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Genome-wide association study of long COVID

Nature Genetics 2025年 1-16页

作者： Lammi, Vilma Nakanishi, Tomoko Jones, Samuel E. Andrews, Shea J. Karjalainen, Juha Cortés, Beatriz O’Brien, Heath E. Ochoa-Guzman, Ana Fulton-Howard, Brian E. Broberg, Martin Haapaniemi, Hele H. Kanai, Masahiro Pirinen, Matti Schmidt, Axel Mitchell, Ruth E. Mousas, Abdou Mangino, Massimo Huerta-Chagoya, Alicia Sinnott-Armstrong, Nasa Cirulli, Elizabeth T. Vaudel, Marc Kwong, Alex S. F. Maiti, Amit K. Marttila, Minttu M. Posner, Daniel C. Rodriguez, Alexis A. Batini, Chiara Minnai, Francesca Dearman, Anna R. Warmerdam, C. A. Robert Sequeros, Celia B. Winkler, Thomas W. Jordan, Daniel M. Rešcenko, Raimonds Miano, Lorenzo Lane, Jacqueline M. Chung, Ryan K. Guillen-Guio, Beatriz Leavy, Olivia C. Carvajal-Silva, Laura Aguilar-Valdés, Kevin Frangione, Erika Guare, Lindsay Vergasova, Ekaterina Marouli, Eirini Striano, Pasquale Zainulabid, Ummu Afeera Kumar, Ashutosh Ahmad, Hajar Fauzan Edahiro, Ryuya Azekawa, Shuhei Maj, Carlo Pensel, Max C. Miller, Abigail Nöthen, Markus M. Behzad, Pari Schultz, Sonja Heggemann, Julia Balla, Daniella Morrison, David R. Mooser, Vincent Perley, Danielle Ragoussis, Jiannis Rousseau, Simon Shi, Fangyi Lathrop, G. Mark Yanishevsky, Solomia Laurent, Laetitia Auld, Daniel Bertrand, Mylene Boisclair, Ariane Bourque, Guillaume Bujold, David Durand, Madeleine Adra, Darin St-Cyr, Janick Niemi, Mari E. K. Iyengar, Sudha K. Cai, Tianxi Cho, Kelly Sarvadhavabhatla, Sannidhi Donaire, Maria Sophia Valenzuela-Jorquera, Héctor Lamoza, Eduardo Arévalo, Tamara V. Retamales-Ortega, Rocío Sanhueza, Sergio Selman, Carolina S. Silva, Andrea X. Alarcon, Teresa A. Martínez, Matías F. Quiroga, Romina Zuñiga-Pacheco, Paula Zapata-Contreras, Daniela Yáñez, Cristian E. Quiñones, Luis A. Tobar-Calfucoy, Eduardo A. Monardes-Ramírez, Virginia A. Signore, Iskra A. Guajardo, Lissette G. Figueroa, Alvaro Oróstica, Karen Y. Muñoz, Christian A. Fuentes-Guajardo, Macarena Bocchieri, Pamela Cabrera, Camilo Echeverria, Cesar A. Cerpa, Leslie C. Donoso, Gerardo Gutiérrez-Richards, Scarlett Nova-Lamperti, Estefania Saez Hidalgo Institute for Molecular Medicine Finland (FIMM) Helsinki Institute of Life Science (HiLIFE) University of Helsinki Helsinki Finland Department of Human Genetics McGill University Montreal QC Canada Centre for Clinical Epidemiology Department of Medicine Lady Davis Institute Jewish General Hospital McGill University Montreal QC Canada Kyoto-McGill International Collaborative Program in Genomic Medicine Graduate School of Medicine Kyoto University Kyoto Japan Department of Genome Informatics Graduate School of Medicine the University of Tokyo Tokyo Japan Research Fellow Japan Society for the Promotion of Science Tokyo Japan Department of Psychiatry and Behavioral Sciences University of California San Francisco San Francisco CA United States Program in Medical and Population Genetics Broad Institute of Harvard and MIT Cambridge MA United States Stanley Center for Psychiatric Research Broad Institute of Harvard and MIT Cambridge MA United States Analytic and Translational Genetics Unit Massachusetts General Hospital Boston MA United States Genomes for Life-GCAT Lab CORE Program Germans Trias i Pujol Research Institute (IGTP) Badalona Spain Grup de REcerca en Impacte de les Malalties Cròniques i les seves Trajectòries (GRIMTra) Barcelona Spain Sano Genetics Limited London United Kingdom Unidad de Biología Molecular y Medicina Genómica Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán Mexico City Mexico Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York City NY United States Broad Institute Cambridge MA United States Analytical and Translational Genetics Unit Massachusetts General Hospital Harvard Medical School Boston MA United States Department of Mathematics and Statistics University of Helsinki Helsinki Finland Department of Public Health University of Helsinki Helsinki Finland Institute of Human Genetics University of Bonn School of Medicine and University Hospital Bonn Bonn Germany MRC Integrat

Infections can lead to persistent symptoms and diseases such as shingles after varicella zoster or rheumatic fever after streptococcal infections. Similarly, severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) infection can result in long coronavirus disease (COVID), typically manifesting as fatigue, pulmonary symptoms and cognitive dysfunction. The biological mechanisms behind long COVID remain unclear. We performed a genome-wide association study for long COVID including up to 6,450 long COVID cases and 1,093,995 population controls from 24 studies across 16 countries. We discovered an association of FOXP4 with long COVID, independent of its previously identified association with severe COVID-19. The signal was replicated in 9,500 long COVID cases and 798,835 population controls. Given the transcription factor FOXP4’s role in lung physiology and pathology, our findings highlight the importance of lung function in the pathophysiology of long COVID. © The Author(s) 2025.

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Community-developed checklists for publishing images and image analyses

arXiv

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arXiv 2023年

作者： Schmied, Christopher Nelson, Michael S. Avilov, Sergiy Bakker, Gert-Jan Bertocchi, Cristina Bischof, Johanna Boehm, Ulrike Brocher, Jan Carvalho, Mariana Chiritescu, Catalin Christopher, Jana Cimini, Beth A. Conde-Sousa, Eduardo Ebner, Michael Ecker, Rupert Eliceiri, Kevin Fernandez-Rodriguez, Julia Gaudreault, Nathalie Gelman, Laurent Grunwald, David Gu, Tingting Halidi, Nadia Hammer, Mathias Hartley, Matthew Held, Marie Jug, Florian Kapoor, Varun Koksoy, Ayse Aslihan Lacoste, Judith Le Dévédec, Sylvia Le Guyader, Sylvie Liu, Penghuan Martins, Gabriel G. Mathur, Aastha Miura, Kota Llopis, Paula Montero Nitschke, Roland North, Alison Parslow, Adam C. Payne-Dwyer, Alex Plantard, Laure Ali, Rizwan Schroth-Diez, Britta Schütz, Lucas Scott, Ryan T. Seitz, Arne Selchow, Olaf Sharma, Ved P. Spitaler, Martin Srinivasan, Sathya Strambio-De-Castillia, Caterina Taatjes, Douglas Tischer, Christian Jambor, HelenaKlara Fondazione Human Technopole Viale Rita Levi-Montalcini 1 Milano20157 Italy Department of Biomedical Engineering University of Wisconsin-Madison MadisonWI53706 United States Max Planck Institute of Immunobiology and Epigenetics Freiburg79108 Germany Medical BioSciences department Radboud University Medical Centre Nijmegen Netherlands Laboratory for Molecular mechanics of cell adhesions Pontificia Universidad Católica de Chile Santiago Chile Osaka University Graduate School of Engineering Science Japan Euro-BioImaging ERIC Bio-Hub Meyerhofstr. 1 Heidelberg69117 Germany Carl Zeiss AG Carl-Zeiss-Straße 22 Oberkochen73447 Germany BioVoxxel Scientific Image Processing and Analysis Eugen-Roth-Strasse 8 Ludwigshafen67071 Germany Nanophotonics and BioImaging Facility at INL International Iberian Nanotechnology Laboratory 4715-330 Portugal Phi Optics Inc. 1800 S. Oak St Ste 106 ChampaignIL61820 United States Biochemistry Center Heidelberg Heidelberg University Germany Imaging Platform Broad Institute CambridgeMA02142 United States i3S Instituto de Investigação e Inovação Em Saúde and INEB Instituto de Engenharia Biomédica Universidade do Porto Porto Portugal Translational Research Institute Queensland University of Technology 37 Kent Street WoolloongabbaQLD4102 Australia School of Biomedical Sciences Faculty of Health Queensland University of Technology BrisbaneQLD4059 Australia TissueGnostics GmbH Vienna1020 Austria Department of Medical Physics and Biomedical Engineering University of Wisconsin-Madison MadisonWI53706 United States Centre for Cellular Imaging Core Facility Sahlgrenska Academy University of Gothenburg Sweden Allen Institute for Cell Science SeattleWA United States Friedrich Miescher Institute for Biomedical Research Basel Switzerland RNA Therapeutics Institute University of Massachusetts Chan Medical School WorcesterMA01605 United States University of Oklahoma NormanOK United States Advanced Light Microscopy Unit Ce

Images document scientific discoveries and are prevalent in modern biomedical research. Microscopy imaging in particular is currently undergoing rapid technological advancements. However for scientists wishing to publish the obtained images and image analyses results, there are to date no unified guidelines. Consequently, microscopy images and image data in publications may be unclear or difficult to interpret. Here we present community-developed checklists for preparing light microscopy images and image analysis for publications. These checklists offer authors, readers, and publishers key recommendations for image formatting and annotation, color selection, data availability, and for reporting image analysis workflows. The goal of our guidelines is to increase the clarity and reproducibility of image figures and thereby heighten the quality and explanatory power of microscopy data is in publications. © 2023, CC BY-SA.

关键词： Image analysis

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Polarimetric geometric modeling for mm-VLBI observations of black holes

arXiv

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arXiv 2023年

作者： Roelofs, Freek Johnson, Michael D. Chael, Andrew Janssen, Michael Wielgus, Maciek Broderick, Avery E. Akiyama, Kazunori Alberdi, Antxon Alef, Walter Algaba, Juan Carlos Anantua, Richard Asada, Keiichi Azulay, Rebecca Bach, Uwe Baczko, Anne-Kathrin Ball, David Baloković, Mislav Barrett, John Bauböck, Michi Benson, Bradford A. Bintley, Dan Blackburn, Lindy Blundell, Raymond Bouman, Katherine L. Bower, Geoffrey C. Boyce, Hope Bremer, Michael Brinkerink, Christiaan D. Brissenden, Roger Britzen, Silke Broguiere, Dominique Bronzwaer, Thomas Bustamante, Sandra Byun, Do-Young Carlstrom, John E. Ceccobello, Chiara Chan, Chi-Kwan Chang, Dominic O. Chatterjee, Koushik Chatterjee, Shami Chen, Ming-Tang Chen, Yongjun Cheng, Xiaopeng Cho, Ilje Christian, Pierre Conroy, Nicholas S. Conway, John E. Cordes, James M. Crawford, Thomas M. Crew, Geoffrey B. Cruz-Osorio, Alejandro Cui, Yuzhu Dahale, Rohan Davelaar, Jordy De Laurentis, Mariafelicia Deane, Roger Dempsey, Jessica Desvignes, Gregory Dexter, Jason Dhruv, Vedant Doeleman, Sheperd S. Dougal, Sean Dzib, Sergio A. Eatough, Ralph P. Emami, Razieh Falcke, Heino Farah, Joseph Fish, Vincent L. Fomalont, Ed Ford, H. Alyson Foschi, Marianna Fraga-Encinas, Raquel Freeman, William T. Friberg, Per Fromm, Christian M. Fuentes, Antonio Galison, Peter Gammie, Charles F. García, Roberto Gentaz, Olivier Georgiev, Boris Goddi, Ciriaco Gold, Roman Gómez-Ruiz, Arturo I. Gómez, José L. Gu, Minfeng Gurwell, Mark Hada, Kazuhiro Haggard, Daryl Haworth, Kari Hecht, Michael H. Hesper, Ronald Heumann, Dirk Ho, Luis C. Ho, Paul Honma, Mareki Huang, Chih-Wei L. Huang, Lei Hughes, David H. Ikeda, Shiro Impellizzeri, C.M. Violette Inoue, Makoto Issaoun, Sara James, David J. Jannuzi, Buell T. Jeter, Britton Jiang, Wu Jiménez-Rosales, Alejandra Jorstad, Svetlana Joshi, Abhishek V. Jung, Taehyun Karami, Mansour Karuppusamy, Ramesh Kawashima, Tomohisa Keating, Garrett K. Kettenis, Mark Kim, Dong-Jin Kim, Jae-Young Kim, Jongsoo Kim, Junhan Kino, Motoki Koay, Jun Yi Kocherlakota, Prashant Kofuji, Yutaro Koch, Center for Astrophysics Harvard & Smithsonian 60 Garden Street CambridgeMA02138 United States Black Hole Initiative Harvard University 20 Garden Street CambridgeMA02138 United States Radboud University P.O. Box 9010 Nijmegen6500 GL Netherlands Black Hole Initiative Harvard University 20 Garden Street CambridgeMA02138 United States Princeton Gravity Initiative Princeton University Jadwin Hall PrincetonNJ08544 United States Max-Planck-Institut für Radioastronomie Auf dem Hügel 69 BonnD-53121 Germany Perimeter Institute for Theoretical Physics 31 Caroline Street North WaterlooONN2L 2Y5 Canada Department of Physics and Astronomy University of Waterloo 200 University Avenue West WaterlooONN2L 3G1 Canada Waterloo Centre for Astrophysics University of Waterloo WaterlooONN2L 3G1 Canada Massachusetts Institute of Technology Haystack Observatory 99 Millstone Road WestfordMA01886 United States National Astronomical Observatory of Japan 2-21-1 Osawa Mitaka Tokyo181-8588 Japan Instituto de Astrofísica de Andalucía-CSIC Glorieta de la Astronomía s/n GranadaE-18008 Spain Department of Physics Faculty of Science Universiti Malaya Kuala Lumpur50603 Malaysia Department of Physics & Astronomy The University of Texas at San Antonio One UTSA Circle San AntonioTX78249 United States Institute of Astronomy and Astrophysics Academia Sinica 11F of Astronomy-Mathematics Building AS/NTU No. 1 Sec. 4 Roosevelt Rd. Taipei10617 Taiwan Departament d’Astronomia i Astrofísica Universitat de València C. Dr. Moliner 50 València BurjassotE-46100 Spain Observatori Astronòmic Universitat de València C. Catedrático José Beltrán 2 València PaternaE-46980 Spain Department of Space Earth and Environment Chalmers University of Technology Onsala Space Observatory OnsalaSE-43992 Sweden Steward Observatory Department of Astronomy University of Arizona 933 N. Cherry Ave. TucsonAZ85721 United States Yale Center for Astronomy & Astrophysics Yale Universit

The Event Horizon Telescope (EHT) is a millimeter very-long-baseline interferometry (VLBI) array which has imaged the apparent shadows of the supermassive black holes M87∗ and Sagittarius A∗. Polarimetric data from these observations contain a wealth of information on the black hole and accretion flow properties. In this work, we develop polarimetric geometric modeling methods for mm-VLBI data, focusing on approaches that fit data products with differing degrees of invariance to broad classes of calibration errors. We establish a fitting procedure using a polarimetric "m-ring" model to approximate the image structure near a black hole. By fitting this model to synthetic EHT data from general relativistic magnetohydrodynamic (GRMHD) models, we show that the linear and circular polarization structure can be successfully approximated with relatively few model parameters. We then fit this model to EHT observations of M87∗ taken in 2017. In total intensity and linear polarization, the m-ring fits are consistent with previous results from imaging methods. In circular polarization, the m-ring fits indicate the presence of event-horizon-scale circular polarization structure, with a persistent dipolar asymmetry and orientation across several days. The same structure was recovered independently of observing band, used data products, and model assumptions. Despite this broad agreement, imaging methods do not produce similarly consistent results. Our circular polarization results, which imposed additional assumptions on the source structure, should thus be interpreted with some caution. Polarimetric geometric modeling provides a useful and powerful method to constrain the properties of horizon-scale polarized emission, particularly for sparse arrays like the EHT. © 2023, CC BY.

关键词： Polarimeters

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Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data

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National science Review 2016年第2期3卷 240-251页

作者： Yong Wang Rui Jiang Wing Hung Wong Department of Statistics Department of Biomedical Data ScienceBio-X ProgramStanford University Academy of Mathematics and Systems Science National Center for Mathematics and Interdisciplinary SciencesChinese Academy of Sciences MOE Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic and Systems BiologyTNLISTDepartment of AutomationTsinghua University

Cell packs a lot of genetic and regulatory information through a structure known as chromatin,*** is wrapped around histone proteins and is tightly packed in a remarkable *** express a gene in a specific coding region,the chromatin would open up and DNA loop may be formed by interacting enhancers and ***,the mediator and cohesion complexes,sequence-specific transcription factors,and RNA polymerase Ⅱ are recruited and work together to elaborately regulate the expression *** is in pressing need to understand how the information,about when,where,and to what degree genes should be expressed,is embedded into chromatin structure and gene regulatory *** to large consortia such as Encyclopedia of DNA Elements(ENCODE) and Roadmap Epigenomic projects,extensive data on chromatin accessibility and transcript abundance are available across many tissues and cell *** rich data offer an exciting opportunity to model the causal regulatory ***,we will review the current experimental approaches,foundational data,computational problems,interpretive frameworks,and integrative models that will enable the accurate interpretation of regulatory ***,we will discuss the efforts to organize,analyze,model,and integrate the DNA accessibility data,transcriptional data,and functional genomic regions *** believe that these efforts will eventually help us understand the information flow within the cell and will influence research directions across many fields.

关键词： gene regulatory network open chromatin DNA accessibility transcription factor colocalization statistical model data integration

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The unified maximum a posteriori (MAP) framework for neuronal system identification

arXiv

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arXiv 2018年

作者： Wu, Michael C.-K. Deniz, Fatma Prenger, Ryan J. Gallant, Jack L. PROS San FranciscoCA94607 United States Biophysics Program University of California BerkeleyCA94720 United States Berkeley Institute for Data Science University of California BerkeleyCA94720 United States Helen Wills Neuroscience Institute University of California BerkeleyCA94720 United States International Computer Science Institute BerkeleyCA94704 United States Department of Physics University of California BerkeleyCA94720 United States Department of Psychology University of California BerkeleyCA94720 United States University of California at Berkeley Department of Psychology 2121 Berkeley Way BerkeleyCA94720 United States

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Incremental Fermi Large Area Telescope Fourth Source Catalog

arXiv

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arXiv 2022年

作者： Abdollahi, S. Acero, F. Baldini, L. Ballet, Jean Bastieri, D. Bellazzini, R. Berenji, B. Berretta, A. Bissaldi, E. Blandford, R.D. Bloom, E. Bonino, R. Brill, A. Britto, R.J. Bruel, P. Burnett, T.H. Buson, S. Cameron, R.A. Caputo, R. Caraveo, P.A. Castro, D. Chaty, S. Cheung, C.C. Chiaro, G. Cibrario, N. Ciprini, S. Coronado-Blázquez, J. Crnogorcevic, M. Cutini, S. D'Ammando, F. De Gaetano, S. Digel, S.W. Di Lalla, N. Dirirsa, F. Di Venere, L. Domínguez, A. Fallah Ramazani, V. Fegan, S.J. Ferrara, E.C. Fiori, A. Fleischhack, H. Franckowiak, A. Fukazawa, Y. Funk, S. Fusco, P. Galanti, G. Gammaldi, V. Gargano, F. Garrappa, S. Gasparrini, D. Giacchino, F. Giglietto, N. Giordano, F. Giroletti, M. Glanzman, T. Green, D. Grenier, I.A. Grondin, M.-H. Guillemot, L. Guiriec, S. Gustafsson, M. Harding, A.K. Hays, E. Hewitt, J.W. Horan, D. Hou, X. Jóhannesson, G. Karwin, C. Kayanoki, T. Kerr, M. Kuss, M. Landriu, D. Larsson, S. Latronico, L. Lemoine-Goumard, M. Li, J. Liodakis, I. Longo, F. Loparco, F. Lott, B. Lubrano, P. Maldera, S. Malyshev, D. Manfreda, A. Martí-Devesa, G. Mazziotta, M.N. Mereu, I. Meyer, M. Michelson, P.F. Mirabal, N. Mitthumsiri, W. Mizuno, T. Moiseev, A.A. Monzani, M.E. Morselli, A. Moskalenko, I.V. Negro, M. Nuss, E. Omodei, N. Orienti, M. Orlando, E. Paneque, D. Pei, Z. Perkins, J.S. Persic, M. Pesce-Rollins, M. Petrosian, V. Pillera, R. Poon, H. Porter, T.A. Principe, G. Rainò, S. Rando, R. Rani, B. Razzano, M. Razzaque, S. Reimer, A. Reimer, O. Reposeur, T. Sánchez-Conde, M. Saz Parkinson, P.M. Scotton, L. Serini, D. Sgrò, C. Siskind, E.J. Smith, D.A. Spandre, G. Spinelli, P. Sueoka, K. Suson, D.J. Tajima, H. Tak, D. Thayer, J.B. Thompson, D.J. Torres, D.F. Troja, E. Valverde, J. Wood, K. Zaharijas, G. IRAP Université de Toulouse CNRS UPS CNES ToulouseF-31028 France Université Paris Saclay Université Paris Cité CEA CNRS AIM Gif-sur-Yvette F-91191 France Università di Pisa Istituto Nazionale di Fisica Nucleare Sezione di Pisa PisaI-56127 Italy Istituto Nazionale di Fisica Nucleare Sezione di Padova PadovaI-35131 Italy Dipartimento di Fisica e Astronomia "G. Galilei" Università di Padova PadovaI-35131 Italy Center for Space Studies and Activities "G. Colombo" University of Padova Via Venezia 15 PadovaI-35131 Italy Istituto Nazionale di Fisica Nucleare Sezione di Pisa PisaI-56127 Italy California State University Los Angeles Department of Physics and Astronomy Los AngelesCA90032 United States Dipartimento di Fisica Università degli Studi di Perugia PerugiaI-06123 Italy Dipartimento di Fisica "M. Merlin" Università e del Politecnico di Bari via Amendola 173 BariI-70126 Italy Istituto Nazionale di Fisica Nucleare Sezione di Bari BariI-70126 Italy W. W. Hansen Experimental Physics Laboratory Kavli Institute for Particle Astrophysics and Cosmology Department of Physics SLAC National Accelerator Laboratory Stanford University StanfordCA94305 United States Istituto Nazionale di Fisica Nucleare Sezione di Torino TorinoI-10125 Italy Dipartimento di Fisica Università degli Studi di Torino TorinoI-10125 Italy NASA Postdoctoral Program NASA Goddard Space Flight Center GreenbeltMD20771 United States Department of Physics University of the Free State P.O. Box 339 Bloemfontein9300 South Africa Laboratoire Leprince-Ringuet École Polytechnique CNRS IN2P3 PalaiseauF-91128 France Department of Physics University of Washington SeattleWA98195-1560 United States Institut für Theoretische Physik and Astrophysik Universität Würzburg WürzburgD-97074 Germany NASA Goddard Space Flight Center GreenbeltMD20771 United States INAF-Istituto di Astrofisica Spaziale e Fisica Cosmica Milano via E. Bassini 15 MilanoI-20133 Italy Harvard-Smithsoni

We present an incremental version (4FGL-DR3, for data Release 3) of the fourth Fermi-LAT catalog of γ-ray sources. Based on the first twelve years of science data in the energy range from 50 MeV to 1 TeV, it contains 6658 sources. The analysis improves on that used for the 4FGL catalog over eight years of data: more sources are fit with curved spectra, we introduce a more robust spectral parameterization for pulsars, and we extend the spectral points to 1 TeV. The spectral parameters, spectral energy distributions, and associations are updated for all sources. Light curves are rebuilt for all sources with 1 yr intervals (not 2 month intervals). Among the 5064 original 4FGL sources, 16 were deleted, 112 are formally below the detection threshold over 12 yr (but are kept in the list), while 74 are newly associated, 10 have an improved association, and seven associations were withdrawn. Pulsars are split explicitly between young and millisecond pulsars. Pulsars and binaries newly detected in LAT sources, as well as more than 100 newly classified blazars, are reported. We add three extended sources and 1607 new point sources, mostly just above the detection threshold, among which eight are considered identified, and 699 have a plausible counterpart at other wavelengths. We discuss the degree-scale residuals to the global sky model and clusters of soft unassociated point sources close to the Galactic plane, which are possibly related to limitations of the interstellar emission model and missing extended sources. © 2022, CC BY.

关键词： Pulsars

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A Nonlinear Dimensionality Reduction Framework Using Smooth Geodesics

arXiv

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arXiv 2017年

作者： Gajamannage, Kelum Paffenroth, Randy Bollt, Erik M. Department of Mathematical Sciences Worcester Polytechnic Institute WorcesterMA01609 United States Department of Mathematical Sciences Department of Computer Science and Data Science Program Worcester Polytechnic Institute WorcesterMA01609 United States Clarkson Center for Complex Systems Science Clarkson University PotsdamNY13676 United States

Existing dimensionality reduction methods are adept at revealing hidden underlying manifolds arising from high-dimensional data and thereby producing a low-dimensional representation. However, the smoothness of the manifolds produced by classic techniques over sparse and noisy data is not guaranteed. In fact, the embedding generated using such data may distort the geometry of the manifold and thereby produce an unfaithful embedding. Herein, we propose a framework for nonlinear dimensionality reduction that generates a manifold in terms of smooth geodesics that is designed to treat problems in which manifold measurements are either sparse or corrupted by noise. Our method generates a network structure for given high-dimensional data using a nearest neighbors search and then produces piecewise linear shortest paths that are defined as geodesics. Then, we fit points in each geodesic by a smoothing spline to emphasize the smoothness. The robustness of this approach for sparse and noisy datasets is demonstrated by the implementation of the method on synthetic and real-world *** Codes 68T05 Copyright © 2017, The Authors. All rights reserved.

关键词： Nonlinear analysis

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Author Correction: Experimental and real-world evidence supporting the computational repurposing of bumetanide for APOE4-related Alzheimer's disease

Nature aging

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Nature aging 2021年第12期1卷 1202页

作者： Alice Taubes Phil Nova Kelly A Zalocusky Idit Kosti Mesude Bicak Misha Y Zilberter Yanxia Hao Seo Yeon Yoon Tomiko Oskotsky Silvia Pineda Bin Chen Emily A Aery Jones Krishna Choudhary Brian Grone Maureen E Balestra Fayzan Chaudhry Ishan Paranjpe Jessica De Freitas Nicole Koutsodendris Nuo Chen Celine Wang William Chang Alice An Benjamin S Glicksberg Marina Sirota Yadong Huang Gladstone Institute of Neurological Disease Gladstone Institutes San Francisco CA USA. Biomedical Sciences Graduate Program University of California San Francisco CA USA. Gladstone Center for Translational Advancement Gladstone Institutes San Francisco CA USA. Department of Neurology University of California San Francisco CA USA. Bakar Computational Health Sciences Institute University of California San Francisco CA USA. Department of Pediatrics University of California San Francisco CA USA. Hasso Plattner Institute for Digital Health at Mount Sinai Icahn School of Medicine at Mount Sinai New York NY USA. Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai New York NY USA. Department of Surgery University of California San Francisco CA USA. Gladstone Institute of Data Science and Biotechnology Gladstone Institutes San Francisco CA USA. Development and Stem Cell Biology Graduate Program University of California San Francisco CA USA. Bakar Computational Health Sciences Institute University of California San Francisco CA USA. marina.sirota@ucsf.edu. Department of Pediatrics University of California San Francisco CA USA. marina.sirota@ucsf.edu. Gladstone Institute of Neurological Disease Gladstone Institutes San Francisco CA USA. yadong.huang@gladstone.ucsf.edu. Biomedical Sciences Graduate Program University of California San Francisco CA USA. yadong.huang@gladstone.ucsf.edu. Gladstone Center for Translational Advancement Gladstone Institutes San Francisco CA USA. yadong.huang@gladstone.ucsf.edu. Department of Neurology University of California San Francisco CA USA. yadong.huang@gladstone.ucsf.edu. Department of Pathology University of California San Francisco CA USA. yadong.huang@gladstone.ucsf.edu.

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Author Correction: Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition

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Nature genetics 2023年第6期55卷 1080页

作者： Bernardo Rodriguez-Martin Eva G Alvarez Adrian Baez-Ortega Jorge Zamora Fran Supek Jonas Demeulemeester Martin Santamarina Young Seok Ju Javier Temes Daniel Garcia-Souto Harald Detering Yilong Li Jorge Rodriguez-Castro Ana Dueso-Barroso Alicia L Bruzos Stefan C Dentro Miguel G Blanco Gianmarco Contino Daniel Ardeljan Marta Tojo Nicola D Roberts Sonia Zumalave Paul A Edwards Joachim Weischenfeldt Montserrat Puiggròs Zechen Chong Ken Chen Eunjung Alice Lee Jeremiah A Wala Keiran M Raine Adam Butler Sebastian M Waszak Fabio C P Navarro Steven E Schumacher Jean Monlong Francesco Maura Niccolo Bolli Guillaume Bourque Mark Gerstein Peter J Park David C Wedge Rameen Beroukhim David Torrents Jan O Korbel Iñigo Martincorena Rebecca C Fitzgerald Peter Van Loo Haig H Kazazian Kathleen H Burns Peter J Campbell Jose M C Tubio Department of Zoology Genetics and Physical Anthropology Universidade de Santiago de Compostela Santiago de Compostela Spain. 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. Transmissible Cancer Group Department of Veterinary Medicine University of Cambridge Cambridge UK. The Biomedical Research Centre (CINBIO) Universidade de Vigo Vigo Spain. Wellcome Sanger Institute Wellcome Genome Campus Cambridge UK. Genome Data Science Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology (BIST) Barcelona Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA) Barcelona Spain. The Francis Crick Institute London UK. Department of Human Genetics University of Leuven Leuven Belgium. Genomes and Disease Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Graduate School of Medical Science and Engineering Korea Advanced Institute of Science and Technology Daejeon South Korea. Cancer Ageing and Somatic Mutation Programme Wellcome Sanger Institute Cambridge UK. Department of Biochemistry Genetics and Immunology University of Vigo Vigo Spain. Galicia Sur Health Research Institute Vigo Spain. Faculty of Science and Technology University of Vic-Central University of Catalonia (UVic-UCC) Vic Spain. Barcelona Supercomputing Center (BSC) Barcelona Spain. Experimental Cancer Genetics Wellcome Sanger Institute Cambridge UK. Oxford Big Data Institute University of Oxford Oxford UK. DNA Repair and Genome Integrity Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS) Universidade de Santiago de Compostela Santiago de Compostela Spain. Department of Biochemistry and Molecular Biology Universidade de Santiago de Compostela Santiago de Compostela Spain. Medical R

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Digital is the New Blood: Enabling the Present and the Future

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Alzheimer's & Dementia 2023年第S21期19卷

作者： Rhoda Au Zachary T Popp Spencer Low Phillip H Hwang Ileana De Anda-Duran Stephanie Li Salman Rahman Huitong Ding Akwaugo Igwe Cody Karjadi Ting Fang Alvin Ang Sherral A. Devine Ashita S Gurnani Jesse B. Mez Lindsay A. Farrer Preeti Sunderaraman Honghuang Lin Vijaya B. Kolachalama Boston University School of Public Health Boston MA USA Framingham Heart Study Boston University School of Medicine Boston MA USA Davos Alzheimer’s Collaborative Philadelphia PA USA Department of Epidemiology Boston University School of Public Health Boston MA USA Boston University Chobanian & Avedisian School of Medicine Boston MA USA Department of Neurology Boston University Chobanian & Avedisian School of Medicine Boston MA USA Boston University Alzheimer’s Disease Research Center Boston University Chobanian & Avedisian School of Medicine Boston MA USA Department of Anatomy and Neurobiology Boston University Chobanian & Avedisian School of Medicine Boston MA USA Framingham Heart Study Boston University Chobanian & Avedisian School of Medicine Boston MA USA Boston University School of Public Heatlh Boston MA USA Tulane School of Public Health and Tropical Medicine New Orleans LA USA Slone Epidemiology Center Boston University Chobanian & Avedisian School of Medicine Boston MA USA Framigham Heart Study - Boston University Framingham MA USA Boston University Bioinformatics Program Boston MA USA Departments of Medicine (Biomedical Genetics) Neurology Ophthalmology Biostatistics and Epidemiology Boston University Schools of Medicine and Public Health Boston MA USA Department of Neurology - Boston University Chobanian & Avedisian School of Medicine Boston MA USA University of Massachusetts Medical School Worcester MA USA Framingham Heart Study/Boston University BOSTON MA USA Hariri Institute for Computing and Computational Science & Engineering Boston University Boston MA USA College of Arts & Sciences Boston University Boston MA USA Faculty of Computing & Data Sciences Boston University Boston MA USA Boston University Alzheimer’s Disease Center Boston University Chobanian & Avedisian School of Medicine Boston MA USA Whitaker Cardiovascular Institute Boston University Chobanian & Avedisian School of Medicine Boston MA USA

Background Digital is the new blood, where collection, use, and storage of raw digital data streams enabled by technology-embedded sensors are replacing analog methods. Analyses of digital data extend beyond current applications, analogous to previously stored blood currently be used for omics/biomarker research. Today digital technologies are used to measure Alzheimer’s disease (AD)-related clinical symptoms (e.g., cognition, function, and behavior), but future possibilities remain to be determined. Importantly, digital data collection can go beyond current intermittent sampling by employing internet-connected applications and devices that allow real-time monitoring and accurate detection of changes, even within a widely heterogeneous spectrum. Method Beginning in 2005, the Framingham Heart Study (FHS) began digitally recording participants’ spoken responses to neuropsychological (NP) test questions, and in 2011 extended to a digital pen to record written responses. The emergence of wearable devices and smartphone applications has led to an expanded use of digital technologies beyond recordings during NP assessments. The Boston University Alzheimer’s Disease Research Center (BU ADRC) leverages digital sensors in multiple internet-connected devices that longitudinally collect digital data, in both in-person and remote settings. Result The first publication involving FHS digital data was in 2016; the remaining (n> 17) have been from 2020-current. Digital data measuring cognition, function and behavior are being collected through the BU ADRC, where results to date indicate nearly 100% and 75% uptake of active and passive engagement applications, respectively, and 95% uptake for wearable devices (n = 60). Longitudinal assessments include > 3 months for ∼50 participants; > 1 year for n∼21 participants. Conclusion Opportunities for improved trial outcome measurement are evident in the broad range of outcomes digital sensors capture beyond traditional research methodologi

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