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Genome-wide association study of long COVID

Nature Genetics 2025年 1-16页

作者： Vilma Lammi Tomoko Nakanishi Samuel E. Jones Juha Karjalainen Martin Broberg Hele H. Haapaniemi Matti Pirinen Mari E. K. Niemi Mattia Cordioli Mark J. Daly Andrea Ganna Hanna M. Ollila J. Brent Richards Yukinori Okada Shea J. Andrews Beatriz Cortés Rafael de Cid Susana Iraola-Guzmán Natalia Blay Xavier Farré Heath E. O’Brien Thompson Hannah Patrick J. Short Ana Ochoa-Guzman Michelle Duran-Gomez Brian E. Fulton-Howard Masahiro Kanai Axel Schmidt Daniella Balla Julia Heggemann Sonja Schultz Pari Behzad Markus M. Nöthen Abigail Miller Kerstin U. Ludwig Ruth E. Mitchell George Davey Smith Nicholas J. Timpson Abdou Mousas Evangelos Evangelou Evangelia Ntzani Konstantinos K. Tsilidis Massimo Mangino Alicia Huerta-Chagoya Nasa Sinnott-Armstrong Elizabeth T. Cirulli Francisco Tanudjaja Efren Sandoval Nicole L. Washington Simon White Alexandre Bolze Kelly M. Schiabor Barrett Marc Vaudel Alex S. F. Kwong Amit K. Maiti Minttu M. Marttila Daniel C. Posner Alexis A. Rodriguez Chiara Batini Beatriz Guillen-Guio Olivia C. Leavy Anna L. Guyatt Catherine John Louise V. Wain Francesca Minnai Anna R. Dearman Benedict Hignell Meena Kumari C. A. Robert Warmerdam Lude H. Franke Celia B. Sequeros Søren Brunak David Westergaard Karina Banasik Thomas W. Winkler Iris M. Heid Daniel M. Jordan Ryan C. Thompson Alexander W. Charney Laura G. Sloofman Nicole W. Simons Noam D. Beckmann Raimonds Rešcenko Vita Rovite Peculis Raitis Monta Briviba Janis Klovinš Laura Ansone Lorenzo Miano Flora Peyvandi Francesco Malvestiti Nicola Montano Alessandra Bandera Francesco Bruno Arturo Blasi Jacqueline M. Lane Jakob M. Cherry Ryan K. Chung Laura Carvajal-Silva Kevin Aguilar-Valdés Leslie C. Cerpa Tamara V. Arévalo Eduardo Lamoza Alicia Colombo Ricardo A. Verdugo Erika Frangione Xu Xinyi Jennifer Taher Jordan Lerner-Ellis Lindsay Guare Shefali S. Verma Ekaterina Vergasova Michil Trofimov Layal Shaheen Nikolay Plotnikov Anna Kim Dmitrii Kharitonov Alexei Kamelin Alexander Rakitko Eirini Marouli Pasquale Striano Ummu Afeera Zainulabid Ashutosh Kumar Hajar Fa Institute for Molecular Medicine Finland (FIMM) Helsinki Institute of Life Science (HiLIFE) University of Helsinki Helsinki Finland Department of Human Genetics McGill University Montreal Quebec Canada Centre for Clinical Epidemiology Department of Medicine Lady Davis Institute Jewish General Hospital McGill University Montreal Quebec Canada Kyoto-McGill International Collaborative Program in Genomic Medicine Graduate School of Medicine Kyoto University Kyoto Japan Department of Genome Informatics Graduate School of Medicine the University of Tokyo Tokyo Japan Research Fellow Japan Society for the Promotion of Science Tokyo Japan Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA USA Stanley Center for Psychiatric Research Broad Institute of Harvard and MIT Cambridge MA USA Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA USA Department of Mathematics and Statistics University of Helsinki Helsinki Finland Department of Public Health University of Helsinki Helsinki Finland Broad Institute Cambridge MA USA Analytical and Translational Genetics Unit Massachusetts General Hospital Harvard Medical School Boston MA USA Center for Genomic Medicine Massachusetts General Hospital Boston MA USA Anesthesia Critical Care and Pain Medicine Massachusetts General Hospital and Harvard Medical School Boston MA USA Broad Institute of MIT and Harvard Cambridge MA USA Department of Twin Research King’s College London London UK 5 Prime Sciences Inc Montreal Quebec Canada Department of Epidemiology Biostatistics and Occupational Health McGill University Montreal Quebec Canada Department of Statistical Genetics Osaka University Graduate School of Medicine Suita Japan Laboratory for Systems Genetics RIKEN Center for Integrative Medical Sciences Yokohama Japan Laboratory of Statistical Immunology Immunology Frontier Research Center (WPI-IFReC) Osaka University Suita Japan Departmen

Infections can lead to persistent symptoms and diseases such as shingles after varicella zoster or rheumatic fever after streptococcal infections. Similarly, severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infection can result in long coronavirus disease (COVID), typically manifesting as fatigue, pulmonary symptoms and cognitive dysfunction. The biological mechanisms behind long COVID remain unclear. We performed a genome-wide association study for long COVID including up to 6,450 long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We discovered an association ofFOXP4with long COVID, independent of its previously identified association with severe COVID-19. The signal was replicated in 9,500 long COVID cases and 798,835 population controls. Given the transcription factor FOXP4’s role in lung physiology and pathology, our findings highlight the importance of lung function in the pathophysiology of long COVID.

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

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The Lancet HIV 2021年第10期8卷 e633-e651页

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

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

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Global, regional, and national incidence of six major immune-mediated inflammatory diseases: findings from the global burden of disease study 2019

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eClinicalMedicine 2023年 64卷 102193-102193页

作者： Wu, Dongze Jin, Yingzhao Xing, Yuhan Abate, Melsew Dagne Abbasian, Mohammadreza Abbasi-Kangevari, Mohsen Abbasi-Kangevari, Zeinab Abd-Allah, Foad Abdelmasseh, Michael Abdollahifar, Mohammad-Amin Abdulah, Deldar Morad Abedi, Aidin Abedi, Vida Abidi, Hassan Aboagye, Richard Gyan Abolhassani, Hassan Abuabara, Katrina Abyadeh, Morteza Addo, Isaac Yeboah Adeniji, Kayode Nelson Adepoju, Abiola Victor Adesina, Miracle Ayomikun Adnani, Qorinah Estiningtyas Sakilah Afarideh, Mohsen Aghamiri, Shahin Agodi, Antonella Agrawal, Anurag Arriagada, Constanza Elizabeth Aguilera Ahmad, Aqeel Ahmad, Danish Ahmad, Sohail Ahmadi, Ali Ahmed, Ayman Aithala, Janardhana P. Ajadi, Abdullateef Abiodun Ajami, Marjan Akbarzadeh-Khiavi, Mostafa Alahdab, Fares AlBataineh, Mohammad T. Alemi, Sharifullah Al-Gheethi, Adel Ali Saeed Ali, Liaqat Alif, Sheikh Mohammad Almazan, Joseph Uy Almustanyir, Sami Alqahtani, Jaber S. Alqasmi, Ibrahim Altaf, Ihsan Ullah Khan Alvis-Guzman, Nelson Alvis-Zakzuk, Nelson J. Al-Worafi, Yaser Mohammed Aly, Hany Amani, Reza Amu, Hubert Amusa, Ganiyu Adeniyi Andrei, Catalina Liliana Ansar, Adnan Ansariniya, Hossein Anyasodor, Anayochukwu Edward Arabloo, Jalal Arefnezhad, Reza Arulappan, Judie Asghari-Jafarabadi, Mohammad Ashraf, Tahira Atata, Jamila Abdulhamid Athari, Seyyed Shamsadin Atlaw, Daniel Atout, Maha Moh'd Wahbi Aujayeb, Avinash Awan, Asma Tahir Ayatollahi, Haleh Azadnajafabad, Sina Azzam, Ahmed Y. Badawi, Alaa Badiye, Ashish D. Bagherieh, Sara Baig, Atif Amin Bantie, Berihun Bantie Barchitta, Martina Bardhan, Mainak Barker-Collo, Suzanne Lyn Barone-Adesi, Francesco Batra, Kavita Bayileyegn, Nebiyou Simegnew Behnoush, Amir Hossein Belgaumi, Uzma Iqbal Bemanalizadeh, Maryam Bensenor, Isabela M. Beyene, Kebede A. Bhagavathula, Akshaya Srikanth Bhardwaj, Pankaj Bhaskar, Sonu Bhat, Ajay Nagesh Bitaraf, Saeid Bitra, Veera R. Boloor, Archith Bora, Kaustubh Botelho, João Silva Buchbinder, Rachelle Calina, Daniela Cámera, Luis Alberto Carvalho, Andre F. Chan, Jeffrey Shi Kai Chattu, Vijay Kumar Abebe, Endeshaw Chekol Department of Rheumatology and Immunology Sichuan Provincial People's Hospital School of Medicine University of Electronic Science and Technology of China China Department of Medicine & Therapeutics The Chinese University of Hong Kong Hong Kong Department of Paediatrics The Chinese University of Hong Kong Hong Kong School of Pharmacy The Chinese University of Hong Kong Hong Kong Jockey Club School of Public Health and Primary Care The Chinese University of Hong Kong Hong Kong Department of Nursing Woldia University Woldia Ethiopia Department of Orthopedic Surgery Harvard University Boston MA United States Postgraduate Medical Education Harvard University Boston MA United States Maternal Fetal Care Center Harvard University Boston MA United States Department of Health Policy and Oral Epidemiology Harvard University Boston MA United States Division of General Internal Medicine Harvard University Boston MA United States Department of Orthopaedic Surgery Shahid Beheshti University of Medical Sciences Tehran Iran Social Determinants of Health Research Center Shahid Beheshti University of Medical Sciences Tehran Iran Department of Biotechnology Shahid Beheshti University of Medical Sciences Tehran Iran Department of Epidemiology Shahid Beheshti University of Medical Sciences Tehran Iran National Nutrition and Food Technology Research Institute Shahid Beheshti University of Medical Sciences Tehran Iran Department of Immunology Shahid Beheshti University of Medical Sciences Tehran Iran Department of Neurology Shahid Beheshti University of Medical Sciences Tehran Iran Department of Medical Genetics Shahid Beheshti University of Medical Sciences Tehran Iran Center for Comprehensive Genetic Services Shahid Beheshti University of Medical Sciences Tehran Iran Cancer Research Center Shahid Beheshti University of Medical Sciences Tehran Iran Department of Health Economics and Statistics Shahid Beheshti University of Medical Sciences Tehran Iran Functional Neuro

Background: The causes for immune-mediated inflammatory diseases (IMIDs) are diverse and the incidence trends of IMIDs from specific causes are rarely studied. The study aims to investigate the pattern and trend of IMIDs from 1990 to 2019. Methods: We collected detailed information on six major causes of IMIDs, including asthma, inflammatory bowel disease, multiple sclerosis, rheumatoid arthritis, psoriasis, and atopic dermatitis, between 1990 and 2019, derived from the Global Burden of Disease study in 2019. The average annual percent change (AAPC) in number of incidents and age standardized incidence rate (ASR) on IMIDs, by sex, age, region, and causes, were calculated to quantify the temporal trends. Findings: In 2019, rheumatoid arthritis, atopic dermatitis, asthma, multiple sclerosis, psoriasis, inflammatory bowel disease accounted 1.59%, 36.17%, 54.71%, 0.09%, 6.84%, 0.60% of overall new IMIDs cases, respectively. The ASR of IMIDs showed substantial regional and global variation with the highest in High SDI region, High-income North America, and United States of America. Throughout human lifespan, the age distribution of incident cases from six IMIDs was quite different. Globally, incident cases of IMIDs increased with an AAPC of 0.68 and the ASR decreased with an AAPC of −0.34 from 1990 to 2019. The incident cases increased across six IMIDs, the ASR of rheumatoid arthritis increased (0.21, 95% CI 0.18, 0.25), while the ASR of asthma (AAPC = −0.41), inflammatory bowel disease (AAPC = −0.72), multiple sclerosis (AAPC = −0.26), psoriasis (AAPC = −0.77), and atopic dermatitis (AAPC = −0.15) decreased. The ASR of overall and six individual IMID increased with SDI at regional and global level. Countries with higher ASR in 1990 experienced a more rapid decrease in ASR. Interpretation: The incidence patterns of IMIDs varied considerably across the world. Innovative prevention and integrative management strategy are urgently needed to mitigate the increasing ASR of rh

关键词： Global burden of disease study Immune-mediated inflammatory disease Incidence Trend

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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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Nat Genet:单细胞分析解开结直肠癌细胞的神秘面纱

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现代生物医学进展 2017年第15期17卷 I0003-I0003页

作者： Huipeng Li, Elise T Courtois, Debarka Sengupta, Yuliana Tan Shyam Prabhakar Elise T Courtois, Yuliana Tan Paul Robson Debarka Sengupta Kok Hao Chen, Jolene Jie Lin Goh Paul Jongjoon Choi Say Li Kong, Axel M Hillmer Iain Beehuat Tan Clarinda Chua Iain Beehuat Tan Lim Kiat Hon Wah Siew Tan Mark Wong Lawrence J K Wee Iain Beehuat Tan Paul Robson Paul Robson Paul Robson Computational and Systems Biology Genome Institute of Singapore Singapore Developmental Cellomics Laboratory Genome Institute of 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 Cancer Therapeutics and Stratified Oncology Genome Institute of Singapore Singapore Department of Medical Oncology National Cancer Centre Singapore Singapore Department of Pathology Singapore General Hospital Singapore Department of Colorectal Surgery Singapore General Hospital Singapore Data Analytics Department Institute for Infocomm Research Singapore Program in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore The Jackson Laboratory for Genomic Medicine Farmington Connecticut USA Department of Genetics and Genome Sciences Institute for Systems Genomics University of Connecticut Farmington Connecticut USA Department of Biological Sciences National University of Singapore Singapore.

结合单细胞基因组学和计算机技术，一个研究团队（包括来自杰克逊实验室（JAx）单细胞生物学主任Paul Robson博士在内）鉴定出了11种结直肠癌肿瘤的癌细胞组成及邻近的非癌细胞。这对于更好的肿瘤靶向诊断和治疗很重要。”使用单细胞测... 详细信息

结合单细胞基因组学和计算机技术，一个研究团队（包括来自杰克逊实验室（JAx）单细胞生物学主任Paul Robson博士在内）鉴定出了11种结直肠癌肿瘤的癌细胞组成及邻近的非癌细胞。这对于更好的肿瘤靶向诊断和治疗很重要。”使用单细胞测序。”JAX科学家、这篇发表在Nature Genetics上的文章共同第一作者Elise Courtois说道。”我们可以根据肿瘤中的细胞组成将结直肠癌进一步分类。因为每种亚型的肿瘤病人生存率存在差别，我们的方法将为肿瘤医生提供更多的关于肿瘤预后和治疗的信息。”

关键词：单细胞分析结直肠癌癌细胞 Nat 细胞组成肿瘤病计算机技术细胞生物学

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26th Annual Computational Neuroscience Meeting (CNS*2017): Part 3 Antwerp, Belgium. 15-20 July 2017 Abstracts

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BMC NEUROscience 2017年第SUPPL 1期18卷 95-176页

作者： [Anonymous] Department of Neuroscience Yale University New Haven CT 06520 USA Department Physiology & Pharmacology SUNY Downstate Brooklyn NY 11203 USA NYU School of Engineering 6 MetroTech Center Brooklyn NY 11201 USA Departament de Matemàtica Aplicada Universitat Politècnica de Catalunya Barcelona 08028 Spain Institut de Neurobiologie de la Méditerrannée (INMED) INSERM UMR901 Aix-Marseille Univ Marseille France Center of Neural Science New York University New York NY USA Aix-Marseille Univ INSERM INS Inst Neurosci Syst Marseille France Laboratoire de Physique Théorique et Modélisation CNRS UMR 8089 Université de Cergy-Pontoise 95300 Cergy-Pontoise Cedex France Department of Mathematics and Computer Science ENSAT Abdelmalek Essaadi’s University Tangier Morocco Laboratory of Natural Computation Department of Information and Electrical Engineering and Applied Mathematics University of Salerno 84084 Fisciano SA Italy Department of Medicine University of Salerno 84083 Lancusi SA Italy Dipartimento di Fisica Università degli Studi Aldo Moro Bari and INFN Sezione Di Bari Italy Data Analysis Department Ghent University Ghent Belgium Coma Science Group University of Liège Liège Belgium Cruces Hospital and Ikerbasque Research Center Bilbao Spain BIOtech Department of Industrial Engineering University of Trento and IRCS-PAT FBK 38010 Trento Italy Department of Data Analysis Ghent University Ghent 9000 Belgium The Wellcome Trust Centre for Neuroimaging University College London London WC1N 3BG UK Department of Electronic Engineering NED University of Engineering and Technology Karachi Pakistan Blue Brain Project École Polytechnique Fédérale de Lausanne Lausanne Switzerland Departement of Mathematics Swansea University Swansea Wales UK Laboratory for Topology and Neuroscience at the Brain Mind Institute École polytechnique fédérale de Lausanne Lausanne Switzerland Institute of Mathematics University of Aberdeen Aberdeen Scotland UK Department of Integrativ

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

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Nature genetics 2018年第12期50卷 1754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 Igor Cima Min-Han Tan 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. Institute of Bioengineering and Nanotechnology 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.

In the version of the article published, the author list is not accurate. Igor Cima and Min-Han Tan should have been authors, appearing after Mark Wong in the author list, while Paul Jongjoon Choi should not have been listed as an author. Igor Cima and Min-Han Tan both have the affiliation Institute of Bioengineering and Nanotechnology, Singapore, Singapore, and their contributions should have been noted in the Author Contributions section as "I.C. preprocessed Primary Cell Atlas data with inputs from M.-H.T." The following description of the contribution of Paul Jongjoon Choi should not have appeared: "P.J.C. supported the smFISH experiments." In the 'RCA: global panel' section of the Online Methods, the following sentence should have appeared as the second sentence, "An expression atlas of human primary cells (the Primary Cell Atlas) was preprocessed similarly to in ref. 55," with new reference 55 (Cima, I. et al. Tumor-derived circulating endothelial cell clusters in colorectal cancer. science Transl. Med. 8, 345ra89, 2016).

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Proceedings from the 9th annual conference on the science of dissemination and implementation: Washington, DC, USA. 14-15 December 2016

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Implement Sci 2017年第SUPPL 1期12卷 48-48页

作者： David Chambers Lisa Simpson Gila Neta Ulrica von Thiele Schwarz Antoinette Percy-Laurry Gregory A. Aarons Ross Brownson Amanda Vogel Shannon Wiltsey Stirman Kenneth Sherr Rachel Sturke Wynne E. Norton Allyson Varley Cynthia Vinson Lisa Klesges Suzanne Heurtin-Roberts M. Rashad Massoud Leighann Kimble Arne Beck Claire Neely Jennifer Boggs Carmel Nichols Wen Wan Erin Staab Neda Laiteerapong Nathalie Moise Ravi Shah Susan Essock Margaret Handley Amy Jones Jay Carruthers Karina Davidson Lauren Peccoralo Lloyd Sederer Todd Molfenter Ashley Scudder Sarah Taber-Thomas Kristen Schaffner Amy Herschell Eva Woodward Jeffery Pitcock Mona Ritchie JoAnn Kirchner Julia E. Moore Sobia Khan Shusmita Rashid Jamie Park Melissa Courvoisier Sharon Straus Daniel Blonigen Allison Rodriguez Luisa Manfredi Andrea Nevedal Joel Rosenthal David Smelson Christine Timko Nicole Stadnick Jennifer Regan Miya Barnett Anna Lau Lauren Brookman-Frazee Erick Guerrero Karissa Fenwick Yinfei Kong Gregory Aarons Rebecca Lengnick-Hall Benjamin Henwood Nina Sayer Craig Rosen Robert Orazem Brandy Smith Lindsey Zimmerman David Lounsbury Rachel Kimerling Jodie A. Trafton Steven Lindley Rahul Bhargava Hal Roberts Laura Gibson Gabriel J. Escobar Vincent Liu Benjamin Turk Arona Ragins Patricia Kipnis Ashley Ketterer Gruszkowski Michael W. Kennedy Emily Rentschler Drobek Lior Turgeman Aleksandra Sasha Milicevic Terrence L. Hubert Larissa Myaskovsky Youxu C. Tjader Robert J. Monte Kathryn G. Sapnas Edmond Ramly Diane R Lauver Christie M Bartels Shereef Elnahal Andrea Ippolito Hillary Peabody Carolyn Clancy Randall Cebul Thomas Love Douglas Einstadter Shari Bolen Brook Watts Vera Yakovchenko Angela Park William Lukesh Donald R. Miller David Thornton Mari-Lynn Drainoni Allen L. Gifford Shawna Smith Julia Kyle Mark S Bauer Daniel Eisenberg Celeste Liebrecht Michelle Barbaresso Amy Kilbourne Elyse Park Giselle Perez Jamie Ostroff Sarah Greene Michael Parchman Brian Austin Eric Larson Stefanie Ferreri Chris Shea Megan Smith Kea Turner Jennifer Bacci Kyle Bigham Geoffr Division of Cancer Control and Population Sciences National Cancer Institute Rockville MD 20850 USA AcademyHealth Washington DC 20009 USA Department of Learning Informatics Management and Ethics Karolinska Institutet Stockholm 17177 Sweden Department of Psychiatry University of California San Diego San Diego CA 92093 USA George Warren Brown School of Social Work Washington University in St. Louis St. Louis MO 63130 USA Center for Global Health National Cancer Institute Rockville MD 20850 USA Dissemination and Training Division VA National Center for PTSD Palo Alto CA 94305 USA Department of Global Health University of Washington Seattle WA 98105 USA Center for Global Health Studies Fogarty International Center National Institutes of Health Bethesda MD 20912 USA School of Public Health University of Alabama at Birmingham Birmingham AL 35243 USA School of Public Health University of Memphis Memphis TN 38152 USA USAID Applying Science to Strengthen and Improve Systems (ASSIST) Project Bethesda Maryland 20814 USA Institute for Health Research Kaiser Permanente Denver CO 80231 USA ICSI Institute for Clinical Systems Improvement Bloomington MN 55425 USA Medicine University of Chicago Chicago IL 60637 USA Medicine Columbia University Medical Center New York NY 10032 USA Psychiatry Columbia University New York NY 10032 USA General Internal Medicine Epidemiology and Biostatistics University of California San Francisco San Francisco CA 94110 USA New York State Office of Mental Health New York NY 10001 USA Medicine Icahn School of Medicine at Mount Sinai New York NY 10029 USA Center for Health Enhancement System Studies University of Wisconsin Madison WI 53706 USA Department of Psychiatry University of Pittsburgh Pittsburgh PA 15213 USA Psychology University at Buffalo Buffalo NY 14260 USA Department of Psychology West Virginia University Morgantown WV 26506 USA MIRECC VA North Little Rock AR 72114 USA QUERI for Team-Based Behavioral Health Centr

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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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11th German Conference on Chemoinformatics (GCC 2015) Abstracts

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JOURNAL OF CHEMINFORMATICS 2016年第SUPPL 1期8卷 1-27页

作者： [Anonymous] GDCh-CIC Division Associated Board Member Beilstein-Institut zur Förderung der Chemischen Wissenschaften Trakehner Str. 7-9 60487 Frankfurt Germany. ufechner@beilstein-institut.de. Division Medicinal Chemistry Amsterdam Institute for Molecules Medicines and Systems (AIMMS) VU University Amsterdam The Netherlands. Centre for Bioinformatics Uni Hamburg Bundesstr. 43 20146 Hamburg Germany. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. stefan.guessregen@***. Sanofi-Aventis Deutschland GmbH 65926 Frankfurt am Main Germany. GlaxoSmithKline Stevenage SG1 2NY UK. nicola.j.richmond@***. Discngine Paris 75011 France. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. marwin.segler@wwu.de. Organisch-Chemisches Institut Westfälische Wilhelms-Universität Münster Germany. Bundeskriminalamt Wiesbaden Central Analytics II 65173 Wiesbaden Germany. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. shea@chem.ucsb.edu. Department of Chemistry and Biochemistry University of California Santa Barbara CA 93111 USA. Chemistry Department Ludwig-Maximilians-Universität München Butenandtstr. 7 81377 Munich Germany. Inorganic Chemistry and Center for Nanointegration University of Duisburg-Essen Essen Germany. CAM-D Technologies Essen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. Institute for Bioinformatics and Chemoinformatics Westphalian University of Applied Sciences Recklinghausen Germany. achim.zielesny@w-hs.de. Leiden University Leiden Netherlands. j.fraaije@chem.leidenuniv.nl. Culgi BV Berlin Germany. Physikalische Chemie III TU Dortmund 44227 Dortmund Germany. stefan.kast@tu-dortmund.de. Centre for Molecular Informatics Department of Chemistry University of Cambridge Lensfield Road Cambridge CB2 1EW United Kingdom. kcb27@cam.ac.uk. Centre for Molecular Informatics Department of Chemistry

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