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International Symposium on Biomedical Imaging

作者： Ruida Cheng Nathan Lay Francesca Mertan Baris Turkbey Holger R. Roth Le Lu William Gandler Evan S. McCreedy Thomas Pohida Peter Choyke Matthew J. McAuliffe Ronald M. Summers Imaging Sciences Laboratory Center for Information Technology Imaging Biomarkers and CAD Laboratory Clinical Center Molecular Imaging Program Computational Bioscience and Engineering Laboratory Center for Information Technology

ISBN: (纸本)9781509011735

Automatic MR whole prostate segmentation is a challenging task. Recent approaches have attempted to harness the capabilities of deep learning for MR prostate segmentation to tackle pixel-level labeling tasks. Patch-based and hierarchical features-based deep CNN models were used to delineate the prostate boundary. To further investigate this problem, we introduce a Holistically-Nested Edge Detector (HED) MRI prostate deep learning segmentation and 3D surface reconstruction model that facilitate the registration of multi-parametric MRI with histopathology slides from radical prostatectomy specimens and targeted biopsy specimens. Application of this technique combines deep learning and computer aided design to provide a generalized solution to construct a high-resolution 3D prostate surface from MRI images in three orthogonal views. The performance of the segmentation is evaluated with MRI scans of 100 patients in 4-fold cross-validation. We achieve a mean Dice Similarity of 88.6%.

关键词： Prostate segmentation HED Deep learning

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Digital is the New Blood: Enabling the Present and the Future

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Alzheimer's & Dementia 2023年第S21期19卷

作者： Rhoda Au Zachary T Popp Spencer Low Phillip H Hwang Ileana De Anda-Duran Stephanie Li Salman Rahman Huitong Ding Akwaugo Igwe Cody Karjadi Ting Fang Alvin Ang Sherral A. Devine Ashita S Gurnani Jesse B. Mez Lindsay A. Farrer Preeti Sunderaraman Honghuang Lin Vijaya B. Kolachalama Boston University School of Public Health Boston MA USA Framingham Heart Study Boston University School of Medicine Boston MA USA Davos Alzheimer’s Collaborative Philadelphia PA USA Department of Epidemiology Boston University School of Public Health Boston MA USA Boston University Chobanian & Avedisian School of Medicine Boston MA USA Department of Neurology Boston University Chobanian & Avedisian School of Medicine Boston MA USA Boston University Alzheimer’s Disease Research Center Boston University Chobanian & Avedisian School of Medicine Boston MA USA Department of Anatomy and Neurobiology Boston University Chobanian & Avedisian School of Medicine Boston MA USA Framingham Heart Study Boston University Chobanian & Avedisian School of Medicine Boston MA USA Boston University School of Public Heatlh Boston MA USA Tulane School of Public Health and Tropical Medicine New Orleans LA USA Slone Epidemiology Center Boston University Chobanian & Avedisian School of Medicine Boston MA USA Framigham Heart Study - Boston University Framingham MA USA Boston University Bioinformatics Program Boston MA USA Departments of Medicine (Biomedical Genetics) Neurology Ophthalmology Biostatistics and Epidemiology Boston University Schools of Medicine and Public Health Boston MA USA Department of Neurology - Boston University Chobanian & Avedisian School of Medicine Boston MA USA University of Massachusetts Medical School Worcester MA USA Framingham Heart Study/Boston University BOSTON MA USA Hariri Institute for Computing and Computational Science & Engineering Boston University Boston MA USA College of Arts & Sciences Boston University Boston MA USA Faculty of Computing & Data Sciences Boston University Boston MA USA Boston University Alzheimer’s Disease Center Boston University Chobanian & Avedisian School of Medicine Boston MA USA Whitaker Cardiovascular Institute Boston University Chobanian & Avedisian School of Medicine Boston MA USA

Background Digital is the new blood, where collection, use, and storage of raw digital data streams enabled by technology-embedded sensors are replacing analog methods. Analyses of digital data extend beyond current applications, analogous to previously stored blood currently be used for omics/biomarker research. Today digital technologies are used to measure Alzheimer’s disease (AD)-related clinical symptoms (e.g., cognition, function, and behavior), but future possibilities remain to be determined. Importantly, digital data collection can go beyond current intermittent sampling by employing internet-connected applications and devices that allow real-time monitoring and accurate detection of changes, even within a widely heterogeneous spectrum. Method Beginning in 2005, the Framingham Heart Study (FHS) began digitally recording participants’ spoken responses to neuropsychological (NP) test questions, and in 2011 extended to a digital pen to record written responses. The emergence of wearable devices and smartphone applications has led to an expanded use of digital technologies beyond recordings during NP assessments. The Boston University Alzheimer’s Disease Research Center (BU ADRC) leverages digital sensors in multiple internet-connected devices that longitudinally collect digital data, in both in-person and remote settings. Result The first publication involving FHS digital data was in 2016; the remaining (n> 17) have been from 2020-current. Digital data measuring cognition, function and behavior are being collected through the BU ADRC, where results to date indicate nearly 100% and 75% uptake of active and passive engagement applications, respectively, and 95% uptake for wearable devices (n = 60). Longitudinal assessments include > 3 months for ∼50 participants; > 1 year for n∼21 participants. Conclusion Opportunities for improved trial outcome measurement are evident in the broad range of outcomes digital sensors capture beyond traditional research methodologi

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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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Mycorrhizal symbioses and tree diversity in global forest communities

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Science Advances 2025年第24期11卷

作者： Feng Jiang Xucai Pu Bernhard Schmid Peter B. Reich Jingjing Liang Akane O. Abbasi Jesús Aguirre-Gutiérrez Angelica Maria Almeyda Zambrano Jan Altman Juan Gabriel Álvarez-González Luciana F. Alves Bienvenu H. K. Amani Christian Ammer Gerardo A. Aymard Naveen Babu Kanda Meredith L. Bastian Jean-Francois Bastin Marijn Bauters Pascal Boeckx Svetlana N. Bondarchuk Alexander Bondarev Francis Q. Brearley Sophie Brennan Jaime Briseño-Reyes Eben N. Broadbent Goran Češljar Han Y. H. Chen Chelsea Chisholm WookJin Choi Emil Cienciala Connie J. Clark Alessio Collalti José Javier Corral-Rivas Javid Ahmad Dar Selvadurai Dayanandan Sergio de-Miguel Ashaq Ahmad Dar Géraldine Derroire Ilija Djordjevic Tran Van Do Jiří Doležal Aurélie Dourdain Teresa Eyre Adandé Belarmain Fandohan Lorenzo Frizzera Roberto Cazzolla Gatti Damiano Gianelle M. Socorro González Elizondo Elisa Grieco David J. Harris Andy Hector Bruno Hérault Cang Hui Nobuo Imai Andrzej M. Jagodziński Chengjun Ji Lin Jiang Carlos A. Joly Viktor N. Karminov Kuswata Kartawinata Justin N. Kassi Elizabeth Kearsley Gunnar Keppel Mohammed Latif Khan Carine Klauberg Kirill A. Korznikov Subashree Kothandaraman Florian Kraxner Leonid Krivobokov Dmitry Kucher Amit Kumar Anna Kvashnina Gaia Vaglio Laurin Rodrigo Vieira Leite Moses B. Libalah Ekaterina S. Lonkina Huicui Lu Shan Luo Yuan Luo Emma Mackintosh Andrew R. Marshall Rodolfo Vásquez Martínez Radim Matula William McDonald Ayyappan Narayanan María Guadalupe Nava-Miranda Jagadeesan Naveenkumar Abel Monteagudo Mendoza Stanisław Miścicki Tatyana Moskalyuk Liudmila Mukhortova Sharif A. Mukul Gert-Jan Nabuurs Victor J. Neldner Radovan Nevenic Anny E. N’Guessan Michael Ngugi Alain Paquette Elena I. Parfenova Marc Parren Narayanaswamy Parthasarathy Pablo L. Peri Sebastian Pfautsch Maria T. F. Piedade Galina Polyakova Axel Dalberg Poulsen John R. Poulsen Hans Pretzsch Mirco Rodeghiero Ervan Rutishauser Purabi Saikia Philippe Saner Dmitry Schepaschenko Jochen Schöngart Eric B. Searle Douglas Sheil Zehao Shen Stephanie Shooner Anatoly Sh Institute of Ecology and State Key Laboratory for Vegetation Structure Function and Construction (VegLab) College of Urban and Environmental Sciences Peking University Beijing China. Remote Sensing Laboratories Department of Geography University of Zürich Zürich Switzerland. Department of Forest Resources University of Minnesota St Paul MN 55108 USA. Hawkesbury Institute for the Environment Western Sydney University Penrith New South Wales Australia. Institute for Global Change Biology and School for Environment and Sustainability University of Michigan Ann Arbor MI 48109 USA. Forest Advanced Computing and Artificial Intelligence Laboratory (FACAI) Department of Forestry and Natural Resources Purdue University West Lafayette IN USA. Environmental Change Institute School of Geography and the Environment University of Oxford Oxford UK. Leverhulme Centre for Nature Recovery University of Oxford Oxford UK OX13QY. Spatial Ecology and Conservation (SPEC) Lab Center for Latin American Studies University of Florida Gainesville FL 32611 USA. Institute of Botany of the Czech Academy of Sciences Třeboň Czech Republic. Faculty of Forestry and Wood Sciences Czech University of Life Sciences Prague Czech Republic. Departamento de Ingeniería Agroforestal Universidad de Santiago de Compostela Lugo Spain. Center for Tropical Research Institute of the Environment and Sustainability University of California Los Angeles Los Angeles CA 90095 USA. Université Jean Lorougnon Guédé Unité de Formation et de Recherche en Agroforesterie BP 150 Daloa Ivory Coast. Université Nangui Abrogoua Unité de Formation et de Recherche en Sciences de la Nature 02 BP 801 Abidjan 02 Laboratoire d’Écologie et du Développement durable (LEDD) Abidjian Ivory Coast. Silviculture and Forest Ecology Georg August-University of Göttingen Göttingen Germany. UNELLEZ-Guanare Programa de Ciencias del Agro y el Mar Herbario Universitario (PORT) Portuguesa Venezuela. Jardín Botánico de Bogotá José Cele

Unraveling the mechanisms underlying the maintenance of species diversity is a central pursuit in ecology. It has been hypothesized that ectomycorrhizal (EcM) in contrast to arbuscular mycorrhizal fungi can reduce tree species diversity in local communities, which remains to be tested at the global scale. To address this gap, we analyzed global forest inventory data and revealed that the relationship between tree species richness and EcM tree proportion varied along environmental gradients. Specifically, the relationship is more negative at low latitudes and in moist conditions but is unimodal at high latitudes and in arid conditions. The negative association of EcM tree proportion on species diversity at low latitudes and in humid conditions is likely due to more negative plant-soil microbial interactions in these regions. These findings extend our knowledge on the mechanisms shaping global patterns in plant species diversity from a belowground view.

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Correction: Phenotate: crowdsourcing phenotype annotations as exercises in undergraduate classes

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Genetics in medicine : official journal of the American College of Medical Genetics 2020年第8期22卷 1427页

作者： Willie H Chang Pouria Mashouri Alexander X Lozano Brittney Johnstone Mia Husić Annie Olry Sylvie Maiella Tugce B Balci Sarah L Sawyer Peter N Robinson Ana Rath Michael Brudno Centre for Computational Medicine The Hospital For Sick Children Toronto ON Canada. Department of Computer Science Princeton University Princeton NJ USA. Faculty of Medicine University of Toronto Toronto ON Canada. Department of Materials Science & Engineering Stanford University Stanford CA USA. Sunnybrook Health Sciences Centre Toronto ON Canada. Orphanet Institut national de la santé et de la recherche médicale Paris France. Medical Genetics Program of Southwestern Ontario London Health Sciences Centre London ON Canada. Department of Genetics Children's Hospital of Eastern Ontario and Children's Hospital of Eastern Ontario Research Institute University of Ottawa Ottawa ON Canada. The Jackson Laboratory for Genomic Medicine Farmington CT USA. Institute for Systems Genomics University of Connecticut Farmington CT USA. Centre for Computational Medicine The Hospital For Sick Children Toronto ON Canada. brudno@cs.toronto.edu. Department of Computer Science University of Toronto Toronto ON Canada. brudno@cs.toronto.edu. Genetics and Genome Biology Program The Hospital for Sick Children Toronto ON Canada. brudno@cs.toronto.edu. University Health Network Toronto ON Canada. brudno@cs.toronto.edu.

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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Analysis of more than 400,000 women provides case-control evidence for BRCA1 and BRCA2 variant classification

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Nature communications 2025年第1期16卷 4852页

作者： Maria Zanti Denise G O'Mahony Michael T Parsons Leila Dorling Joe Dennis Nicholas J Boddicker Wenan Chen Chunling Hu Marc Naven Kristia Yiangou Thomas U Ahearn Christine B Ambrosone Irene L Andrulis Antonis C Antoniou Paul L Auer Caroline Baynes Clara Bodelon Natalia V Bogdanova Stig E Bojesen Manjeet K Bolla Kristen D Brantley Nicola J Camp Archie Campbell Jose E Castelao Melissa H Cessna Jenny Chang-Claude Fei Chen Georgia Chenevix-Trench Don M Conroy Kamila Czene Arcangela De Nicolo Susan M Domchek Thilo Dörk Alison M Dunning A Heather Eliassen D Gareth Evans Peter A Fasching Jonine D Figueroa Henrik Flyger Manuela Gago-Dominguez Montserrat García-Closas Gord Glendon Anna González-Neira Felix Grassmann Andreas Hadjisavvas Christopher A Haiman Ute Hamann Steven N Hart Mikael B A Hartman Weang-Kee Ho James M Hodge Reiner Hoppe Sacha J Howell Anna Jakubowska Elza K Khusnutdinova Yon-Dschun Ko Peter Kraft Vessela N Kristensen James V Lacey Jingmei Li Geok Hoon Lim Sara Lindström Artitaya Lophatananon Craig Luccarini Arto Mannermaa Maria Elena Martinez Dimitrios Mavroudis Roger L Milne Kenneth Muir Katherine L Nathanson Rocio Nuñez-Torres Nadia Obi Janet E Olson Julie R Palmer Mihalis I Panayiotidis Alpa V Patel Paul D P Pharoah Eric C Polley Muhammad U Rashid Kathryn J Ruddy Emmanouil Saloustros Elinor J Sawyer Marjanka K Schmidt Melissa C Southey Veronique Kiak-Mien Tan Soo Hwang Teo Lauren R Teras Diana Torres Amy Trentham-Dietz Thérèse Truong Celine M Vachon Qin Wang Jeffrey N Weitzel Siddhartha Yadav Song Yao Gary R Zirpoli Melissa S Cline Peter Devilee Sean V Tavtigian David E Goldgar Fergus J Couch Douglas F Easton Amanda B Spurdle Kyriaki Michailidou Biostatistics Unit The Cyprus Institute of Neurology & Genetics Nicosia Cyprus. Department of Medical Genetics Oslo University Hospital Oslo Norway. Population Health Program QIMR Berghofer Medical Research Institute Brisbane Queensland Australia. Centre for Cancer Genetic Epidemiology Department of Public Health and Primary Care University of Cambridge Cambridge UK. Department of Quantitative Health Sciences Division of Computational Biology Mayo Clinic Rochester MN USA. Department of Laboratory Medicine and Pathology Mayo Clinic Rochester MN USA. Division of Cancer Epidemiology and Genetics National Cancer Institute National Institutes of Health Department of Health and Human Services Bethesda MD USA. Department of Cancer Prevention and Control Roswell Park Comprehensive Cancer Institute Buffalo NY USA. Fred A. Litwin Center for Cancer Genetics Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital Toronto Ontario Canada. Department of Molecular Genetics University of Toronto Toronto Ontario Canada. Division of Biostatistics Data Science Institute and Cancer Center Medical College of Wisconsin Milwaukee WI USA. Centre for Cancer Genetic Epidemiology Department of Oncology University of Cambridge Cambridge UK. Department of Population Science American Cancer Society Atlanta GA USA. Radiation Oncology Research Unit Hannover Medical School Hannover Germany. Copenhagen General Population Study Herlev and Gentofte Hospital Copenhagen University Hospital Herlev Denmark. Department of Clinical Biochemistry Herlev and Gentofte Hospital Copenhagen University Hospital Herlev Denmark. Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark. Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA. Department of Internal Medicine and Huntsman Cancer Institute University of Utah Salt Lake City UT USA. Centre for Genomic and Experimental Medicine Institute of Genetics & Cancer The University of Ed

Clinical genetic testing identifies variants causal for hereditary cancer, information that is used for risk assessment and clinical management. Unfortunately, some variants identified are of uncertain clinical significance (VUS), complicating patient management. Case-control data is one evidence type used to classify VUS. As an initiative of the Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) Analytical Working Group we analyze germline sequencing data of BRCA1 and BRCA2 from 96,691 female breast cancer cases and 302,116 controls from three studies: the BRIDGES study of the Breast Cancer Association Consortium, the Cancer Risk Estimates Related to Susceptibility consortium, and the UK Biobank. We observe 11,207 BRCA1 and BRCA2 variants, with 6909 being coding, covering 23.4% of BRCA1 and BRCA2 VUS in ClinVar and 19.2% of ClinVar curated (likely) benign or pathogenic variants. Case-control likelihood ratio (ccLR) evidence is highly consistent with ClinVar assertions for (likely) benign or pathogenic variants; exhibiting 99.1% sensitivity and 95.3% specificity for BRCA1 and 93.3% sensitivity and 86.6% specificity for BRCA2. This approach provides case-control evidence for 787 unclassified variants; these include 579 with strong or moderate benign evidence and 10 with strong pathogenic evidence for which ccLR evidence is sufficient to alter clinical classification.

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Dense sampling of bird diversity increases power of comparative genomics (vol 587, pg 252, 2020)

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NATURE 2021年第7856期592卷 E24-E24页

作者： Feng, Shaohong Stiller, Josefin Deng, Yuan Armstrong, Joel Fang, Qi Reeve, Andrew Hart Xie, Duo Chen, Guangji Guo, Chunxue Faircloth, Brant C. Petersen, Bent Wang, Zongji Zhou, Qi Diekhans, Mark Chen, Wanjun Andreu-Sanchez, Sergio Margaryan, Ashot Howard, Jason Travis Parent, Carole Pacheco, George Sinding, Mikkel-Holger S. Puetz, Lara Cavill, Emily Ribeiro, Angela M. Eckhart, Leopold Fjeldsa, Jon Hosner, Peter A. Brumfield, Robb T. Christidis, Les Bertelsen, Mads F. Sicheritz-Ponten, Thomas Tietze, Dieter Thomas Robertson, Bruce C. Song, Gang Borgia, Gerald Claramunt, Santiago Lovette, Irby J. Cowen, Saul J. Njoroge, Peter Dumbacher, John Philip Ryder, Oliver A. Fuchs, Jerome Bunce, Michael Burt, David W. Cracraft, Joel Meng, Guanliang Hackett, Shannon J. Ryan, Peter G. Jonsson, Knud Andreas Jamieson, Ian G. da Fonseca, Rute R. Braun, Edward L. Houde, Peter Mirarab, Siavash Suh, Alexander Hansson, Bengt Ponnikas, Suvi Sigeman, Hanna Stervander, Martin Frandsen, Paul B. van der Zwan, Henriette van der Sluis, Rencia Visser, Carina Balakrishnan, Christopher N. Clark, Andrew G. Fitzpatrick, John W. Bowman, Reed Chen, Nancy Cloutier, Alison Sackton, Timothy B. Edwards, Scott V. Foote, Dustin J. Shakya, Subir B. Sheldon, Frederick H. Vignal, Alain Soares, Andre E. R. Shapiro, Beth Gonzalez-Solis, Jacob Ferrer-Obiol, Joan Rozas, Julio Riutort, Marta Tigano, Anna Friesen, Vicki Dalen, Love Urrutia, Araxi O. Szekely, Tamas Liu, Yang Campana, Michael G. Corvelo, Andre Fleischer, Robert C. Rutherford, Kim M. Gemmell, Neil J. Dussex, Nicolas Mouritsen, Henrik Thiele, Nadine Delmore, Kira Liedvogel, Miriam Franke, Andre Hoeppner, Marc P. Krone, Oliver Fudickar, Adam M. Mila, Borja Ketterson, Ellen D. Fidler, Andrew Eric Friis, Guillermo Parody-Merino, Angela M. Battley, Phil F. Cox, Murray P. Lima, Nicholas Costa Barroso Prosdocimi, Francisco Parchman, Thomas Lee Schlinger, Barney A. Loiselle, Bette A. Blake, John G. Lim, Haw Chuan Day, Lainy B. Fuxjager, Matthew J. Baldwin, Maude W. Braun, Michael J. Wirthlin, Morgan Dikow, China National GeneBank BGI-Shenzhen Shenzhen China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Kunming China BGI-Shenzhen Shenzhen China Villum Centre for Biodiversity Genomics Section for Ecology and Evolution Department of Biology University of Copenhagen Copenhagen Denmark BGI Education Center University of Chinese Academy of Sciences Shenzhen China MOE Laboratory of Biosystems Homeostasis and Protection Life Sciences Institute Zhejiang University Hangzhou China Department of Neuroscience and Developmental Biology University of Vienna Vienna Austria Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China James D. Watson Institute of Genome Sciences Hangzhou China UC Santa Cruz Genomics Institute UC Santa Cruz Santa Cruz CA USA Natural History Museum of Denmark University of Copenhagen Copenhagen Denmark Center for Macroecology Evolution and Climate GLOBE Institute University of Copenhagen Copenhagen Denmark Department of Biological Sciences Louisiana State University Baton Rouge LA USA Museum of Natural Science Louisiana State University Baton Rouge LA USA Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio) Faculty of Applied Sciences AIMST University Kedah Malaysia Section for Evolutionary Genomics The GLOBE Institute Faculty of Health and Medical Sciences University of Copenhagen Copenhagen Denmark Institute of Molecular Biology National Academy of Sciences Yerevan Armenia University Museum Norwegian University of Science and Technology Trondheim Norway Center for Reproductive Medicine The 2nd Affiliated Hospital School of Medicine Zhejiang University Hangzhou China Novogene Durham NC USA Duke University Medical Center Durham NC USA The Rockefeller University New York NY USA Howard Hughes Medical Institute Chevy Chase MD USA Department of Dermatology Medical University of Vienna Vienna Austria

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FinnGen provides genetic insights from a well-phenotyped isolated population (vol 613, pg 508, 2023)

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NATURE 2023年第7952期615卷 E19-E19页

作者： Kurki, Mitja I. Karjalainen, Juha Palta, Priit Sipila, Timo P. Kristiansson, Kati Donner, Kati M. Reeve, Mary P. Laivuori, Hannele Aavikko, Mervi Kaunisto, Mari A. Loukola, Anu Lahtela, Elisa Mattsson, Hannele Laiho, Paivi Parolo, Pietro Della Briotta Lehisto, Arto A. Kanai, Masahiro Mars, Nina Ramo, Joel Kiiskinen, Tuomo Heyne, Henrike O. Veerapen, Kumar Rueger, Sina Lemmela, Susanna Zhou, Wei Ruotsalainen, Sanni Parn, Kalle Hiekkalinna, Tero Koskelainen, Sami Paajanen, Teemu Llorens, Vincent Gracia-Tabuenca, Javier Siirtola, Harri Reis, Kadri Elnahas, Abdelrahman G. Sun, Benjamin Foley, Christopher N. Aalto-Setala, Katriina Alasoo, Kaur Arvas, Mikko Auro, Kirsi Biswas, Shameek Bizaki-Vallaskangas, Argyro Carpen, Olli Chen, Chia-Yen Dada, Oluwaseun A. Ding, Zhihao Ehm, Margaret G. Eklund, Kari Farkkila, Martti Finucane, Hilary Ganna, Andrea Ghazal, Awaisa Graham, Robert R. Green, Eric M. Hakanen, Antti Hautalahti, Marco Hedman, Asa K. Hiltunen, Mikko Hinttala, Reetta Hovatta, Iiris Hu, Xinli Huertas-Vazquez, Adriana Huilaja, Laura Hunkapiller, Julie Jacob, Howard Jensen, Jan-Nygaard Joensuu, Heikki John, Sally Julkunen, Valtteri Jung, Marc Junttila, Juhani Kaarniranta, Kai Kahonen, Mika Kajanne, Risto Kallio, Lila Kalviainen, Reetta Kaprio, Jaakko Kerimov, Nurlan Kettunen, Johannes Kilpelainen, Elina Kilpi, Terhi Klinger, Katherine Kosma, Veli-Matti Kuopio, Teijo Kurra, Venla Laisk, Triin Laukkanen, Jari Lawless, Nathan Liu, Aoxing Longerich, Simonne Magi, Reedik Makela, Johanna Makitie, Antti Malarstig, Anders Mannermaa, Arto Maranville, Joseph Matakidou, Athena Meretoja, Tuomo Mozaffari, Sahar V. Niemi, Mari E. K. Niemi, Marianna Niiranen, Teemu O'Donnell, Christopher J. Obeidat, Ma'En Okafo, George Ollila, Hanna M. Palomaki, Antti Palotie, Tuula Partanen, Jukka Paul, Dirk S. Pelkonen, Margit Pendergrass, Rion K. Petrovski, Slave Pitkaranta, Anne Platt, Adam Pulford, David Punkka, Eero Pussinen, Pirkko Raghavan, Neha Rahimov, Fedik Rajpal, Deepak Renaud, Nicole A. Riley-Gillis, Bridget Rodosthenous, Rodostheni Institute for Molecular Medicine Finland (FIMM) Helsinki Institute of Life Science (HiLIFE) University of Helsinki Helsinki Finland Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA Stanley Center for Psychiatric Research Broad Institute of Harvard and MIT Cambridge MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Estonian Genome Centre Institute of Genomics University of Tartu Tartu Estonia Medical and Clinical Genetics University of Helsinki and Helsinki University Hospital Helsinki Finland Department of Obstetrics and Gynecology Tampere University Hospital Tampere Finland Faculty of Medicine and Health Technology Center for Child Adolescent and Maternal Health University of Tampere Tampere Finland Department of Biomedical Informatics Harvard Medical School Boston MA USA Digital Health Center Hasso Plattner Institute for Digital Engineering University of Potsdam Potsdam Potsdam Germany Hasso Plattner Institute for Digital Health at Mount Sinai Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York NY USA Finnish Institute for Health and Welfare (THL) Helsinki Finland Department of Public Health University of Helsinki Helsinki Finland Anesthesia Critical Care and Pain Medicine Massachusetts General Hospital Boston MA USA Abdominal Center Endocrinology Helsinki University Hospital Helsinki Finland Folkhalsan Research Center Helsinki Finland Research Program of Clinical and Molecular Metabolism University of Helsinki Helsinki Finland Biocenter Oulu University of Oulu Oulu Finland Computational Medicine Center for Life Course Health Research Faculty of Medicine University of Oulu Oulu Finland Turku University Hospital and University of Turku Turku Finland University of Turku Turku Finland Helsinki Biobank University of Helsinki and Hospital District of Helsinki and Uusimaa Helsinki Finland TAUCHI Research Center

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Global, regional, and national sex-specific burden and control of the HIV epidemic, 1990–2019, for 204 countries and territories: the Global Burden of Diseases Study 2019

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The Lancet HIV 2021年第10期8卷 e633-e651页

作者： Jahagirdar, Deepa Walters, Magdalene K. Novotney, Amanda Brewer, Edmond D. Frank, Tahvi D. Carter, Austin Biehl, Molly H. Abbastabar, Hedayat Abhilash, E.S. Abu-Gharbieh, Eman Abu-Raddad, Laith Jamal Adekanmbi, Victor Adeyinka, Daniel Adedayo Adnani, Qorinah Estiningtyas Sakilah Afzal, Saira Aghababaei, Soodabeh Ahinkorah, Bright Opoku Ahmad, Sajjad Ahmadi, Keivan Ahmadi, Sepideh Ahmadpour, Ehsan Ahmed, Muktar Beshir Rashid, Tarik Ahmed Salih, Yusra Ahmed Aklilu, Addis Akram, Tayyaba Akunna, Chisom Joyqueenet Al Hamad, Hanadi Alahdab, Fares Alanezi, Fahad Mashhour Aleksandrova, Ekaterina A. Alene, Kefyalew Addis Ali, Liaqat Alipour, Vahid Almustanyir, Sami Alvis-Guzman, Nelson Ameyaw, Edward Kwabena Amu, Hubert Andrei, Catalina Liliana Andrei, Tudorel Anvari, Davood Arabloo, Jalal Aremu, Olatunde Arulappan, Judie Atnafu, Desta Debalkie Quintanilla, Beatriz Paulina Ayala Ayza, Muluken Altaye Azari, Samad Darshan, B.B. Banach, Maciej Bärnighausen, Till Winfried Barra, Fabio Barrow, Amadou Basu, Sanjay Bazargan-Hejazi, Shahrzad Belay, Habtamu Gebrehana Berheto, Tezera Moshago Bezabhe, Woldesellassie Mequanint Bezabih, Yihienew Mequanint Bhagavathula, Akshaya Srikanth Bhardwaj, Nikha Bhardwaj, Pankaj Bhattacharyya, Krittika Bibi, Sadia Bijani, Ali Bisignano, Catherine Bolarinwa, Obasanjo Afolabi Boloor, Archith Boltaev, Azizbek A. Briko, Nikolay Ivanovich Buonsenso, Danilo Burkart, Katrin Butt, Zahid A. Cao, Chao Charan, Jaykaran Chatterjee, Souranshu Chattu, Soosanna Kumary Chattu, Vijay Kumar Choudhari, Sonali Gajanan Chu, Dinh-Toi Couto, Rosa A.S. Cowden, Richard G. Dachew, Berihun Assefa Dadras, Omid Dagnew, Amare Belachew Dahlawi, Saad M.A. Dai, Xiaochen Dandona, Lalit Dandona, Rakhi das Neves, José Degenhardt, Louisa Demeke, Feleke Mekonnen Desta, Abebaw Alemayehu Deuba, Keshab Dhamnetiya, Deepak Dhungana, Govinda Prasad Dianatinasab, Mostafa Diaz, Daniel Djalalinia, Shirin Doan, Linh Phuong Dorostkar, Fariba Edinur, Hisham Atan Effiong, Andem Eftekharzadeh, Sahar El Sayed Zaki, Maysaa Elayedath, Rajesh Elhadi, Institute for Health Metrics and Evaluation University of Washington Seattle WA United States Department of Health Metrics Sciences School of Medicine University of Washington Seattle WA United States Division of Allergy and Infectious Diseases University of Washington Seattle WA United States Department of Global Health University of Washington Seattle WA United States School of Social Work University of Washington Seattle WA United States Department of Medicine University of Washington Seattle WA United States Vagelos College of Physicians and Surgeones Columbia University Medical Center New York NY United States Division of Data Analytics and Delivery for Impact WHO Geneva Switzerland Advanced Diagnostic and Interventional Radiology Research Centre Tehran University of Medical Sciences Tehran Iran Multiple Sclerosis Research Centre Tehran University of Medical Sciences Tehran Iran School of Public Health Tehran University of Medical Sciences Tehran Iran Department of Epidemiology and Biostatistics Tehran University of Medical Sciences Tehran Iran Paediatric Chronic Kidney Disease Research Centre Tehran University of Medical Sciences Tehran Iran Department of Psychiatry Tehran University of Medical Sciences Tehran Iran Metabolomics and Genomics Research Centre Tehran University of Medical Sciences Tehran Iran Sina Trauma and Surgery Research Centre Tehran University of Medical Sciences Tehran Iran Research Centre for Immunodeficiencies Tehran University of Medical Sciences Tehran Iran Non-Communicable Diseases Research Centre Tehran University of Medical Sciences Tehran Iran Department of Botany Sree Narayana Guru College Chelannur Kozhikode India Clinical Sciences Department University of Sharjah Sharjah United Arab Emirates Mass Communication Department University of Sharjah Sharjah United Arab Emirates Department of Health-Care Policy and Research Weill Cornell Medical College in Qatar Doha Qatar Department of Population Medicine Ca

Background: The sustainable development goals (SDGs) aim to end HIV/AIDS as a public health threat by 2030. Understanding the current state of the HIV epidemic and its change over time is essential to this effort. This study assesses the current sex-specific HIV burden in 204 countries and territories and measures progress in the control of the epidemic. Methods: To estimate age-specific and sex-specific trends in 48 of 204 countries, we extended the Estimation and Projection Package Age-Sex Model to also implement the spectrum paediatric model. We used this model in cases where age and sex specific HIV-seroprevalence surveys and antenatal care-clinic sentinel surveillance data were available. For the remaining 156 of 204 locations, we developed a cohort-incidence bias adjustment to derive incidence as a function of cause-of-death data from vital registration systems. The incidence was input to a custom Spectrum model. To assess progress, we measured the percentage change in incident cases and deaths between 2010 and 2019 (threshold >75% decline), the ratio of incident cases to number of people living with HIV (incidence-to-prevalence ratio threshold <0·03), and the ratio of incident cases to deaths (incidence-to-mortality ratio threshold <1·0). Findings: In 2019, there were 36·8 million (95% uncertainty interval [UI] 35·1–38·9) people living with HIV worldwide. There were 0·84 males (95% UI 0·78–0·91) per female living with HIV in 2019, 0·99 male infections (0·91–1·10) for every female infection, and 1·02 male deaths (0·95–1·10) per female death. Global progress in incident cases and deaths between 2010 and 2019 was driven by sub-Saharan Africa (with a 28·52% decrease in incident cases, 95% UI 19·58–35·43, and a 39·66% decrease in deaths, 36·49–42·36). Elsewhere, the incidence remained stable or increased, whereas deaths generally decreased. In 2019, the global incidence-to-prevalence ratio was 0·05 (95% UI 0·05–0·06) and the global incidence-to-mortality ratio was

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Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes

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Nature 2022年第7909期605卷 E3页

作者： Jill E Moore Michael J Purcaro Henry E Pratt Charles B Epstein Noam Shoresh Jessika Adrian Trupti Kawli Carrie A Davis Alexander Dobin Rajinder Kaul Jessica Halow Eric L Van Nostrand Peter Freese David U Gorkin Yin Shen Yupeng He Mark Mackiewicz Florencia Pauli-Behn Brian A Williams Ali Mortazavi Cheryl A Keller Xiao-Ou Zhang Shaimae I Elhajjajy Jack Huey Diane E Dickel Valentina Snetkova Xintao Wei Xiaofeng Wang Juan Carlos Rivera-Mulia Joel Rozowsky Jing Zhang Surya B Chhetri Jialing Zhang Alec Victorsen Kevin P White Axel Visel Gene W Yeo Christopher B Burge Eric Lécuyer David M Gilbert Job Dekker John Rinn Eric M Mendenhall Joseph R Ecker Manolis Kellis Robert J Klein William S Noble Anshul Kundaje Roderic Guigó Peggy J Farnham J Michael Cherry Richard M Myers Bing Ren Brenton R Graveley Mark B Gerstein Len A Pennacchio Michael P Snyder Bradley E Bernstein Barbara Wold Ross C Hardison Thomas R Gingeras John A Stamatoyannopoulos Zhiping Weng University of Massachusetts Medical School Program in Bioinformatics and Integrative Biology Worcester MA USA. The Broad Institute of Harvard and MIT Cambridge MA USA. Department of Genetics School of Medicine Stanford University Palo Alto CA USA. Cold Spring Harbor Laboratory Functional Genomics Cold Spring Harbor NY USA. Altius Institute for Biomedical Sciences Seattle WA USA. Department of Medicine University of Washington School of Medicine Seattle WA USA. Department of Cellular and Molecular Medicine Institute for Genomic Medicine Stem Cell Program Sanford Consortium for Regenerative Medicine University of California San Diego La Jolla CA USA. Program in Computational and Systems Biology Massachusetts Institute of Technology Cambridge MA USA. Center for Epigenomics Department of Cellular and Molecular Medicine University of California San Diego La Jolla CA USA. Ludwig Institute for Cancer Research University of California San Diego La Jolla CA USA. Institute for Human Genetics Department of Neurology University of California San Francisco San Francisco CA USA. Genomics Analysis Laboratory The Salk Institute for Biological Studies La Jolla CA USA. HudsonAlpha Institute for Biotechnology Huntsville AL USA. Division of Biology and Biological Engineering California Institute of Technology Pasadena CA USA. Department of Developmental and Cell Biology University of California Irvine Irvine CA USA. Department of Biochemistry and Molecular Biology The Pennsylvania State University University Park PA USA. Environmental Genomics and Systems Biology Division Lawrence Berkeley National Laboratory Berkeley CA USA. Department of Genetics and Genome Sciences Institute for Systems Genomics UConn Health Farmington CT USA. Département de Biochimie et Médecine Moléculaire Université de Montréal Montréal Quebec Canada. Division of Experimental Medicine McGill University Montreal Quebec Canada. Institut de Recherches Cliniques de Montréal (IR

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