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arXiv 2022年

作者： Bano, Sophia Casella, Alessandro Vasconcelos, Francisco Qayyum, Abdul Benzinou, Abdesslam Mazher, Moona Meriaudeau, Fabrice Lena, Chiara Cintorrino, Ilaria Anita De Paolis, Gaia Romana Biagioli, Jessica Grechishnikova, Daria Jiao, Jing Bai, Bizhe Qiao, Yanyan Bhattarai, Binod Gaire, Rebati Raman Subedi, Ronast Vazquez, Eduard Plotka, Szymon Lisowska, Aneta Sitek, Arkadiusz Attilakos, George Wimalasundera, Ruwan David, Anna L. Paladini, Dario Deprest, Jan De Momi, Elena Mattos, Leonardo S. Moccia, Sara Stoyanov, Danail Department of Computer Science University College London United Kingdom Department of Advanced Robotics Istituto Italiano di Tecnologia Italy Department of Electronics Information and Bioengineering Politecnico di Milano Italy The BioRobotics Institute Department of Excellence in Robotics and AI Scuola Superiore Sant'Anna Italy Fetal Medicine Unit Elizabeth Garrett Anderson Wing University College London Hospital United Kingdom EGA Institute for Women's Health Faculty of Population Health Sciences University College London United Kingdom Department of Development and Regeneration University Hospital Leuven Belgium Department of Fetal and Perinatal Medicine Istituto Giannina Gaslini Italy ENIB UMR CNRS 6285 LabSTICC 29238 France Department of Computer Engineering and Mathematics University Rovira i Virgili Spain ImViA Laboratory University of Bourgogne Franche-Comté France Physics Department Lomonosov Moscow State University Russia Fudan University China Medical Computer Vision and Robotics Group Department of Mathematical and Computational Sciences University of Toronto Canada Co. Ltd China NepAL Applied Mathematics and Informatics Institute for Research Nepal Redev Technology United Kingdom Sano Center for Computational Medicine Poland Quantitative Healthcare Analysis Group Informatics Institute University of Amsterdam Amsterdam Netherlands Center for Advanced Medical Computing and Simulation Massachusetts General Hospital Harvard Medical School BostonMA United States

Fetoscopy laser photocoagulation is a widely adopted procedure for treating Twin-to-Twin Transfusion Syndrome (TTTS). The procedure involves photocoagulation pathological anastomoses to restore a physiological blood exchange among twins. The procedure is particularly challenging, from the surgeon's side, due to the limited field of view, poor manoeuvrability of the fetoscope, poor visibility due to amniotic fluid turbidity, and variability in illumination. These challenges may lead to increased surgery time and incomplete ablation of pathological anastomoses, resulting in persistent TTTS. Computer-assisted intervention (CAI) can provide TTTS surgeons with decision support and context awareness by identifying key structures in the scene and expanding the fetoscopic field of view through video mosaicking. research in this domain has been hampered by the lack of high-quality data to design, develop and test CAI algorithms. Through the Fetoscopic Placental Vessel Segmentation and Registration (FetReg2021) challenge, which was organized as part of the MICCAI2021 Endoscopic Vision (EndoVis) challenge, we released the first large-scale multi-center TTTS dataset for the development of generalized and robust semantic segmentation and video mosaicking algorithms with a focus on creating drift-free mosaics from long duration fetoscopy videos. For this challenge, we released a dataset of 2060 images, pixel-annotated for vessels, tool, fetus and background classes, from 18 in-vivo TTTS fetoscopy procedures and 18 short video clips of an average length of 411 frames for developing placental scene segmentation and frame registration for mosaicking techniques. Seven teams participated in this challenge and their model performance was assessed on an unseen test dataset of 658 pixel-annotated images from 6 fetoscopic procedures and 6 short clips. The challenge provided an opportunity for creating generalized solutions for fetoscopic scene understanding and mosaicking. In this paper,

关键词： Pixels

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Quantitative Prediction of Aggregation-Induced Emission: A Full Quantum Mechanical Approach to the Optical Spectra

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advanced Materials 2020年第28期59卷 11647-11652页

作者： Zhang, Wei Liu, Jinfeng Jin, Xinsheng Gu, Xinggui Zeng, Xiao Cheng He, Xiao Li, Hui Beijing Advanced Innovation Center for Soft Matter Science and Engineering Beijing University of Chemical Technology Beijing100029 China Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development School of Chemistry and Molecular Engineering East China Normal University Shanghai200062 China Department of Basic Medicine and Clinical Pharmacy China Pharmaceutical University Nanjing210009 China Department of Chemistry University of Nebraska LincolnNE68588 United States NYU-ECNU Center for Computational Chemistry at NYU Shanghai Shanghai200062 China

Full quantum mechanical (FQM) calculation of the excited state of aggregation-induced-emission (AIE) materials is highly sought but still a challenging tosh Herein, we employed the recently developed electrostatically embedded generalized molecular fractionation (EE-GMF) method, a method based on the systematic fragmentation approach, to predict, for the first time, the spectra of a prototype AIE fluorophore: di(p-methoxylphenyl)dibenzofidvene (FTPE). Compared to the single molecular or QM/MM calculations, the EE-GMF method shows significantly improved accuracy, nearly reproducing the experimental optical spectra of FTPE in both condensed phases. Importantly, we show that the conventional restriction of the intramolecular rotation mechanism cannot fully account for AIE, whereas the two-body intermolecular quantum mechanical interaction plays a crucial role in AIE. © 2020 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

关键词： Emission spectroscopy

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The need to implement FAIR principles in biomolecular simulations

arXiv

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arXiv 2024年

作者： Amaro, R. Åqvist, J. Bahar, I. Battistini, F. Bellaiche, A. Beltran, D. Biggin, P.C. Bonomi, M. Bowman, G.R. Bryce, R. Bussi, G. Carloni, P. Case, D. Cavalli, A. Chang, C.A. Cheatham, T.E. Cheung, M.S. Chipot, C. Chong, L.T. Choudhary, P. Cisneros, G.A. Clementi, C. Collepardo-Guevara, R. Coveney, P. Covino, R. Crawford, T.D. Dal Peraro, M. de Groot, B. Delemotte, L. De Vivo, M. Essex, J. Fraternali, F. Gao, J. Gelpí, J.L. Gervasio, F.L. Gonzalez-Nilo, F.D. Grubmüller, H. Guenza, M.G. Guzman, H.V. Harris, S. Head-Gordon, T. Hernandez, R. Hospital, A. Huang, N. Huang, X. Hummer, G. Iglesias-Fernández, J. Jensen, J.H. Jha, S. Jiao, W. Jorgensen, W.L. Kamerlin, S.C.L. Khalid, S. Laughton, C. Levitt, M. Limongelli, V. Lindahl, E. Lindorff-Larsen, K. Loverde, S. Lundborg, M. Luo, Y.L. Luque, F.J. Lynch, C.I. MacKerell, A. Magistrato, A. Marrink, S.J. Martin, H. McCammon, J.A. Merz, K. Moliner, V. Mulholland, A. Murad, S. Naganathan, A.N. Nangia, S. Noe, F. Noy, A. Oláh, J. O'Mara, M. Ondrechen, M.J. Onuchic, J.N. Onufriev, A. Osuna, S. Palermo, G. Panchenko, A.R. Pantano, S. Parish, C. Parrinello, M. Perez, A. Perez-Acle, T. Perilla, J.R. Pettitt, B.M. Pietropaolo, A. Piquemal, J.-P. Poma, A. Praprotnik, M. Ramos, M.J. Ren, P. Reuter, N. Roitberg, A. Rosta, E. Rovira, C. Roux, B. Röthlisberger, U. Sanbonmatsu, K. Schlick, T. Shaytan, A.K. Simmerling, C. Smith, J.C. Sugita, Y. Świderek, K. Taiji, M. Tao, P. Tikhonova, I.G. Tirado-Rives, J. Tuñón, I. Van Der Kamp, M.W. Van der Spoel, D. Velankar, S. Voth, G.A. Wade, R. Warshel, A. Welborn, V.V. Wetmore, S. Wong, C.F. Yang, L.-W. Zacharias, M. Orozco, M. Department of Molecular Biology University of California San DiegoCA United States Department of Cell and Molecular Biology Uppsala University Uppsala Sweden Laufer Center for Physical and Quantitative Biology Renaissance School of Medicine Stony Brook University Stony BrookNY United States Department of Biochemistry and Cell Biology Renaissance School of Medicine Stony Brook University Stony BrookNY United States Barcelona Spain European Molecular Biology Laboratory European Bioinformatics Institute Hinxton United Kingdom Structural Bioinformatics and Computational Biochemistry Department of Biochemistry University of Oxford Oxford United Kingdom Institut Pasteur Université Paris Cité CNRS UMR 3528 Computational Structural Biology Unit Paris France Department of Biochemistry and Biophysics University of Pennsylvania PhiladelphiaPA United States Division of Pharmacy and Optometry University of Manchester Manchester United Kingdom Scuola Internazionale Superiore di Studi Avanzati-SISSA Trieste Italy Computational Biomedicine Institute of Advanced Simulations IAS-5 Institute for Neuroscience and Medicine INM-9 Forschungszentrum Jülich GmbH Jülich Germany Department of Physics and Universitätsklinikum RWTH Aachen University Aachen Germany Department of Chemistry & Chemical Biology Rutgers University PiscatawayNJ United States Istituto Italiano di Tecnologia Drug Discovery and Development Bologna Italy Lausanne Switzerland Department of Chemistry University of California RiversideCA United States Department of Medicinal Chemistry College of Pharmacy University of Utah Salt Lake CityUT United States Department of Physics University of Washington SeattleWA United States Pacific Northwest National Laboratory RichlandWA United States LIA CNRS-UIUC UMR n°7019 Université de Lorraine Vandœuvre-lès-Nancy France Department of Physics University of Illinois at Urbana-Champaign UrbanaIL United States Department of Biochemistry and Molecular Biol

The communities that embraced data archiving efforts decades ago are now, in the era of data-driven biology, those gaining the most from the AI revolution. The structural biology community was a pioneer in this regard by establishing the Protein Data Bank (PDB) in 1971 and making data accessible using the FAIR (Findable, Accessible, Interoperable and Reusable) principles even before these were articulated [1, 2]. The genomics/bioinformatics community has followed the example, establishing many widely used databases [3, 4]. By contrast, molecular simulation has been anchored in usage paradigms dating back to the seventies, when molecular dynamics (MD) simulation was first applied to study biomacromolecules [5]. At that time, MD was used by theoretical physicists and chemists in "proof of concept" simulations. Still, fifty years later, MD has evolved into a cornerstone molecular biology technique that can provide accurate quantitative analysis and property prediction. MD is now employed by tens of thousands of researchers worldwide, accounting for roughly 15% of global supercomputer usage. Unfortunately, these rich and costly data are not systematically maintained, and when further analyses are required, simulations have to be rerun-an unacceptable situation from scientific, environmental and sustainability standpoints. In this letter, we argue for a collaborative endeavor to archive MD simulation data and describe ongoing efforts to establish cost-effective and sustainable data archiving strategies. © 2024, CC BY-NC-SA.

关键词： Biotic

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FUTURE-AI: International consensus guideline for trustworthy and deployable artificial intelligence in healthcare

arXiv

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arXiv 2023年

作者： Lekadir, Karim Feragen, Aasa Fofanah, Abdul Joseph Frangi, Alejandro F. Buyx, Alena Emelie, Anais Lara, Andrea Porras, Antonio R. Chan, An-Wen Navarro, Arcadi Glocker, Ben Botwe, Benard O. Khanal, Bishesh Beger, Brigit Wu, Carol C. Cintas, Celia Langlotz, Curtis P. Rueckert, Daniel Mzurikwao, Deogratias Fotiadis, Dimitrios I. Zhussupov, Doszhan Ferrante, Enzo Meijering, Erik Weicken, Eva González, Fabio A. Asselbergs, Folkert W. Prior, Fred Krestin, Gabriel P. Collins, Gary S. Tegenaw, Geletaw S. Kaissis, Georgios Misuraca, Gianluca Tsakou, Gianna Dwivedi, Girish Kondylakis, Haridimos Jayakody, Harsha Woodruf, Henry C. Mayer, Horst Joachim Aerts, Hugo JWL Walsh, Ian Chouvarda, Ioanna Buvat, Irène Tributsch, Isabell Rekik, Islem Duncan, James Kalpathy-Cramer, Jayashree Zahir, Jihad Park, Jinah Mongan, John Gichoya, Judy W. Schnabel, Julia A. Kushibar, Kaisar Riklund, Katrine Mori, Kensaku Marias, Kostas Amugongo, Lameck M. Fromont, Lauren A. Maier-Hein, Lena Alberich, Leonor Cerdá Rittner, Leticia Phiri, Lighton Marrakchi-Kacem, Linda Donoso-Bach, Lluís Martí-Bonmatí, Luis Cardoso, M. Jorge Bobowicz, Maciej Shabani, Mahsa Tsiknakis, Manolis Zuluaga, Maria A. Bielikova, Maria Fritzsche, Marie-Christine Camacho, Marina Linguraru, Marius George Wenzel, Markus De Bruijne, Marleen Tolsgaard, Martin G. Ghassemi, Marzyeh Ashrafuzzaman, Md Goisauf, Melanie Yaqub, Mohammad Abadía, Mónica Cano Mahmoud, Mukhtar M.E. Elattar, Mustafa Rieke, Nicola Papanikolaou, Nikolaos Lazrak, Noussair Díaz, Oliver Salvado, Olivier Pujol, Oriol Sall, Ousmane Guevara, Pamela Gordebeke, Peter Lambin, Philippe Brown, Pieta Abolmaesumi, Purang Dou, Qi Lu, Qinghua Osuala, Richard Nakasi, Rose Zhou, S. Kevin Napel, Sandy Colantonio, Sara Albarqouni, Shadi Joshi, Smriti Carter, Stacy Klein, Stefan Petersen, Steffen E. Aussó, Susanna Awate, Suyash Raviv, Tammy Riklin Cook, Tessa Mutsvangwa, Tinashe E.M. Rogers, Wendy A. Niessen, Wiro J. Puig-Bosch, Xènia Zeng, Yi Mohammed, Yunusa G. Aquino, Yves Saint James Salahuddin, Zohaib Starmans, Martijn P.A. Department de Matemàtiques i Informàtica Universitat de Barcelona Barcelona Spain Barcelona Spain DTU Compute Technical University of Denmark Kgs Lyngby Denmark Department of Mathematics and Computer Science Faculty of Science and Technology Milton Margai Technical University Freetown Sierra Leone Center for Computational Imaging & Simulation Technologies in Biomedicine Schools of Computing and Medicine University of Leeds Leeds United Kingdom Cardiovascular Science and Electronic Engineering Departments KU Leuven Leuven Belgium Institute of History and Ethics in Medicine Technical University of Munich Munich Germany Faculty of Engineering of Systems Informatics and Sciences of Computing Galileo University Guatemala City Guatemala Department of Biostatistics and Informatics Colorado School of Public Health University of Colorado Anschutz Medical Campus AuroraCO United States Department of Medicine Women’s College Research Institute University of Toronto Toronto Canada Universitat Pompeu Fabra BarcelonaBeta Brain Research Center Barcelona Spain Department of Computing Imperial College London London United Kingdom School of Biomedical & Allied Health Sciences University of Ghana Accra Ghana Department of Midwifery & Radiography School of Health & Psychological Sciences City University of London United Kingdom Kathmandu Nepal European Heart Network Brussels Belgium Department of Thoracic Imaging University of Texas MD Anderson Cancer Center Houston United States IBM Research Africa Nairobi Kenya Departments of Radiology Medicine and Biomedical Data Science Stanford University School of Medicine Stanford United States Institute for AI and Informatics in Medicine Klinikum rechts der Isar Technical University Munich Munich Germany Department of Computing Imperial College London London United Kingdom Muhimbili University of Health and Allied Sciences Dar es Salaam Tanzania United Republic of Ioannina Greece Almaty AI Lab Almaty Kazakhstan

Background: Despite major advances in artificial intelligence (AI) research for healthcare, the deployment and adoption of AI technologies remain limited in clinical practice. In recent years, concerns have been raised about the clinical, technical, ethical and legal risks associated with healthcare AI. To increase adoption in the real world, it is essential that AI technologies are trusted and accepted by patients, clinicians, health organisations and authorities. This paper describes the FUTURE-AI framework as the first international consensus guideline for trustworthy AI in healthcare. Methods: The FUTURE-AI consortium was founded in 2021 and now comprises 117 interdisciplinary experts from 50 countries representing all continents, including AI scientists, clinical researchers, biomedical ethicists, and social scientists. Over a two-year period, the consortium established guiding principles and best practices for trustworthy and deployable AI through an iterative process comprising an in-depth literature review, a modified Delphi survey, and online consensus meetings. Findings: The FUTURE-AI framework was established based on six guiding principles for trustworthy AI in healthcare, i.e. Fairness, Universality, Traceability, Usability, Robustness and Explainability. Through consensus, a set of 30 best practices were defined, addressing technical, clinical, socio-ethical and legal dimensions of trustworthy AI. The recommendations cover the entire lifecycle of healthcare AI, from design, development and validation to regulation, deployment, and monitoring. Interpretation: FUTURE-AI is a structured, risk-informed framework which provides guidance for constructing healthcare AI tools that will be trusted, deployed and adopted in real-world clinical practice. researchers are encouraged to take the recommendations into account in proof-of-concept stages to facilitate future translation towards clinical practice of healthcare AI. Copyright © 2023, The Authors. All rights

关键词： Clinical research

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Synergy of Binary Substitutions for Improving the Cycle Performance in LiNiO2 Revealed by Ab Initio Materials Informatics

arXiv

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arXiv 2020年

作者： Yoshida, Tomohiro Maezono, Ryo Hongo, Kenta Department of Computer-Aided Engineering and Development Sumitomo Metal Mining Co. Ltd. 3-5 Sobiraki-cho NiihamaEhime792-0001 Japan School of Information Science JAIST Asahidai 1-1 IshikawaNomi923-1292 Japan Computational Engineering Applications Unit RIKEN 2-1 Hirosawa SaitamaWako351-0198 Japan Research Center for Advanced Computing Infrastructure JAIST Asahidai 1-1 NomiIshikawa923-1292 Japan Center for Materials Research by Information Integration Research and Services Division of Materials Data and Integrated System National Institute for Materials Science 1-2-1 Sengen TsukubaIbaraki305-0047 Japan PRESTO Japan Science and Technology Agency 4-1-8 Honcho SaitamaKawaguchi-shi322-0012 Japan

We explore LiNiO2-based cathode materials with two-element substitutions by an ab initio simulation based materials informatics (AIMI) approach. According to our previous study, a higher cycle performance strongly correlates with less structural change during charge–discharge cycles;the latter can be used for evaluating the former. However, if we target the full substitution space, full simulations are infeasible even for all binary combinations. To circumvent such an exhaustive search, we rely on Bayesian optimization. Actually, by searching only 4% of all the combinations, our AIMI approach discovered two promising combinations, Cr-Mg and Cr-Re, whereas each atom itself never improved the performance. We conclude that the synergy never emerges from a common strategy restricted to combinations of "good" elements that individually improve the performance. In addition, we propose a guideline for the binary substitutions by elucidating the mechanism of crystal structure change. Copyright © 2020, The Authors. All rights reserved.

关键词： Binary alloys

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

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NATURE 2023年第7948期614卷 E38-E38页

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

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

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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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The repertoire of mutational signatures in human cancer (vol 578, pg 94, 2020)

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NATURE 2023年第7948期614卷 E41-E41页

作者： Alexandrov, Ludmil B. Kim, Jaegil Haradhvala, Nicholas J. Huang, Mi Ni Ng, Alvin Wei Tian Wu, Yang Boot, Arnoud Covington, Kyle R. Gordenin, Dmitry A. Bergstrom, Erik N. Islam, S. M. Ashiqul Lopez-Bigas, Nuria Klimczak, Leszek J. McPherson, John R. Morganella, Sandro Sabarinathan, Radhakrishnan Wheeler, David A. Mustonen, Ville Getz, Gad Rozen, Steven G. Stratton, Michael R. Department of Cellular and Molecular Medicine Department of Bioengineering Moores Cancer Center University of California San Diego CA USA Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Department of Cellular and Molecular Medicine and Department of Bioengineering University of California San Diego La Jolla CA USA UC San Diego Moores Cancer Center San Diego CA USA University of California San Diego San Diego CA USA Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Massachusetts General Hospital Boston MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Laboratory for Medical Science Mathematics RIKEN Center for Integrative Medical Sciences Yokohama Japan Computational Biology Program Ontario Institute for Cancer Research Toronto ON Canada Programme in Cancer & Stem Cell Biology Duke-NUS Medical School Singapore Singapore Centre for Computational Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Duke-NUS Medical School Singapore Singapore Programme in Cancer and Stem Cell Biology Centre for Computational Biology Duke-NUS Medical School Singapore Singapore SingHealth Duke-NUS Institute of Precision Medicine National Heart Centre Singapore Singapore Singapore Cancer Science Institute of Singapore National University of Singapore Singapore Singapore Institute of Molecular and Cell Biology Singapore Singapore Laboratory of Cancer Epigenome Division of Medical Science National Cancer Centre Singapore Singapore Singapore Duke-NUS Medical School Singapore Singapore Human Genome Sequencing Center Baylor College of Medicine Houston TX USA Dan L. Duncan Cancer Center Baylor College of Medicine Houston TX USA Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA Genome Integrity and Structural Biology Laboratory National Ins

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The evolutionary history of 2,658 cancers (vol 578, pg 122, 2020)

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NATURE 2023年第7948期614卷 E42-E42页

作者： Gerstung, Moritz Jolly, Clemency Leshchiner, Ignaty Dentro, Stefan C. Gonzalez, Santiago Rosebrock, Daniel Mitchell, Thomas J. Rubanova, Yulia Anur, Pavana Yu, Kaixian Tarabichi, Maxime Deshwar, Amit Wintersinger, Jeff Kleinheinz, Kortine Vazquez-Garcia, Ignacio Haase, Kerstin Jerman, Lara Sengupta, Subhajit Macintyre, Geoff Malikic, Salem Donmez, Nilgun Livitz, Dimitri G. Cmero, Marek Demeulemeester, Jonas Schumacher, Steven Fan, Yu Yao, Xiaotong Lee, Juhee Schlesner, Matthias Boutros, Paul C. Bowtell, David D. Zhu, Hongtu Getz, Gad Imielinski, Marcin Beroukhim, Rameen Sahinalp, S. Cenk Ji, Yuan Peifer, Martin Markowetz, Florian Mustonen, Ville Yuan, Ke Wang, Wenyi Morris, Quaid D. Spellman, Paul T. Wedge, David C. Van Loo, Peter European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Wellcome Sanger Institute Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany University of Ljubljana Ljubljana Slovenia The Francis Crick Institute London UK Big Data Institute University of Oxford Oxford UK Wellcome Sanger Institute Wellcome Genome Campus Hinxton UK Big Data Institute Li Ka Shing Centre University of Oxford Oxford UK University of Cambridge Cambridge UK Cambridge University Hospitals NHS Foundation Trust Cambridge UK Department of Applied Mathematics and Theoretical Physics Centre for Mathematical Sciences University of Cambridge Cambridge UK Department of Epidemiology and Biostatistics Memorial Sloan Kettering Cancer Center New York NY USA Department of Statistics Columbia University New York NY USA Department of Haematology University of Cambridge Cambridge UK University of Leuven Leuven Belgium Broad Institute of MIT and Harvard Cambridge MA USA Center for Cancer Research Massachusetts General Hospital Charlestown MA USA Department of Pathology Massachusetts General Hospital Boston MA USA Harvard Medical School Boston MA USA Center for Cancer Research Massachusetts General Hospital Boston MA USA Dana-Farber Cancer Institute Boston MA USA Department of Medical Oncology Dana-Farber Cancer Institute Boston MA USA Department of Cancer Biology Dana-Farber Cancer Institute Boston MA USA Oxford NIHR Biomedical Research Centre Oxford UK Oxford NIHR Biomedical Research Centre University of Oxford Oxford UK University of Toronto Toronto Ontario Canada Vector Institute Toronto Ontario Canada Vector Institute Toronto ON Canada Department of Computer Science University of Toronto Toronto ON Canada Ontario Institute for Cancer Research Toronto Ontario Canada University of California Los Angeles

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Genomic basis for RNA alterations in cancer (vol 578, pg 129, 2020)

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NATURE 2023年第7948期614卷 E37-E37页

作者： Calabrese, Claudia Davidson, Natalie R. Demircioglu, Deniz Fonseca, Nuno A. He, Yao Lehmann, Kjong-Van Liu, Fenglin Shiraishi, Yuichi Soulette, Cameron M. Urban, Lara Greger, Liliana Li, Siliang Liu, Dongbing Perry, Marc D. Xiang, Qian Zhang, Fan Zhang, Junjun Bailey, Peter Erkek, Serap Hoadley, Katherine A. Hou, Yong Huska, Matthew R. Kilpinen, Helena Korbel, Jan O. Marin, Maximillian G. Markowski, Julia Nandi, Tannistha Pan-Hammarstrom, Qiang Pedamallu, Chandra Sekhar Siebert, Reiner Stark, Stefan G. Su, Hong Tan, Patrick Waszak, Sebastian M. Yung, Christina Zhu, Shida Awadalla, Philip Creighton, Chad J. Meyerson, Matthew Ouellette, B. F. Francis Wu, Kui Yang, Huanming Brazma, Alvis Brooks, Angela N. Goke, Jonathan Ratsch, Gunnar Schwarz, Roland F. Stegle, Oliver Zhang, Zemin European Molecular Biology Laboratory European Bioinformatics Institute Hinxton UK European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Cambridge UK Genome Biology Unit European Molecular Biology Laboratory (EMBL) Heidelberg Germany CIBIO/InBIO - Research Center in Biodiversity and Genetic Resources Universidade do Porto Vairão Portugal Berlin Institute for Medical Systems Biology Max Delbruck Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) partner site Berlin Germany German Cancer Research Center (DKFZ) Heidelberg Germany Berlin Institute for Medical Systems Biology Max Delbrück Center for Molecular Medicine Berlin Germany German Cancer Consortium (DKTK) Partner site Berlin Berlin Germany European Molecular Biology Laboratory Genome Biology Unit Heidelberg Germany Division of Computational Genomics and Systems Genetics German Cancer Research Center (DKFZ) Heidelberg Germany ETH Zurich Zurich Switzerland Memorial Sloan Kettering Cancer Center New York NY USA Weill Cornell Medical College New York NY USA SIB Swiss Institute of Bioinformatics Lausanne Switzerland University Hospital Zurich Zurich Switzerland Computational Biology Center Memorial Sloan Kettering Cancer Center New York NY USA Department of Biology ETH Zurich Zürich Switzerland Department of Computer Science ETH Zurich Zurich Switzerland Korea University Seoul South Korea Computational and Systems Biology Program Memorial Sloan Kettering Cancer Center New York NY USA Department of Physiology and Biophysics Weill Cornell Medicine New York NY USA Institute for Computational Biomedicine Weill Cornell Medicine New York NY USA Controlled Department and Institution New York NY USA Englander Institute for Precision Medicine Weill Cornell Medicine New York NY USA National University of Singapore Singapore Singapore Genome Institute of Singapore Singapore Singapore Computational and Systems Biology Genome Institute of Singap

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