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Patterns of somatic structural variation in human cancer genomes (vol 578, pg 112, 2020)

NATURE 2023年第7948期614卷 E38-E38页

作者： Li, Yilong Roberts, Nicola D. Wala, Jeremiah A. Shapira, Ofer Schumacher, Steven E. Kumar, Kiran Khurana, Ekta Waszak, Sebastian Korbel, Jan O. Haber, James E. Imielinski, Marcin Weischenfeldt, Joachim Beroukhim, Rameen Campbell, Peter J. Cancer Genome Project Wellcome Trust Sanger Institute Hinxton UK Totient Inc Cambridge MA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Haematology University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Korea Advanced Institute of Science and Technology Daejeon South Korea Department of Zoology Genetics and Physical Anthropology University of Santiago de Compostela Santiago de Compostela Spain Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) University of Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) University of Vigo Vigo Spain Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain Department of Zoology Genetics and Physical Anthropology (CiMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain The Broad Institute of Harvard and MIT Cambridge MA USA Bioinformatics and Integrative Genomics Harvard University Cambridge MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Harvard Medical School Boston MA USA Massachusetts General Hospital Center for Cancer Research Charlestown MA USA Dana-Farber Cancer Institute Boston MA USA Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute and Harvard Medical School Boston MA USA Weill Cornell Medical College New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine Ne

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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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Exposure-associated DNA methylation among people exposed to multiple industrial pollutants

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Clinical epigenetics 2024年第1期16卷 111页

作者： Chi-Hsin Sally Chen Tzu-Hsuen Yuan Tzu-Pin Lu Hsin-Ying Lee Yi-Hsuen Chen Liang-Chuan Lai Mong-Hsun Tsai Eric Y Chuang Chang-Chuan Chan Institute of Environmental and Occupational Health Sciences College of Public Health National Taiwan University Taipei Taiwan. Department of Health and Welfare College of City Management University of Taipei Taipei Taiwan. Institute of Epidemiology and Preventive Medicine College of Public Health National Taiwan University Taipei Taiwan. Institute of Health Data Analytics and Statistics College of Public Health National Taiwan University Taipei Taiwan. Graduate Institute of Physiology College of Medicine National Taiwan University Taipei Taiwan. Institute of Biotechnology College of Bio-Resources and Agriculture National Taiwan University Taipei Taiwan. Department of Electrical Engineering College of Electrical Engineering and Computer Science National Taiwan University Taipei Taiwan. chuangey@ntu.edu.tw. Biomedical Technology and Device Research Laboratories Industrial Technology Research Institute Hsinchu Taiwan. chuangey@ntu.edu.tw. Research and Development Center for Medical Devices National Taiwan University Taipei Taiwan. chuangey@ntu.edu.tw. Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan. chuangey@ntu.edu.tw. Institute of Environmental and Occupational Health Sciences College of Public Health National Taiwan University Taipei Taiwan. ccchan@ntu.edu.tw.

BACKGROUND:Current research on the epigenetic repercussions of exposure to a combination of pollutants is limited. This study aims to discern DNA methylation probes associated with exposure to multiple pollutants, ser... 详细信息

BACKGROUND:Current research on the epigenetic repercussions of exposure to a combination of pollutants is limited. This study aims to discern DNA methylation probes associated with exposure to multiple pollutants, serving as early effect markers, and single-nucleotide polymorphisms (SNPs) as surrogate indicators for population susceptibility. The investigation involved the analysis of urine exposure biomarkers for 11 heavy metals (vanadium, arsenic, mercury, cadmium, chromium, nickel, lead, manganese, copper, strontium, thallium), polycyclic aromatic hydrocarbon (PAHs) (1-hydroxypyrene), genome-wide DNA methylation sequencing, and SNPs array on all study participants. The data were integrated with metabolomics information and analyzed both at a community level based on proximity to home addresses relative to the complex and at an individual level based on exposure biomarker concentrations. RESULTS:On a community level, 67 exposure-related CpG probes were identified, while 70 CpG probes were associated with urine arsenic concentration, 2 with mercury, and 46 with vanadium on an individual level. These probes were annotated to genes implicated in cancers and chronic kidney disease. Weighted quantile sum regression analysis revealed that vanadium, mercury, and 1-hydroxypyrene contributed the most to cg08238319 hypomethylation. cg08238319 is annotated to the aryl hydrocarbon receptor repressor (AHRR) gene, and AHRR hypomethylation was correlated with an elevated risk of lung cancer. AHRR was further linked to deregulations in phenylalanine metabolism, alanine, aspartate, and glutamate metabolism, along with heightened oxidative stress. Additionally, three SNPs (rs11085020, rs199442, and rs10947050) corresponding to exposure-related CpG probes exhibited significant interaction effects with multiple heavy metals and PAHs exposure, and have been implicated in cancer progression and respiratory diseases. CONCLUSION:Our findings underscore the pivotal role of AHRR methylatio

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The Past, Present, and Future of the Brain Imaging data Structure (BIDS)

arXiv

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arXiv 2023年

作者： Poldrack, Russell A. Markiewicz, Christopher J. Appelhoff, Stefan Ashar, Yoni K. Auer, Tibor Baillet, Sylvain Bansal, Shashank Beltrachini, Leandro Bénar, Christian G. Bertazzoli, Giacomo Bhogawar, Suyash Blair, Ross W. Bortoletto, Marta Boudreau, Mathieu Brooks, Teon L. Calhoun, Vince D. Castelli, Filippo Maria Clement, Patricia Cohen, Alexander L. Cohen-Adad, Julien D'Ambrosio, Sasha de Hollander, Gilles de la Iglesia-Vayá, María de la Vega, Alejandro Delorme, Arnaud Devinsky, Orrin Draschkow, Dejan Duff, Eugene Paul DuPre, Elizabeth Earl, Eric Esteban, Oscar Feingold, Franklin W. Flandin, Guillaume Galassi, Anthony Gallitto, Giuseppe Ganz, Melanie Gau, Rémi Gholam, James Ghosh, Satrajit S. Giacomel, Alessio Gillman, Ashley G. Gleeson, Padraig Gramfort, Alexandre Guay, Samuel Guidali, Giacomo Halchenko, Yaroslav O. Handwerker, Daniel A. Hardcastle, Nell Herholz, Peer Hermes, Dora Honey, Christopher J. Innis, Robert B. Ioanas, Horea-Ioan Jahn, Andrew Karakuzu, Agah Keator, David B. Kiar, Gregory Kincses, Balint Laird, Angela R. Lau, Jonathan C. Lazari, Alberto Legarreta, Jon Haitz Li, Adam Li, Xiangrui Love, Bradley C. Lu, Hanzhang Maumet, Camille Mazzamuto, Giacomo Meisler, Steven L. Mikkelsen, Mark Mutsaerts, Henk Nichols, Thomas E. Nikolaidis, Aki Nilsonne, Gustav Niso, Guiomar Norgaard, Martin Okell, Thomas W. Oostenveld, Robert Ort, Eduard Park, Patrick J. Pawlik, Mateusz Pernet, Cyril R. Pestilli, Franco Petr, Jan Phillips, Christophe Poline, Jean-Baptiste Pollonini, Luca Raamana, Pradeep Reddy Ritter, Petra Rizzo, Gaia Robbins, Kay A. Rockhill, Alexander P. Rogers, Christine Rokem, Ariel Rorden, Chris Routier, Alexandre Saborit-Torres, Jose Manuel Salo, Taylor Schirner, Michael Smith, Robert E. Spisak, Tamas Sprenger, Julia Swann, Nicole C. Szinte, Martin Takerkart, Sylvain Thirion, Bertrand Thomas, Adam G. Torabian, Sajjad Varoquaux, Gael Voytek, Bradley Welzel, Julius Wilson, Martin Yarkoni, Tal Gorgolewski, Krzysztof J. Department of Psychology Stanford University StanfordCA United States Max Planck Institute for Human Development Berlin Germany University of Colorado Anschutz Medical Campus AuroraCO United States School of Psychology University of Surrey Guildford United Kingdom McConnell Brain Imaging Centre Montréal Neurological Institute McGill University Montréal Canada Department of Bioengineering University of California San Diego La Jolla CA United States School of Physics Astronomy Cardiff University Wales United Kingdom Institut de Neurosciences des Systèmes Marseille France Neurophysiology Lab IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli Brescia Italy Center for Mind/Brain Sciences - CIMeC University of Trento TN Rovereto Italy Brigham and Women’s Hospital BostonMA United States Massachusetts General Hospital BostonMA United States Harvard Medical School BostonMA United States Rackspace Technology San AntonioTX United States NeuroPoly Lab Polytechnique Montréal MontréalQC Canada Georgia State Georgia Tech Emory AtlantaGA United States University of Florence Sesto Fiorentino Italy Bioretics srl Cesena Italy Department of Medical Imaging Ghent University Hospital Ghent Belgium Department of Diagnostic Sciences Ghent University Ghent Belgium Department of Neurology Boston Children's Hospital BostonMA United States Dipartimento di Scienze della Salute dell'Università degli Studi di Milano Milan Italy Department of Clinical and Experimental Epilepsy University College London United Kingdom Zurich Center for Neuroeconomics Department of Economics University of Zurich Zurich Switzerland UMIB-FISABIO Valencia Spain The University of Texas at Austin AustinTX United States SCCN University of California San Diego La Jolla CA United States Department of Neurology NYU Langone Medical Center New YorkNY United States Department of Experimental Psychology University of Oxford Oxford United Kingdom UK Dementia Research Ins

The Brain Imaging data Structure (BIDS) is a community-driven standard for the organization of data and metadata from a growing range of neuroscience modalities. This paper is meant as a history of how the standard ha... 详细信息

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Author Correction: Why rankings of biomedical image analysis competitions should be interpreted with care

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Nature communications 2019年第1期10卷 588页

作者： Lena Maier-Hein Matthias Eisenmann Annika Reinke Sinan Onogur Marko Stankovic Patrick Scholz Tal Arbel Hrvoje Bogunovic Andrew P Bradley Aaron Carass Carolin Feldmann Alejandro F Frangi Peter M Full Bram van Ginneken Allan Hanbury Katrin Honauer Michal Kozubek Bennett A Landman Keno März Oskar Maier Klaus Maier-Hein Bjoern H Menze Henning Müller Peter F Neher Wiro Niessen Nasir Rajpoot Gregory C Sharp Korsuk Sirinukunwattana Stefanie Speidel Christian Stock Danail Stoyanov Abdel Aziz Taha Fons van der Sommen Ching-Wei Wang Marc-André Weber Guoyan Zheng Pierre Jannin Annette Kopp-Schneider Division of Computer Assisted Medical Interventions (CAMI) German Cancer Research Center (DKFZ) 69120 Heidelberg Germany. l.maier-hein@dkfz.de. Division of Computer Assisted Medical Interventions (CAMI) German Cancer Research Center (DKFZ) 69120 Heidelberg Germany. Centre for Intelligent Machines McGill University Montreal QC H3A0G4 Canada. Christian Doppler Laboratory for Ophthalmic Image Analysis Department of Ophthalmology Medical University Vienna 1090 Vienna Austria. Science and Engineering Faculty Queensland University of Technology Brisbane QLD 4001 Australia. Department of Electrical and Computer Engineering Department of Computer Science Johns Hopkins University Baltimore MD 21218 USA. CISTIB - Center for Computational Imaging & Simulation Technologies in Biomedicine The University of Leeds Leeds Yorkshire LS2 9JT UK. Department of Radiology and Nuclear Medicine Medical Image Analysis Radboud University Center 6525 GA Nijmegen The Netherlands. Institute of Information Systems Engineering TU Wien 1040 Vienna Austria. Complexity Science Hub Vienna 1080 Vienna Austria. Heidelberg Collaboratory for Image Processing (HCI Heidelberg University 69120 Heidelberg Germany. Centre for Biomedical Image Analysis Masaryk University 60200 Brno Czech Republic. Electrical Engineering Vanderbilt University Nashville TN 37235-1679 USA. Institute of Medical Informatics Universität zu Lübeck 23562 Lübeck Germany. Division of Medical Image Computing (MIC) German Cancer Research Center (DKFZ) 69120 Heidelberg Germany. Institute for Advanced Studies Department of Informatics Technical University of Munich 80333 Munich Germany. Information System Institute HES-SO Sierre 3960 Switzerland. Departments of Radiology Nuclear Medicine and Medical Informatics Erasmus MC 3015 GD Rotterdam The Netherlands. Department of Computer Science University of Warwick Coventry CV4 7AL UK. Department of Radiation Oncology Massachusetts General Hospital Boston MA

In the original version of this Article the values in the rightmost column of Table 1 were inadvertently shifted relative to the other columns. This has now been corrected in the PDF and HTML versions of the Article.

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Correction: Assessing real-world gait with digital technology? Validation, insights and recommendations from the Mobilise-D consortium

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Journal of neuroengineering and rehabilitation 2024年第1期21卷 71页

作者： M Encarna Micó-Amigo Tecla Bonci Anisoara Paraschiv-Ionescu Martin Ullrich Cameron Kirk Abolfazl Soltani Arne Küderle Eran Gazit Francesca Salis Lisa Alcock Kamiar Aminian Clemens Becker Stefano Bertuletti Philip Brown Ellen Buckley Alma Cantu Anne-Elie Carsin Marco Caruso Brian Caulfield Andrea Cereatti Lorenzo Chiari Ilaria D'Ascanio Bjoern Eskofier Sara Fernstad Marcel Froehlich Judith Garcia-Aymerich Clint Hansen Jeffrey M Hausdorff Hugo Hiden Emily Hume Alison Keogh Felix Kluge Sarah Koch Walter Maetzler Dimitrios Megaritis Arne Mueller Martijn Niessen Luca Palmerini Lars Schwickert Kirsty Scott Basil Sharrack Henrik Sillén David Singleton Beatrix Vereijken Ioannis Vogiatzis Alison J Yarnall Lynn Rochester Claudia Mazzà Silvia Del Din Translational and Clinical Research Institute Faculty of Medical Sciences Newcastle University Newcastle Upon Tyne UK. Department of Mechanical Engineering and Insigneo Institute for in Silico Medicine The University of Sheffield Sheffield UK. Laboratory of Movement Analysis and Measurement Ecole Polytechnique Federale de Lausanne Lausanne Switzerland. Machine Learning and Data Analytics Lab Department of Artificial Intelligence in Biomedical Engineering Friedrich-Alexander-Universität Erlangen Nürnberg Erlangen Germany. Center for the Study of Movement Cognition and Mobility Neurological Institute Tel Aviv Sourasky Medical Center Tel Aviv Israel. Department of Biomedical Sciences University of Sassari Sassari Italy. Department of Electronics and Telecommunications Politecnico di Torino Turin Italy. National Institute for Health and Care Research (NIHR) Newcastle Biomedical Research Centre (BRC) Newcastle University and The Newcastle Upon Tyne Hospitals NHS Foundation Trust Newcastle Upon Tyne UK. Robert Bosch Gesellschaft für Medizinische Forschung Stuttgart Germany. The Newcastle Upon Tyne Hospitals NHS Foundation Trust Newcastle Upon Tyne UK. School of Computing Newcastle University Newcastle Upon Tyne UK. Barcelona Institute for Global Health (ISGlobal) Barcelona Spain. Universitat Pompeu Fabra Barcelona Catalonia Spain. CIBER Epidemiología y Salud Pública (CIBERESP) Madrid Spain. Insight Centre for Data Analytics University College Dublin Dublin Ireland. School of Public Health Physiotherapy and Sports Science University College Dublin Dublin Ireland. Department of Electrical Electronic and Information Engineering «Guglielmo Marconi» University of Bologna Bologna Italy. Health Sciences and Technologies-Interdepartmental Center for Industrial Research (CIRI-SDV) University of Bologna Bologna Italy. Grünenthal GmbH Aachen Germany. Department of Neurology University Medical Center Schleswig-Holstein Campus Kiel Kiel Germany. Sagol School of Neuroscien

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Publisher Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

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Nature genetics 2023年第1期55卷 166页

作者： Huipeng Li Elise T Courtois Debarka Sengupta Yuliana Tan Kok Hao Chen Jolene Jie Lin Goh Say Li Kong Clarinda Chua Lim Kiat Hon Wah Siew Tan Mark Wong Paul Jongjoon Choi Lawrence J K Wee Axel M Hillmer Iain Beehuat Tan Paul Robson Shyam Prabhakar Computational and Systems Biology Genome Institute of Singapore Singapore Singapore. Developmental Cellomics Laboratory Genome Institute of Singapore Singapore Singapore. Department of Computer Science and Engineering and Center for Computational Biology Indraprastha Institute of Information Technology Delhi India. Synthetic Biology Genome Institute of Singapore Singapore Singapore. Cancer Therapeutics and Stratified Oncology Genome Institute of Singapore Singapore Singapore. Department of Medical Oncology National Cancer Centre Singapore Singapore Singapore. Department of Pathology Singapore General Hospital Singapore Singapore. Department of Colorectal Surgery Singapore General Hospital Singapore Singapore. Data Analytics Department Institute for Infocomm Research Singapore Singapore. Cancer Therapeutics and Stratified Oncology Genome Institute of Singapore Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Department of Medical Oncology National Cancer Centre Singapore Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Program in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore. iain.tan.b.h@singhealth.com.sg. Developmental Cellomics Laboratory Genome Institute of Singapore Singapore Singapore. paul.robson@***. The Jackson Laboratory for Genomic Medicine Farmington Connecticut USA. paul.robson@***. Department of Genetics and Genome Sciences Institute for Systems Genomics University of Connecticut Farmington Connecticut USA. paul.robson@***. Department of Biological Sciences National University of Singapore Singapore Singapore. paul.robson@***. Computational and Systems Biology Genome Institute of Singapore Singapore Singapore. prabhakars@gis.a-star.edu.sg.

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

arXiv

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arXiv 2024年

作者： Kazerooni, Anahita Fathi Khalili, Nastaran Liu, Xinyang Gandhi, Deep Jiang, Zhifan Anwar, Syed Muhammed Albrecht, Jake Adewole, Maruf Anazodo, Udunna Anderson, Hannah Baid, Ujjwal Bergquist, Timothy Borja, Austin J. Calabrese, Evan Chung, Verena Conte, Gian-Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Franson, Andrea Gottipati, Anurag Haldar, Shuvanjan Iglesias, Juan Eugenio Janas, Anastasia Johansen, Elaine Jones, Blaise V. Khalili, Neda 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 Rudie, Jeffrey D. Sanchez-Montano, Mariana Shaikh, Ibraheem Salman Sheth, Nakul Tu, Wenxin Wang, Chunhao Ware, Jeffrey B. Wiestler, Benedikt Zapaishchykova, Anna Bornhorst, Miriam Deutsch, Michelle Fouladi, Maryam Lazow, Margot Mikael, Leonie Hummel, Trent Kann, Benjamin de Blank, Peter Hoffman, Lindsey Aboian, Mariam Nabavizadeh, Ali Packer, Roger Bakas, Spyridon Resnick, Adam Rood, Brian Vossough, Arastoo 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 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 Division of Computational Pathology Department of Pathology and Laboratory Medicine Indiana University School of Medicine IndianapolisIN United States Department of Neurosurgery The University of Southern California CA United States Department of Radiology Duke University Medical Center DurhamNC 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 C. S. Mott Children’s Hospital University of Michigan MI 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 OH United States Helmholtz AI Helmholtz Munich Germany Department of Radiation Oncology Duke University Medical Center DurhamNC United States Department of Radiology Children’s Health Orange County CA United States Department of Applied Mathematics and Computer Science Technical University of De

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 d... 详细信息

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The Brain Tumor Segmentation (BraTS-METS) Challenge 2023: Brain Metastasis Segmentation on Pre-treatment MRI

arXiv

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arXiv 2023年

作者： Moawad, Ahmed W. Janas, Anastasia Baid, Ujjwal Ramakrishnan, Divya Saluja, Rachit Ashraf, Nader Jekel, Leon Amiruddin, Raisa Adewole, Maruf Albrecht, Jake Anazodo, Udunna Aneja, Sanjay Anwar, Syed Muhammad Bergquist, Timothy Calabrese, Evan Chiang, Veronica Chung, Verena Conte, Gian Marco Marco Dako, Farouk Eddy, James Ezhov, Ivan Familiar, Ariana Farahani, Keyvan Iglesias, Juan Eugenio Jiang, Zhifan Johanson, Elaine Kazerooni, Anahita Fathi Kofler, Florian Krantchev, Kiril LaBella, Dominic Van Leemput, Koen Li, Hongwei Bran Linguraru, Marius George Link, Katherine E. Liu, Xinyang Maleki, Nazanin Meier, Zeke Menze, Bjoern H. Moy, Harrison Osenberg, Klara Piraud, Marie Reitman, Zachary Shinohara, Russel Takeshi Tahon, Nourel hoda Nada, Ayman Velichko, Yuri S. Wang, Chunhao Wiestler, Benedikt Wiggins, Walter Shafique, Umber Willms, Klara Avesta, Arman Bousabarah, Khaled Chakrabarty, Satrajit Gennaro, Nicolo Holler, Wolfgang Kaur, Manpreet LaMontagne, Pamela Lin, MingDe Lost, Jan Marcus, Daniel S. Maresca, Ryan Merkaj, Sarah Nada, Ayaman Pedersen, Gabriel Cassinelli von Reppert, Marc Sotiras, Aristeidis Teytelboym, Oleg Tillmans, Niklas Westerhoff, Malte Youssef, Ayda Godfrey, Devon Floyd, Scott Rauschecker, Andreas Villanueva-Meyer, Javier Pflüger, Irada Cho, Jaeyoung Bendszus, Martin Brugnara, Gianluca Cramer, Justin Perez-Carillo, Gloria Guzman J. Johnson, Derek R. Kam, Anthony Kwan, Benjamin Yin Ming Lai, Lillian Lall, Neil U. Memon, Fatima Patro, Satya Narayana Petrovic, Bojan So, Tiffany Y. Thompson, Gerard Wu, Lei Schrickel, E. Brooke Bansal, Anu Barkhof, Frederik Besada, Cristina Chu, Sammy Druzgal, Jason Dusoi, Alexandru Farage, Luciano Feltrin, Fabricio Fong, Amy Fung, Steve H. Gray, R. Ian Ikuta, Ichiro Iv, Michael Postma, Alida A. Mahajan, Amit Joyner, David Krumpelman, Chase Letourneau-Guillon, Laurent Lincoln, Christie M. Maros, Mate E. Miller, Elka Morón, Fanny Nimchinsky, Esther A. Ozsarlak, Ozkan Patel, Uresh Rohatgi, Saurabh Saha, Atin Sayah, Anousheh Schwartz, Eric D. Shih, Robert Shiroishi, Mark Trinity health Mid Atlantic Hosiptals DarbyPA United States Department of Radiology and Biomedical Imaging Yale School of Medicine New HavenCT United States Division of Computational Pathology Department of Pathology and Laboratory Medicine School of Medicine Indiana University IndianapolisIN United States Department of Electical and Computer Engineering Cornell University Cornell Tech New YorkNY United States Department of Radiology Weill Cornell Medicine New YorkNY United States ImagineQuant Children’s Hospital of Philadelphia PhiladelphiaPA United States College of Medicine Alfaisal University Riyadh Saudi Arabia DKFZ Division of Translational Neurooncology The WTZ German Cancer Consortium DKTK Partner Site University Hospital Essen Essen Germany Medical Artificial Intelligence Lab Crestview Radiology Lagos Nigeria Sage Bionetworks SeattleWA United States Montreal Neurological Institute McGill University Montreal Canada lab Crestview Radiology Lagos Nigeria Department of Therapeutic Radiology Yale School of Medicine New HavenCT United States Sheikh Zayed Institute for Pediatric Surgical Innovation Children’s National Hospital WashingtonDC United States Department of Radiology Mayo Clinic RochesterMN United States Department of Radiology Duke University Medical Center DurhamNC United States Department of Neurosurgery Yale School of Medicine New HavenCT United States Center for Global Health Perelman School of Medicine University of Pennsylvania PA United States Department of Informatics Technical University Munich Germany Children’s Hospital of Philadelphia University of Pennsylvania PhiladelphiaPA United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD United States Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital BostonMA United States Children’s National Hospital WashingtonDC United States PrecisionFDA U.S. Food and Drug Administration S

The translation of AI-generated brain metastases (BM) segmentation into clinical practice relies heavily on diverse, high-quality annotated medical imaging datasets. The BraTS-METS 2023 challenge has gained momentum f... 详细信息

The translation of AI-generated brain metastases (BM) segmentation into clinical practice relies heavily on diverse, high-quality annotated medical imaging datasets. The BraTS-METS 2023 challenge has gained momentum for testing and benchmarking algorithms using rigorously annotated internationally compiled real-world datasets. This study presents the results of the segmentation challenge and characterizes the challenging cases that impacted the performance of the winning algorithms. Untreated brain metastases on standard anatomic MRI sequences (T1, T2, FLAIR, T1PG) from eight contributed international datasets were annotated in stepwise method: published UNET algorithms, student, neuroradiologist, final approver neuroradiologist. Segmentations were ranked based on lesion-wise Dice and Hausdorff distance (HD95) scores. False positives (FP) and false negatives (FN) were rigorously penalized, receiving a score of 0 for Dice and a fixed penalty of 374 for HD95. The mean scores for the teams were calculated. Eight datasets comprising 1303 studies were annotated, with 402 studies (3076 lesions) released on Synapse as publicly available datasets to challenge competitors. Additionally, 31 studies (139 lesions) were held out for validation, and 59 studies (218 lesions) were used for testing. Segmentation accuracy was measured as rank across subjects, with the winning team achieving a LesionWise mean score of 7.9. The Dice score for the winning team was 0.65 ± 0.25. Common errors among the leading teams included false negatives for small lesions and misregistration of masks in space. The Dice scores and lesion detection rates of all algorithms diminished with decreasing tumor size, particularly for tumors smaller than 100 mm3. In conclusion, algorithms for BM segmentation require further refinement to balance high sensitivity in lesion detection with the minimization of false positives and negatives. The BraTS-METS 2023 challenge successfully curated well-annotated, diverse d

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Methods for Evaluating Medical Tests and Biomarkers

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Diagnostic and Prognostic Research 2017年第1期1卷 1-34页

作者： Gowri Gopalakrishna Miranda Langendam Patrick Bossuyt Mariska Leeflang Rob Scholten Anna Noel-Storr James Thomas Iain Marshall Byron Wallace Penny Whiting Clare Davenport Gowri GopalaKrishna Isabel de Salis Sue Mallett Robert Wolff Marie Westwood Jos Kleinen Richard Riley Gary Collins Hans Reitsma Karel Moons Antonia Zapf Katharina Kramer Annika Hoyer Oliver Kuss J. Ensor R. D. Riley J. J. Deeks E. C. Martin Gerta Rücker Martin Schumacher Susanne Steinhauser Joie Ensor Kym Snell Brian Willis Jon Deeks Thomas Debray Lavinia Ferrante di Ruffano Sian Taylor-Phillips Chris Hyde Stuart A. Taylor Gauraang Batnagar Lavinia Ferrante Di Ruffano Farah Seedat Aileen Clarke Sarah Byron Frances Nixon Rebecca Albrow Thomas Walker Carla Deakin Zhivko Zhelev Harriet Hunt Yaling Yang Lucy Abel James Buchanan Thomas Fanshawe Bethany Shinkins Laure Wynants Sabine Van Huffel Jan Verbakel Dirk Timmerman Ben Van Calster Aeliko Zwinderman Jason Oke Jack O’Sullivan Rafael Perera Brian Nicholson Hannah L. Bromley Tracy E. Roberts Adele Francis Denniis Petrie G. Bruce Mann Kinga Malottki Holly Smith Lucinda Billingham Alice Sitch Oke Gerke Mie Holm-Vilstrup Eivind Antonsen Segtnan Ulrich Halekoh Poul Flemming Høilund-Carlsen Bernard G. Francq Jac Dinnes Julie Parkes Walter Gregory Jenny Hewison Peter Selby Doug Altman William Rosenberg Julien Asselineau Paul Perez Aïssatou Paye Emilie Bessede Cécile Proust-Lima Christiana Naaktgeboren Joris de Groot Johannes Reitsma Anne Rutjes Emmanuel Ogundimu Jonathan Cook Yannick Le Manach Yvonne Vergouwe Romin Pajouheshnia Rolf Groenwold Karen Moons Linda Peelen Bavo De Cock Daan Nieboer Ewout W. Steyerberg Micael J. Pencina Jennifer Cooper Nick Parsons Chris Stinton Steve Smith Andy Dickens Rachel Jordan Alexandra Enocson David Fitzmaurice Peymane Adab Charles Boachie Gaj Vidmar Karoline Freeman Martin Connock Rachel Court Carl Moons Jessica Harris Zoe Plummer Barnaby Reeves Chris Rogers Andrew Mumford Kurtis Lee Veerle Verheyden Gianni D. Angelini Gavin J. Murphy Jeremy Huddy Melody Ni George Hanna Department of Clinical Epidemiology Biostatistics & Bioinformatics Academic Medical Center University of Amsterdam Amsterdam The Netherlands Department of Clinical Epidemiology and Biostatistics Academic Medical Center University of Amsterdam Amsterdam Netherlands Cochrane Netherlands Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht Netherlands Cochrane Dementia and Cognitive Improvement Group University of Oxford Oxford UK EPPI-Centre Department of Social Science University College London London UK Division of Health and Social Care Research King’s College London London UK College of Computer and Information Science Northeastern University Boston USA University Hospitals Bristol NHS Foundation Trust School of Social and Community Medicine Bristol UK Institute of Applied Health Research University of Birmingham Birmingham UK School of Social and Community Medicine University of Bristol Bristol UK Kleijnen Systematic Reviews Ltd York UK Research Institute for Primary Care and Health Sciences Keele University Keele UK Centre for Statistics in Medicine Nuffield Department of Orthopaedics Rheumatology and Musculoskeletal Sciences University of Oxford Oxford UK Julius Center for Health Sciences and Primary Care University Medical Center Utrecht Utrecht The Netherlands Cochrane Netherlands University Medical Center Utrecht Utrecht The Netherlands Julius Center for Health Sciences and Primary Care University Medical Center Utrecht 3584 CG Utrecht Netherlands Department of Medical Statistics University Medical Center Göttingen Göttingen Germany Institute for Biometry and Epidemiology German Diabetes Center Leibniz Institute for Diabetes Research at Heinrich Heine University Düsseldorf Germany Manchester Pharmacy School University of Manchester Manchester UK Institute for Medical Biometry and Statistics Faculty of Medicine and Medical Center – University of Freiburg Stefan-Meier-Str. 26 79104 Freiburg Germany

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