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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: Brain clocks capture diversity and disparities in aging and dementia across geographically diverse populations

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Nature medicine 2024年第12期30卷 3779页

作者： Sebastian Moguilner Sandra Baez Hernan Hernandez Joaquín Migeot Agustina Legaz Raul Gonzalez-Gomez Francesca R Farina Pavel Prado Jhosmary Cuadros Enzo Tagliazucchi Florencia Altschuler Marcelo Adrián Maito María E Godoy Josephine Cruzat Pedro A Valdes-Sosa Francisco Lopera John Fredy Ochoa-Gómez Alfredis Gonzalez Hernandez Jasmin Bonilla-Santos Rodrigo A Gonzalez-Montealegre Renato Anghinah Luís E d'Almeida Manfrinati Sol Fittipaldi Vicente Medel Daniela Olivares Görsev G Yener Javier Escudero Claudio Babiloni Robert Whelan Bahar Güntekin Harun Yırıkoğulları Hernando Santamaria-Garcia Alberto Fernández Lucas David Huepe Gaetano Di Caterina Marcio Soto-Añari Agustina Birba Agustin Sainz-Ballesteros Carlos Coronel-Oliveros Amanuel Yigezu Eduar Herrera Daniel Abasolo Kerry Kilborn Nicolás Rubido Ruaridh A Clark Ruben Herzog Deniz Yerlikaya Kun Hu Mario A Parra Pablo Reyes Adolfo M García Diana L Matallana José Alberto Avila-Funes Andrea Slachevsky María I Behrens Nilton Custodio Juan F Cardona Pablo Barttfeld Ignacio L Brusco Martín A Bruno Ana L Sosa Ortiz Stefanie D Pina-Escudero Leonel T Takada Elisa Resende Katherine L Possin Maira Okada de Oliveira Alejandro Lopez-Valdes Brian Lawlor Ian H Robertson Kenneth S Kosik Claudia Duran-Aniotz Victor Valcour Jennifer S Yokoyama Bruce Miller Agustin Ibanez Latin American Brain Health Institute Universidad Adolfo Ibañez Santiago de Chile Chile. Cognitive Neuroscience Center Universidad de San Andrés Buenos Aires Argentina. Department of Neurology Massachusetts General Hospital and Harvard Medical School Boston MA USA. Universidad de los Andes Bogota Colombia. Global Brain Health Institute (GBHI) University of California San Francisco CA USA. Global Brain Health Institute (GBHI) Trinity College Dublin Dublin Ireland. The University of California Santa Barbara (UCSB) Santa Barbara CA USA. Escuela de Fonoaudiología Universidad San Sebastián Santiago de Chile Chile. Grupo de Bioingeniería Decanato de Investigación Universidad Nacional Experimental del Táchira San Cristóbal Venezuela. Advanced Center for Electrical and Electronic Engineering Universidad Técnica Federico Santa María Valparaíso Chile. University of Buenos Aires Buenos Aires Argentina. The Clinical Hospital of Chengdu Brain Sciences Institute University of Electronic Sciences and Technology of China Chengdu China. Technology of China Chengdu China. Cuban Neuroscience Center La Habana Cuba. Grupo de Neurociencias de Antioquia (GNA) University of Antioquia Medellín Colombia. Department of Psychology Master Program of Clinical Neuropsychology Universidad Surcolombiana Neiva Neiva Colombia. Department of Psychology Universidad Cooperativa de Colombia Arauca Colombia. Neurocognition and Psychophysiology Laboratory Universidad Surcolombiana Neiva Colombia. Reference Center of Behavioural Disturbances and Dementia School of Medicine University of Sao Paulo Sao Paulo Brazil. Traumatic Brain Injury Cognitive Rehabilitation Out-Patient Center University of Sao Paulo Sao Paulo Brazil. Center for Social and Cognitive Neuroscience School of Psychology Universidad Adolfo Ibáñez Santiago Chile. Neuropsychology and Clinical Neuroscience Laboratory (LANNEC) Physiopathology Program-Institute of Biomedical Sciences (ICBM) Neuroscience and East Neuroscience Dep

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Centenarian clocks: epigenetic clocks for validating claims of exceptional longevity

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GEROSCIENCE 2023年第3期45卷 1817-1835页

作者： Dec, Eric Clement, James Cheng, Kaiyang Church., George M. Fossel., Michael B. Rehkopf, David. H. Rosero-Bixby, Luis Kobor, Michael S. Lin, David TS. Lu, Ake T. Fei, Zhe Guo, Wei Chew, Yap Ching Yang, Xiaojing Putra, Sulistyo E. Dwi Reiner, Alex P. Correa, Adolfo Vilalta, Adrian Pirazzini, Chiara Passarino, Giuseppe Monti, Daniela Arosio, Beatrice Garagnani, Paolo Franceschi, Claudio Horvath, Steve University of California Department of Pediatrics Division of Genetics and Genomic Medicine Irvine USA (GRID:grid.266093.8) (ISNI:0000 0001 0668 7243) Betterhumans Inc. Gainesville USA (GRID:grid.266093.8) University of Ferrara Department of Chemical Pharmaceutical and Agricultural Sciences Ferrara Italy (GRID:grid.8484.0) (ISNI:0000 0004 1757 2064) University of California Los Angeles Medical Informatics David Geffen School of Medicine Los Angeles USA (GRID:grid.19006.3e) (ISNI:0000 0000 9632 6718) Harvard Medical School Department of Genetics Boston USA (GRID:grid.38142.3c) (ISNI:***) Wyss Institute for Biologically Inspired Engineering Harvard University Cambridge USA (GRID:grid.38142.3c) (ISNI:***) Telocyte LLC Grand Rapids USA (GRID:grid.38142.3c) Stanford University Epidemiology & Population Health and Medicine School of Medicine Stanford USA (GRID:grid.168010.e) (ISNI:***) Universidad de Costa Rica Centro Centroamericano de Población San Pedro Costa Rica (GRID:grid.412889.e) (ISNI:0000 0004 1937 0706) University of British Columbia Edwin S.H. Leong Healthy Aging Program Centre for Molecular Medicine and Therapeutics Vancouver Canada (GRID:grid.17091.3e) (ISNI:0000 0001 2288 9830) University of California Los Angeles Dept. of Human Genetics David Geffen School of Medicine Los Angeles USA (GRID:grid.19006.3e) (ISNI:0000 0000 9632 6718) Altos Labs San Diego USA (GRID:grid.518162.9) (ISNI:0000 0005 0774 3285) University of California Los Angeles Dept. of Biostatistics Fielding School of Public Health Los Angeles USA (GRID:grid.19006.3e) (ISNI:0000 0000 9632 6718) Zymo Research Corp Irvine USA (GRID:grid.19006.3e) University of Surabaya Department of Biology Faculty of Biotechnology Surabaya Indonesia (GRID:grid.444430.3) (ISNI:0000 0000 8739 9595) Public Health Sciences Division Fred Hutchinson Cancer Research Center Seattle USA (GRID:grid.270240.3) (ISNI:0000 0001 2180 1622) University of Mississippi Medical Center Medicine and Population Health Science Ja

Claims surrounding exceptional longevity are sometimes disputed or dismissed for lack of credible evidence. Here, we present three DNA methylation-based age estimators (epigenetic clocks) for verifying age claims of centenarians. The three centenarian clocks were developed based on n = 7039 blood and saliva samples from individuals older than 40, including n = 184 samples from centenarians, 122 samples from semi-supercentenarians (aged 105 +), and 25 samples from supercentenarians (aged 110 +). The oldest individual was 115 years old. Our most accurate centenarian clock resulted from applying a neural network model to a training set composed of individuals older than 40. An epigenome-wide association study of age in different age groups revealed that age effects in young individuals (age < 40) are correlated (r = 0.55) with age effects in old individuals (age > 90). We present a chromatin state analysis of age effects in centenarians. The centenarian clocks are expected to be useful for validating claims surrounding exceptional old age.

关键词： Centenarian clocks Epigenetic clocks Longevity

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Author Correction: A consensus protocol for functional connectivity analysis in the rat brain

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Nature neuroscience 2023年 2023 Apr 18页

作者： Joanes Grandjean Gabriel Desrosiers-Gregoire Cynthia Anckaerts Diego Angeles-Valdez Fadi Ayad David A Barrière Ines Blockx Aleksandra Bortel Margaret Broadwater Beatriz M Cardoso Marina Célestine Jorge E Chavez-Negrete Sangcheon Choi Emma Christiaen Perrin Clavijo Luis Colon-Perez Samuel Cramer Tolomeo Daniele Elaine Dempsey Yujian Diao Arno Doelemeyer David Dopfel Lenka Dvořáková Claudia Falfán-Melgoza Francisca F Fernandes Caitlin F Fowler Antonio Fuentes-Ibañez Clément M Garin Eveline Gelderman Carla E M Golden Chao C G Guo Marloes J A G Henckens Lauren A Hennessy Peter Herman Nita Hofwijks Corey Horien Tudor M Ionescu Jolyon Jones Johannes Kaesser Eugene Kim Henriette Lambers Alberto Lazari Sung-Ho Lee Amanda Lillywhite Yikang Liu Yanyan Y Liu Alejandra López-Castro Xavier López-Gil Zilu Ma Eilidh MacNicol Dan Madularu Francesca Mandino Sabina Marciano Matthew J McAuslan Patrick McCunn Alison McIntosh Xianzong Meng Lisa Meyer-Baese Stephan Missault Federico Moro Daphne M P Naessens Laura J Nava-Gomez Hiroi Nonaka Juan J Ortiz Jaakko Paasonen Lore M Peeters Mickaël Pereira Pablo D Perez Marjory Pompilus Malcolm Prior Rustam Rakhmatullin Henning M Reimann Jonathan Reinwald Rodrigo Triana Del Rio Alejandro Rivera-Olvera Daniel Ruiz-Pérez Gabriele Russo Tobias J Rutten Rie Ryoke Markus Sack Piergiorgio Salvan Basavaraju G Sanganahalli Aileen Schroeter Bhedita J Seewoo Erwan Selingue Aline Seuwen Bowen Shi Nikoloz Sirmpilatze Joanna A B Smith Corrie Smith Filip Sobczak Petteri J Stenroos Milou Straathof Sandra Strobelt Akira Sumiyoshi Kengo Takahashi Maria E Torres-García Raul Tudela Monica van den Berg Kajo van der Marel Aran T B van Hout Roberta Vertullo Benjamin Vidal Roël M Vrooman Victora X Wang Isabel Wank David J G Watson Ting Yin Yongzhi Zhang Stefan Zurbruegg Sophie Achard Sarael Alcauter Dorothee P Auer Emmanuel L Barbier Jürgen Baudewig Christian F Beckmann Nicolau Beckmann Guillaume J P C Becq Erwin L A Blezer Radu Bolbos Susann Boretius Sandrine Bouvard Eike Budinger Joseph D Buxbaum Diana Cash Victor Donders Institute for Brain Behaviour and Cognition Radboud University Nijmegen The Netherlands. joanes.grandjean@radboudumc.nl. Department for Medical Imaging Radboud University Medical Center Nijmegen The Netherlands. joanes.grandjean@radboudumc.nl. Cerebral Imaging Centre Douglas Mental Health University Institute Verdun QC Canada. Integrated Program in Neuroscience McGill University Montreal QC Canada. Bio-imaging Lab University of Antwerp Antwerp Belgium. µNEURO Research Centre of Excellence University of Antwerp Antwerp Belgium. Instituto de Neurobiología Universidad Nacional Autónoma de México Campus Juriquilla Querétaro Mexico. Biological and Biomedical Engineering McGill University Montreal QC Canada. McConnell Brain Imaging Centre McGill University Montreal QC Canada. Montreal Neurological Institute McGill University Montreal QC Canada. UMR INRAE/CNRS 7247 Physiologie des Comportements et de la Reproduction Physiologie de la reproduction et des comportements Centre de recherche INRAE de Nouzilly Tours France. Department of Neurology and Neurosurgery McGill University Montreal QC Canada. Center for Animal MRI University of North Carolina at Chapel Hill Chapel Hill NC USA. Department of Neurology University of North Carolina at Chapel Hill Chapel Hill NC USA. Biomedical Research Imaging Center University of North Carolina at Chapel Hill Chapel Hill NC USA. Preclinical MRI Champalimaud Research Champalimaud Centre for the Unknown Lisbon Portugal. Laboratoire des Maladies Neurodégénératives Molecular Imaging Research Center (MIRCen) Université Paris-Saclay Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA) CNRS Fontenay-aux-Roses France. Departamento de Neurobiología Conductual y Cognitiva Instituto de Neurobiología Universidad Nacional Autónoma de México Campus Juriquilla Querétaro México. Translational Neuroimaging and Neural Control Group High-Field Magnetic Resonance Max Planck Institute for Biological Cyberneti

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Characterization of the complete mitochondrial genome of Mauritian sardinella, Sardinella jussieu (Lacepède, 1803), collected in the Banten Bay, Indonesia

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Fisheries and Aquatic Sciences 2017年第1期20卷 26.1-26.9页

作者： Sektiana, Sinar Pagi Andriyono, Sapto Kim, Hyun-Woo Pukyong National University Interdisciplinary Program of Biomedical Mechanical and Electrical Engineering Busan 48513 South Korea Pukyong National University Department of Marine Biology Busan 48513 South Korea Jakarta Fisheries University Aquaculture Technology Study Program Jl. AUP Pasar Minggu Jakarta Selatan Jakarta 12520 Indonesia Fisheries and Marine Faculty C Campus Jl. Mulyorejo Surabaya 60115 Indonesia Universitas Airlangga Surabaya East Java Indonesia

Fishes in genus Sardinella are small pelagic species, which plays an important role in marine ecosystem as the first consumer. Those species are also commercially important, whose total catch reaches 278,600 tons in 2011 in Indonesia, but their identification has been difficult for their morphological similarity. In this study, we reported Sardinella jussieu for the first time in Indonesian coastal area (Banten Bay, Indonesia, 6° 0' 50.00" S-106° 10' 21.00" E). We were able to confirm the species by both its morphological characteristics including the black spot at dorsal fin origin, the dusky pigmentation at caudal fin, 31 total scute numbers, and DNA sequence identity in the GenBank database by the molecular analysis. Its total mitochondrial genome was determined by the combination of next-generation sequencing and typical PCR strategy. The total mitochondrial genome of Sardinella jussieu (16,695 bp) encoded 13 proteins, 2 ribosomal RNAs, 22 transfer RNAs, and the putative control region. All protein-coding genes started with ATG and typical stop codon and ended with TAA or TAG except for ND4 in which AGA is used. Phylogenetic analyses of both COI region and full mitochondrial genome showed that S. jussieu is most closely related to Sardinella albella and Sardinella gibbosa. © 2017 The Author(s).

关键词： Barcode Indonesia Mitochondrial genome Next-generation sequencing Sardinella

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The IBEX Knowledge-Base: Achieving more together with open science

arXiv

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arXiv 2024年

作者： Radtke, Andrea J. Anidi, Ifeanyichukwu Arakkal, Leanne Arroyo-Mejias, Armando Beuschel, Rebecca T. Börner, Katy Chu, Colin J. Clark, Beatrice Clatworthy, Menna R. Colautti, Jake Croteau, Joshua Denha, Saven Dever, Rose Dutra, Walderez O. Fritzsche, Sonja Fullam, Spencer Gerner, Michael Y. Gola, Anita Gollob, Kenneth J. Hernandez, Jonathan M. Hor, Jyh Liang Ichise, Hiroshi Jing, Zhixin Jonigk, Danny Kandov, Evelyn Kastenmüller, Wolfgang Koenig, Joshua F.E. Kothurkar, Aanandita Kreins, Alexandra Y. Lamborn, Ian Lin, Yuri Morais, Katia Luciano Pereira Lunich, Aleksandra Luz, Jean C.S. MacDonald, Ryan B. Makranz, Chen Maltez, Vivien I. Moriaty, Ryan V. Ocampo-Godinez, Juan M. Olyntho, Vitoria M. Padhan, Kartika Remmert, Kirsten Richoz, Nathan Schrom, Edward C. Shang, Wanjing Shi, Lihong Shih, Rochelle M. Speranza, Emily Stierli, Salome Teichmann, Sarah A. Veres, Tibor Z. Vierhout, Megan Wachter, Brianna T. Wade-Vallance, Adam K. Williams, Margaret Zangger, Nathan Germain, Ronald N. Yaniv, Ziv Lymphocyte Biology Section Center for Advanced Tissue Imaging Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health BethesdaMD United States Critical Care Medicine and Pulmonary Branch National Heart Lung and Blood Institute National Institutes of Health BethesdaMD United States Lymphocyte Biology Section Laboratory of Immune System Biology National Institute of Allergy and Infectious Diseases National Institutes of Health BethesdaMD United States Department of Intelligent Systems Engineering Indiana University BloomingtonIN United States UCL Institute of Ophthalmology NIHR Moorfields Biomedical Research Centre London United Kingdom Cambridge Institute for Therapeutic Immunology and Infectious Diseases University of Cambridge Department of Medicine Molecular Immunity Unit Laboratory of Molecular Biology Cambridge United Kingdom McMaster Immunology Research Centre Schroeder Allergy and Immunology Research Institute Department of Medicine Faculty of Health Sciences McMaster University HamiltonON Canada Department of Business Development BioLegend Inc. San DiegoCA United States Functional Immunogenomics Unit National Institute of Arthritis and Musculoskeletal and Skin Diseases National Institutes of Health BethesdaMD United States Laboratory of Cell-Cell Interactions Department of Morphology Institute of Biological Sciences Universidade Federal de Minas Gerais MG Belo Horizonte Brazil Spatial Proteomics Group Berlin Germany Division of Rheumatology Rush University Medical Center ChicagoIL United States Department of Immunology University of Washington School of Medicine SeattleWA United States Robin Chemers Neustein Laboratory of Mammalian Cell Biology and Development The Rockefeller University New YorkNY United States Hospital Israelita Albert Einstein SP Sao Paulo Brazil Surgical Oncology Program National Cancer Institute National Institutes of Health BethesdaMD United St

Iterative Bleaching Extends multipleXity (IBEX) is a versatile method for highly multiplexed imaging of diverse tissues. Based on open science principles, we created the IBEX Knowledge-Base, a resource for reagents, p... 详细信息

关键词： Cleaning

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QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results

arXiv

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arXiv 2021年

作者： Mehta, Raghav Filos, Angelos Baid, Ujjwal Sako, Chiharu McKinley, Richard Rebsamen, Michael Dätwyler, Katrin Meier, Raphael Radojewski, Piotr Murugesan, Gowtham Krishnan Nalawade, Sahil Ganesh, Chandan Wagner, Ben Yu, Fang F. Fei, Baowei Madhuranthakam, Ananth J. Maldjian, Joseph A. Daza, Laura Gómez, Catalina Arbeláez, Pablo Dai, Chengliang Wang, Shuo Reynaud, Hadrien Mo, Yuanhan Angelini, Elsa Guo, Yike Bai, Wenjia Banerjee, Subhashis Pei, Linmin Murat, A.K. Rosas-González, Sarahi Zemmoura, Ilyess Tauber, Clovis Vu, Minh H. Nyholm, Tufve Löfstedt, Tommy Ballestar, Laura Mora Vilaplana, Veronica McHugh, Hugh Talou, Gonzalo Maso Wang, Alan Patel, Jay Chang, Ken Hoebel, Katharina Gidwani, Mishka Arun, Nishanth Gupta, Sharut Aggarwal, Mehak Singh, Praveer Gerstner, Elizabeth R. Kalpathy-Cramer, Jayashree Boutry, Nicolas Huard, Alexis Vidyaratne, Lasitha Rahman, Md Monibor Iftekharuddin, Khan M. Chazalon, Joseph Puybareau, Elodie Tochon, Guillaume Ma, Jun Cabezas, Mariano Llado, Xavier Oliver, Arnau Valencia, Liliana Valverde, Sergi Amian, Mehdi Soltaninejad, Mohammadreza Myronenko, Andriy Hatamizadeh, Ali Feng, Xue Dou, Quan Tustison, Nicholas Meyer, Craig Shah, Nisarg A. Talbar, Sanjay Weber, Marc-André Mahajan, Abhishek Jakab, Andras Wiest, Roland Fathallah-Shaykh, Hassan M. Nazeri, Arash Milchenko, Mikhail Marcus, Daniel Kotrotsou, Aikaterini Colen, Rivka Freymann, John Kirby, Justin Davatzikos, Christos Menze, Bjoern Bakas, Spyridon Gal, Yarin Arbel, Tal McGill University MontrealQC Canada Group University of Oxford Oxford United Kingdom University of Pennsylvania PhiladelphiaPA United States Department of Radiology Perelman School of Medicine The University of Pennsylvania PhiladelphiaPA United States Department of Pathology and Laboratory Medicine Perelman School of Medicine University of Pennsylvania PhiladelphiaPA United States University Institute of Diagnostic and Interventional Neuroradiology University of Bern Inselspital Bern University Hospital Bern Switzerland Department of Radiology University of Texas Southwestern Medical Center DallasTX United States Department of Bioengineering University of Texas DallasTX United States Advanced Imaging Research Center University of Texas Southwestern Medical Center DallasTX United States Universidad de los Andes Bogotá Colombia Data Science Institute Imperial College London London United Kingdom NIHR Imperial BRC ITMAT Data Science Group Imperial College London London United Kingdom Department of Brain Sciences Imperial College London London United Kingdom Machine Intelligence Unit Indian Statistical Institute Kolkata India Department of CSE University of Calcutta Kolkata India Department of Information Technology Uppsala University Uppsala Sweden Department of Diagnostic Radiology The University of Pittsburgh Medical Center PittsburghPA United States UMR U1253 iBrain Université de Tours Inserm Tours France Department of Radiation Sciences Umeå University Umeå Sweden Department of Computing Science Umeå University Umeå Sweden Signal Theory and Communications Department Universitat Politècnica de Catalunya Barcelona Tech Barcelona Spain Faculty of Medical and Health Sciences University of Auckland Auckland New Zealand Radiology Department Auckland City Hospital Auckland New Zealand Auckland Bioengineering Institute University of Auckland New Zealand Athinoula A. Martinos Center for Biomedical Imaging Department of Radiology

Deep learning (DL) models have provided state-of-the-art performance in various medical imaging benchmarking challenges, including the Brain Tumor Segmentation (BraTS) challenges. However, the task of focal pathology multi-compartment segmentation (e.g., tumor and lesion sub-regions) is particularly challenging, and potential errors hinder translating DL models into clinical workflows. Quantifying the reliability of DL model predictions in the form of uncertainties could enable clinical review of the most uncertain regions, thereby building trust and paving the way toward clinical translation. Several uncertainty estimation methods have recently been introduced for DL medical image segmentation tasks. Developing scores to evaluate and compare the performance of uncertainty measures will assist the end-user in making more informed decisions. In this study, we explore and evaluate a score developed during the BraTS 2019 and BraTS 2020 task on uncertainty quantification (QU-BraTS) and designed to assess and rank uncertainty estimates for brain tumor multi-compartment segmentation. This score (1) rewards uncertainty estimates that produce high confidence in correct assertions and those that assign low confidence levels at incorrect assertions, and (2) penalizes uncertainty measures that lead to a higher percentage of under-confident correct assertions. We further benchmark the segmentation uncertainties generated by 14 independent participating teams of QU-BraTS 2020, all of which also participated in the main BraTS segmentation task. Overall, our findings confirm the importance and complementary value that uncertainty estimates provide to segmentation algorithms, highlighting the need for uncertainty quantification in medical image analyses. Finally, in favor of transparency and reproducibility, our evaluation code is made publicly available at https://***/RagMeh11/QU-BraTS. © 2021, CC BY.

关键词： Benchmarking

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Toward an automatic system for computer-aided assessment in facial palsy

arXiv

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arXiv 2019年

作者： Guarin, Diego L. Yunusova, Yana Taati, Babak Dusseldorp, Joseph R. Mohan, Suresh Tavares, Joana van Veen, Martinus M. Fortier, Emily Hadlock, Tessa A. Jowett, Nate KITE Toronto Rehabilitation Institute University Health Network TorontoON Canada Department of Otolaryngology/Head and Neck Surgery Massachusetts Eye and Ear Infirmary Harvard Medical School Boston United States Department of Speech Language Pathology University of Toronto TorontoON Canada Hurvitz Brain Sciences Program Sunnybrook Research Institute ON Canada Department of Computer Science University of Toronto TorontoON Canada Institute of Biomaterials and Biomedical Engineering University of Toronto TorontoON Canada Department of Plastic and Reconstructive Surgery Royal Australasian College of Surgeons University of Sydney Sydney Australia Faculty of Health Sciences Brasilia University Brasilia Brazil

Importance: Quantitative assessment of facial function is challenging, and subjective grading scales such as House-Brackmann, Sunnybrook, and eFACE have well-recognized limitations. Machine learning approaches to facial landmark localization carry great clinical potential as they enable high-throughput automated quantification of relevant facial metrics from photographs and videos. However, the translation from research settings to clinical application still requires important improvements. Objective: To develop a novel machine learning algorithm for fast and accurate localization of facial landmarks in photographs of facial palsy patients and utilize this technology as part of an automated computer-aided diagnosis system. Design, Setting, and Participants: Portrait photographs of eight expressions obtained from 200 facial palsy patients and 10 healthy participants were manually annotated, by localizing 68 facial landmarks in each photograph, by three trained clinicians using a custom graphical user interface. A novel machine learning model for automated facial landmark localization was trained using this disease-specific database. Algorithm accuracy was compared to manual markings and the output of a model trained using a larger database consisting only of healthy subjects. Main Outcomes and measurements: Root mean square error normalized by the inter-ocular distance (NRMSE) of facial landmark localization between prediction of machine learning algorithm and manually localized landmarks. Results: Publicly available algorithms for facial landmark localization provide poor localization accuracy when applied to photographs of patients compared to healthy controls (NRMSE, 8.56 ± 2.16 vs. 7.09 ± 2.34, p Copyright © 2019, The Authors. All rights reserved.

关键词： Photography

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Author Correction: Stretchable, dynamic covalent polymers for soft, long-lived bioresorbable electronic stimulators designed to facilitate neuromuscular regeneration

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Nature communications 2021年第1期12卷 415页

作者： Yeon Sik Choi Yuan-Yu Hsueh Jahyun Koo Quansan Yang Raudel Avila Buwei Hu Zhaoqian Xie Geumbee Lee Zheng Ning Claire Liu Yameng Xu Young Joong Lee Weikang Zhao Jun Fang Yujun Deng Seung Min Lee Abraham Vázquez-Guardado Iwona Stepien Ying Yan Joseph W Song Chad Haney Yong Suk Oh Wentai Liu Hong-Joon Yoon Anthony Banks Matthew R MacEwan Guillermo A Ameer Wilson Z Ray Yonggang Huang Tao Xie Colin K Franz Song Li John A Rogers Center for Bio-Integrated Electronics Northwestern University Evanston IL 60208 USA. Querrey Simpson Institute for Biotechnology Northwestern University Evanston IL 60208 USA. Department of Materials Science and Engineering Northwestern University Evanston IL 60208 USA. Department of Bioengineering University of California Los Angeles Los Angeles CA 90095 USA. Division of Plastic and Reconstructive Surgery Department of Surgery National Cheng Kung University Hospital College of Medicine National Cheng Kung University Tainan 70456 Taiwan. International Research Center for Wound Repair and Regeneration National Cheng Kung University Tainan 70456 Taiwan. School of Biomedical Engineering Korea University Seoul 02841 Republic of Korea. Interdisciplinary Program in Precision Public Health Korea University Seoul 02841 Republic of Korea. Department of Mechanical Engineering Northwestern University Evanston IL 60208 USA. Department of Medicine University of California Los Angeles Los Angeles CA 90095 USA. State Key Laboratory of Structural Analysis for Industrial Equipment Dalian University of Technology 116024 Dalian China. Department of Engineering Mechanics Dalian University of Technology 116024 Dalian China. International Research Center for Computational Mechanics Dalian University of Technology 116024 Dalian China. State Key Laboratory of Chemical Engineering College of Chemical and Biological Engineering Zhejiang University 310027 Hangzhou China. Department of Biomedical Engineering Northwestern University Evanston IL 60208 USA. State Key Laboratory of Mechanical System and Vibration Shanghai Jiao Tong University 200240 Shanghai China. Center for Developmental Therapeutics Chemistry Life Processes Institute Northwestern University Evanston IL 60208 USA. Department of Neurological Surgery Washington University School of Medicine St. Louis MO 63110 USA. Center for Advanced Molecular Imaging Northwestern University Evanston IL

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Author Correction: Apoptotic stress causes mtDNA release during senescence and drives the SASP

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Nature 2024年第7995期625卷 E15页

作者： Stella Victorelli Hanna Salmonowicz James Chapman Helene Martini Maria Grazia Vizioli Joel S Riley Catherine Cloix Ella Hall-Younger Jair Machado Espindola-Netto Diana Jurk Anthony B Lagnado Lilian Sales Gomez Joshua N Farr Dominik Saul Rebecca Reed George Kelly Madeline Eppard Laura C Greaves Zhixun Dou Nicholas Pirius Karolina Szczepanowska Rebecca A Porritt Huijie Huang Timothy Y Huang Derek A Mann Claudio Akio Masuda Sundeep Khosla Haiming Dai Scott H Kaufmann Emmanouil Zacharioudakis Evripidis Gavathiotis Nathan K LeBrasseur Xue Lei Alva G Sainz Viktor I Korolchuk Peter D Adams Gerald S Shadel Stephen W G Tait João F Passos Department of Physiology and Biomedical Engineering Mayo Clinic Rochester MN USA. Robert and Arlene Kogod Center on Aging Mayo Clinic Rochester MN USA. Biosciences Institute Faculty of Medical Sciences Campus for Ageing and Vitality Newcastle University Newcastle upon Tyne UK. ReMedy International Research Agenda Unit IMol Polish Academy of Sciences Warsaw Poland. Cancer Research UK Scotland Institute Glasgow UK. School of Cancer Sciences University of Glasgow Glasgow UK. Institute of Developmental Immunology Biocenter Medical University of Innsbruck Innsbruck Austria. Wellcome Centre for Mitochondrial Research Biosciences Institute Newcastle University Newcastle upon Tyne UK. Center for Regenerative Medicine Department of Medicine Massachusetts General Hospital Boston MA USA. Harvard Stem Cell Institute Harvard University Cambridge MA USA. Sanford Burnham Prebys Medical Discovery Institute La Jolla CA USA. Degenerative Diseases Program Sanford Burnham Prebys Medical Discovery Institute La Jolla CA USA. Newcastle Fibrosis Research Group Biosciences Institute Newcastle University Newcastle upon Tyne UK. Department of Gastroenterology and Hepatology School of Medicine Koç University Istanbul Turkey. Instituto de Bioquímica Médica Leopoldo de Meis Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil. Division of Oncology Research and Department of Molecular Pharmacology and Experimental Therapeutics Mayo Clinic Rochester MN USA. Department of Biochemistry Department of Medicine Montefiore Einstein Cancer Center Wilf Family Cardiovascular Research Institute Institute for Aging Research Albert Einstein College of Medicine New York NY USA. Cancer Genome and Epigenetics Program Sanford Burnham Prebys Medical Discovery Institute La Jolla CA USA. Salk Institute for Biological Studies La Jolla CA USA. Department of Pathology Yale University School of Medicine New Haven CT USA. Cancer Research UK Scotland Institute Glasgow UK. Stephen.T

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