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Non-invasive biopsy diagnosis of diabetic kidney disease via deep learning applied to retinal images: a population-based study

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The Lancet Digital Health 2025年第5期7卷 100868页

作者： Meng, Ziyao Guan, Zhouyu Yu, Shujie Wu, Yilan Zhao, Yaoning Shen, Jie Lim, Cynthia Ciwei Chen, Tingli Yang, Dawei Ran, An Ran He, Feng Hamzah, Haslina Singh, Sarkaaj Abd Raof, Anis Syazwani Lee-Boey, Jian Wen Samuel Lim, Soo-Kun Sun, Xufang Ge, Shuwang Xu, Gang Su, Hua Cheng, Yang Lu, Feng Liao, Xiaofei Jin, Hai Deng, Chenxin Ruan, Lei Zhang, Cuntai Wu, Chan Dai, Rongping Jin, Yixiao Wang, Wenxiao Li, Tingyao Liu, Ruhan Li, Jiajia Shu, Jia Lu, Yuwei Wang, Xiangning Wu, Qiang Qin, Yiming Tang, Jin Sheng, Xiaohua Jiao, Qiong Yang, Xiaokang Guo, Minyi McKay, Gareth J Hogg, Ruth E Liew, Gerald Chee, Evelyn Yi Lyn Hsu, Wynne Lee, Mong Li Szeto, Simon Luk, Andrea O Y Chan, Juliana C N Cheung, Carol Y Tan, Gavin Siew Wei Tham, Yih-Chung Cheng, Ching-Yu Sabanayagam, Charumathi Lim, Lee-Ling Jia, Weiping Li, Huating Sheng, Bin Wong, Tien Yin Shanghai Belt and Road International Joint Laboratory of Intelligent Prevention and Treatment for Metabolic Diseases Department of Computer Science and Engineering School of Electronic Information and Electrical Engineering Institute for Proactive Healthcare Shanghai Jiao Tong University Department of Endocrinology and Metabolism Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai Diabetes Institute Shanghai Clinical Centre for Diabetes Shanghai Key Laboratory of Diabetes Mellitus Shanghai China MOE Key Laboratory of AI School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai China Beijing Tsinghua Changgung Hospital Eye Center School of Clinical Medicine Tsinghua Medicine Tsinghua University Beijing China Medical Records and Statistics Office Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Shanghai China Department of Renal Medicine Singapore General Hospital SingHealth-Duke Academic Medical Centre Singapore Singapore Department of Ophthalmology Shanghai Health and Medical Center Wuxi China Department of Ophthalmology and Visual Sciences The Chinese University of Hong Kong Hong Kong Special Administrative Region China Singapore Eye Research Institute Singapore National Eye Centre Singapore Department of Medicine Faculty of Medicine Universiti Malaya Kuala Lumpur Malaysia Department of Ophthalmology Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Hubei Wuhan China Department of Nephrology Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan China Department of Nephrology Union Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan China Department of Ophthalmology Union Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan China National Engineering Research Centre for Big Dat

Background: Improving the accessibility of screening diabetic kidney disease (DKD) and differentiating isolated diabetic nephropathy from non-diabetic kidney disease (NDKD) are two major challenges in the field of diabetes care. We aimed to develop and validate an artificial intelligence (AI) deep learning system to detect DKD and isolated diabetic nephropathy from retinal fundus images. Methods: In this population-based study, we developed a retinal image-based AI-deep learning system, DeepDKD, pretrained using 734 084 retinal fundus images. First, for DKD detection, we used 486 312 retinal images from 121 578 participants in the Shanghai Integrated Diabetes Prevention and Care System for development and internal validation, and ten multi-ethnic datasets from China, Singapore, Malaysia, Australia, and the UK (65 406 participants) for external validation. Second, to differentiate isolated diabetic nephropathy from NDKD, we used 1068 retinal images from 267 participants for development and internal validation, and three multi-ethnic datasets from China, Malaysia, and the UK (244 participants) for external validation. Finally, we conducted two proof-of-concept studies: a prospective real-world study with 3 months' follow-up to evaluate the effectiveness of DeepDKD in screening DKD;and a longitudinal analysis of the effectiveness of DeepDKD in differentiating isolated diabetic nephropathy from NDKD on renal function changes with 4·6 years' follow-up. Findings: For detecting DKD, DeepDKD achieved an area under the receiver operating characteristic curve (AUC) of 0·842 (95% CI 0·838–0·846) on the internal validation dataset and AUCs of 0·791–0·826 across external validation datasets. For differentiating isolated diabetic nephropathy from NDKD, DeepDKD achieved an AUC of 0·906 (0·825–0·966) on the internal validation dataset and AUCs of 0·733–0·844 across external validation datasets. In the prospective study, compared with the metadata model, DeepDKD could detect DKD wit

关键词： Deep learning

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CMRxRecon2024: A Multi-Modality, Multi-View K-Space dataset Boosting Universal Machine Learning for Accelerated Cardiac MRI

arXiv

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arXiv 2024年

作者： Wang, Zi Wang, Fanwen Qin, Chen Lyu, Jun Ouyang, Cheng Wang, Shuo Li, Yan Yu, Mengyao Zhang, Haoyu Guo, Kunyuan Shi, Zhang Li, Qirong Xu, Ziqiang Zhang, Yajing Li, Hao Hua, Sha Chen, Binghua Sun, Longyu Sun, Mengting Li, Qin Chu, Ying-Hua Bai, Wenjia Qin, Jing Zhuang, Xiahai Prieto, Claudia Young, Alistair Markl, Michael Wang, He Wu, Lianming Yang, Guang Qu, Xiaobo Wang, Chengyan Department of Electronic Science Fujian Provincial Key Laboratory of Plasma and Magnetic Resonance National Institute for Data Science in Health and Medicine Xiamen University Xiamen China Department of Bioengineering and Imperial-X Imperial College London London United Kingdom Cardiovascular Research Centre Royal Brompton Hospital London United Kingdom Department of Electrical and Electronic Engineering & Imperial-X Imperial College London London United Kingdom Psychiatry Neuroimaging Laboratory Brigham and Women’s Hospital Harvard Medical School Boston United States Department of Computing Department of Brain Sciences Imperial College London London United Kingdom Digital Medical Research Center School of Basic Medical Sciences Fudan University Shanghai China Department of Radiology Ruijin Hospital Shanghai Jiao Tong University School of Medicine Shanghai China Human Phenome Institute Fudan University Shanghai China Department of Radiology Zhongshan Hospital Fudan University Shanghai China School of Health Science and Engineering University of Shanghai for Science and Technology Shanghai China GE Healthcare Beijing China Institute of Science and Technology for Brain-Inspired Intelligence Fudan University Shanghai China Department of Cardiovascular Medicine Ruijin Hospital Lu Wan Branch Shanghai Jiao Tong University School of Medicine Shanghai China Department of Radiology Ren Ji Hospital School of Medicine Shanghai Jiao Tong University Shanghai China Siemens Healthineers Ltd. Shanghai China School of Nursing The Hong Kong Polytechnic University Hong Kong School of Data Science Fudan University Shanghai China School of Engineering Pontificia Universidad Católica de Chile Santiago Chile School of Biomedical Engineering and Imaging Sciences King’s College London London United Kingdom Millenium Institute for Intelligent Healthcare Engineering Santiago Chile Department of Radiology Feinberg School of Medicine Northwestern University Chicago Unit

The released CMRxRecon2024 dataset is currently the largest and most protocol-diverse publicly available k-space dataset including multi-modality and multi-view cardiac MRI data from 330 healthy volunteers, and each o... 详细信息

关键词： Adversarial machine learning

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Gut microbiota and diabetes: From correlation to causality and mechanism

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World Journal of Diabetes 2020年第7期11卷 293-308页

作者： Wei-Zheng Li Kyle Stirling Jun-Jie Yang Lei Zhang Microbiome-X Beijing Advanced Innovation Center for Big Data-Based Precision MedicineSchool of Medicine and EngineeringKey Laboratory of Big Data-Based Precision MedicineBeihang UniversityBeijing 100191China School of Biological Science and Medical Engineering Beihang UniversityBeijing 100191China Luddy School of Informatics Computing and EngineeringIndiana UniversityBloomingtonIN 47408United States The Crisis Technologies Innovation Lab Indiana UniversityThe Information Technology Services and the Pervasive Technology InstituteBloomingtonIN 47408United States Shandong Institute of Industrial Technology for Health Sciences and Precision Medicine Jinan 250000Shandong ProvinceChina College of Life Science Qilu Normal UniversityJinan 250000Shandong ProvinceChina Microbiome Research Center Shandong Institutes for Food and Drug ControlJinan 250000Shandong ProvinceChina Shandong Children’s Microbiome Center Qilu Children's Hospital of Shandong UniversityJinan 250000Shandong ProvinceChina Microbiological Laboratory Lin Yi People’s HospitalLinyi 276000Shandong ProvinceChina Qingdao Human Microbiome Center The Affiliated Central Hospital of Qingdao UniversityQingdao 266000Shandong ProvinceChina Institute for Medical Dataology Cheeloo College of MedicineShandong UniversityJinan 250000Shandong ProvinceChina Department of Biostatistics School of Public HealthCheeloo College of MedicineShandong UniversityJinan 250000Shandong ProvinceChina Shandong Children’s Microbiome Center Research Institute of PediatricsQilu Children's HospitalCheeloo College of MedicineShandong Universityand Jinan Children's HospitalJinan 250022Shandong ProvinceChina

In this review,we summarize the recent microbiome studies related to diabetes disease and discuss the key findings that show the early emerging potential causal roles for *** a global scale,diabetes causes a significant negative impact to the health status of human *** review covers type 1 diabetes and type 2 *** examine promising studies which lead to a better understanding of the potential mechanism of microbiota in diabetes *** appears that the human oral and gut microbiota are deeply interdigitated with *** is that *** studies of the human microbiome are capturing the attention of scientists and healthcare practitioners worldwide by focusing on the interplay of gut microbiome and *** studies focus on the role and the potential impact of intestinal microflora in *** paint a clear picture of how strongly microbes are linked and associated,both positively and negatively,with the fundamental and essential parts of diabetes in *** microflora seems to have an endless capacity to impact and transform *** conclude that there is clear and growing evidence of a close relationship between the microbiota and diabetes and this is worthy of future investments and research efforts.

关键词： Diabetes Microbiota Causality Mechanism Type 1 diabetes Type 2 diabetes Insulin resistance Inflammation Metabolites

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Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

arXiv

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arXiv 2025年

作者： Sun, Yingying Jun, A. Liu, Zhiwei Sun, Rui Qian, Liujia Payne, Samuel H. Bittremieux, Wout Ralser, Markus Li, Chen Chen, Yi Dong, Zhen Perez-Riverol, Yasset Khan, Asif Sander, Chris Aebersold, Ruedi Vizcaíno, Juan Antonio Krieger, Jonathan R. Yao, Jianhua Wen, Han Zhang, Linfeng Zhu, Yunping Xuan, Yue Sun, Benjamin Boyang Qiao, Liang Hermjakob, Henning Tang, Haixu Gao, Huanhuan Deng, Yamin Zhong, Qing Chang, Cheng Bandeira, Nuno Li, Ming Weinan, E. Sun, Siqi Yang, Yuedong Omenn, Gilbert S. Zhang, Yue Xu, Ping Fu, Yan Liu, Xiaowen Overall, Christopher M. Wang, Yu Deutsch, Eric W. Chen, Luonan Cox, Jürgen Demichev, Vadim He, Fuchu Huang, Jiaxing Jin, Huilin Liu, Chao Li, Nan Luan, Zhongzhi Song, Jiangning Yu, Kaicheng Wan, Wanggen Wang, Tai Zhang, Kang Zhang, Le Bell, Peter A. Mann, Matthias Zhang, Bing Guo, Tiannan Affiliated Hangzhou First People’s Hospital State Key Laboratory of Medical Proteomics School of Medicine Westlake University Zhejiang Province Hangzhou China Westlake Center for Intelligent Proteomics Westlake Laboratory of Life Sciences and Biomedicine Zhejiang Province Hangzhou China Biology Department Brigham Young University ProvoUT84602 United States Department of Computer Science University of Antwerp Antwerp2020 Belgium Department of Biochemistry CharitéUniversitätsmedizin Berlin Berlin Germany Biomedicine Discovery Institute Department of Biochemistry and Molecular Biology Monash University MelbourneVICVIC 3800 Australia Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Harvard Medical School Ludwig Center at Harvard United States Harvard Medical School Broad Institute Ludwig Center at Harvard Dana-Farber Cancer Institute United States Department of Biology Institute of Molecular Systems Biology ETH Zürich Zürich Switzerland Bruker Ltd. MiltonONL9T 6P4 Canada AI for Life Sciences Lab Tencent Shenzhen518057 China State Key Laboratory of Medical Proteomics AI for Science Institute Beijing100080 China Beijing Institute of Lifeomics Beijing102206 China Thermo Fisher Scientific GmbH Hanna-Kunath Str. 11 Bremen28199 Germany Informatics and Predictive Sciences Research Bristol Myers Squibb United States Department of Chemistry Fudan University Songhu Road 2005 Shanghai200438 China Department of Computer Science Luddy School of Informatics Computing and Engineering Indiana University IN47408 United States ProCan® Children’s Medical Research Institute Faculty of Medicine and Health The University of Sydney WestmeadNSW Australia La Jolla CA United States Central China Institute of Artificial Intelligence University of Waterloo Canada AI for Science Institute Center for Machine Learning Research School of Mathematical Sciences Peking University China Research Institute of Intelligent Complex Systems Fudan U

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis;improving peptide and protein identification and quantification;characterizing protein-protein interactions and protein complexes;advancing spatial and perturbation proteomics;integrating multi-omics data;and ultimately enabling AI-empowered virtual cells. © 2025, CC BY.

关键词： Biotic

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Radiomics based on dual-energy CT for noninvasive prediction of cervical lymph node metastases in patients with nasopharyngeal carcinoma

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Radiography (London, England : 1995) 2025年第4期31卷 102989页

作者： L Li D Yang Y Wu R Sun Y Qin M Kang X Deng M Bu Z Li Z Zeng X Zeng M Jiang B T Chen Department of Radiology First Affiliated Hospital of Guangxi Medical University Nanning 530021 Guangxi PR China. Department of Radiology Guizhou Provincial People Hospital No.83 East Zhongshan Road Nanming District Guizhou Province 550000 Guiyang PR China Engineering Research Center of Text Computing & Cognitive Intelligence Ministry of Education Key Laboratory of Intelligent Medical Image Analysis and Precise Diagnosis of Guizhou Province State Key Laboratory of Public Big Data College of Computer Science and Technology Guizhou University No. 2870 Huaxi Avenue South Guiyang 550025 Guizhou PR China. Department of Radiology Guizhou Provincial People Hospital No.83 East Zhongshan Road Nanming District Guizhou Province 550000 Guiyang PR China. Department of Nuclear Medicine First Affiliated Hospital of Guangxi Medical University Nanning 530021 Guangxi PR China. Department of Radiation Oncology First Affiliated Hospital of Guangxi Medical University Nanning 530021 Guangxi PR China. Department of Radiology Guizhou Provincial People Hospital No.83 East Zhongshan Road Nanming District Guizhou Province 550000 Guiyang PR China. Electronic address: zengxianchun04@***. Department of Radiology First Affiliated Hospital of Guangxi Medical University Nanning 530021 Guangxi PR China. Electronic address: jmlgxmu@***. Department of Diagnostic Radiology City of Hope National Medical Center Duarte CA USA.

INTRODUCTION:To develop and validate a machine learning model based on dual-energy computed tomography (DECT) for predicting cervical lymph node metastases (CLNM) in patients diagnosed with nasopharyngeal carcinoma (NPC). METHODS:This prospective single-center study enrolled patients with NPC and the study assessment included both DECT and 18F-fluorodeoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT). Radiomics features were extracted from each region of interest (ROI) for cervical lymph nodes using arterial and venous phase images at 100 keV and 150 keV, either individually as non-fusion models or combined as fusion models on the DECT images. The performance of the random forest (RF) models, combined with radiomics features, was evaluated by area under the receiver operating characteristic curve (AUC) analysis. DeLong's test was employed to compare model performances, while decision curve analysis (DCA) assessed the clinical utility of the predictive models. RESULTS:Sixty-six patients with NPC were included for analysis, which was divided into a training set (n = 42) and a validation set (n = 22). A total of 13 radiomic models were constructed (4 non-fusion models and 9 fusion models). In the non-fusion models, when the threshold value exceeded 0.4, the venous phase at 100 keV (V100) (AUC, 0.9667; 95 % confidence interval [95 % CI], 0.9363-0.9901) model exhibited a higher net benefit than other non-fusion models. The V100 + V150 fusion model achieved the best performance, with an AUC of 0.9697 (95 % CI, 0.9393-0.9907). CONCLUSION:DECT-based radiomics effectively diagnosed CLNM in patients with NPC and may potentially be a valuable tool for clinical decision-making. IMPLICATIONS FOR PRACTICE:This study improved pre-operative evaluation, treatment strategy selection, and prognostic evaluation for patients with nasopharyngeal carcinoma by combining DECT and radiomics to predict cervical lymph node status prior to treatment.

关键词： Cervical lymph node metastases (CLNM) Dual-energy computed tomography (DECT) Machine learning model Nasopharyngeal carcinoma (NPC) Radiomics

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Correction: White matter diffusion estimates in obsessive-compulsive disorder across 1653 individuals: machine learning findings from the ENIGMA OCD Working Group

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Molecular psychiatry 2024年第4期29卷 1216页

作者： Bo-Gyeom Kim Gakyung Kim Yoshinari Abe Pino Alonso Stephanie Ameis Alan Anticevic Paul D Arnold Srinivas Balachander Nerisa Banaj Nuria Bargalló Marcelo C Batistuzzo Francesco Benedetti Sara Bertolín Jan Carl Beucke Irene Bollettini Silvia Brem Brian P Brennan Jan K Buitelaar Rosa Calvo Miguel Castelo-Branco Yuqi Cheng Ritu Bhusal Chhatkuli Valentina Ciullo Ana Coelho Beatriz Couto Sara Dallaspezia Benjamin A Ely Sónia Ferreira Martine Fontaine Jean-Paul Fouche Rachael Grazioplene Patricia Gruner Kristen Hagen Bjarne Hansen Gregory L Hanna Yoshiyuki Hirano Marcelo Q Höxter Morgan Hough Hao Hu Chaim Huyser Toshikazu Ikuta Neda Jahanshad Anthony James Fern Jaspers-Fayer Selina Kasprzak Norbert Kathmann Christian Kaufmann Minah Kim Kathrin Koch Gerd Kvale Jun Soo Kwon Luisa Lazaro Junhee Lee Christine Lochner Jin Lu Daniela Rodriguez Manrique Ignacio Martínez-Zalacaín Yoshitada Masuda Koji Matsumoto Maria Paula Maziero Jose M Menchón Luciano Minuzzi Pedro Silva Moreira Pedro Morgado Janardhanan C Narayanaswamy Jin Narumoto Ana E Ortiz Junko Ota Jose C Pariente Chris Perriello Maria Picó-Pérez Christopher Pittenger Sara Poletti Eva Real Y C Janardhan Reddy Daan van Rooij Yuki Sakai João Ricardo Sato Cinto Segalas Roseli G Shavitt Zonglin Shen Eiji Shimizu Venkataram Shivakumar Noam Soreni Carles Soriano-Mas Nuno Sousa Mafalda Machado Sousa Gianfranco Spalletta Emily R Stern S Evelyn Stewart Philip R Szeszko Rajat Thomas Sophia I Thomopoulos Daniela Vecchio Ganesan Venkatasubramanian Chris Vriend Susanne Walitza Zhen Wang Anri Watanabe Lidewij Wolters Jian Xu Kei Yamada Je-Yeon Yun Mojtaba Zarei Qing Zhao Xi Zhu Paul M Thompson Willem B Bruin Guido A van Wingen Federica Piras Fabrizio Piras Dan J Stein Odile A van den Heuvel Helen Blair Simpson Rachel Marsh Jiook Cha Department of Psychology College of Social Sciences Seoul National University Seoul Republic of Korea. Department of Brain and Cognitive Sciences College of Natural Sciences Seoul National University Seoul Republic of Korea. Graduate School of Medical Science Kyoto Prefectural University of Medicine Department of Psychiatry Kyoto City Japan. Bellvitge Biomedical Research Insitute-IDIBELL Bellvitge University Hospital Barcelona Spain. CIBER of Mental Health (CIBERSAM) Carlos III Health Institute Madrid Spain. Department of Clinical Sciences University of Barcelona Barcelona Spain. The Margaret and Wallace McCain Centre for Child Youth & Family Mental Health and Campbell Family Mental Health Research Institute Centre for Addiction and Mental Health Toronto ON Canada. Department of Psychiatry University of Toronto Toronto ON Canada. Program in Neurosciences and Mental Health The Hospital for Sick Children Toronto ON Canada. Department of Psychiatry Yale University School of Medicine New Haven CT 06510 USA. The Mathison Centre for Mental Health Research & Education Hotchkiss Brain Institute Cumming School of Medicine University of Calgary Calgary AB Canada. Departments of Psychiatry and Medical Genetics Cumming School of Medicine University of Calgary Calgary AB Canada. OCD clinic Department of Psychiatry National Institute of Mental Health And Neurosciences (NIMHANS) Bangalore India. Laboratory of Neuropsychiatry Department of Clinical and Neuroscience and Neurorehabilitation IRCCS Santa Lucia Foundation Rome Italy. Center of Image Diagnostic Hospital Clínic de Barcelona Barcelona Spain. Magnetic Resonance Image Core Facility Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) Barcelona Spain. Departamento e Instituto de Psiquiatria do Hospital das Clinicas IPQ HCFMUSP Faculdade de Medicina Universidade de Sao Paulo Sao Paulo SP Brazil. Department of Methods and Techniques in Psychology Pontifical Catholic University São Paulo SP

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Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits (vol 50, pg 1412, 2018)

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NATURE GENETICS 2018年第12期50卷 1755-1755页

作者： Evangelou, Evangelos Warren, Helen R. Mosen-Ansorena, David Mifsud, Borbala Pazoki, Raha Gao, He Ntritsos, Georgios Dimou, Niki Cabrera, Claudia P. Karaman, Ibrahim Fu Liang Ng Evangelou, Marina Witkowska, Katarzyna Tzanis, Evan Hellwege, Jacklyn N. Giri, Ayush Edwards, Digna R. Velez Sun, Yan V. Cho, Kelly Gaziano, J. Michael Wilson, Peter W. F. Tsao, Philip S. Kovesdy, Csaba P. Esko, Tonu Magi, Reedik Milani, Lili Almgren, Peter Boutin, Thibaud Debette, Stephanie Ding, Jun Giulianini, Franco Holliday, Elizabeth G. Jackson, Anne U. Li-Gao, Ruifang Lin, Wei-Yu Luan, Jian'an Mangino, Massimo Oldmeadow, Christopher Prins, Bram Peter Qian, Yong Sargurupremraj, Muralidharan Shah, Nabi Surendran, Praveen Theriault, Sebastien Verweij, Niek Willems, Sara M. Zhao, Jing-Hua Amouyel, Philippe Connell, John de Mutsert, Renee Doney, Alex S. F. Farrall, Martin Menni, Cristina Morris, Andrew D. Noordam, Raymond Pare, Guillaume Poulter, Neil R. Shields, Denis C. Stanton, Alice Thom, Simon Abecasis, Goncalo Amin, Najaf Arking, Dan E. Ayers, Kristin L. Barbieri, Caterina M. Batini, Chiara Bis, Joshua C. Blake, Tineka Bochud, Murielle Boehnke, Michael Boerwinkle, Eric Boomsma, Dorret I. Bottinger, Erwin P. Braund, Peter S. Brumat, Marco Campbell, Archie Campbell, Harry Chakravarti, Aravinda Chambers, John C. Chauhan, Ganesh Ciullo, Marina Cocca, Massimiliano Collins, Francis Cordell, Heather J. Davies, Gail de Borst, Martin H. de Geus, Eco J. Deary, Ian J. Deelen, Joris Del Greco, Fabiola M. Demirkale, Cumhur Yusuf Dorr, Marcus Ehret, Georg B. Elosua, Roberto Enroth, Stefan Erzurumluoglu, A. Mesut Ferreira, Teresa Franberg, Mattias Franco, Oscar H. Gandin, Ilaria Gasparini, Paolo Giedraitis, Vilmantas Gieger, Christian Girotto, Giorgia Goel, Anuj Gow, Alan J. Gudnason, Vilmundur Guo, Xiuqing Gyllensten, Ulf Hamsten, Anders Harris, Tamara B. Harris, Sarah E. Hartman, Catharina A. Havulinna, Aki S. Hicks, Andrew A. Hofer, Edith Hofman, Albert Hottenga, Jouke-Jan Huffman, Jennifer E. Hwang, Shih-Jen Ingelsson, Erik James, Alan Jansen Department of Epidemiology and Biostatistics Imperial College London London UK Department of Hygiene and Epidemiology University of Ioannina Medical School Ioannina Greece William Harvey Research Institute Barts and The London School of Medicine and Dentistry Queen Mary University of London London UK National Institute for Health Research Barts Cardiovascular Biomedical Research Center Queen Mary University of London London UK MRC-PHE Centre for Environment and Health Imperial College London London UK Department of Mathematics Imperial College London London UK Division of Epidemiology Department of Medicine Institute for Medicine and Public Health Vanderbilt Genetics Institute Vanderbilt University Medical Center Tennessee Valley Healthcare System (626)/Vanderbilt University Nashville TN USA Vanderbilt Genetics Institute Vanderbilt Epidemiology Center Department of Obstetrics and Gynecology Vanderbilt University Medical Center Tennessee Valley Health Systems VA Nashville TN USA Department of Epidemiology Emory University Rollins School of Public Health Atlanta GA USA Department of Biomedical Informatics Emory University School of Medicine Atlanta GA USA Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) VA Boston Healthcare System Boston MA USA Division of Aging Department of Medicine Brigham and Women’s Hospital Department of Medicine Harvard Medical School Boston MA USA Atlanta VAMC and Emory Clinical Cardiovascular Research Institute Atlanta GA USA VA Palo Alto Health Care System Division of Cardiovascular Medicine Stanford University School of Medicine Stanford CA USA Nephrology Section Memphis VA Medical Center and University of Tennessee Health Science Center Memphis TN USA Estonian Genome Center University of Tartu Tartu Estonia Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA Department Clinical Sciences Malmö Lund University Malmö Sweden MRC Human Genetics Un

High blood pressure is a highly heritable and modifiable risk factor for cardiovascular disease. We report the largest genetic association study of blood pressure traits (systolic, diastolic and pulse pressure) to date in over 1 million people of European ancestry. We identify 535 novel blood pressure loci that not only offer new biological insights into blood pressure regulation but also highlight shared genetic architecture between blood pressure and lifestyle exposures. Our findings identify new biological pathways for blood pressure regulation with potential for improved cardiovascular disease prevention in the future.

关键词： Cardiovascular diseases Genome informatics Genome-wide association studies

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Identifying the best machine learning algorithms for brain tumor segmentation, progression assessment, and overall survival prediction in the BRATS challenge

arXiv

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arXiv 2018年

作者： Bakas, Spyridon Reyes, Mauricio Jakab, Andras Bauer, Stefan Rempfler, Markus Crimi, Alessandro Shinohara, Russell Takeshi Berger, Christoph Ha, Sung Min Rozycki, Martin Prastawa, Marcel Alberts, Esther Lipkova, Jana Freymann, John Kirby, Justin Bilello, Michel Fathallah-Shaykh, Hassan M. Wiest, Roland Kirschke, Jan Wiestler, Benedikt Colen, Rivka Kotrotsou, Aikaterini Lamontagne, Pamela Marcus, Daniel Milchenko, Mikhail Nazeri, Arash Weber, Marc-Andr Mahajan, Abhishek Baid, Ujjwal Gerstner, Elizabeth Kwon, Dongjin Acharya, Gagan Agarwal, Manu Alam, Mahbubul Albiol, Alberto Albiol, Antonio Albiol, Francisco J. Alex, Varghese Allinson, Nigel Amorim, Pedro H.A. Amrutkar, Abhijit Anand, Ganesh Andermatt, Simon Arbel, Tal Arbelaez, Pablo Avery, Aaron Azmat, Muneeza Pranjal, B. Bai, Wenjia Banerjee, Subhashis Barth, Bill Batchelder, Thomas Batmanghelich, Kayhan Battistella, Enzo Beers, Andrew Belyaev, Mikhail Bendszus, Martin Benson, Eze Bernal, Jose Bharath, Halandur Nagaraja Biros, George Bisdas, Sotirios Brown, James Cabezas, Mariano Cao, Shilei Cardoso, Jorge M. Carver, Eric N. Casamitjana, Adri Castillo, Laura Silvana Cat, Marcel Cattin, Philippe Cérigues, Albert Chagas, Vinicius S. Chandra, Siddhartha Chang, Yi-Ju Chang, Shiyu Chang, Ken Chazalon, Joseph Chen, Shengcong Chen, Wei Chen, Jefferson W. Chen, Zhaolin Cheng, Kun Choudhury, Ahana Roy Chylla, Roger Clrigues, Albert Colleman, Steven Colmeiro, Ramiro German Rodriguez Combalia, Marc Costa, Anthony Cui, Xiaomeng Dai, Zhenzhen Dai, Lutao Daza, Laura Alexandra Deutsch, Eric Ding, Changxing Dong, Chao Dong, Shidu Dudzik, Wojciech Eaton-Rosen, Zach Egan, Gary Escudero, Guilherme Estienne, Tho Everson, Richard Fabrizio, Jonathan Fan, Yong Fang, Longwei Feng, Xue Ferrante, Enzo Fidon, Lucas Fischer, Martin French, Andrew P. Fridman, Naomi Fu, Huan Fuentes, David Gao, Yaozong Gates, Evan Gering, David Gholami, Amir Gierke, Willi Glocker, Ben Gong, Mingming Gonzlez-Vill, Sandra Grosges, T. Guan, Yuanfang Guo, Sheng Gupta, Sudeep Han, Woo-Sup Han, Il Song Harmuth, Ko Center for Biomedical Image Computing and Analytics University of Pennsylvania PhiladelphiaPA United States 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 Institute for Surgical Technology and Biomechanics University of Bern Bern Switzerland Center for MR-Research University Children's Hospital Zurich Zurich Switzerland Support Centre for Advanced Neuroimaging Inselspital Institute for Diagnostic and Interventional Neuroradiology Bern University Hospital Bern Switzerland University Hospital of Zurich Zurich Switzerland Center for Clinical Epidemiology and Biostatistics University of Pennsylvania Philadelphia United States Image-Based Biomedical Modeling Group Technical University of Munich Munich Germany Icahn School of Medicine Mount Sinai Health System New YorkNY United States Leidos Biomedical Research Inc. Frederick National Laboratory for Cancer Research FrederickMD21701 United States Cancer Imaging Program National Cancer Institute National Institutes of Health BethesdaMD20814 United States Department of Neurology University of Alabama at Birmingham BirminghamAL United States Department of Diagnostic Radiology University of Texas MD Anderson Cancer Center HoustonTX United States Department of Psychology Washington University St. LouisMO United States Neuroimaging Informatics and Analysis Center Washington University St. LouisMO United States Department of Radiology Washington University St. LouisMO United States Institute of Diagnostic and Interventional Radiology Pediatric Radiology and Neuroradiology University Medical Center Rostock Ernst-Heydemann-Str. 6 Rostock18057 Germany Tata Memorial Centre Homi Bhabha National Institute Mumbai India Shri Guru Gobind Singhji Institute of Engineering and Technology Nanded India NVIDIA Santa Clara

Gliomas are the most common primary brain malignancies, with different degrees of aggressiveness, variable prognosis and various heterogeneous histologic sub-regions, i.e., peritumoral edematous/invaded tissue, necrotic core, active and non-enhancing core. This intrinsic heterogeneity is also portrayed in their radio-phenotype, as their sub-regions are depicted by varying intensity profiles disseminated across multi-parametric magnetic resonance imaging (mpMRI) scans, reflecting varying biological properties. Their heterogeneous shape, extent, and location are some of the factors that make these tumors difficult to resect, and in some cases inoperable. The amount of resected tumor is a factor also considered in longitudinal scans, when evaluating the apparent tumor for potential diagnosis of progression. Furthermore, there is mounting evidence that accurate segmentation of the various tumor sub-regions can offer the basis for quantitative image analysis towards prediction of patient overall survival. This study assesses the state-of-the-art machine learning (ML) methods used for brain tumor image analysis in mpMRI scans, during the last seven instances of the International Brain Tumor Segmentation (BraTS) challenge, i.e., 2012-2018. Specifically, we focus on i) evaluating segmentations of the various glioma sub-regions in pre-operative mpMRI scans, ii) assessing potential tumor progression by virtue of longitudinal growth of tumor sub-regions, beyond use of the RECIST/RANO criteria, and iii) predicting the overall survival from pre-operative mpMRI scans of patients that underwent gross total resection. Finally, we investigate the challenge of identifying the best ML algorithms for each of these tasks, considering that apart from being diverse on each instance of the challenge, the multi-institutional mpMRI BraTS dataset has also been a continuously evolving/growing dataset. Copyright © 2018, The Authors. All rights reserved.

关键词： Tumors

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