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arXiv 2024年

作者： Willett, Francis R. Li, Jingyuan Le, Trung Fan, Chaofei Chen, Mingfei Shlizerman, Eli Chen, Yue Zheng, Xin Okubo, Tatsuo S. Benster, Tyler Lee, Hyun Dong Kounga, Maxwell Buchanan, E. Kelly Zoltowski, David Linderman, Scott W. Henderson, Jaimie M. Department of Neurosurgery Stanford University United States Department of Electrical & Computer Engineering University of Washington United States Department of Computer Science Stanford University United States Department of Applied Mathematics University of Washington United States China Neurosciences Phd Program Stanford University United States Wu Tsai Neurosciences Institute Department of Statistics Stanford University United States

Speech brain-computer interfaces aim to decipher what a person is trying to say from neural activity alone, restoring communication to people with paralysis who have lost the ability to speak intelligibly. The Brain-to-Text Benchmark’24 and associated competition was created to foster the advancement of decoding algorithms that convert neural activity to text. Here, we summarize the lessons learned from the competition ending on June 1, 2024 (the top 4 entrants also presented their experiences in a recorded webinar). The largest improvements in accuracy were achieved using an ensembling approach, where the output of multiple independent decoders was merged using a fine-tuned large language model (an approach used by all 3 top entrants). Performance gains were also found by improving how the baseline recurrent neural network (RNN) model was trained, including by optimizing learning rate scheduling and by using a diphone training objective. Improving upon the model architecture itself proved more difficult, however, with attempts to use deep state space models or transformers not yet appearing to offer a benefit over the RNN baseline. The benchmark will remain open indefinitely to support further work towards increasing the accuracy of brain-to-text algorithms. © 2024, CC BY.

关键词： Recurrent neural networks

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Mutually beneficial confluence of structure-based modeling of protein dynamics and machine learning methods

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Current Opinion in Structural Biology 2023年 78卷 102517页

作者： Banerjee, Anupam Saha, Satyaki Tvedt, Nathan C. Yang, Lee-Wei Bahar, Ivet Computational and Systems Biology University of Pittsburgh School of Medicine Pittsburgh 15261 PA United States Computational and Applied Mathematics and Statistics The College of William and Mary Williamsburg 23185 VA United States Institute of Bioinformatics and Structural Biology and PhD Program in Biomedical Artificial Intelligence National Tsing Hua University Hsinchu 300044 Taiwan Physics Division National Center for Theoretical Sciences Taipei 106319 Taiwan

Proteins sample an ensemble of conformers under physiological conditions, having access to a spectrum of modes of motions, also called intrinsic dynamics. These motions ensure the adaptation to various interactions in the cell, and largely assist in, if not determine, viable mechanisms of biological function. In recent years, machine learning frameworks have proven uniquely useful in structural biology, and recent studies further provide evidence to the utility and/or necessity of considering intrinsic dynamics for increasing their predictive ability. Efficient quantification of dynamics-based attributes by recently developed physics-based theories and models such as elastic network models provides a unique opportunity to generate data on dynamics for training ML models towards inferring mechanisms of protein function, assessing pathogenicity, or estimating binding affinities. © 2022 The Authors

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Mathematical modeling and mechanisms of HIV latency for personalized anti latency therapies

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npj Systems Biology and Applications 2025年第1期11卷 1-11页

作者： Gianmarco Rasi Nicola Cotugno Paolo Palma Elena Emili Jessica M. Conway Research Unit of Clinical Immunology and Vaccinology Bambino Gesù Children’s Hospital IRCCS 00165 Rome Italy PhD Program in Immunology Molecular Medicine and Applied Biotechnology University of Rome “Tor Vergata” 00133 Rome Italy Department of Systems Medicine University of Rome “Tor Vergata” 00133 Roma Italy Department of Mathematics and Center for Infectious Disease Dynamics Pennsylvania State University University Park PA USA

Combination antiretroviral therapy controls human immunodeficiency virus-1 (HIV) but cannot eradicate latent proviruses in immune cells, which reactivate upon treatment interruption. Anti-latency therapies like “shock-and-kill” are being developed but are yet to succeed due to the complexity of latency mechanisms. This review discusses recent advances in understanding HIV latency via mathematical modeling, covering key regulatory factors and models to predict latency reversal, highlighting gaps to guide future therapeutic approaches.

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IN VITRO POPULATION GROWTH OF HUMAN GLIOBLASTOMAS: REAL PATIENTS AND CURVE FITTING

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Hematology, Transfusion and Cell Therapy 2025年 47卷 103807-103807页

作者： Diego Samuel Rodrigues Letícia Fernanda Alves João Frederico da Costa Azevedo Meyer Moníze Valéria Ramos da Silva Natália Barreto Catarina Raposo Faculdade de Tecnologia Universidade Estadual de Campinas (UNICAMP) Limeira SP Brazil PhD Program in Applied Mathematics Universidade Estadual de Campinas (UNICAMP) Campinas SP Brazil Instituto de Matemática Estatística e Computação Científica Universidade Estadual de Campinas (UNICAMP) Campinas SP Brazil Faculdade de Ciências Farmacêuticas Universidade Estadual de Campinas (UNICAMP) Campinas SP Brazil

Introduction/Justification For more than a century, a variety of ordinary differential equation growth models have been used to describe and predict the proliferation of human malignancies. Indeed, in the field of mathematical oncology, the growth of cell populations over time is typically represented by sigmoidal functions, such as logistic or Gompertz curves and their generalizations. These models are particularly focused on understanding and predicting the proliferation of cancer cells, including those from human glioblastomas, which can be very aggressive brain tumors with a survival rate of less than two years. Objectives This research examines in vitro cell cultures of five lines of human glioblastoma using curve fitting and numerical parameter estimation of real datasets to separately describe the growth profile of all these cell populations lineages over time. Materials and Methods Cell culture experiments were performed in the Advanced Therapeutics Laboratory at FCF-UNICAMP. These included a well-established human glioblastoma cell line (NG97) and four other glioblastoma cell lines derived from clinical patients designated N07, C03, L09 and J01. Twelve repeated time series of experiments were collected for each cell line. Cell counting was performed daily on days 1 to 6. The drda R package was used for curve fitting of the measured data aiming to determine the intrinsic growth rate and other parameters for each of the five cell lines. The 5-parameter generalized logistic curve was used, and all the resulting models were analyzed under statistical criteria such as the Akaike Information Criterion (AIC) and the Bayesian Information Criterion (BIC). Results Curve fitting analysis revealed significant diversity in the population growth of different cell lines. The drda R package proved to be highly effective in capturing these different behaviors and the unique sigmoidal shapes associated with them. Notably, the population growth of NG97 cells showed the least

关键词： Generalized Logistic Function Glioblastomas Mathematical Oncology

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QUANTIFYING INTERSPECIFIC COMPETITION BETWEEN CANCER AND NORMAL CELLS USING USING NONLINEAR MIXED EFFECTS AND ORDINARY DIFFERENTIAL EQUATION MODELING

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Hematology, Transfusion and Cell Therapy 2025年 47卷 103779-103779页

作者： Letícia Fernanda Alves Mauro César Cafundó Morais João Frederico Costa Azevedo Meyer Diego Samuel Rodrigues PhD Program in Applied Mathematics Universidade Estadual de Campinas (UNICAMP) Campinas SP Brazil Department of Clinical Analysis Faculdade de Ciências Farmacêuticas Universidade de São Paulo (USP) São Paulo SP Brazil Instituto de Matemática Estatística e Computação Científica Universidade Estadual de Campinas (UNICAMP) Campinas SP Brazil Faculdade de Tecnologia Universidade Estadual de Campinas (UNICAMP) Limeira SP Brazil

Introduction/Justification Tumor growth has been widely studied through various methodologies. In mathematical oncology, researchers use ordinary differential equations (ODEs) to analyze tumor dynamics. These models present meaningful parameters to link mathematical theory with experimental data. For in vitro cocultures, parameters quantifying cellular competition clarify interactions between tumor and normal cells. Objectives This research investigates the interaction between cancer and normal cells during competition, focusing on the in vitro growth of SK-MEL-147 (metastatic melanoma) and HaCaT (immortalized epithelial cells) cell lines. Using an ODE model with cell numbers as dependent variables, we quantify interspecific competition through the parameters α_{12} (impact of SK-MEL-147 on HaCaT) and α_{21} (impact of HaCaT on SK-MEL-147). Materials and Methods The in vitro cell growth experiments from Morais \textit{et al}., (2017), https://***/10.1038/s41598-017-07553-6, allowed us to estimate parameters for Gatenby's 1996 ODE model. We used a nonlinear mixed effects model from NLMEModeling (https://***/10.48550/arXiv.2011.06879) to account for observation errors and biological variability. Results The curve fitting matched the experimental data for both cell types. Parameter estimates showed that SK-MEL-147 cells experienced stronger inhibition from HaCaT cells than the reverse, suggesting normal cells hinder cancer cell growth upon contact. Conclusion Nonlinear mixed effects modeling successfully fit Gatenby's mathematical model to the experimental data, providing competition parameters that clarified interspecific interactions in tumor dynamics. Such models can predict cell growth behavior, supporting experimental design and reducing the need for preliminary \textit{in vitro} tests.

关键词： HaCaT Cell Lineage SK-MEL-147 Cell Lineage Skin cancer

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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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Call to Action: Data, Diversity, and STEM Education

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Change 2018年第2期50卷 40-47页

作者： Jones, Jason Williams, Aaron Whitaker, Shanta Yingling, Stephanie Inkelas, Karen Gates, John Jason Jones is the Assistant Director of the Office of Diversity and Engagement at the University of Virginia School of Engineering and Applied Science. Throughout his years at UVA he has worked in the Contemplative Sciences Center Curry School of Education Women’s Center and the Office of the Dean of Students. Aaron Williams is the Senior Data Research Scientist in the Office of Diversity and Engagement at the University of Virginia School of Engineering and Applied Science. Before joining UVA Williams worked as a principal data analyst at a Fortune 100 financial technology company building models and reporting dashboards from enterprise scale data warehouses. Shanta Whitaker is a health policy consultant at Logistics Management Institute (LMI) a management consulting firm based in Tysons VA. Before switching to health policy Dr. Whitaker was the Associate Director of the Health Professions Advising Program at Yale University. Stephanie Yingling is a government consultant at Logistics Management Institute (LMI) a management consulting firm based in Tysons VA. An Air Force veteran she is also a PhD candidate pursuing her research in the field of Education focusing areas of Organizational Leadership and Science Technology Engineering and Mathematics (STEM) Inclusion. Karen Kurotsuchi Inkelas is an Associate Professor in the Higher Education Program Curry School of Education at the University of Virginia. She also serves as Research Director for the Crafting Success for Underrepresented Scientists and Engineers Initiative as well as a Research Director of Undergraduate Initiatives for the Contemplative Sciences Center. John Gates is the Associate Dean and Chief Diversity Officer in the University of Virginia School of Engineering and Applied Science. He is also the Principal and Chief Strategist for Criticality Management Consulting.

To meet projected labor demands in science and engineering, the workforce of the future must be educated today in increasing numbers. Indeed, science, technology, engineering, and mathematics (STEM) underpin the government's ability to defend the nation and to assure the vitality of the economy. STEM jobs are the fastest growing occupational category and, by 2020, 65% of all jobs in the U.S. will require a post-secondary degree with STEM literacy skills (Carnevale, Smith, & Strohl, 2013). However, according to the U.S. Department of Education, less than 25 percent of college students pursuing bachelor's degrees will be specializing in STEM fields (National Center for Education Statistics, 2012). In addition, the current STEM workforce is predominantly male and White or Asian, even as women and racial and ethnic minority groups are projected to comprise greater percentages of the U.S. population in the coming decades. To meet the growing global demand for a STEM workforce, every segment of the U.S. population will need to be engaged in a successful STEM education. A first critical step will be for academia, government, and nongovernmental agencies to understand the challenges diverse students face in their quest to join the STEM workforce. The goal of the project described in this article is to close the achievement gap of underrepresented minority and underserved students (URMS) and to contribute to addressing the STEM crisis facing the nation. In addition to the longitudinal, five phase research project outlined in this article, UVA Engineering's Office of Diversity and Education (ODE) will work to assemble a comprehensive clearinghouse of survey and records data on factors related to STEM education from sources such as admissions, student affairs, student health, academic records and campus-wide surveys in institutional research offices, and UVA's own research and work.

关键词： STEM Education Achievement Gap Disproportionate Representation Minority Group Students Equal Education Higher Education Mixed Methods Research Longitudinal Studies Racial Differences Gender Differences Socioeconomic Status First Generation College Students At Risk Students Information Management Grade Point AverageVirginia

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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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Author Correction: Genomic footprints of activated telomere maintenance mechanisms in cancer (Dec, 10.1038/s41467-019-13824-9, 2022)

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NATURE COMMUNICATIONS 2022年第1期13卷 1-1页

作者： Sieverling, Lina Hong, Chen Koser, Sandra D. Ginsbach, Philip Kleinheinz, Kortine Hutter, Barbara Braun, Delia M. Cortes-Ciriano, Isidro Xi, Ruibin Kabbe, Rolf Park, Peter J. Eils, Roland Schlesner, Matthias Brors, Benedikt Rippe, Karsten Jones, David T. W. Feuerbach, Lars Division of Applied Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Faculty of Biosciences Heidelberg University 69120 Heidelberg Germany Division of Applied Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Faculty of Biosciences Heidelberg University Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) 69120 Heidelberg Germany Department for Bioinformatics and Functional Genomics Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant 69120 Heidelberg Germany Division of Theoretical Bioinformatics German Cancer Research Center (DKFZ) Heidelberg Germany Institute of Pharmacy and Molecular Biotechnology and BioQuant Heidelberg University Heidelberg Germany German Cancer Consortium (DKTK) Heidelberg Germany National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany Heidelberg Center for Personalized Oncology (DKFZ-HIPO) German Cancer Research Center (DKFZ) Heidelberg Germany German Cancer Consortium (DKTK) German Cancer Research Center (DKFZ) Heidelberg Germany Division of Chromatin Networks German Cancer Research Center (DKFZ) and BioQuant 69120 Heidelberg Germany Department of Biomedical Informatics Harvard Medical School Boston Massachusetts 02115 USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge CB2 1EW UK Ludwig Center at Harvard Medical School Boston Massachusetts 02115 USA Department of Biomedical Informatics Harvard Medical School Boston MA USA Department of Chemistry Centre for Molecular Science Informatics University of Cambridge Cambridge UK Ludwig Center at Harvard Medical School Boston MA USA School of Mathematical Sciences and Center for Statistical Science Peking University Beijing 100871 China Heidelberg University Heidelberg Germany New BIH Digital Health Center Berlin Institute of Health (BIH) and Charité - Universitätsmedizin Berlin Berlin Germany Bioi

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Changing life expectancy in European countries 1990–2021: a subanalysis of causes and risk factors from the Global Burden of Disease Study 2021

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The Lancet Public Health 2025年第3期10卷 e172-e188页

作者： Steel, Nicholas Bauer-Staeb, Clarissa Maria Mercedes Ford, John A. Abbafati, Cristiana Abdalla, Mohammed Altigani Abdelkader, Atef Abdi, Parsa Zuñiga, Roberto Ariel Abeldaño Abiodun, Olugbenga Olusola Abolhassani, Hassan Abu-Gharbieh, Eman Abukhadijah, Hana J. Abu-Zaid, Ahmed Addo, Isaac Yeboah Addolorato, Giovanni Adekanmbi, Victor Adetunji, Juliana Bunmi Adeyeoluwa, Temitayo Esther Agardh, Emilie E. Agyemang-Duah, Williams Ahmad, Danish Ahmed, Ayman Ahmed, Syed Anees Akinosoglou, Karolina Akkaif, Mohammed Ahmed Al Awaidy, Salah Al Hasan, Syed Mahfuz Al Zaabi, Omar Ali Mohammed Aldridge, Robert W. Algammal, Abdelazeem M. Al-Gheethi, Adel Ali Saeed Ali, Abid Ali, Mohammed Usman Ali, Syed Shujait Ali, Waad Alicandro, Gianfranco Alif, Sheikh Mohammad Al-Jumaily, Adel Allebeck, Peter Alrawashdeh, Ahmad Al-Rifai, Rami H. Alsabri, Mohammed A. Alshahrani, Najim Z. Aluh, Deborah Oyine Al-Wardat, Mohammad Al-Zyoud, Walid A. Amiri, Sohrab Anderlini, Deanna Andrei, Catalina Liliana Anil, Abhishek Anvari, Saeid Anyasodor, Anayochukwu Edward Appiah, Seth Christopher Yaw Aquilano, Michele Arabloo, Jalal Arafat, Mosab Areda, Demelash Aremu, Abdulfatai Armani, Keivan Armocida, Benedetta Ärnlöv, Johan Asaduzzaman, Muhammad Astell-Burt, Thomas Aujayeb, Avinash Ausloos, Marcel Azadnajafabad, Sina Aziz, Shahkaar Azzam, Ahmed Y. Babu, Giridhara Rathnaiah Badache, Andreea Corina Badiye, Ashish D. Bahramian, Saeed Baig, Atif Amin Baker, Jennifer L. Bansal, Hansi Bärnighausen, Till Winfried Barone, Mark Thomaz Ugliara Barrow, Amadou Barteit, Sandra Bashir, Shahid Bashiru, Hameed Akande Basso, João Diogo Bastan, Mohammad-Mahdi Basu, Sanjay Batra, Kavita Bauckneht, Matteo Baune, Bernhard T. Beghi, Massimiliano Beiranvand, Maryam Béjot, Yannick Bell, Michelle L. Bello, Olorunjuwon Omolaja Belo, Luis Beloukas, Apostolos Beneke, Alice A. Bettencourt, Paulo J.G. Bhagavathula, Akshaya Srikanth Bhala, Neeraj Bhaskar, Sonu Bisulli, Francesca Bjørge, Tone Bodunrin, Aadam Olalekan Carvajal, Alejandro Botero Bouaoud, Souad Brayne, Carol Brenner, H Department of Primary Care and Public Health University of East Anglia Norwich United Kingdom Office for Health Improvement and Disparities Department of Health and Social Care London United Kingdom Department of Legal and Economic Studies La Sapienza University Rome Italy Rome Italy Hull York Medical School University of Hull Hull United Kingdom Department of Mathematics and Sciences Ajman University Ajman United Arab Emirates Department of Medicine Memorial University St. John's NL Canada Postgraduate Department University of Sierra Sur Miahuatlan de Porfirio Diaz Mexico Yhteiskuntadatatieteen keskus (Centre for Social Data Science) Helsinki Finland Department of Internal Medicine Federal Medical Centre Abuja Nigeria Research Center for Immunodeficiencies Tehran University of Medical Sciences Tehran Iran Department of Medical Biochemistry and Biophysics Karolinska Institutet (Karolinska Institute) Stockholm Sweden Department of Clinical Sciences University of Sharjah Sharjah United Arab Emirates Department of Biopharmaceutics and Clinical Pharmacy University of Jordan Amman Jordan Medical Research Center Hamad Medical Corporation Doha Qatar Department of Biochemistry and Molecular Medicine Alfaisal University Riyadh Saudi Arabia College of Graduate Health Sciences University of Tennessee Memphis TN United States School of Medicine Sydney NSW Australia Centre for Social Research in Health University of New South Wales Sydney NSW Australia Internal Medicine and Alcohol Related Disease Unit Fondazione Policlinico Universitario A. Gemelli IRCCS Rome Italy Department of Medical and Surgical Sciences Università Cattolica di Roma (Catholic University of Rome) Rome Italy Department of Obstetrics and Gynecology University of Texas Medical Branch Galveston TX United States Department of Biochemistry Osun State University Osogbo Nigeria Department of Pharmacology and Therapeutics University of Medical Sciences Ondo Ondo Nigeria Department of Veteri

Background: Decades of steady improvements in life expectancy in Europe slowed down from around 2011, well before the COVID-19 pandemic, for reasons which remain disputed. We aimed to assess how changes in risk factors and cause-specific death rates in different European countries related to changes in life expectancy in those countries before and during the COVID-19 pandemic. Methods: We used data and methods from the Global Burden of Diseases, Injuries, and Risk Factors Study 2021 to compare changes in life expectancy at birth, causes of death, and population exposure to risk factors in 16 European Economic Area countries (Austria, Belgium, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, and Sweden) and the four UK nations (England, Northern Ireland, Scotland, and Wales) for three time periods: 1990–2011, 2011–19, and 2019–21. Changes in life expectancy and causes of death were estimated with an established life expectancy cause-specific decomposition method, and compared with summary exposure values of risk factors for the major causes of death influencing life expectancy. Findings: All countries showed mean annual improvements in life expectancy in both 1990–2011 (overall mean 0·23 years [95% uncertainty interval [UI] 0·23 to 0·24]) and 2011–19 (overall mean 0·15 years [0·13 to 0·16]). The rate of improvement was lower in 2011–19 than in 1990–2011 in all countries except for Norway, where the mean annual increase in life expectancy rose from 0·21 years (95% UI 0·20 to 0·22) in 1990–2011 to 0·23 years (0·21 to 0·26) in 2011–19 (difference of 0·03 years). In other countries, the difference in mean annual improvement between these periods ranged from –0·01 years in Iceland (0·19 years [95% UI 0·16 to 0·21] vs 0·18 years [0·09 to 0·26]), to –0·18 years in England (0·25 years [0·24 to 0·25] vs 0·07 years [0·06 to 0·08]). In 2019–21, there was an overall decrease in mean annual life expectancy a

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