de Janeiro68542 Brazil Redesign Science Inc. 180 Varick St. New YorkNY10014 United States EaStCHEM School of Chemistry University of Edinburgh EH9 3FJ United Kingdom Department of Chemistry and Biochemistry Brooklyn College The City University of New York NY United States Ph.D. Program in Chemistry Ph.D. Program in Biochemistry The Graduate Center of the City University of New York New YorkNY United States Stream HPC Koningin Wilhelminaplein 1 - 40601 Amsterdam1062 HG Netherlands Computational and Systems Biology Program Sloan Kettering Institute Memorial Sloan Kettering Cancer Center New YorkNY10065 United States Key Laboratory of Structural Biology of Zhejiang Province School of Life Sciences Westlake University 18 Shilongshan Road Zhejiang Hangzhou310024 China Department of Mathematics and Computer Science Freie Universität Berlin Arnimallee 12 Berlin14195 Germany The Open Force Field Initiative Open Molecular Software Foundation DavisCA95616 United States Andreessen Horowitz 2865 Sand Hill Rd Menlo ParkCA94025 United States Department of Structural Biology Stanford University StanfordCA94305 United States Charité Universitätsmedizin Berlin In silico Toxicology and Structural Bioinformatics Virchowweg 6 Berlin10117 Germany Laboratory of Computational Biology National Heart Lung and Blood Institute National Institutes of Health BethesdaMD20892 United States Entos Inc. 9310 Athena Circle La Jolla CA92037 United States College of Engineering Virginia Polytechnic Institute State University BlacksburgVA24061 United States Simons Center for Computational Physical Chemistry Center for Data Science New York University 24 Waverly Place New YorkNY10004 United States T

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost. Copyright © 2023, The Authors. All rights reserved.

关键词： Machine learning

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Harmonized-Multinational qEEG norms (HarMNqEEG)

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NEUROIMAGE 2022年 256卷 119190-119190页

作者： Li, Min Wang, Ying Lopez-Naranjo, Carlos Hu, Shiang Reyes, Ronaldo Cesar Garcia Paz-Linares, Deirel Areces-Gonzalez, Ariosky Hamid, Aini Ismafairus Abd Evans, Alan C. Savostyanov, Alexander N. Calzada-Reyes, Ana Villringer, Arno Tobon-Quintero, Carlos A. Garcia-Agustin, Daysi Yao, Dezhong Dong, Li Aubert-Vazquez, Eduardo Reza, Faruque Razzaq, Fuleah Abdul Omar, Hazim Abdullah, Jafri Malin Galler, Janina R. Ochoa-Gomez, John F. Prichep, Leslie S. Galan-Garcia, Lidice Morales-Chacon, Lilia Valdes-Sosa, Mitchell J. Trondle, Marius Zulkifly, Mohd Faizal Mohd Rahman, Muhammad Riddha Bin Abdul Milakhina, Natalya S. Langer, Nicolas Rudych, Pavel Koenig, Thomas Virues-Alba, Trinidad A. Lei, Xu Bringas-Vega, Maria L. Bosch-Bayard, Jorge F. Valdes-Sosa, Pedro Antonio [a]The Clinical Hospital of Chengdu Brain Science Institute MOE Key Lab for Neuroinformation School of Life Science and Technology University of Electronic Science and Technology of China Chengdu China [b]Cuban Center for Neurocience La Habana Cuba [c]McGill Centre for Integrative Neuroscience Ludmer Centre for Neuroinformatics and Mental Health Montreal Neurological Institute Canada [d]Department of Neurosciences School of Medical Sciences Universiti Sains Malaysia Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [e]Brain and Behaviour Cluster School of Medical Sciences Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [f]Hospital Universiti Sains Malaysia Universiti Sains Malaysia Health Campus Kota Bharu Kelantan 16150 Malaysia [g]Humanitarian Institute Novosibirsk State University Novosibirsk 630090 Russia [h]Laboratory of Psychophysiology of Individual Differences Federal State Budgetary Scientific Institution Scientific Research Institute of Neurosciences and Medicine Novosibirsk 630117 Russia [i]Laboratory of Psychological Genetics at the Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences Novosibirsk 630090 Russia [j]University of Pinar del Río “Hermanos Saiz Montes de Oca” Pinar del Río Cuba [k]Department of Neurology Max Planck Institute for Human Cognitive and Brain Sciences Leipzig Germany [l]Department of Cognitive Neurology University Hospital Leipzig Leipzig Germany [m]Center for Stroke Research Charité-Universitätsmedizin Berlin Berlin Germany [n]Grupo Neuropsicología y Conducta - GRUNECO Faculty of Medicine Universidad de Antioquia Colombia [o]Research Department Institución Prestadora de Servicios de Salud IPS Universitaria Colombia [p]The Cuban center aging longevity and health Havana Cuba [q]Research Unit of NeuroInformation Chinese Academy of Medical Sciences Chengdu 2019RU035 China [r]School of Electrical Engineering Zhengzhou University Zhengzhou 4500

This paper extends frequency domain quantitative electroencephalography (qEEG) methods pursuing higher sensitivity to detect Brain Developmental Disorders. Prior qEEG work lacked integration of cross-spectral information omitting important functional connectivity descriptors. Lack of geographical diversity precluded accounting for site-specific variance, increasing qEEG nuisance variance. We ameliorate these weaknesses. (i) Create lifespan Riemannian multinational qEEG norms for cross-spectral tensors. These norms result from the HarMNqEEG project fostered by the Global Brain Consortium. We calculate the norms with data from 9 countries, 12 devices, and 14 studies, including 1564 subjects. Instead of raw data, only anonymized metadata and EEG cross spectral tensors were shared. After visual and automatic quality control, developmental equations for the mean and standard deviation of qEEG traditional and Riemannian DPs were calculated using additive mixed-effects models. We demonstrate qEEG "batch effects " and provide methods to calculate harmonized z-scores. (ii) We also show that harmonized Riemannian norms produce z-scores with increased diagnostic accuracy predicting brain dysfunction produced by malnutrition in the first year of life and detecting COVID induced brain dysfunction. (iii) We offer open code and data to calculate different individual z-scores from the HarMNqEEG dataset. These results contribute to developing bias-free, low-cost neuroimaging technologies applicable in various health settings.

关键词： Quantitative EEG EEG cross-spectrum Riemannian geometry Batch effects Z-score Harmonization Malnutrition Covid induced brain dysfunction Developmental Brain Chart

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OS12.7.A Characterization of intra-tumoral heterogeneity and differential immune activation during malignant progression of meningiomas on single cell level

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Neuro-Oncology 2021年第SUPPLEMENT_2期23卷 ii15-ii16页

作者： Blume, C Dogan, H Schweizer, L Wick, W Weller, M Mann, M Kalamarides, M von Deimling, A Schlesner, M Sahm, F CCU Neuropathology German Cancer Research Centre (DKFZ) Heidelberg Germany Dept. of Neuropathology University Hospital Heidelberg Heidelberg Germany Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany German Cancer Research Centre (DKFZ) Heidelberg Germany Department of Neurology and Neurooncology Program National Center for Tumor Diseases Heidelberg University Hospital Heidelberg Germany Department of Neurology Clinical Neuroscience Center University Hospital and University of Zürich Zürich Switzerland NNF Center for Protein Research Faculty of Health Sciences University of Copenhagen Copenhagen Denmark Sorbonne Université and Department of Neurosurgery Pitié Salpêtrière Hospital Paris France Biomedical Informatics Data Mining and Data Analytics Faculty of Applied Computer Science and Medical Faculty University of Augsburg Augsburg Germany

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OPTIMADE, an API for exchanging materials data

arXiv

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arXiv 2021年

作者： Andersen, Casper W. Armiento, Rickard Blokhin, Evgeny Conduit, Gareth J. Dwaraknath, Shyam Evans, Matthew L. Fekete, Ádám Gopakumar, Abhijith Gražulis, Saulius Merkys, Andrius Mohamed, Fawzi Oses, Corey Pizzi, Giovanni Rignanese, Gian-Marco Scheidgen, Markus Talirz, Leopold Toher, Cormac Winston, Donald Aversa, Rossella Choudhary, Kamal Colinet, Pauline Curtarolo, Stefano Di Stefano, Davide Draxl, Claudia Er, Suleyman Esters, Marco Fornari, Marco Giantomassi, Matteo Govoni, Marco Hautier, Geoffroy Hegde, Vinay Horton, Matthew K. Huck, Patrick Huhs, Georg Hummelshøj, Jens Kariryaa, Ankit Kozinsky, Boris Kumbhar, Snehal Liu, Mohan Marzari, Nicola Morris, Andrew J. Mostofi, Arash A. Persson, Kristin A. Petretto, Guido Purcell, Thomas Ricci, Francesco Rose, Frisco Scheffler, Matthias Speckhard, Daniel Uhrin, Martin Vaitkus, Antanas Villars, Pierre Waroquiers, David Wolverton, Chris Wu, Michael Yang, Xiaoyu École Polytechnique Fédérale de Lausanne Lausanne1015 Switzerland Materials Design and Informatics Unit Department of Physics Chemistry and Biology Linköping University Sweden Tilde Materials Informatics Straßmannstraße 25 Berlin10249 Germany Materials Platform for Data Science Sepapaja 6 Tallinn15551 Estonia Theory of Condensed Matter Group Cavendish Laboratory 19 J.J. Thomson Avenue CambridgeCB3 0HE United Kingdom Lawrence Berkeley Labs BerkeleyCA United States Chemin des Étoiles 8 Louvain-la-Neuve1348 Belgium Department of Physics King's College London London United Kingdom Department of Materials Science and Engineering Northwestern University EvanstonIL60208 United States Institute of Biotechnology Life Science Center Vilnius University Saulétekio av. 7 VilniusLT-10257 Lithuania Institute of Computer Science Faculty of Mathematics and Informatics Vilnius University Naugarduko g. 24 VilniusLT-03225 Lithuania Fritz-Haber-Institut der Max-Planck-Gesellschaft Faradayweg 4-6 Berlin14195 Germany Center for Autonomous Materials Design Duke University DurhamNC27708 United States Department of Mechanical Engineering and Materials Science Duke University DurhamNC27708 United States Humboldt-Universität zu Berlin Institut für Physik and IRIS Adlershof Berlin12489 Germany École Polytechnique Fédérale de Lausanne Sion1951 Switzerland Trieste34136 Italy Hermann-von-Helmholtz-Platz 1 Eggenstein-Leopoldshafen76344 Germany Materials Measurement Laboratory National Institute of Standards and Technology GaithersburgMD20899 United States Ansys 300 Rustat House 62 Clifton Rd CambridgeCB1 7EG United Kingdom De Zaale 20 Eindhoven5612 AJ Netherlands Department of Physics and Science of Advanced Materials Program Central Michigan University Mount PleasantMI48859 United States Argonne National Laboratory LemontIL60439 United States Thayer School of Engineering Dartmouth College HanoverNH03755 United States Los AltosCA940

The Open databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v1.0, which is already supported by many leading databases and several software packages. We illustrate the advantages of the OPTIMADE API through worked examples on each of the public materials databases that support the full API specification. © 2021, CC BY.

关键词： Specifications

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Association analyses of more than 140,000 men identify 63 new prostate cancer susceptibility loci (vol 50, pg 928, 2018)

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NATURE GENETICS 2019年第2期51卷 363-363页

作者： Schumacher, Fredrick R. Al Olama, Ali Amin Berndt, Sonja I. Benlloch, Sara Ahmed, Mahbubl Saunders, Edward J. Dadaev, Tokhir Leongamornlert, Daniel Anokian, Ezequiel Cieza-Borrella, Clara Goh, Chee Brook, Mark N. Sheng, Xin Fachal, Laura Dennis, Joe Tyrer, Jonathan Muir, Kenneth Lophatananon, Artitaya Stevens, Victoria L. Gapstur, Susan M. Carter, Brian D. Tangen, Catherine M. Goodman, Phyllis J. Thompson, Ian M., Jr. Batra, Jyotsna Chambers, Suzanne Moya, Leire Clements, Judith Horvath, Lisa Tilley, Wayne Risbridger, Gail P. Gronberg, Henrik Aly, Markus Nordstrom, Tobias Pharoah, Paul Pashayan, Nora Schleutker, Johanna Tammela, Teuvo L. J. Sipeky, Csilla Auvinen, Anssi Albanes, Demetrius Weinstein, Stephanie Wolk, Alicja Hakansson, Niclas West, Catharine M. L. Dunning, Alison M. Burnet, Neil Mucci, Lorelei A. Giovannucci, Edward Andriole, Gerald L. Cussenot, Olivier Cancel-Tassin, Geraldine Koutros, Stella Freeman, Laura E. Beane Sorensen, Karina Dalsgaard Orntoft, Torben Falck Borre, Michael Maehle, Lovise Grindedal, Eli Marie Neal, David E. Donovan, Jenny L. Hamdy, Freddie C. Martin, Richard M. Travis, Ruth C. Key, Tim J. Hamilton, Robert J. Fleshner, Neil E. Finelli, Antonio Ingles, Sue Ann Stern, Mariana C. Rosenstein, Barry S. Kerns, Sarah L. Ostrer, Harry Lu, Yong-Jie Zhang, Hong-Wei Feng, Ninghan Mao, Xueying Guo, Xin Wang, Guomin Sun, Zan Giles, Graham G. Southey, Melissa C. MacInnis, Robert J. FitzGerald, Liesel M. Kibel, Adam S. Drake, Bettina F. Vega, Ana Gomez-Caamano, Antonio Szulkin, Robert Eklund, Martin Kogevinas, Manolis Llorca, Javier Castano-Vinyals, Gemma Penney, Kathryn L. Stampfer, Meir Park, Jong Y. Sellers, Thomas A. Lin, Hui-Yi Stanford, Janet L. Cybulski, Cezary Wokolorczyk, Dominika Lubinski, Jan Ostrander, Elaine A. Geybels, Milan S. Nordestgaard, Borge G. Nielsen, Sune F. Weischer, Maren Bisbjerg, Rasmus Roder, Martin Andreas Iversen, Peter Brenner, Hermann Cuk, Katarina Holleczek, Bernd Maier, Christiane Luedeke, Manuel Schnoeller, Thomas Kim, Jeri Logothetis, Christopher J. John, E Department of Population and Quantitative Health Sciences Case Western Reserve University Cleveland USA Seidman Cancer Center University Hospitals Cleveland USA Royal Marsden NHS Foundation Trust London UK Department of Public Health and Primary Care Centre for Cancer Genetic Epidemiology University of Cambridge Strangeways Research Laboratory Cambridge UK Department of Clinical Neurosciences University of Cambridge Cambridge UK Division of Cancer Epidemiology and Genetics National Cancer Institute NIH Bethesda USA Institute of Cancer Research London UK Department of Preventive Medicine Keck School of Medicine University of Southern California/Norris Comprehensive Cancer Center Los Angeles USA Fundación Pública Galega de Medicina Xenómica–SERGAS Grupo de Medicina Xenómica CIBERER IDIS Santiago de Compostela Spain Department of Oncology Centre for Cancer Genetic Epidemiology Strangeways Laboratory University of Cambridge Cambridge UK Division of Population Health Health Services Research and Primary Care University of Manchester Manchester UK Warwick Medical School University of Warwick Coventry UK Epidemiology Research Program American Cancer Society Atlanta USA SWOG Statistical Center Fred Hutchinson Cancer Research Center Seattle USA CHRISTUS Santa Rosa Hospital–Medical Center San Antonio USA Institute of Health and Biomedical Innovation and School of Biomedical Sciences Queensland University of Technology Brisbane Australia Australian Prostate Cancer Research Centre–Qld Translational Research Institute Brisbane Australia Menzies Health Institute of Queensland Griffith University Nathan Australia Cancer Council Queensland Fortitude Valley Australia Chris O’Brien Lifehouse (COBLH) Camperdown Australia Garvan Institute of Medical Research Sydney Australia Dame Roma Mitchell Cancer Research Centre University of Adelaide Adelaide Australia Monash Biomedicine Discovery Institute Cancer Program Prostate Cancer Research Program Department of Anatom

In the version of this article initially published, the name of author Manuela Gago-Dominguez was misspelled as Manuela Gago Dominguez. The error has been corrected in the HTML and PDF version of the article.

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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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