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The overlapping burden of the three leading causes of disability and death in sub-Saharan African children

Nature Communications 2022年第1期13卷 1-14页

作者： Reiner, Robert C. Welgan, Catherine A. Troeger, Christopher E. Baumann, Mathew M. Weiss, Daniel J. Deshpande, Aniruddha Blacker, Brigette F. Miller-Petrie, Molly K. Earl, Lucas Bhatt, Samir Abolhassani, Hassan Abosetugn, Akine Eshete Abu-Gharbieh, Eman Adekanmbi, Victor Adetokunboh, Olatunji O. Aghaali, Mohammad Aji, Budi Alahdab, Fares Al-Aly, Ziyad Alhassan, Robert Kaba Ali, Saqib Alizade, Hesam Aljunid, Syed Mohamed Almasi-Hashiani, Amir Al-Mekhlafi, Hesham M. Altirkawi, Khalid A. Alvis-Guzman, Nelson Amare, Azmeraw T. Amini, Saeed Amugsi, Dickson A. Ancuceanu, Robert Andrei, Catalina Liliana Ansari, Fereshteh Anvari, Davood Appiah, Seth Christopher Yaw Arabloo, Jalal Aremu, Olatunde Atout, Maha Moh’d Wahbi Ausloos, Marcel Ausloos, Floriane Ayanore, Martin Amogre Aynalem, Yared Asmare Azene, Zelalem Nigussie Badawi, Alaa Baig, Atif Amin Banach, Maciej Bedi, Neeraj Bhagavathula, Akshaya Srikanth Bhandari, Dinesh Bhardwaj, Nikha Bhardwaj, Pankaj Bhattacharyya, Krittika Bhutta, Zulfiqar A. Bijani, Ali Birhanu, Tesega Tesega Mengistu Bitew, Zebenay Workneh Boloor, Archith Brady, Oliver J. Butt, Zahid A. Car, Josip Carvalho, Felix Casey, Daniel C. Chattu, Vijay Kumar Chowdhury, Mohiuddin Ahsanul Kabir Chu, Dinh-Toi Coelho, Camila H. Cook, Aubrey J. Damiani, Giovanni Daoud, Farah Gela, Jiregna Darega Darwish, Amira Hamed Daryani, Ahmad Das, Jai K. Davis Weaver, Nicole Deribe, Kebede Desalew, Assefa Dharmaratne, Samath Dhamminda Dianatinasab, Mostafa Diaz, Daniel Djalalinia, Shirin Dorostkar, Fariba Dubljanin, Eleonora Duko, Bereket Dwyer-Lindgren, Laura Effiong, Andem El Sayed Zaki, Maysaa El Tantawi, Maha Enany, Shymaa Fattahi, Nazir Feigin, Valery L. Fernandes, Eduarda Ferrara, Pietro Fischer, Florian Foigt, Nataliya A. Folayan, Morenike Oluwatoyin Foroutan, Masoud Frostad, Joseph Jon Fukumoto, Takeshi Gaidhane, Abhay Motiramji Gebrekrstos, Hailemikael Gebrekidan G. K. Gebremeskel, Leake Gebreslassie, Assefa Ayalew Gething, Peter W. Gezae, Kebede Embaye Ghadiri, Keyghobad Ghashghaee, Ahmad Golechha, Mahaveer Gubar 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 Malaria Atlas Project University of Oxford Oxford United Kingdom Imperial College London London United Kingdom Department of Laboratory Medicine Karolinska University Hospital Huddinge Sweden Research Center for Immunodeficiencies Tehran University of Medical Sciences Tehran Iran Department of Public Health Debre Berhan University Debre Berhan Ethiopia Department of Clinical Sciences University of Sharjah Sharjah United Arab Emirates Population Health Sciences King’s College London London United Kingdom Centre of Excellence for Epidemiological Modelling and Analysis Stellenbosch University Stellenbosch South Africa Department of Global Health Stellenbosch University Cape Town South Africa Department of Epidemiology and Biostatistics Qom University of Medical Sciences Qom Iran Faculty of Medicine and Public Health Jenderal Soedirman University Purwokerto Indonesia Mayo Evidence-based Practice Center Mayo Clinic Foundation for Medical Education and Research Rochester MN United States John T. Milliken Department of Internal Medicine Washington University in St. Louis St. Louis MO United States Clinical Epidemiology Center Department of Veterans Affairs St Louis MO United States Institute of Health Research University of Health and Allied Sciences Ho Ghana Department of Information Systems College of Economics and Political Science Sultan Qaboos University Muscat Oman Infectious and Tropical Disease Research Center Hormozgan University of Medical Sciences Bandar Abbas Iran Department of Health Policy and Management Kuwait University Safat Kuwait International Centre for Casemix and Clinical Coding National University of Malaysia Bandar Tun Razak Malaysia Department of Epidemiology Arak University of Medical Sciences Arak Iran Medical Research Center

Despite substantial declines since 2000, lower respiratory infections (LRIs), diarrhoeal diseases, and malaria remain among the leading causes of nonfatal and fatal disease burden for children under 5 years of age (under 5), primarily in sub-Saharan Africa (SSA). The spatial burden of each of these diseases has been estimated subnationally across SSA, yet no prior analyses have examined the pattern of their combined burden. Here we synthesise subnational estimates of the burden of LRIs, diarrhoea, and malaria in children under-5 from 2000 to 2017 for 43 sub-Saharan countries. Some units faced a relatively equal burden from each of the three diseases, while others had one or two dominant sources of unit-level burden, with no consistent pattern geographically across the entire subcontinent. Using a subnational counterfactual analysis, we show that nearly 300 million DALYs could have been averted since 2000 by raising all units to their national average. Our findings are directly relevant for decision-makers in determining which and targeting where the most appropriate interventions are for increasing child survival. © 2022, The Author(s).

关键词： Biogeography Epidemiology Infectious diseases Malaria

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Global burden of 369 diseases and injuries in 204 countries and territories, 1990–2019: a systematic analysis for the Global Burden of Disease Study 2019

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The Lancet 2020年第10258期396卷 1204-1222页

作者： Abbafati, Cristiana Abbas, Kaja M. Abbasi, Mohammad Abbasifard, Mitra Abbasi-Kangevari, Mohsen Abbastabar, Hedayat Abd-Allah, Foad Abdelalim, Ahmed Abdollahi, Mohammad Abdollahpour, Ibrahim Abedi, Aidin Abedi, Parisa Abegaz, Kedir Hussein Abolhassani, Hassan Abosetugn, Akine Eshete Aboyans, Victor Abrams, Elissa M. Abreu, Lucas Guimarães Abrigo, Michael R.M. Abu Haimed, Abdulaziz Khalid Abualhasan, Ahmed Abu-Gharbieh, Eman Abu-Raddad, Laith Jamal Abushouk, Abdelrahman I. Acebedo, Alyssa Ackerman, Ilana N. Adabi, Maryam Adair, Tim Adamu, Abdu A. Adebayo, Oladimeji M. Adedeji, Isaac Akinkunmi Adekanmbi, Victor Adelson, Jaimie D. Adeoye, Abiodun Moshood Adetokunboh, Olatunji O. Adham, Davoud Advani, Shailesh M. Afarideh, Mohsen Afshari, Mahdi Afshin, Ashkan Agardh, Emilie E. Agarwal, Gina Agasthi, Pradyumna Agesa, Kareha M. Aghaali, Mohammad Aghamir, Seyed Mohammad Kazem Agrawal, Anurag Ahmad, Tauseef Ahmadi, Alireza Ahmadi, Keivan Ahmadi, Mehdi Ahmadieh, Hamid Ahmadpour, Ehsan Ahmed, Muktar Beshir Aji, Budi Akalu, Temesgen Yihunie Akinyemi, Rufus Olusola Akinyemiju, Tomi Akombi, Blessing Akunna, Chisom Joyqueenet Alahdab, Fares Al-Aly, Ziyad Alam, Khurshid Alam, Noore Alam, Samiah Alam, Tahiya Alanezi, Fahad Mashhour Alanzi, Turki M. Albertson, Samuel B. Alcalde-Rabanal, Jacqueline Elizabeth Alema, Niguse Meles Alemu, Biresaw Wassihun Alemu, Yihun Mulugeta Alhabib, Khalid F. Alhassan, Robert Kaba Ali, Muhammad Ali, Saqib Alicandro, Gianfranco Alijanzadeh, Mehran Alinia, Cyrus Alipour, Vahid Alizade, Hesam Aljunid, Syed Mohamed Alla, François Allebeck, Peter Almadi, Majid Abdulrahman Hamad Almasi, Ali Almasi-Hashiani, Amir Almasri, Nihad A. Al-Mekhlafi, Hesham M. Almulhim, Abdulaziz M. Alonso, Jordi Al-Raddadi, Rajaa M. Altirkawi, Khalid A. Alumran, Arwa Khalid Alvis-Guzman, Nelson Alvis-Zakzuk, Nelson J. Amare, Azmeraw T. Amare, Bekalu Amini, Saeed Amini-Rarani, Mostafa Aminorroaya, Arya Amiri, Fatemeh Amit, Arianna Maever L. Amugsi, Dickson A. Amul, Gianna Gayle Herrera Anbesu, Etsay Woldu Ancuceanu, Robert Anderl Department of Juridical and Economic Studies La Sapienza University Rome Italy Department of Infectious Disease Epidemiology London School of Hygiene and Tropical Medicine London United Kingdom Social Determinants of Health Research Center Tehran Iran Department of Neurology Cairo University Cairo Egypt School of Pharmacy Tehran Iran The Institute of Pharmaceutical Sciences (TIPS) Tehran Iran Neuroscience Research Center Isfahan University of Medical Sciences Isfahan Iran Biostatistics Department Near East University Nicosia Cyprus Biostatistics and Health Informatics Madda Walabu University Bale Robe Ethiopia Research Center for Immunodeficiencies Tehran Iran Karolinska University Hospital Huddinge Sweden Department of Cardiology Dupuytren University Hospital Limoges France University of Limoges Limoges France Department of Pediatric Dentistry Federal University of Minas Gerais Belo Horizonte Brazil Department of Research Philippine Institute for Development Studies Quezon City Philippines Department of Healthcare Policy and Research Weill Cornell Medical College in Qatar Doha Qatar Harvard Medical School Boston MA United States Department of Medicine Ain Shams University Cairo Egypt Hamadan University of Medical Sciences Hamadan Iran School of Medicine Cardiff University Cardiff United Kingdom School of Laboratory Medicine and Science University College Hospital Ibadan Ibadan Nigeria Institute of Cardiovascular Diseases University of Ibadan Ibadan Nigeria Centre of Excellence for Epidemiological Modelling and Analysis Stellenbosch University Cape Town South Africa Department of Global Health Stellenbosch University Cape Town South Africa School of Health Ardabil University of Medical Science Ardabil Iran Social Behavioral Research Branch National Institute of Health Bethesda MD United States Department of Oncology Georgetown University Washington DC DC United States Department of Health Metrics Sciences School of Medicine Seattle WA

Background: In an era of shifting global agendas and expanded emphasis on non-communicable diseases and injuries along with communicable diseases, sound evidence on trends by cause at the national level is essential. The Global Burden of Diseases, Injuries, and Risk Factors Study (GBD) provides a systematic scientific assessment of published, publicly available, and contributed data on incidence, prevalence, and mortality for a mutually exclusive and collectively exhaustive list of diseases and injuries. Methods: GBD estimates incidence, prevalence, mortality, years of life lost (YLLs), years lived with disability (YLDs), and disability-adjusted life-years (DALYs) due to 369 diseases and injuries, for two sexes, and for 204 countries and territories. Input data were extracted from censuses, household surveys, civil registration and vital statistics, disease registries, health service use, air pollution monitors, satellite imaging, disease notifications, and other sources. Cause-specific death rates and cause fractions were calculated using the Cause of Death Ensemble model and spatiotemporal Gaussian process regression. Cause-specific deaths were adjusted to match the total all-cause deaths calculated as part of the GBD population, fertility, and mortality estimates. Deaths were multiplied by standard life expectancy at each age to calculate YLLs. A Bayesian meta-regression modelling tool, DisMod-MR 2.1, was used to ensure consistency between incidence, prevalence, remission, excess mortality, and cause-specific mortality for most causes. Prevalence estimates were multiplied by disability weights for mutually exclusive sequelae of diseases and injuries to calculate YLDs. We considered results in the context of the Socio-demographic Index (SDI), a composite indicator of income per capita, years of schooling, and fertility rate in females younger than 25 years. Uncertainty intervals (UIs) were generated for every metric using the 25th and 975th ordered 1000 draw value

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ON-OFF Neuromorphic ISING Machines using Fowler-Nordheim Annealers

arXiv

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arXiv 2024年

作者： Chen, Zihao Xiao, Zhili Akl, Mahmoud Leugring, Johannes Olajide, Omowuyi Malik, Adil Dennler, Nik Harper, Chad Bose, Subhankar Gonzalez, Hector A. Eshraghian, Jason Pignari, Riccardo Urgese, Gianvito Andreou, Andreas G. Shankar, Sadasivan Mayr, Christian Cauwenberghs, Gert Chakrabartty, Shantanu Department of Electrical and Systems Engineering Washington University in St. Louis One Brookings Drive St. LouisMO63130 United States Department of Bioengineering University of California 9500 Gilman Dr La Jolla San DiegoCA92093 United States SpiNNcloud Systems GmbH Freibergerstr. 37 Dresden01067 Germany Department of Electrical and computer engineering Johns Hopkins University 3400 N. Charles Street BaltimoreMD21218 United States SLAC National Accelerator Laboratory 2575 Sand Hill Road Menlo ParkCA94025 United States Department of Electrical and Electronic Engineering Imperial College London Exhibition Rd LondonSW7 2AZ United Kingdom International Centre for Neuromorphic Engineering Western Sydney University Penrith Second Ave KingswoodNSW2747 Australia Department of Physics University of California Berkeley University Avenue and Oxford St BerkeleyCA94720 United States Department of Electrical and Computer Engineering University of California Santa Cruz 1156 High Street Santa CruzCA95064 United States Politecnico di Torino Address: Corso Duca degli Abruzzi 24 Torino10129 Italy Redwood Center for Theoretical Neuroscience Helen Wills Neuroscience Institute University of California Berkeley University Avenue and Oxford St BerkeleyCA94720 United States Biocomputation Group University of Hertfordshire Exhibition Rd LondonSW7 2AZ United Kingdom Materials Science and Engineering Stanford University 450 Jane Stanford Way StanfordCA94305 United States Highly-Parallel VLSI-Systems and Neuro-Microelectronics Technische Universität Dresden Mommsenstraße 12 Dresden01069 Germany Scads.AI: Center for scalable data analytics and artificial intelligence Strehlener Street 12 14 Dresden01069 Germany

We introduce NeuroSA, a neuromorphic architecture specifically designed to ensure asymptotic convergence to the ground state of an Ising problem using an annealing process that is governed by the physics of quantum mechanical tunneling using Fowler-Nordheim (FN). The core component of NeuroSA consists of a pair of asynchronous ON-OFF neurons, which effectively map classical simulated annealing (SA) dynamics onto a network of integrate-and-fire (IF) neurons. The threshold of each ON-OFF neuron pair is adaptively adjusted by an FN annealer which replicates the optimal escape mechanism and convergence of SA, particularly at low temperatures. To validate the effectiveness of our neuromorphic Ising machine, we systematically solved various benchmark MAX-CUT combinatorial optimization problems. Across multiple runs, NeuroSA consistently generates solutions that approach the state-of-the-art level with high accuracy (greater than 99%), and without any graph-specific hyperparameter tuning. For practical illustration, we present results from an implementation of NeuroSA on the SpiNNaker2 platform, highlighting the feasibility of mapping our proposed architecture onto a standard neuromorphic accelerator platform. © 2024, CC BY-NC-SA.

关键词： Simulated annealing

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An Open-Source Knowledge Graph Ecosystem for the Life sciences

arXiv

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arXiv 2023年

作者： Callahan, Tiffany J. Tripodi, Ignacio J. Stefanski, Adrianne L. Cappelletti, Luca Taneja, Sanya B. Wyrwa, Jordan M. Casiraghi, Elena Matentzoglu, Nicolas A. Reese, Justin Silverstein, Jonathan C. Hoyt, Charles Tapley Boyce, Richard D. Malec, Scott A. Unni, Deepak R. Joachimiak, Marcin P. Robinson, Peter N. Mungall, Christopher J. Cavalleri, Emanuele Fontana, Tommaso Valentini, Giorgio Mesiti, Marco Gillenwater, Lucas A. Santangelo, Brook Vasilevsky, Nicole A. Hoehndorf, Robert Bennett, Tellen D. Ryan, Patrick B. Hripcsak, George Kahn, Michael G. Bada, Michael Baumgartner, William A. Hunter, Lawrence E. Computational Bioscience Program University of Colorado Anschutz Medical Campus AuroraCO80045 United States Department of Biomedical Informatics Columbia University Irving Medical Center New YorkNY10032 United States Computer Science Department Interdisciplinary Quantitative Biology University of Colorado Boulder BoulderCO80301 United States AnacletoLab Computer Science Department University of Milan 20122 Italy Intelligent Systems Program University of Pittsburgh PittsburghPA15260 United States Department of Physical Medicine and Rehabilitation School of Medicine University of Colorado Anschutz Medical Campus AuroraCO80045 United States Division of Environmental Genomics and Systems Biology Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Semanticly Ltd Athens Greece Department of Biomedical Informatics University of Pittsburgh School of Medicine PittsburghPA15206 United States Laboratory of Systems Pharmacology Harvard Medical School BostonMA02115 United States Division of Translational Informatics University of New Mexico School of Medicine AlbuquerqueNM87131 United States SIB Swiss Institute of Bioinformatics Basel Switzerland Berlin Institute of Health at Charité-Universitatsmedizin Berlin10117 Germany ELLIS European Laboratory for Learning and Intelligent Systems Germany Department of Biomedical Informatics University of Colorado School of Medicine AuroraCO80045 United States Data Collaboration Center Critical Path Institute 1840 E River Rd. Suite 100 TucsonAZ85718 United States Computer Electrical and Mathematical Sciences & Engineering Division Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia Department of Pediatrics University of Colorado School of Medicine AuroraCO80045 United States Janssen Research and Development RaritanNJ08869 United States Division of General Internal Medicine University of Colorado School of Medicine A

translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability. © 2023, CC BY.

关键词： Ecosystems

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Operational Research: Methods and Applications

arXiv

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arXiv 2023年

作者： Petropoulos, Fotios Laporte, Gilbert Aktas, Emel Alumur, Sibel A. Archetti, Claudia Ayhan, Hayriye Battarra, Maria Bennell, Julia A. Bourjolly, Jean-Marie Boylan, John E. Breton, Michèle Canca, David Charlin, Laurent Chen, Bo Cicek, Cihan Tugrul Cox, Louis Anthony Currie, Christine S.M. Demeulemeester, Erik Ding, Li Disney, Stephen M. Ehrgott, Matthias Eppler, Martin J. Erdogan, Güneş Fortz, Bernard Franco, L. Alberto Frische, Jens Greco, Salvatore Gregory, Amanda J. Hämäläinen, Raimo P. Herroelen, Willy Hewitt, Mike Holmström, Jan Hooker, John N. Işık, Tugçe Johnes, Jill Kara, Bahar Y. Karsu, Özlem Kent, Katherine Köhler, Charlotte Kunc, Martin Kuo, Yong-Hong Letchford, Adam N. Leung, Janny Li, Dong Li, Haitao Lienert, Judit Ljubić, Ivana Lodi, Andrea Lozano, Sebastián Lurkin, Virginie Martello, Silvano McHale, Ian G. Midgley, Gerald Morecroft, John D.W. Mutha, Akshay Oguz, Ceyda Petrovic, Sanja Pferschy, Ulrich Psaraftis, Harilaos N. Rose, Sam Saarinen, Lauri Salhi, Said Song, Jing-Sheng Sotiros, Dimitrios Stecke, Kathryn E. Strauss, Arne K. Tarhan, Istenç Thielen, Clemens Toth, Paolo Van Woensel, Tom Vanden Berghe, Greet Vasilakis, Christos Vaze, Vikrant Vigo, Daniele Virtanen, Kai Wang, Xun Weron, Rafal White, Leroy Yearworth, Mike Yıldırım, E. Alper Zaccour, Georges Zhao, Xuying School of Management University of Bath Bath United Kingdom Makridakis Open Forecasting Center University of Nicosia Nicosia Cyprus Department of Decision Sciences HEC Montréal Montreal Canada Molde University College Molde Norway Cranfield School of Management Cranfield University Cranfield United Kingdom Department of Management Sciences University of Waterloo Waterloo Canada ESSEC Business School in Paris Department of Information Systems Decision Sciences and Statistics Cergy France H. Milton Stewart School of Industrial and Systems Engineering Georgia Institute of Technology Atlanta United States Centre for Decision Research Leeds University Business School University of Leeds Leeds United Kingdom Université du Québec à Montréal Montreal Canada Centre for Marketing Analytics and Forecasting Lancaster University Management School Lancaster University Lancaster United Kingdom School of Engineering Department of Industrial Engineering and Management Science I University of Seville Seville Spain Mila-Quebec AI Institute Montreal Canada Warwick Business School University of Warwick Coventry United Kingdom Department of Industrial Engineering Atilim University Ankara Turkey Department of Business Analytics University of Colorado School of Business Denver United States Cox Associates Denver United States Mathematical Sciences University of Southampton Southampton United Kingdom Faculty of Economics and Business Research Center for Operations Management KU Leuven Leuven Belgium Durham University Business School Durham University Durham United Kingdom Center for Simulation Analytics and Modelling University of Exeter Business School Exeter United Kingdom Department of Management Science Lancaster University Management School Lancaster University Lancaster United Kingdom University of St. Gallen St. Gallen Switzerland HEC - Management School of the University of Liège Liège Belgium Département d'Informatique Université Libre de Bruxelles Bruss

Throughout its history, Operational Research has evolved to include a variety of methods, models and algorithms that have been applied to a diverse and wide range of contexts. This encyclopedic article consists of two main sections: methods and applications. The first aims to summarise the up-to-date knowledge and provide an overview of the state-of-the-art methods and key developments in the various subdomains of the field. The second offers a wide-ranging list of areas where Operational Research has been applied. The article is meant to be read in a nonlinear fashion. It should be used as a point of reference or first-port-of-call for a diverse pool of readers: academics, researchers, students, and practitioners. The entries within the methods and applications sections are presented in alphabetical order. The authors dedicate this paper to the 2023 Turkey/Syria earthquake victims. We sincerely hope that advances in OR will play a role towards minimising the pain and suffering caused by this and future catastrophes. © 2023, CC BY.

关键词： Decision making

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The Minimum Information about CLinical Artificial Intelligence Checklist for Generative Modeling Research (MI-CLAIM-GEN)

arXiv

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arXiv 2024年

作者： Miao, Brenda Y. Chen, Irene Y. Williams, Christopher Y.K. Davidson, Jaysón Garcia-Agundez, Augusto Sun, Shenghuan Zack, Travis Saria, Suchi Arnaout, Rima Quer, Giorgio Sadaei, Hossein J. Torkamani, Ali Beaulieu-Jones, Brett Yu, Bin Gianfrancesco, Milena Butte, Atul J. Norgeot, Beau Sushil, Madhumita Bakar Computational Health Sciences Institute University of California San Francisco San FranciscoCA United States UCSF-UC Berkeley Joint Program in Computational Precision Health University of California Berkeley University of California San Francisco BerkeleyCA United States Department of Electrical Engineering and Computer Sciences University of California Berkeley BerkeleyCA United States Berkeley AI Research University of California Berkeley BerkeleyCA United States Department of Medicine Division of Rheumatology University of California San Francisco San FranciscoCA United States Helen Diller Family Comprehensive Cancer Center University of California San Francisco San FranciscoCA United States Center for Data-driven Insights and Innovation University of California Office of the President OaklandCA United States Bayesian Health New YorkNY10282 United States Department of Computer Science Johns Hopkins University Whiting School of Engineering BaltimoreMD United States Department of Health Policy & Management Johns Hopkins University Bloomberg School of Public Health BaltimoreMD United States Department of Medicine Johns Hopkins Medicine BaltimoreMD21205 United States Departments of Medicine Radiology and Pediatrics University of California San Francisco San FranciscoCA United States Scripps Research Translational Institute La Jolla CA United States Department of Integrative Structural and Computational Biology Scripps Research La Jolla CA92037 United States Department of Medicine University of Chicago ChicagoIL United States Department of Statistics University of California Berkeley BerkeleyCA United States Center for Computational Biology University of California Berkeley BerkeleyCA United States Qualified Health PBC Palo AltoCA United States

Recent advances in generative models, including large language models (LLMs), vision language models (VLMs), and diffusion models, have accelerated the field of natural language and image processing in medicine and marked a significant paradigm shift in how biomedical models can be developed and deployed. While these models are highly adaptable to new tasks, scaling and evaluating their usage presents new challenges not addressed in previous frameworks. In particular, the ability of these models to produce useful outputs with little to no specialized training data ("zero-" or "few-shot" approaches), as well as the open-ended nature of their outputs, necessitate the development of new guidelines for robust reporting of clinical generative model research. In response to gaps in standards and best practices for the development of clinical AI tools identified by US Executive Order 141103 and several emerging national networks for clinical AI evaluation, we begin to formalize some of these guidelines by building on the original MI-CLAIM checklist. The new checklist, MI-CLAIM-GEN (Table 1), aims to address differences in training, evaluation, interpretability, and reproducibility of new generative models compared to non-generative ("predictive") AI models. This MI-CLAIM-GEN checklist also seeks to clarify cohort selection reporting with unstructured clinical data and adds additional items on alignment with ethical standards for clinical AI research. © 2024, CC BY.

关键词： Generative adversarial networks

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Deconvolving Immunologic Networks of the AML Marrow Microenvironment with Spatial Multi-Omic Profiling

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Blood 2024年 144卷 928-928页

作者： Katie Maurer Florian Raths Kenneth Gouin Cameron Y Park Michael Lawson Jake Koh Martin Fabani Kenneth J. Livak Jerome Ritz Robert J. Soiffer Eli Glezer Catherine J. Wu Elham Azizi Harvard Medical School Boston MA Broad Institute of MIT and Harvard Cambridge MA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA Singular Genomics San Diego CA Irving Institute for Cancer Dynamics Columbia University New York NY Department of Biomedical Engineering Columbia University New York NY Translational Immunogenomics Lab Dana-Farber Cancer Institute Boston MA Dana-Farber Cancer Inst. Boston MA Brigham and Women's Hospital Boston MA Herbert Irving Comprehensive Cancer Center Columbia University New York NY Data Science Institute Columbia University New York Department of Computer Science Columbia University New York

The spatial organization of “immune hubs” in tumor microenvironments has gained recognition across histologies and tissues. Bone marrow offers a valuable platform for investigating immune hubs in the context of acute myeloid leukemia (AML) following hematopoietic stem cell transplant (HSCT). This setting may provide fresh insights into mechanisms of relapse and maintenance of remission after donor lymphocyte infusion (DLI). While it is generally understood that DLI exerts its effects through a graft-versus-leukemia (GVL) response, the specific cellular players and spatial organization driving GVL remain unidentified. Addressing this question can inform the rational design of cancer cellular therapies. A major challenge for spatial transcriptomic assays interrogating bone marrow samples is RNA degradation due to decalcification in addition to that caused by formalin fixation and paraffin embedding (FFPE). Furthermore, existing spatial platforms lack single-cell resolution and their throughput is generally limited to a small number of samples. To address these constraints, Singular Genomics is developing the G4XTM, an in-situ next-generation sequencing (NGS) platform that enables rapid sample throughput (up to 20-fold greater than existing platforms), and enables combined readouts of transcriptomics, proteomics, and fluorescent H&E staining in the same FFPE section. We used a pre-release version of the G4X to analyze bone marrow biopsies of patients with relapsed AML before and after treatment with DLI. We profiled 24 specimens (6 responder [R] pre-DLI, 7 R post-DLI, 5 non-responder [NR] pre-DLI, 6 NR post-DLI), aiming to elucidate the spatial relationships of immune cellular networks in the marrow microenvironment. Our targeted transcript panel included 153 immune- and marrow-related genes defining specific T cell subsets and other immune cell lineages, as well as 8 protein markers (CD3, CD4, CD8, CD45RA, HLA-DR, CD34, KI67, ATPase). We filtered out cells with transc

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GREGoR: Accelerating Genomics for Rare Diseases

arXiv

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arXiv 2024年

作者： Dawood, Moez Heavner, Ben Wheeler, Marsha M. Ungar, Rachel A. LoTempio, Jonathan Wiel, Laurens Berger, Seth Bernstein, Jonathan A. Chong, Jessica X. Délot, Emmanuèle C. Eichler, Evan E. Gibbs, Richard A. Lupski, James R. Shojaie, Ali Talkowski, Michael E. Wagner, Alex H. Wei, Chia-Lin Wellington, Christopher Wheeler, Matthew T. Carvalho, Claudia M.B. Gifford, Casey A. May, Susanne Miller, Danny E. Rehm, Heidi L. Sedlazeck, Fritz J. Vilain, Eric O'Donnell-Luria, Anne Posey, Jennifer E. Chadwick, Lisa H. Bamshad, Michael J. Montgomery, Stephen B. Human Genome Sequencing Center Baylor College of Medicine HoustonTX United States Department of Molecular and Human Genetics Baylor College of Medicine HoustonTX United States Medical Scientist Training Program Baylor College of Medicine HoustonTX United States Department of Biostatistics University of Washington SeattleWA United States Department of Genetics School of Medicine Stanford University StanfordCA United States Department of Pathology School of Medicine Stanford University Stanford CA United States Stanford Center for Biomedical Ethics School of Medicine Stanford University Stanford CA United States Institute for Clinical and Translational Science University of California IrvineCA United States Division of Cardiovascular Medicine School of Medicine Stanford University Stanford CA United States Division of Genetics and Metabolism Children’s National Rare Disease Institute WashingtonDC United States Center for Genetic Medicine Research Children’s National Rare Disease Institute WashingtonDC United States Department of Genomics and Precision Medicine George Washington University WashingtonDC United States Department of Pediatrics School of Medicine Stanford University Stanford CA United States Department of Pediatrics Dvision of Genetic Medicine University of Washington SeattleWA United States Brotman Baty Institute for Precision Medicine University of Washington SeattleWA United States Department of Genome Sciences University of Washington SeattleWA United States Howard Hughes Medical Institute University of Washington SeattleWA United States Department of Pediatrics Baylor College of Medicine HoustonTX United States Center for Genomic Medicine Massachusetts General Hospital BostonMA United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard BostonMA United States Department of Neurology Massachusetts General Hospital Harvard Medical School BostonMA United States Stanley Center for

Rare diseases are collectively common, affecting approximately one in twenty individuals worldwide. In recent years, rapid progress has been made in rare disease diagnostics due to advances in DNA sequencing, development of new computational and experimental approaches to prioritize genes and genetic variants, and increased global exchange of clinical and genetic data. However, more than half of individuals suspected to have a rare disease lack a genetic diagnosis. The Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium was initiated to study thousands of challenging rare disease cases and families and apply, standardize, and evaluate emerging genomics technologies and analytics to accelerate their adoption in clinical practice. Further, all data generated, currently representing ~7500 individuals from ~3000 families, is rapidly made available to researchers worldwide via the Genomic data science Analysis, Visualization, and Informatics Lab-space (AnVIL) to catalyze global efforts to develop approaches for genetic diagnoses in rare diseases (https://***/data). The majority of these families have undergone prior clinical genetic testing but remained unsolved, with most being exome-negative. Here, we describe the collaborative research framework, datasets, and discoveries comprising GREGoR that will provide foundational resources and substrates for the future of rare disease genomics. © 2024, CC BY.

关键词： Genome

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Corrigendum to "Dissemination in time and space in presymptomatic granulin mutation carriers: A spatial chronnectome study" [Neurobiology of Aging Volume 108, December 2021, Pages 155-167]

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Neurobiology of aging 2022年 119卷 140-144页

作者： Enrico Premi Marcello Giunta Armin Iraji Srinivas Rachakonda VinceD Calhoun Stefano Gazzina Alberto Benussi Roberto Gasparotti Silvana Archetti Martina Bocchetta Dave Cash Emily Todd Georgia Peakman Rhian Convery John C van Swieten Lize Jiskoot Raquel Sanchez-Valle Fermin Moreno Robert Laforce Caroline Graff Matthis Synofzik Daniela Galimberti JamesB Rowe Mario Masellis Carmela Tartaglia Elizabeth Finger Rik Vandenberghe Alexandre de Mendonça Fabrizio Tagliavini Chris R Butler Isabel Santana Alexander Gerhard Isabelle Le Ber Florence Pasquier Simon Ducharme Johannes Levin Adrian Danek Sandro Sorbi Markus Otto Jonathan D Rohrer Barbara Borroni Stroke Unit Azienda Socio Sanitaria Territoriale Spedali Civili Brescia Brescia Italy. Centre for Neurodegenerative Disorders Department of Clinical and Experimental Sciences University of Brescia Brescia Italy. Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University Georgia Institute of Technology Emory University Atlanta GA USA. Tri-institutional Center for Translational Research in Neuroimaging and Data Science (TReNDS) Georgia State University Georgia Institute of Technology Emory University Atlanta GA USA Departments of Psychology and Computer Science Georgia State University Atlanta GA USA Department of Electrical and Computer Engineering Georgia Institute of Technology Atlanta GA USA. Neurophysiology Unit Azienda Socio Sanitaria Territoriale Spedali Civili Brescia Brescia Italy. Neuroradiology Unit University of Brescia Brescia Italy. Laboratory Unit Azienda Socio Sanitaria Territoriale Spedali Civili Brescia Brescia Italy. Department of Neurodegenerative Disease Dementia Research Centre UCL Institute of Neurology Queen Square London UK. Department of Neurology Erasmus Medical Centre Rotterdam the Netherlands. Alzheimer's disease and Other Cognitive Disorders Unit Neurology Service Hospital Clinic University of Barcelona Barcelona Spain. Cognitive Disorders Unit Department of Neurology Donostia University Hospital San Sebastian Gipuzkoa Spain. Clinique Interdisciplinaire de Memoire Department des Sciences Neurologiques CHU de Quebec and Faculte de Medecine Universite Laval Quebec Canada. Center for Alzheimer Research Division of Neurogeriatrics Department of Neurobiology Care Sciences and Society Bioclinicum Karolinska Institutet Solna Sweden. Department of Neurodegenerative Diseases Hertie-Institute for Clinical Brain Research and Center of Neurology University of Tubingen Tubingen Germany. Fondazione Ca' Granda IRCCS Ospedale Policlinico Milan Italy University of Milan

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Brain age acceleration as biomarker of Alzheimer’s disease progression: Functional network connectivity analysis

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Alzheimer's & Dementia 2021年第S1期17卷

作者： Mohammad S.E. Sendi David H Salat Vince D Calhoun School of Electrical and Computer Engineering (ECE) at the Georgia Institute of Technology Atlanta GA USA Tri-Institutional Georgia State University/Georgia Institute of Technology/Emory University Center for Translational Research in Neuroimaging and Data Science Atlanta GA USA Wallace H. Coulter Department of Biomedical Engineering at Emory University and Georgia Tech Atlanta GA USA Neuroimaging Research for Veterans Center VA Boston Healthcare System Boston MA USA Massachusetts General Hospital Charlestown MA USA Harvard Medical School Boston MA USA Georgia State University Atlanta GA USA

Background The brain age gap, the difference between an individual’s brain predicted age and chronological age, is used as a brain disease biomarker and aging. To date, although previous studies utilized mostly structural magnetic resonance imaging (MRI) data to predict brain age, less work has used functional network connectivity (FNC) from resting-state functional MRI (rs-fMRI) to indicate brain age and its link with Alzheimer’s disease (AD) progression. This study aims to estimate brain age from FNC and introduce it as a biomarker of AD progression. Method This study used 1091 rs-fMRI data and the chronological age at the time of scanning, ranging from 42-95, from the Open Access Series of Imaging Studies (OASIS)-3 cohort. This dataset includes 1021 healthy subjects (HC) and 70 AD patients. We used group independent component analysis to estimate 53 components for the whole-brain. Then, FNC feature, in total 1378, of each subject was calculated by applying the Pearson correlation. A support vector regression (SVR) was trained on 951 HC subjects in which FNC features and the chronological age was served as predictor and prediction output, respectively. We then tested the trained model on 70 HC (age mean± sd: 73.66± 7.47) and 70 AD (age mean± sd: 73.34± 7.51) subjects to predict their brain age. Result The correlation between predicted brain age and the chronological age of HC test data was R=0.73, (p=5.3e -13 , N=70), while the correlation between predicted brain age and AD patients' chronological age was R=0.33 (p=0.004, N=70). This result shows that the model based on HC could better predict the HC age than the AD patients. The brain age gap mean and standard deviation for the test HC and AD group was -2.2581± 5.0879 and 2.0814± 7.4520. This result shows that the brain age gap was increased in AD (Cohen’s d=0.68, p<0.001). Conclusion We proved that FNC, estimated from rs-fMRI, could predict the brain age in HC. Also, we found an acceleration in the brain predict

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