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arXiv 2022年

作者： Dumont, Vincent Bowen, Trevor A. Roglans, Roger Dobler, Gregory Sharma, Mohit S. Karpf, Andy Bale, Stuart D. Wickenbrock, Arne Zhivun, Elena Kornack, Tom Wurtele, Jonathan S. Budker, Dmitry Computational Research Division Lawrence Berkeley National Laboratory BerkeleyCA94720 United States Department Of Physics University Of California BerkeleyCA94720-7300 United States Space Sciences Laboratory University Of California BerkeleyCA94720-7300 United States Biden School Of Public Policy And Administration University Of Delaware NewarkDE19716 United States Department Of Physics And Astronomy University Of Delaware NewarkDE19716 United States Data Science Institute University Of Delaware NewarkDE19713 United States Center For Urban Science And Progress New York University BrooklynNY11201 United States Civil And Urban Engineering Tandon School Of Engineering New York University BrooklynNY11201 United States Institut Für Physik Universität Mainz Staudingerweg 7 Mainz55128 Germany Helmholtz Institut Mainz Staudingerweg 18 Mainz55128 Germany Twinleaf LLC 300 Deer Creek Drive PlainsboroNJ08536 United States Johannes Gutenberg-Universität Mainz Mainz55128 Germany Helmholtz Institut Mainz Mainz55128 Germany

We present a comparative analysis of urban magnetic fields between two American cities: Berkeley (California) and Brooklyn Borough of New York City (New York). Our analysis uses data taken over a four-week period during which magnetic field data were continuously recorded using a fluxgate magnetometer of 70 pT/√ Hz sensitivity. We identified significant differences in the magnetic signatures. In particular, we noticed that Berkeley reaches a near-zero magnetic field activity at night whereas magnetic activity in Brooklyn continues during nighttime. We also present auxiliary measurements acquired using magnetoresistive vector magnetometers (VMR), with sensitivity of 300 pT/√ Hz, and demonstrate how cross-correlation, and frequency-domain analysis, combined with data filtering can be used to extract urban magnetometry signals and study local anthropogenic activities. Finally, we discuss the potential of using magnetometer networks to characterize the global magnetic field of cities and give directions for future development. Copyright © 2022, The Authors. All rights reserved.

关键词： Magnetometers

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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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Fusion of convolution neural network, support vector machine and Sobel filter for accurate detection of COVID-19 patients using X-ray images

arXiv

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arXiv 2021年

作者： Sharifrazi, Danial Alizadehsani, Roohallah Roshanzamir, Mohamad Joloudari, Javad Hassannataj Shoeibi, Afshin Jafari, Mahboobeh Hussain, Sadiq Sani, Zahra Alizadeh Hasanzadeh, Fereshteh Khozeimeh, Fahime Khosravi, Abbas Nahavandi, Saeid Panahiazar, Maryam Zare, Assef Shariful Islam, Sheikh Mohammed Rajendra, U. Acharya Department of Computer Engineering School of Technical and Engineering Shiraz Branch Islamic Azad University Shiraz Iran Deakin University Geelong Australia Department of Engineering Fasa Branch Islamic Azad University Post Box No 364 Fasa Fars*** Iran Department of Computer Engineering Faculty of Engineering University of Birjand Birjand Iran Computer Engineering Department Ferdowsi University of Mashhad Mashhad Iran Faculty of Electrical and Computer Engineering Biomedical Data Acquisition Lab K. N. Toosi University of Technology Tehran Iran Electrical and Computer Engineering Faculty Semnan University Semnan Iran System Administrator Dibrugarh University Assam786004 India Rajaie Cardiovascular Medical and Research Center Iran University of Medical Sciences Tehran Iran Omid hospital Iran University of Medical Sciences Tehran Iran Institute for Computational Health Sciences University of California San Francisco United States Faculty of Electrical Engineering Gonabad Branch Islamic Azad University Gonabad Iran Institute for Physical Activity and Nutrition Deakin University Melbourne Australia Cardiovascular Division The George Institute for Global Health Australia Sydney Medical School University of Sydney Australia Department of Electronics and Computer Engineering Ngee Ann Polytechnic Singapore Department of Biomedical Engineering School of Science and Technology Singapore University of Social Sciences Singapore Department of Bioinformatics and Medical Engineering Asia University Taiwan

The coronavirus (COVID-19) is currently the most common contagious disease which is prevalent all over the world. The main challenge of this disease is the primary diagnosis to prevent secondary infections and its spread from one person to another. Therefore, it is essential to use an automatic diagnosis system along with clinical procedures for the rapid diagnosis of COVID-19 to prevent its spread. Artificial intelligence techniques using computed tomography (CT) images of the lungs and chest radiography have the potential to obtain high diagnostic performance for Covid-19 diagnosis. In this study, a fusion of convolutional neural network (CNN), support vector machine (SVM), and Sobel filter is proposed to detect COVID-19 using X-ray images. A new X-ray image dataset was collected and subjected to high pass filter using a Sobel filter to obtain the edges of the images. Then these images are fed to CNN deep learning model followed by SVM classifier with ten-fold cross validation strategy. This method is designed so that it can learn with not many data. Our results show that the proposed CNN-SVM with Sobel filtering (CNN-SVM+Sobel) achieved the highest classification accuracy of 99.02% in accurate detection of COVID-19. It showed that using Sobel filter can improve the performance of CNN. Unlike most of the other researches, this method does not use a pre-trained network. We have also validated our developed model using six public databases and obtained the highest performance. Hence, our developed model is ready for clinical application. Copyright © 2021, The Authors. All rights reserved.

关键词： data mining

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The status of the human gene catalogue

arXiv

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arXiv 2023年

作者： Amaral, Paulo Carbonell-Sala, Silvia De La Vega, Francisco M. Faial, Tiago Frankish, Adam Gingeras, Thomas Guigo, Roderic Harrow, Jennifer L. Hatzigeorgiou, Artemis G. Johnson, Rory Murphy, Terence D. Pertea, Mihaela Pruitt, Kim D. Pujar, Shashikant Takahashi, Hazuki Ulitsky, Igor Varabyou, Ales Wells, Christine A. Yandell, Mark Carninci, Piero Salzberg, Steven L. INSPER Institute of Education and Research SP São Paulo Brazil Dr. Aiguader 88 Catalonia Barcelona08003 Spain Department of Biomedical Data Science Stanford University School of Medicine StanfordCA United States Tempus Labs Inc. ChicagoIL United States Nature Genetics San FranciscoCA United States European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton CambridgeCB10 1SD United Kingdom Department of Functional Genomics Cold Spring Harbor Laboratory Cold Spring HarborNY United States Catalonia Barcelona Spain Centre for Genomics Research Discovery Sciences AstraZeneca Da Vinci Building. Melbourn Science Park RoystonSG8 6HB United Kingdom Universithy of Thessaly Department of Computer Science and Biomedical Informatics Lamia Greece Hellenic Pasteur Institute Athens Greece School of Biology and Environmental Science University College Dublin DublinD04 V1W8 Ireland Conway Institute of Biomedical and Biomolecular Research University College Dublin DublinD04 V1W8 Ireland Department of Medical Oncology Inselspital Bern University Hospital University of Bern Bern3010 Switzerland Department for BioMedical Research University of Bern Bern3008 Switzerland National Center for Biotechnology Information National Library of Medicine National Institutes of Health BethesdaMD20894 United States Center for Computational Biology Johns Hopkins University BaltimoreMD United States Department of Biomedical Engineering Johns Hopkins University BaltimoreMD United States Laboratory for Transcriptome Technology RIKEN Center for Integrative Medical Sciences Kanagawa Yokohama230-0045 Japan Department of Immunology and Regenerative Biology Department of Molecular Neuroscience Weizmann Institute of Science Rehovot76100 Israel Department of Computer Science Johns Hopkins University BaltimoreMD United States Stem Cell Systems Department of Anatomy and Physiology Faculty of Medicine Dentistry and Health Scien

Scientists have been trying to identify all of the genes in the human genome since the initial draft of the genome was published in 2001. Over the intervening years, much progress has been made in identifying protein-coding genes, and the estimated number has shrunk to fewer than 20,000, although the number of distinct protein-coding isoforms has expanded dramatically. The invention of high-throughput RNA sequencing and other technological breakthroughs have led to an explosion in the number of reported non-coding RNA genes, although most of them do not yet have any known function. A combination of recent advances offers a path forward to identifying these functions and towards eventually completing the human gene catalogue. However, much work remains to be done before we have a universal annotation standard that includes all medically significant genes, maintains their relationships with different reference genomes, and describes clinically relevant genetic variants. © 2023, CC BY.

关键词： Genes

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Inclusion of PH Improves Associations Between SARS-CoV-2 RNA Levels in Wastewater and Covid-19 Cases Within Smaller Sewersheds

SSRN

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SSRN 2024年

作者： Lamm, Erik D. Babler, Kristina M. Sharkey, Mark E. Amirali, Ayaaz Beaver, Cynthia Boone, Melinda M. Comerford, Samuel Cooper, Daniel Currall, Benjamin B. Grills, George S. Kobetz, Erin Kumar, Naresh Laine, Jennifer Lamar, Walter E. Lyu, Jiangnan Kennedy, Althea Perritano, Stefan Mason, Christopher E. Reding, Brian D. Roca, Matthew A. Schürer, Stephan C. Shukla, Bhavarth S. Solle, Natasha Schaefer Tallon, John J. Thomas, Collette Tierney, Braden T. Torres, Belkis Venkatpuram, Sreeharsha Vidovic, Dusica Williams, Sion L. Yin, Xue Zarnegarnia, Yalda Solo-Gabriele, Helena M. Department of Chemical Environmental and Materials Engineering University of Miami Coral GablesFL United States Department of Medicine University of Miami Miller School of Medicine MiamiFL United States Sylvester Comprehensive Cancer Center University of Miami Miller School of Medicine MiamiFL United States DataGrade Solutions LLC MiamiFL United States Department of Public Health Sciences University of Miami Miller School of Medicine MiamiFL United States Environmental Health and Safety University of Miami MiamiFL United States Division of Occupational Health Safety & Compliance University of Miami Health System MiamiFL United States Department of Physiology and Biophysics Weill Cornell Medical College New York CityNY United States The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine Weill Cornell Medicine New YorkNY United States The WorldQuant Initiative for Quantitative Prediction Weill Cornell Medicine New YorkNY United States Department of Molecular & Cellular Pharmacology University of Miami Miller School of Medicines MiamiFL United States Institute for Data Science & Computing University of Miami Coral GablesFL United States Facilities and Operations University of Miami Coral GablesFL United States

Measurements of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in wastewater can be used to understand the prevalence of COVID-19 cases within a community. Environmental conditions inclusive of water quality are known to impact wastewater SARS-CoV-2 signals, but they are rarely measured in areas upstream of wastewater treatment plants. The objectives of this study were to report on continuous measurements of environmental parameters (water quality and flow) in the upper reaches of a sewershed and to evaluate whether the inclusion of these environmental parameters improves associations between SARS-CoV-2 RNA levels in wastewater, and COVID-19 prevalence in the sewershed community. Measurements of environmental parameters and SARS-CoV-2 RNA in wastewater spanned different time scales (minutes, hours and weeks) and population scales (building, campus, community). Spearman correlations and stepwise regressions were used to evaluate associations. When comparing SARS-CoV-2 RNA levels directly to environmental parameters from instantaneous measurements or grab samples, results showed inconsistent correlations likely due to short term (minute-scale) variations observed in flow and water quality. For the analysis involving COVID-19 prevalence data which required averaging over weekly time scales, regressions showed that inclusion of environmental parameters, in particular pH, improved correlations between RNA and COVID-19 prevalence. The significance of pH in improving correlations of SARS-CoV-2 with prevalence data was greater for the cluster sewershed scale (populations of a few thousand) than at the community scale (populations of several 100,000). The significance of pH is believed to be related to the properties of the tap water characterized by high pH and low alkalinity, with pH serving as a proxy of fecal waste allowing for an adjustment of the SARS-CoV-2 signal to account for human waste dilution within the sewer system. © 2024, The Authors. All rights

关键词： Coronavirus

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Advancing the Use of Longitudinal Electronic Health Records: Tutorial for Uncovering Real-World Evidence in Chronic Disease Outcomes

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Journal of Medical Internet Research 2025年第1期27卷 e71873页

作者： Huang, Feiqing Hou, Jue Zhou, Ningxuan Greco, Kimberly Lin, Chenyu Sweet, Sara Morini Wen, Jun Shen, Lechen Gonzalez, Nicolas Zhang, Sinian Liao, Katherine P. Cai, Tianrun Xia, Zongqi Bourgeois, Florence T. Cai, Tianxi Department of Biostatistics Harvard T.H. Chan School of Public Health Boston MA United States Harvard-MIT Center for Regulatory Science Harvard Medical School Boston MA United States Division of Biostatistics and Health Data Science School of Public Health University of Minnesota Minneapolis MN United States Department of Biomedical Informatics Harvard Medical School Boston MA United States Department of Engineering University of Toronto Toronto ON Canada Division of Rheumatology Inflammation and Immunity Brigham and Women's Hospital Boston MA United States Department of Neurology University of Pittsburgh Pittsburgh PA United States Computational Health Informatics Program (CHIP) Boston Children's Hospital Boston MA United States Department of Pediatrics Harvard Medical School Boston MA United States

Managing chronic diseases requires ongoing monitoring of disease activity and therapeutic responses to optimize treatment plans. With the growing availability of disease-modifying therapies, it is crucial to investigate comparative effectiveness and long-term outcomes beyond those available from randomized clinical trials. We introduce a comprehensive pipeline for generating reproducible and generalizable real-world evidence on disease outcomes by leveraging electronic health record data. The pipeline first generates scalable disease outcomes by linking electronic health record data with registry data containing a small sample of labeled outcomes. It then applies causal analysis using these scalable outcomes to evaluate therapies for chronic diseases. The implementation of the pipeline is illustrated in a case study based on multiple sclerosis. Our approach addresses challenges in real-world evidence generation for disease activity of chronic conditions, specifically the lack of direct observations on key outcomes and biases arising from imperfect or incomplete data. We present advanced machine learning techniques such as semisupervised and ensemble methods to impute missing outcome data, further incorporating steps for calibrated causal analyses and bias correction. ©Feiqing Huang, Jue Hou, Ningxuan Zhou, Kimberly Greco, Chenyu Lin, Sara Morini Sweet, Jun Wen, Lechen Shen, Nicolas Gonzalez, Sinian Zhang, Katherine P Liao, Tianrun Cai, Zongqi Xia, Florence T Bourgeois, Tianxi Cai.

关键词： calibration causal inference chronic disease outcomes data imputation electronic health records longitudinal disease activity machine learning real-world evidence

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The Obscured Fraction of Quasars at Cosmic Noon

arXiv

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arXiv 2022年

作者： Vijarnwannaluk, Bovornpratch Akiyama, Masayuki Schramm, Malte Ueda, Yoshihiro Matsuoka, Yoshiki Toba, Yoshiki Sawicki, Marcin Gwyn, Stephen Pflugradt, Janek Astronomical Institute Tohoku University Aoba-ku Aramaki Miyagi Sendai980-8578 Japan Graduate School of Science and Engineering Saitama University 255 Shimo-Okubo Sakura-ku Saitama Saitama City338-8570 Japan Department of Astronomy Kyoto University Kitashirakawa-Oiwake-cho Sakyo-ku Kyoto606-8502 Japan Research Center for Space and Cosmic Evolution Ehime University 2-5 Bunkyo-cho Ehime Matsuyama790-8577 Japan National Astronomical Observatory of Japan 2-21-1 Osawa Tokyo Mitaka181-8588 Japan Institute for Computational Astrophysics Department of Astronomy and Physics Saint Mary's University HalifaxNSB3H 3C3 Canada Canadian Astronomy Data Centre NRC-Herzberg 5071 West Saanich Road VictoriaBCV9E 2E7 Canada

Statistical studies of X-ray selected Active Galactic Nuclei (AGN) indicate that the fraction of obscured AGN increases with increasing redshift, and the results suggest that a significant part of the accretion growth occurs behind obscuring material in the early universe. We investigate the obscured fraction of highly accreting X-ray AGN at around the peak epoch of supermassive black hole growth utilizing the wide and deep X-ray and optical/IR imaging datasets. A unique sample of luminous X-ray selected AGNs above z > 2 was constructed by matching the XMM-SERVS X-ray point-source catalog with a PSF-convolved photometric catalog covering from u∗to 4.5μm bands. Photometric redshift, hydrogen column density, and 2-10 keV AGN luminosity of the X-ray selected AGN candidates were estimated. Using the sample of 306 2-10 keV detected AGN at above redshift 2, we estimate the fraction of AGN with log NH(cm-2) > 22, assuming parametric X-ray luminosity and absorption functions. The results suggest that 76-3+4% of luminous quasars (log LX(erg s-1) > 44.5) above redshift 2 are obscured. The fraction indicates an increased contribution of obscured accretion at high redshift than that in the local universe. We discuss the implications of the increasing obscured fraction with increasing redshift based on the AGN obscuration scenarios, which describe obscuration properties in the local universe. Both the obscured and unobscured z > 2 AGN show a broad range of SEDs and morphology, which may reflect the broad variety of host galaxy properties and physical processes associated with the obscuration. © 2022, CC BY.

关键词： Active Galactic Nuclei

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The leap to ordinal: Detailed functional prognosis after traumatic brain injury with a flexible modelling approach

arXiv

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arXiv 2022年

作者： Bhattacharyay, Shubhayu Milosevic, Ioan Wilson, Lindsay Menon, David K. Stevens, Robert D. Steyerberg, Ewout W. Nelson, David W. Ercole, Ari Åkerlund, Cecilia Amrein, Krisztina Andelic, Nada Andreassen, Lasse Anke, Audny Antoni, Anna Audibert, Gérard Azouvi, Philippe Azzolini, Maria Luisa Bartels, Ronald Barzó, Pál Beauvais, Romuald Beer, Ronny Bellander, Bo-Michael Belli, Antonio Benali, Habib Berardino, Maurizio Beretta, Luigi Blaabjerg, Morten Bragge, Peter Brazinova, Alexandra Brinck, Vibeke Brooker, Joanne Brorsson, Camilla Buki, Andras Bullinger, Monika Cabeleira, Manuel Caccioppola, Alessio Calappi, Emiliana Calvi, Maria Rosa Cameron, Peter Lozano, Guillermo Carbayo Carbonara, Marco Cavallo, Simona Chevallard, Giorgio Chieregato, Arturo Citerio, Giuseppe Clusmann, Hans Coburn, Mark Coles, Jonathan Cooper, Jamie D. Correia, Marta Čović, Amra Curry, Nicola Czeiter, Endre Czosnyka, Marek Dahyot-Fizelier, Claire Dark, Paul Dawes, Helen De Keyser, Véronique Degos, Vincent Della Corte, Francesco den Boogert, Hugo Depreitere, Bart Đilvesi, Đula Dixit, Abhishek Donoghue, Emma Dreier, Jens Dulière, Guy-Loup Esser, Patrick Ezer, Erzsébet Fabricius, Martin Feigin, Valery L. Foks, Kelly Frisvold, Shirin Furmanov, Alex Gagliardo, Pablo Galanaud, Damien Gantner, Dashiell Gao, Guoyi George, Pradeep Ghuysen, Alexandre Giga, Lelde Glocker, Ben Golubovic, Jagoš Gomez, Pedro A. Gratz, Johannes Gravesteijn, Benjamin Grossi, Francesca Gruen, Russell L. Gupta, Deepak Haagsma, Juanita A. Haitsma, Iain Helbok, Raimund Helseth, Eirik Horton, Lindsay Huijben, Jilske Hutchinson, Peter J. Jacobs, Bram Jankowski, Stefan Jarrett, Mike Jiang, Ji-Yao Johnson, Faye Jones, Kelly Karan, Mladen Kolias, Angelos G. Kompanje, Erwin Kondziella, Daniel Kornaropoulos, Evgenios Koskinen, Lars-Owe Kovács, Noémi Kowark, Ana Lagares, Alfonso Lanyon, Linda Laureys, Steven Lecky, Fiona Ledoux, Didier Lefering, Rolf Legrand, Valerie Lejeune, Aurelie Levi, Leon Lightfoot, Roger Lingsma, Hester Maas, Andrew I.R. Castaño-León, Ana M. Maegele, Marc Majdan, M Division of Anaesthesia University of Cambridge Addenbrooke's Hospital Cambridge United Kingdom Division of Neurosurgery Department of Clinical Neurosciences Addenbrooke's Hospital University of Cambridge Cambridge United Kingdom Laboratory of Computational Intensive Care Medicine Johns Hopkins University BaltimoreMD United States Division of Psychology University of Stirling Stirling United Kingdom Department of Anesthesiology and Critical Care Medicine Johns Hopkins University BaltimoreMD United States Department of Biomedical Data Sciences Leiden University Medical Center Leiden Netherlands Department of Physiology and Pharmacology Section for Perioperative Medicine and Intensive Care Karolinska Institutet Stockholm Sweden Cambridge Centre for Artificial Intelligence in Medicine Cambridge United Kingdom Division of Surgery and Clinical Neuroscience Department of Physical Medicine and Rehabilitation Oslo University Hospital University of Oslo Oslo Norway Department of Neurosurgery University Hospital Northern Norway Tromso Norway Department of Physical Medicine and Rehabilitation University Hospital Northern Norway Tromso Norway Trauma Surgery Medical University Vienna Vienna Austria Department of Anesthesiology & Intensive Care University Hospital Nancy Nancy France Raymond Poincare Hospital Assistance Publique - Hopitaux de Paris Paris France Department of Anesthesiology & Intensive Care S Raffaele University Hospital Milan Italy Department of Neurosurgery Radboud University Medical Center Nijmegen Netherlands Department of Neurosurgery University of Szeged Szeged Hungary International Projects Management ARTTIC Munchen Germany Department of Neurology Neurological Intensive Care Unit Medical University of Innsbruck Innsbruck Austria Department of Neurosurgery & Anesthesia & Intensive Care Medicine Karolinska University Hospital Stockholm Sweden NIHR Surgical Reconstruction and Microbiology Research Centre Birmingham United Kingdom Anesthesi

When a patient is admitted to the intensive care unit (ICU) after a traumatic brain injury (TBI), an early prognosis is essential for baseline risk adjustment and shared decision making. TBI outcomes are commonly categorised by the Glasgow Outcome Scale - Extended (GOSE) into eight, ordered levels of functional recovery at 6 months after injury. Existing ICU prognostic models predict binary outcomes at a certain threshold of GOSE (e.g., prediction of survival [GOSE > 1]). We aimed to develop ordinal prediction models that concurrently predict probabilities of each GOSE score. From a prospective cohort (n = 1,550, 65 centres) in the ICU stratum of the Collaborative European NeuroTrauma Effectiveness Research in TBI (center-TBI) patient dataset, we extracted all clinical information within 24 hours of ICU admission (1,151 predictors) and 6-month GOSE scores. We analysed the effect of two design elements on ordinal model performance: (1) the baseline predictor set, ranging from a concise set of ten validated predictors to a token-embedded representation of all possible predictors, and (2) the modelling strategy, from ordinal logistic regression to multinomial deep learning. With repeated k-fold cross-validation, we found that expanding the baseline predictor set significantly improved ordinal prediction performance while increasing analytical complexity did not. Half of these gains could be achieved with the addition of eight high-impact predictors to the concise set. At best, ordinal models achieved 0.76 (95% CI: 0.74 - 0.77) ordinal discrimination ability (ordinal c-index) and 57% (95% CI: 54% - 60%) explanation of ordinal variation in 6-month GOSE (Somers' Dxy). Model performance and the effect of expanding the predictor set decreased at higher GOSE thresholds, indicating the difficulty of predicting better functional outcomes shortly after ICU admission. Our results motivate the search for informative predictors that improve confidence in prognosis of higher GOSE a

关键词： Neural network models

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Automatic Extraction of Medication Mentions from Tweets-Overview of the BioCreative VII Shared Task 3 Competition

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database : the journal of biological databases and curation 2023年第2023期2023卷 baac108页

作者： Davy Weissenbacher Karen O'Connor Siddharth Rawal Yu Zhang Richard Tzong-Han Tsai Timothy Miller Dongfang Xu Carol Anderson Bo Liu Qing Han Jinfeng Zhang Igor Kulev Berkay Köprü Raul Rodriguez-Esteban Elif Ozkirimli Ammer Ayach Roland Roller Stephen Piccolo Peijin Han V G Vinod Vydiswaran Ramya Tekumalla Juan M Banda Parsa Bagherzadeh Sabine Bergler João F Silva Tiago Almeida Paloma Martinez Renzo Rivera-Zavala Chen-Kai Wang Hong-Jie Dai Luis Alberto Robles Hernandez Graciela Gonzalez-Hernandez Department of Computational Biomedicine Cedars-Sinai Medical Center Los Angeles CA USA. DBEI The Perelman School of Medicine University of Pennsylvania Philadelphia PA USA. Department of Computer Science and Information Engineering National Central University No. 300 Zhongda Rd Zhongli District Taoyuan 320 Taiwan. IoX Center National Taiwan University Da'an District Section 4 Roosevelt Rd No. 1 Barry Lam Hall Taipei 106 Taiwan. Research Center for Humanities and Social Sciences Academia Sinica No. 128 Section 2 Academia Rd Nangang District Taipei 115 Taiwan. Computational Health Informatics Program Boston Children's Hospital Boston MA USA. Department of Pediatrics Harvard Medical School Boston MA USA. NVIDIA Santa Clara CA USA. Department of Statistics Florida State University Tallahassee FL USA. Data and Analytics Chapter F. Hoffmann-La Roche Ltd Switzerland. Pharmaceutical Research and Early Development Roche Innovation Center Basel Switzerland. Speech and Language Technology Lab DFKI Berlin Germany. Department of Biology Brigham Young University Provo UT USA. Department of Computational Medicine and Bioinformatics Medical School University of Michigan Ann Arbor MI USA. Department of Learning Health Sciences Medical School University of Michigan Ann Arbor MI USA. School of Information University of Michigan Ann Arbor MI USA. Department of Computer Science Georgia State University Atlanta GA USA. CLaC Labs Concordia University Montreal Canada. DETI Institute of Electronics and Informatics Engineering of Aveiro University of Aveiro Portugal. Department of Computation University of A Coruña Spain. Computer Science and Engineering Department Universidad Carlos III de Madrid Madrid Spain. Big Data Laboratory Chunghwa Telecom Laboratories Taoyuan Taiwan. Department of Computer Science National Yang Ming Chiao Tung University Hsinchu Taiwan. Department of Electrical Engineering College of Electrical Engineering and Computer Sci

This study presents the outcomes of the shared task competition BioCreative VII (Task 3) focusing on the extraction of medication names from a Twitter user's publicly available tweets (the user's 'timeline'). In general, detecting health-related tweets is notoriously challenging for natural language processing tools. The main challenge, aside from the informality of the language used, is that people tweet about any and all topics, and most of their tweets are not related to health. Thus, finding those tweets in a user's timeline that mention specific health-related concepts such as medications requires addressing extreme imbalance. Task 3 called for detecting tweets in a user's timeline that mentions a medication name and, for each detected mention, extracting its span. The organizers made available a corpus consisting of 182 049 tweets publicly posted by 212 Twitter users with all medication mentions manually annotated. The corpus exhibits the natural distribution of positive tweets, with only 442 tweets (0.2%) mentioning a medication. This task was an opportunity for participants to evaluate methods that are robust to class imbalance beyond the simple lexical match. A total of 65 teams registered, and 16 teams submitted a system run. This study summarizes the corpus created by the organizers and the approaches taken by the participating teams for this challenge. The corpus is freely available at https://***/tasks/biocreative-vii/track-3/. The methods and the results of the competing systems are analyzed with a focus on the approaches taken for learning from class-imbalanced data.

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Author Correction: Medical history predicts phenome-wide disease onset and enables the rapid response to emerging health threats

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Nature communications 2025年第1期16卷 1507页

作者： Jakob Steinfeldt Benjamin Wild Thore Buergel Maik Pietzner Julius Upmeier Zu Belzen Andre Vauvelle Stefan Hegselmann Spiros Denaxas Harry Hemingway Claudia Langenberg Ulf Landmesser John Deanfield Roland Eils Department of Cardiology Angiology and Intensive Care Medicine Deutsches Herzzentrum der Charité (DHZC) Berlin Germany. Charité - Universitätsmedizin Berlin corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin Klinik/Centrum Berlin Germany. Computational Medicine Berlin Institute of Health (BIH) Charite - University Medicine Berlin Berlin Germany. Friede Springer Cardiovascular Prevention Center@Charite Charite - University Medicine Berlin Berlin Germany. Institute of Cardiovascular Sciences University College London London UK. Center for Digital Health Berlin Institute of Health (BIH) Charite - University Medicine Berlin Berlin Germany. MRC Epidemiology Unit Institute of Metabolic Science University of Cambridge Cambridge UK. Precision Health University Research Institute Queen Mary University of London and Barts NHS Trust London UK. Institute of Health Informatics University College London London UK. Institute for Medical Engineering and Science Massachusetts Institute of Technology Massachusetts USA. Pattern Recognition and Image Analysis Lab University of Münster Münster Germany. British Heart Foundation Data Science Centre London UK. Health Data Research UK London UK. National Institute for Health Research Biomedical Research Centre at University College London Hospitals London UK. Berlin Institute of Health (BIH) Charite - University Medicine Berlin Berlin Germany. DZHK (German Centre for Cardiovascular Research) Partner Site Berlin Berlin Berlin Germany. Center for Digital Health Berlin Institute of Health (BIH) Charite - University Medicine Berlin Berlin Germany. roland.eils@bih-charite.de. Health Data Science Unit Heidelberg University Hospital and BioQuant Heidelberg Germany. roland.eils@bih-charite.de.

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