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Chronic radiation-associated dysphagia in oropharyngeal cancer survivors: Towards age-adjusted dose constraints for deglutitive muscles

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CLINICAL AND TRANSLATIONAL RADIATION ONCOLOGY 2019年 18卷 16-22页

作者： Christopherson, Kaitlin M. Ghosh, Alokananda Sherif, Abdallah Mohamed, Radwan Kamal, Mona Fuller, David Department of Radiation Oncology The University of Texas MD Anderson Cancer Center Houston TX United States Department of Biostatistics and Data Science University of Texas School of Public Health Houston TX United States Department of Clinical Oncology University of Alexandria Alexandria Egypt Department of Emergency Medicine The University of Texas MD Anderson Cancer Center Houston TX United States Baylor College of Medicine Houston TX United States Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown MA United States Department of Radiation Oncology The University of Texas Medical Branch Galveston TX United States Department of Head and Neck Surgery The University of Texas MD Anderson Cancer Center Houston TX United States Department of Thoracic & Head and Neck Oncology The University of Texas MD Anderson Cancer Center Houston TX United States Medical Physics Program The University of Texas Graduate School of Biomedical Sciences Houston TX United States Department of Computer Science University of Illinois at Chicago Chicago IL United States Department of Electrical and Computer Engineering The University of Iowa Iowa City IA United States

Objectives: We sought to model chronic radiation-associated dysphagia (RAD) in patients given intensity-modulated radiation therapy (IMRT) for oropharyngeal squamous cell cancer (OPSCC) as a function of age and dose to non-target swallowing muscles. Methods: We reviewed 300 patients with T1-T4 N0-3 M0 OPSCC given definitive IMRT with concurrent chemotherapy. Chronic RAD was defined as aspiration or stricture on videoflouroscopy/endoscopy, gastrostomy tube, or aspiration pneumonia at >= 12 months after IMRT. Doses to autosegmented regions of interest (ROIs;inferior, middle and superior constrictors, anterior and posterior digastrics, mylo/geniohyoid complex, intrinsic tongue, and gengioglossus) were obtained from DICOM-RT plans and dose-volume histograms. The probability of chronic RAD as a function of mean ROI dose, stratified by age (<50, 50-59, 60-69, or >70 years), was estimated with logistic probability models and subsequent unsupervised nonlinear curves. Results: Chronic RAD was observed in 34 patients (11%). Age was a significant correlate of chronic RAD, both independently and with dose for all muscle groups examined. Distinct muscle-specific dose-response profiles were observed as a function of age (e.g., 5% of patients in their 50 s [but 20% of those 70 +] who received 60 Gy to the superior constrictor had chronic RAD). This effect was stable across all observed muscle ROIs, with a false discovery rate-corrected p < 0.05, for all dose/muscle/age models, suggesting that including age as a covariate improves modeling of chronic RAD. Conclusions: Age at treatment moderates the probability of chronic RAD after chemo-IMRT for OPSCC, with aging muscles showing lower dose thresholds. Uniform dose constraints may not predict toxicity in older patients. (C) 2019 The Authors. Published by Elsevier B.V. on behalf of European Society for Radiotherapy and Oncology.

关键词： Oropharynx IMRT Radiation Toxicity Presbyphagia

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Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition

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database : the journal of biological databases and curation 2023年第2023期2023卷 baac108页

作者： Davy Weissenbacher Karen O'Connor Siddharth Rawal Yu Zhang Richard Tzong-Han Tsai Timothy Miller Dongfang Xu Carol Anderson Bo Liu Qing Han Jinfeng Zhang Igor Kulev Berkay Köprü Raul Rodriguez-Esteban Elif Ozkirimli Ammer Ayach Roland Roller Stephen Piccolo Peijin Han V G Vinod Vydiswaran Ramya Tekumalla Juan M Banda Parsa Bagherzadeh Sabine Bergler João F Silva Tiago Almeida Paloma Martinez Renzo Rivera-Zavala Chen-Kai Wang Hong-Jie Dai Luis Alberto Robles Hernandez Graciela Gonzalez-Hernandez Department of Computational Biomedicine Cedars-Sinai Medical Center Los Angeles CA USA. DBEI The Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Computer Science and Information Engineering National Central University No. 300 Zhongda Rd Zhongli District Taoyuan 320 Taiwan. IoX Center National Taiwan University Da'an District Section 4 Roosevelt Rd No. 1 Barry Lam Hall Taipei 106 Taiwan. Research Center for Humanities and Social Sciences Academia Sinica No. 128 Section 2 Academia Rd Nangang District Taipei 115 Taiwan. Computational Health Informatics Program Boston Children's Hospital Boston MA USA. Department of Pediatrics Harvard Medical School Boston MA USA. NVIDIA Santa Clara CA USA. Department of Statistics Florida State University Tallahassee FL USA. Data and Analytics Chapter F. Hoffmann-La Roche Ltd Switzerland. Pharmaceutical Research and Early Development Roche Innovation Center Basel Switzerland. Speech and Language Technology Lab DFKI Berlin Germany. Department of Biology Brigham Young University Provo UT USA. Department of Computational Medicine and Bioinformatics Medical School University of Michigan Ann Arbor MI USA. Department of Learning Health Sciences Medical School University of Michigan Ann Arbor MI USA. School of Information University of Michigan Ann Arbor MI USA. Department of Computer Science Georgia State University Atlanta GA USA. CLaC Labs Concordia University Montreal Canada. DETI Institute of Electronics and Informatics Engineering of Aveiro University of Aveiro Portugal. Department of Computation University of A Coruña Spain. Computer Science and Engineering Department Universidad Carlos III de Madrid Madrid Spain. Big Data Laboratory Chunghwa Telecom Laboratories Taoyuan Taiwan. Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan. Department of Electrical Engineering College of Electrical Engineering and Computer Sci

This study presents the outcomes of the shared task competition BioCreative VII (Task 3) focusing on the extraction of medication names from a Twitter user's publicly available tweets (the user's 'timeline'). In general, detecting health-related tweets is notoriously challenging for natural language processing tools. The main challenge, aside from the informality of the language used, is that people tweet about any and all topics, and most of their tweets are not related to health. Thus, finding those tweets in a user's timeline that mention specific health-related concepts such as medications requires addressing extreme imbalance. Task 3 called for detecting tweets in a user's timeline that mentions a medication name and, for each detected mention, extracting its span. The organizers made available a corpus consisting of 182 049 tweets publicly posted by 212 Twitter users with all medication mentions manually annotated. The corpus exhibits the natural distribution of positive tweets, with only 442 tweets (0.2%) mentioning a medication. This task was an opportunity for participants to evaluate methods that are robust to class imbalance beyond the simple lexical match. A total of 65 teams registered, and 16 teams submitted a system run. This study summarizes the corpus created by the organizers and the approaches taken by the participating teams for this challenge. The corpus is freely available at https://***/tasks/biocreative-vii/track-3/. The methods and the results of the competing systems are analyzed with a focus on the approaches taken for learning from class-imbalanced data.

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The Brain Tumor Segmentation (BraTS) Challenge 2023: Focus on Pediatrics (CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs)

arXiv

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arXiv 2023年

作者： Kazerooni, Anahita Fathi Khalili, Nastaran Liu, Xinyang Haldar, Debanjan Jiang, Zhifan Anwar, Syed Muhammed Albrecht, Jake Adewole, Maruf Anazodo, Udunna Anderson, Hannah Bagheri, Sina Baid, Ujjwal Bergquist, Timothy Borja, Austin J. Calabrese, Evan Chung, Verena Conte, Gian-Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Haldar, Shuvanjan Iglesias, Juan Eugenio Janas, Anastasia Johansen, Elaine Jones, Blaise V. Kofler, Florian LaBella, Dominic Lai, Hollie Anne Van Leemput, Koen Li, Hongwei Bran Maleki, Nazanin McAllister, Aaron S. Meier, Zeke Menze, Bjoern Moawad, Ahmed W. Nandolia, Khanak K. Pavaine, Julija Piraud, Marie Poussaint, Tina Prabhu, Sanjay P. Reitman, Zachary Rodriguez, Andres Rudie, Jeffrey D. Sanchez-Montano, Mariana Shaikh, Ibraheem Salman Shah, Lubdha M. Sheth, Nakul Shinohara, Russel Taki Tu, Wenxin Viswanathan, Karthik Wang, Chunhao Ware, Jeffrey B. Wiestler, Benedikt Wiggins, Walter Zapaishchykova, Anna Aboian, Mariam Bornhorst, Miriam de Blank, Peter Deutsch, Michelle Fouladi, Maryam Hoffman, Lindsey Kann, Benjamin Lazow, Margot Mikael, Leonie Nabavizadeh, Ali Packer, Roger Resnick, Adam Rood, Brian Vossough, Arastoo Bakas, Spyridon Linguraru, Marius George Children’s Hospital of Philadelphia PhiladelphiaPA United States Department of Neurosurgery University of Pennsylvania PhiladelphiaPA United States University of Pennsylvania PhiladelphiaPA United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Department of Neurosurgery Thomas Jefferson University Hospital PA United States Sage Bionetworks United States Lab Crestview Radiology Lagos Nigeria McGill University MontrealQC Canada Department of Radiology Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Neurosurgery The University of Southern California CA United States Department of Radiology Duke University Medical Center United States Mayo Clinic MN United States Center for Global Health Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Informatics Technical University Munich Germany TranslaTUM - Central Institute for Translational Cancer Research Technical University of Munich Germany Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States Biomedical Engineering Rutgers University New BrunswickNJ United States Athinoula A Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Yale University New HavenCT United States PrecisionFDA U.S. Food and Drug Administration Silver SpringMD United States Cincinnati Children’s Hospital Medical Center United States Helmholtz AI Helmholtz Munich Germany Department of Radiation Oncology Duke University Medical Center United States Department of Radiology Children’s Health Orange County CA United States Department of Applied Mathematics and Computer Science Technical University of Denmark Denmark Department of Radiol

Pediatric tumors of the central nervous system are the most common cause of cancer-related death in children. The five-year survival rate for high-grade gliomas in children is less than 20%. Due to their rarity, the diagnosis of these entities is often delayed, their treatment is mainly based on historic treatment concepts, and clinical trials require multi-institutional collaborations. The MICCAI Brain Tumor Segmentation (BraTS) Challenge is a landmark community benchmark event with a successful history of 12 years of resource creation for the segmentation and analysis of adult glioma. Here we present the CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs 2023 challenge, which represents the first BraTS challenge focused on pediatric brain tumors with data acquired across multiple international consortia dedicated to pediatric neuro-oncology and clinical trials. The BraTS-PEDs 2023 challenge focuses on benchmarking the development of volumentric segmentation algorithms for pediatric brain glioma through standardized quantitative performance evaluation metrics utilized across the BraTS 2023 cluster of challenges. Models gaining knowledge from the BraTS-PEDs multi-parametric structural MRI (mpMRI) training data will be evaluated on separate validation and unseen test mpMRI dataof high-grade pediatric glioma. The CBTN-CONNECT-DIPGR-ASNR-MICCAI BraTS-PEDs 2023 challenge brings together clinicians and AI/imaging scientists to lead to faster development of automated segmentation techniques that could benefit clinical trials, and ultimately the care of children with brain tumors. © 2023, CC BY.

关键词： Tumors

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Author Correction: Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk

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Nature genetics 2023年第10期55卷 1778-1779页

作者： Nick Shrine Abril G Izquierdo Jing Chen Richard Packer Robert J Hall Anna L Guyatt Chiara Batini Rebecca J Thompson Chandan Pavuluri Vidhi Malik Brian D Hobbs Matthew Moll Wonji Kim Ruth Tal-Singer Per Bakke Katherine A Fawcett Catherine John Kayesha Coley Noemi Nicole Piga Alfred Pozarickij Kuang Lin Iona Y Millwood Zhengming Chen Liming Li Sara R A Wijnant Lies Lahousse Guy Brusselle Andre G Uitterlinden Ani Manichaikul Elizabeth C Oelsner Stephen S Rich R Graham Barr Shona M Kerr Veronique Vitart Michael R Brown Matthias Wielscher Medea Imboden Ayoung Jeong Traci M Bartz Sina A Gharib Claudia Flexeder Stefan Karrasch Christian Gieger Annette Peters Beate Stubbe Xiaowei Hu Victor E Ortega Deborah A Meyers Eugene R Bleecker Stacey B Gabriel Namrata Gupta Albert Vernon Smith Jian'an Luan Jing-Hua Zhao Ailin F Hansen Arnulf Langhammer Cristen Willer Laxmi Bhatta David Porteous Blair H Smith Archie Campbell Tamar Sofer Jiwon Lee Martha L Daviglus Bing Yu Elise Lim Hanfei Xu George T O'Connor Gaurav Thareja Omar M E Albagha Karsten Suhre Raquel Granell Tariq O Faquih Pieter S Hiemstra Annelies M Slats Benjamin H Mullin Jennie Hui Alan James John Beilby Karina Patasova Pirro Hysi Jukka T Koskela Annah B Wyss Jianping Jin Sinjini Sikdar Mikyeong Lee Sebastian May-Wilson Nicola Pirastu Katherine A Kentistou Peter K Joshi Paul R H J Timmers Alexander T Williams Robert C Free Xueyang Wang John L Morrison Frank D Gilliland Zhanghua Chen Carol A Wang Rachel E Foong Sarah E Harris Adele Taylor Paul Redmond James P Cook Anubha Mahajan Lars Lind Teemu Palviainen Terho Lehtimäki Olli T Raitakari Jaakko Kaprio Taina Rantanen Kirsi H Pietiläinen Simon R Cox Craig E Pennell Graham L Hall W James Gauderman Chris Brightling James F Wilson Tuula Vasankari Tarja Laitinen Veikko Salomaa Dennis O Mook-Kanamori Nicholas J Timpson Eleftheria Zeggini Josée Dupuis Caroline Hayward Ben Brumpton Claudia Langenberg Stefan Weiss Georg Homuth Carsten Oliver Schmidt Nicole Probst-Hensch Marjo-Riitta Jarvelin Alanna C Morrison Ozren Polasek Igor Department of Population Health Sciences University of Leicester Leicester UK. nick.shrine@leicester.ac.uk. Department of Population Health Sciences University of Leicester Leicester UK. Division of Respiratory Medicine and NIHR Nottingham Biomedical Research Centre University of Nottingham Nottingham UK. Leicester National Institute for Health and Care Research Biomedical Research Centre Glenfield Hospital Leicester UK. Channing Division of Network Medicine Division of Pulmonary and Critical Care Medicine Department of Medicine Brigham and Women's Hospital Boston MA USA. Harvard Medical School Boston MA USA. COPD Foundation Washington DC USA. Department of Clinical Science Unversity of Bergen Bergen Norway. Nuffield Department of Population Health University of Oxford Oxford UK. MRC Population Health Research Unit University of Oxford Oxford UK. Department of Epidemiology and Biostatistics School of Public Health Peking University Health Science Center Beijing China. Department of Respiratory Diseases Ghent Universital Hospital Ghent Belgium. Department of Bioanalysis Faculty of Pharmaceutical Sciences Ghent University Ghent Belgium. Department of Epidemiology Eramus Medical Center Rotterdam The Netherlands. Department of Internal Medicine Eramus Medical Center Rotterdam The Netherlands. Center for Public Health Genomics University of Virginia Charlottesville VA USA. Department of Medicine Columbia University Medical Center New York NY USA. Medical Research Council Human Genetics Unit Institute of Genetics and Cancer University of Edinburgh Edinburgh UK. Human Genetics Center Department of Epidemiology Human Genetics and Environmental Sciences School of Public Health The University of Texas Health Science Center at Houston Houston TX USA. MRC Centre for Environment and Health Department of Epidemiology and Biostatistics School of Public Health Imperial College London London UK. Department of Epidemiology and Public Health Swiss Tropical

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Author Correction: Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries

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Nature genetics 2023年第3期55卷 519-520页

作者： Ceres Fernandez-Rozadilla Maria Timofeeva Zhishan Chen Philip Law Minta Thomas Stephanie Schmit Virginia Díez-Obrero Li Hsu Juan Fernandez-Tajes Claire Palles Kitty Sherwood Sarah Briggs Victoria Svinti Kevin Donnelly Susan Farrington James Blackmur Peter Vaughan-Shaw Xiao-Ou Shu Jirong Long Qiuyin Cai Xingyi Guo Yingchang Lu Peter Broderick James Studd Jeroen Huyghe Tabitha Harrison David Conti Christopher Dampier Mathew Devall Fredrick Schumacher Marilena Melas Gad Rennert Mireia Obón-Santacana Vicente Martín-Sánchez Ferran Moratalla-Navarro Jae Hwan Oh Jeongseon Kim Sun Ha Jee Keum Ji Jung Sun-Seog Kweon Min-Ho Shin Aesun Shin Yoon-Ok Ahn Dong-Hyun Kim Isao Oze Wanqing Wen Keitaro Matsuo Koichi Matsuda Chizu Tanikawa Zefang Ren Yu-Tang Gao Wei-Hua Jia John Hopper Mark Jenkins Aung Ko Win Rish Pai Jane Figueiredo Robert Haile Steven Gallinger Michael Woods Polly Newcomb David Duggan Jeremy Cheadle Richard Kaplan Timothy Maughan Rachel Kerr David Kerr Iva Kirac Jan Böhm Lukka-Pekka Mecklin Pekka Jousilahti Paul Knekt Lauri Aaltonen Harri Rissanen Eero Pukkala Johan Eriksson Tatiana Cajuso Ulrika Hänninen Johanna Kondelin Kimmo Palin Tomas Tanskanen Laura Renkonen-Sinisalo Brent Zanke Satu Männistö Demetrius Albanes Stephanie Weinstein Edward Ruiz-Narvaez Julie Palmer Daniel Buchanan Elizabeth Platz Kala Visvanathan Cornelia Ulrich Erin Siegel Stefanie Brezina Andrea Gsur Peter Campbell Jenny Chang-Claude Michael Hoffmeister Hermann Brenner Martha Slattery John Potter Konstantinos Tsilidis Matthias Schulze Marc Gunter Neil Murphy Antoni Castells Sergi Castellví-Bel Leticia Moreira Volker Arndt Anna Shcherbina Mariana Stern Bens Pardamean Timothy Bishop Graham Giles Melissa Southey Gregory Idos Kevin McDonnell Zomoroda Abu-Ful Joel Greenson Katerina Shulman Flavio Lejbkowicz Kenneth Offit Yu-Ru Su Robert Steinfelder Temitope Keku Bethany van Guelpen Thomas Hudson Heather Hampel Rachel Pearlman Sonja Berndt Richard Hayes Marie Elena Martinez Sushma Thomas Douglas Corley Paul Pharoah Susanna Larsson Yun Yen Heinz-Jo Edinburgh Cancer Research Centre Institute of Genomics and Cancer University of Edinburgh Edinburgh UK. Genomic Medicine Group Instituto de Investigacion Sanitaria de Santiago Santiago de Compostela Spain. Colon Cancer Genetics Group Medical Research Council Human Genetics Unit Institute of Genetics and Cancer University of Edinburgh Edinburgh UK. Danish Institute for Advanced Study Department of Public Health University of Southern Denmark Odense Denmark. Division of Epidemiology Department of Medicine Vanderbilt-Ingram Cancer Center Vanderbilt Epidemiology Center Vanderbilt University Medical Center Nashville TN USA. Division of Genetics and Epidemiology Institute of Cancer Research London UK. Public Health Sciences Division Fred Hutchinson Cancer Research Center Seattle WA USA. Genomic Medicine Institute Cleveland Clinic Cleveland OH USA. Population and Cancer Prevention Program Case Comprehensive Cancer Center Cleveland OH USA. Colorectal Cancer Group ONCOBELL Program Bellvitge Biomedical Research Institute Barcelona Spain. Oncology Data Analytics Program Catalan Institute of Oncology Barcelona Spain. Consortium for Biomedical Research in Epidemiology and Public Health Madrid Madrid Spain. Department of Clinical Sciences Faculty of Medicine University of Barcelona Barcelona Spain. Department of Biostatistics School of Public Health University of Washington Seattle WA USA. Institute of Cancer and Genomic Sciences College of Medical and Dental Sciences University of Birmingham Birmingham UK. Department of Public Health Richard Doll Building University of Oxford Oxford UK. Department of Biomedical Informatics Vanderbilt University School of Medicine Nashville TN USA. Department of Preventive Medicine USC Norris Comprehensive Cancer Center Keck School of Medicine University of Southern California Los Angeles CA USA. Center for Public Health Genomics Department of Public Health Sciences University of Virginia Charlottesville VA USA. De

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Global tracking of marine megafauna space use reveals how to achieve conservation targets

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science 2025年第6751期388卷 1086-1097页

作者： Ana M. M. Sequeira Jorge P. Rodríguez Sarah A. Marley Hannah J. Calich Mirjam van der Mheen Michelle VanCompernolle Lucy M. Arrowsmith Lauren R. Peel Nuno Queiroz Marisa Vedor Ivo da Costa Gonzalo Mucientes Ana Couto Nicolas E. Humphries Sara Abalo-Morla Francisco J. Abascal Debra L. Abercrombie Katya Abrantes F. Alberto Abreu-Grobois André S. Afonso Pedro Afonso Heidi Ahonen Susanne Åkesson Joanna Alfaro-Shigueto Russel D. Andrews Frédéric Angelier Marina Antonopoulou Javier A. Arata Gonzalo Araujo Randall Arauz José Manuel Arcos Igor Arregui Haritz Arrizabalaga Marie Auger-Méthé Steffen Bach Fred Bailleul Robin W. Baird George H. Balazs Susan G. Barco Adam Barnett Warren Baverstock Alastair M. M. Baylis Annalea Beard Juan Bécares Eduardo J. Belda Ian Bell Ashley Bennison Scott R. Benson Diego Bernal Michael L. Berumen Sandra Bessudo Natalia P. A. Bezerra Antonin V. Blaison Gabriela S. Blanco Barbara A. Block Mark Bolton Mark E. Bond Ramón Bonfil Camrin D. Braun Annette C. Broderick Michael de L. Brooke Annabelle M. L. Brooks Edward J. Brooks Ignacio M. Bruno Jennifer M. Burns Michael E. Byrne Steven E. Campana Hamish A. Campbell Richard A. Campbell Aaron Carlisle Ruth H. Carmichael Gemma Carroll Paolo Casale Filipe R. Ceia Demian D. Chapman Taylor K. Chapple Jean-Benoit Charrassin Andre Chiaradia John Chisholm Christopher R. Clarke Thomas A. Clay Christophe Cleguer Elizabeth Clingham Eric E. G. Clua Jesse E. M. Cochran Rochelle Constantine Robert W. Cooper Estelle Crochelet Michelle Cronin Eduardo Cuevas Kayla P. DaCosta Laurent Dagorn Ryan Daly Randall W. Davis P. J. Nico de Bruyn Carlos Delgado-Trejo Thomas Dellinger Solène Derville Stella Diamant Andrew DiMatteo Kara L. Dodge Philip D. Doherty Michael C. Double Alistair D. M. Dove Thomas K Doyle Michael J. Drew Lindsay L. Dubbs Clinton A. J. Duffy Peter H. Dutton Ewan W. J. Edwards Luke D. Einoder Mark V. Erdmann Eduardo Espinoza Nicole Esteban Ana Isabel Fagundes Chris Feare Steven H. Ferguson Luciana C. Ferreira Francesco Ferretti John Filmalter Brittany F Division of Ecology and Evolution Research School of Biology The Australian National University Canberra (Australian Capital Territory) Australia. UWA Oceans Institute and the School of Biological Sciences The University of Western Australia Perth (Western Australia) Australia. Instituto de Física Interdisciplinar y Sistemas Complejos (IFISC) CSIC-UIB Palma de Mallorca Spain. Instituto Mediterráneo de Estudios Avanzados (IMEDEA) CSIC-UIB Esporles Illes Balears Spain. C.A. Illes Balears Universidad Nacional de Educación a Distancia (UNED) Palma Spain. Delegación Territorial en Illes Balears Agencia Estatal de Meteorología (AEMET) Muelle de Poniente s/n Palma Spain. Scotland’s Rural College (SRUC) Craibstone Estate Bucksburn Aberdeen UK. Oceans Graduate School and the UWA Oceans Institute The University of Western Australia Perth (Western Australia) Australia. School of Engineering and the UWA Oceans Institute The University of Western Australia Perth (Western Australia) Australia. Department of Biodiversity Conservation and Attractions Biodiversity and Conservation Science Kensington (Western Australia) Australia. Save Our Seas Foundation Geneva Switzerland. The Manta Trust Catemwood House Norwood Lane Corscombe Dorset UK. Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO) InBIO Laboratório Associado Campus de Vairão Universidade do Porto Vairão Portugal. BIOPOLIS Program in Genomics Biodiversity and Land Planning Campus de Vairao Vairão Portugal. Instituto de Investigaciones Marinas Consejo Superior de Investigaciones Científicas (IIM-CSIC) Vigo Pontevedra Spain. School of Biological Sciences University of Aberdeen Aberdeen UK. Biomathematics and statistics Scotland The kings building Edinburgh Scotland. Marine Biological Association (MBA) The Laboratory Citadel Hill Plymouth UK. Instituto de Investigación para la Gestión Integrada de Zonas Costeras Universitat Politècnica de València Gandia València Spain. Instituto Español de O

The recent Kunming-Montreal Global Biodiversity Framework (GBF) sets ambitious goals but no clear pathway for how zero loss of important biodiversity areas and halting human-induced extinction of threatened species will be achieved. We assembled a multi-taxa tracking dataset (11 million geopositions from 15,845 tracked individuals across 121 species) to provide a global assessment of space use of highly mobile marine megafauna, showing that 63% of the area that they cover is used 80% of the time as important migratory corridors or residence areas. The GBF 30% threshold (Target 3) will be insufficient for marine megafauna’s effective conservation, leaving important areas exposed to major anthropogenic threats. Coupling area protection with mitigation strategies (e.g., fishing regulation, wildlife-traffic separation) will be essential to reach international goals and conserve biodiversity.

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Correction to: CpG‑creating mutations are costly in many human viruses

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Evolutionary Ecology 2020年第3期34卷 361-362页

作者： Caudill, Victoria R. Qin, Sarina Winstead, Ryan Kaur, Jasmeen Tisthammer, Kaho Pineda, E. Geo Solis, Caroline Cobey, Sarah Bedford, Trevor Carja, Oana Eggo, Rosalind M. Koelle, Katia Lythgoe, Katrina Regoes, Roland Roy, Scott Allen, Nicole Aviles, Milo Baker, Brittany A. Bauer, William Bermudez, Shannel Carlson, Corey Castellanos, Edgar Catalan, Francisca L. Chemel, Angeline Katia Elliot, Jacob Evans, Dwayne Fiutek, Natalie Fryer, Emily Goodfellow, Samuel Melvin Hecht, Mordecai Hopp, Kellen Hopson, E. Deshawn Jaberi, Amirhossein Kim, Jennifer Kinney, Christen Lao, Derek Le, Adrienne Lo, Jacky Lopez, Alejandro G. López, Andrea Lorenzo, Fernando G. Luu, Gordon T. Mahoney, Andrew R. Melton, Rebecca L. Nascimento, Gabriela Do Pradhananga, Anjani Rodrigues, Nicole S. Shieh, Annie Sims, Jasmine Singh, Rima Sulaeman, Hasan Thu, Ricky Tran, Krystal Tran, Livia Winters, Elizabeth J. Wong, Albert Pennings, Pleuni S. Department of Biology San Francisco State University San Francisco USA Department of Biology University of Oregon Eugene USA Quantitative Systems Biology Univeristy of California Merced USA Department of Ecology and Evolution University of Chicago Chicago USA Vaccine and Infectious Disease Division Fred Hutchinson Cancer Research Center Seattle USA Department of Computational Biology School of Computer Science Carnegie Mellon University Pittsburgh USA Department of Infectious Disease Epidemiology London School of Hygiene & Tropical Medicine London UK Department of Biology Emory University Atlanta USA Big Data Institute University of Oxford Oxford UK Department of Environmental Systems Science ETH Zurich Zurich Switzerland Department of Neurological Surgery University of California San Francisco USA Department of Organismic and Evolutionary Biology Harvard University Cambridge USA Department of Plant Biology Carnegie Institution for Science Stanford USA Health Sciences Center University of New Mexico Albuquerque USA UCSD Biomed Sciences PhD Program University of California San Diego USA Biochemistry Molecular Cellular and Developmental Biology Graduate Group University of California Davis USA UCSF Tetrad Graduate Program University of California San Francisco USA

In the original article, the co-author name "Jennifer Kim" has been inadvertently missed during the publication process. The complete author group is given in this correction.

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Ontologizing Health Systems data at Scale: Making Translational Discovery a Reality

arXiv

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arXiv 2022年

作者： Callahan, Tiffany J. Stefanski, Adrianne L. Wyrwa, Jordan M. Zeng, Chenjie Ostropolets, Anna Banda, Juan M. Baumgartner, William A. Boyce, Richard D. Casiraghi, Elena Coleman, Ben D. Collins, Janine H. Deakyne-Davies, Sara J. Feinstein, James A. Haendel, Melissa A. Lin, Asiyah Y. Martin, Blake Matentzoglu, Nicolas A. Meeker, Daniella Reese, Justin Sinclair, Jessica Taneja, Sanya B. Trinkley, Katy E. Vasilevsky, Nicole A. Williams, Andrew Zhang, Xingman A. Denny, Joshua C. Robinson, Peter N. Ryan, Patrick Hripcsak, George Bennett, Tellen D. Hunter, Lawrence E. Kahn, Michael G. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States National Human Genome Research Institute National Institutes of Health BethesdaMD20892 United States Department of Computer Science Georgia State University AtlantaGA30303 United States Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15260 United States Computer Science Università degli Studi di Milano Milan20122 Italy Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States The Jackson Laboratory for Genomic Medicine FarmingtonCT06032 United States Department of Haematology University of Cambridge Cambridge United Kingdom Department of Research Informatics & Data Science Analytics Resource Center Children’s Hospital Colorado AuroraCO80045 United States University of Colorado Anschutz School of Medicine AuroraCO80045 United States Center for Health AI University of Colorado Anschutz Medical Campus AuroraCO80045 United States Departments of Biomedical Informatics and Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Semanticly Athens Greece Yale School of Medicine New HavenCT06510 United States HealthLinc ValparaisoIN46383 United States Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Family Medicine University of Colorado Anschutz School of Medicine AuroraCO80045 United States Translational and Integrative Sciences Lab University of Colorado Anschutz Medical Campus AuroraCO80045 United States Tufts Institute for Clinical Research and Health Policy Studies Tufts University Bos

Background: Common data models solve many challenges of standardizing electronic health record (EHR) data, but are unable to semantically integrate all the resources needed for deep phenotyping. Open Biological and Biomedical Ontology (OBO) Foundry ontologies provide computable representations of biological knowledge and enable the integration of heterogeneous data. However, mapping EHR data to OBO ontologies requires significant manual curation and domain expertise. Objective: We introduce OMOP2OBO, an algorithm for mapping Observational Medical Outcomes Partnership (OMOP) vocabularies to OBO ontologies. Results: Using OMOP2OBO, we produced mappings for 92,367 conditions, 8611 drug ingredients, and 10,673 measurement results, which covered 68-99% of concepts used in clinical practice when examined across 24 hospitals. When used to phenotype rare disease patients, the mappings helped systematically identify undiagnosed patients who might benefit from genetic testing. Conclusions: By aligning OMOP vocabularies to OBO ontologies our algorithm presents new opportunities to advance EHR-based deep phenotyping. © 2022, CC BY.

关键词： Ontology

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The 2021 report of the Lancet Countdown on health and climate change: code red for a healthy future

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The Lancet 2021年第10311期398卷 1619-1662页

作者： Romanello, Marina McGushin, Alice Di Napoli, Claudia Drummond, Paul Hughes, Nick Jamart, Louis Kennard, Harry Lampard, Pete Solano Rodriguez, Baltazar Arnell, Nigel Ayeb-Karlsson, Sonja Belesova, Kristine Cai, Wenjia Campbell-Lendrum, Diarmid Capstick, Stuart Chambers, Jonathan Chu, Lingzhi Ciampi, Luisa Dalin, Carole Dasandi, Niheer Dasgupta, Shouro Davies, Michael Dominguez-Salas, Paula Dubrow, Robert Ebi, Kristie L Eckelman, Matthew Ekins, Paul Escobar, Luis E Georgeson, Lucien Grace, Delia Graham, Hilary Gunther, Samuel H Hartinger, Stella He, Kehan Heaviside, Clare Hess, Jeremy Hsu, Shih-Che Jankin, Slava Jimenez, Marcia P Kelman, Ilan Kiesewetter, Gregor Kinney, Patrick L Kjellstrom, Tord Kniveton, Dominic Lee, Jason K W Lemke, Bruno Liu, Yang Liu, Zhao Lott, Melissa Lowe, Rachel Martinez-Urtaza, Jaime Maslin, Mark McAllister, Lucy McMichael, Celia Mi, Zhifu Milner, James Minor, Kelton Mohajeri, Nahid Moradi-Lakeh, Maziar Morrissey, Karyn Munzert, Simon Murray, Kris A Neville, Tara Nilsson, Maria Obradovich, Nick Sewe, Maquins Odhiambo Oreszczyn, Tadj Otto, Matthias Owfi, Fereidoon Pearman, Olivia Pencheon, David Rabbaniha, Mahnaz Robinson, Elizabeth Rocklöv, Joacim Salas, Renee N Semenza, Jan C Sherman, Jodi Shi, Liuhua Springmann, Marco Tabatabaei, Meisam Taylor, Jonathon Trinanes, Joaquin Shumake-Guillemot, Joy Vu, Bryan Wagner, Fabian Wilkinson, Paul Winning, Matthew Yglesias, Marisol Zhang, Shihui Gong, Peng Montgomery, Hugh Costello, Anthony Hamilton, Ian Institute for Global Health University College London London UK United Kingdom Institute for Sustainable Resources University College London London UK United Kingdom UCL Energy Institute University College London London UK United Kingdom Institute for Environmental Design and Engineering University College London London UK United Kingdom Department of Geography University College London London UK United Kingdom The Bartlett School of Sustainable Construction University College London London UK United Kingdom Centre for Human Health and Performance University College London London UK United Kingdom School of Agriculture Policy and Development University of Reading Reading United Kingdom Department of Meteorology University of Reading Reading United Kingdom The Walker Institute University of Reading Reading United Kingdom Department of Health Sciences University of York York United Kingdom Institute for Environment and Human Security United Nations University Bonn Germany Centre on Climate Change and Planetary Health London School of Hygiene & Tropical Medicine London UK United Kingdom Centre for Mathematical Modelling of Infectious Diseases London School of Hygiene & Tropical Medicine London UK United Kingdom Department of Public Health Environments and Society London School of Hygiene & Tropical Medicine London UK United Kingdom Department of Earth System Science Tsinghua University Beijing China Department of Environment Climate Change and Health World Health Organization Geneva Switzerland Institute for Environmental Sciences World Health Organization Geneva Switzerland Centre for Climate Change and Social Transformations School of Psychology Cardiff University Cardiff United Kingdom Yale Center on Climate Change and Health Yale University New Haven CT United States School of Government University of Birmingham Birmingham United Kingdom Economic analysis of Climate Impacts and Policy Centro Euro-Mediterraneo sui Cambiamenti Climatic

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Identification and development of therapeutics for COVID-19

arXiv

引用

arXiv 2021年

作者： Rando, Halie M. Wellhausen, Nils Ghosh, Soumita Lee, Alexandra J. Dattoli, Anna Ada Hu, Fengling Byrd, James Brian Rafizadeh, Diane N. Lordan, Ronan Qi, Yanjun Sun, Yuchen Brueffer, Christian Field, Jeffrey M. Guebila, Marouen Ben Jadavji, Nafisa M. Skelly, Ashwin N. Ramsundar, Bharath Wang, Jinhui Goel, Rishi Raj Park, YoSon Boca, Simina M. Gitter, Anthony Greene, Casey S. Department of Systems Pharmacology and Translational Therapeutics University of Pennsylvania PhiladelphiaPA United States Department of Biochemistry and Molecular Genetics University of Colorado School of Medicine AuroraCO United States Center for Health AI University of Colorado School of Medicine AuroraCO United States Institute of Translational Medicine and Therapeutics Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Biostatistics Epidemiology and Informatics University of Pennsylvania PhiladelphiaPA United States University of Michigan School of Medicine Ann ArborMI United States Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States Department of Chemistry University of Pennsylvania PhiladelphiaPA United States Department of Computer Science University of Virginia CharlottesvilleVA United States Department of Clinical Sciences Lund University Lund Sweden Department of Biostatistics Harvard School of Public Health BostonMA United States Biomedical Science Midwestern University GlendaleAZ United States Department of Neuroscience Carleton University OttawaON Canada Institute for Immunology University of Pennsylvania Perelman School of Medicine Philadelphia United States The DeepChem Project Institute for Immunology University of Pennsylvania PhiladelphiaPA United States SiminaB Innovation Center for BiomedicalInformatics Georgetown University Medical Center WashingtonDC United States Early Biometrics & Statistical Innovation Data Science & Artificial Intelligence R & D AstraZeneca GaithersburgMD United States Department of Biostatistics and Medical Informatics University of Wisconsin-Madison MadisonWI United States Morgridge Institute for Research MadisonWI United States Childhood Cancer Data Lab Alex’s Lemonade Stand Foundation PhiladelphiaPA United States

After emerging in China in late 2019, the novel coronavirus SARS-CoV-2 spread worldwide and as of mid-2021 remains a significant threat globally. Only a few coronaviruses are known to infect humans, and only two cause infections similar in severity to SARS-CoV-2: Severe acute respiratory syndrome-related coronavirus, a closely related species of SARS-CoV-2 that emerged in 2002, and Middle East respiratory syndrome-related coronavirus, which emerged in 2012. Unlike the current pandemic, previous epidemics were controlled rapidly through public health measures, but the body of research investigating severe acute respiratory syndrome and Middle East respiratory syndrome has proven valuable for identifying approaches to treating and preventing novel coronavirus disease 2019 (COVID-19). Building on this research, the medical and scientific communities have responded rapidly to the COVID-19 crisis to identify many candidate therapeutics. The approaches used to identify candidates fall into four main categories: adaptation of clinical approaches to diseases with related pathologies, adaptation based on virological properties, adaptation based on host response, and data-driven identification of candidates based on physical properties or on pharmacological compendia. To date, a small number of therapeutics have already been authorized by regulatory agencies such as the Food and Drug Administration (FDA), while most remain under investigation. The scale of the COVID-19 crisis offers a rare opportunity to collect data on the effects of candidate therapeutics. This information provides insight not only into the management of coronavirus diseases, but also into the relative success of different approaches to identifying candidate therapeutics against an emerging disease. © 2021, CC BY.

关键词： Coronavirus

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