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computationally modeling the physiological impact of the ratio of fats to carbohydrates in the diet on intake among metabolically healthy adults

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Current Developments in Nutrition 2025年

作者： Marie F. Martinez Jessie Heneghan Colleen Weatherwax Timothy H. Moran Britt Burton-Freeman Kavya Velmurugan José M. Ordovás Sarah M. Bartsch Tej D. Shah Jennifer Lee Sarah L. Booth Samantha Kleinberg Kevin L. Chin Kayla de la Haye Alexis Dibbs Sheryl A. Scannell Bruce Y. Lee Public Health Informatics Computational and Operations Research (PHICOR) CUNY Graduate School of Public Health and Health Policy New York City NY Center for Advanced Technology and Communication in Health (CATCH) CUNY Graduate School of Public Health and Health Policy New York City NY Artificial Intelligence Modeling and Informatics for Nutrition Guidance and Systems (AIMINGS) Center Nutrition for Precision Health powered by All of Us Research Program CUNY Graduate School of Public Health and Health Policy New York NY Department of Psychiatry and Behavioral Sciences Johns Hopkins School of Medicine Baltimore MD Department of Food Science and Nutrition Illinois Institute of Technology Chicago IL Jean Mayer USDA Human Nutrition Research Center on Aging Tufts University Boston MA Tufts University School of Medicine Boston MA Stevens Institute of Technology Hoboken NJ Center for Economic and Social Research University of Southern California Los Angeles CA

Background When it comes to how effectively a diet can help reduce or maintain body weight, a key question is how that diet affects a person's hunger, satiety, and subsequent eating. Objective Modeling, from a physiological perspective, how varying the ratio of fats to carbohydrates in a diet impacts hunger, satiety, and subsequent eating among metabolically healthy adults. Methods We developed a model representing an adult, their dietary intake, gastrointestinal tract, hunger/satiety levels, and meal consumption. We simulated agents eating fixed ratios of macronutrients and measured their subsequent eating over 24 hours driven by physiological responses. Results When increasing the proportion of energy from fats relative to carbohydrates, daily calories decrease by on average 149 and 110 calories per 10% increase in fats for males and females, respectively. Additionally, a simulated diet with a relative ratio of energy from fats:carbohydrates of 20%:80% results in individuals snacking after 9PM 93% of days for both sexes, whereas a relative fats:carbohydrates ratio of 80%:20% results in late night snacking approximately 55% and 60% of days for males and females, respectively. Agents consuming at least a 40%:60% relative ratio of energy from fats:carbohydrates can achieve the largest reductions in total calories consumed and late-night snacking compared to consuming higher relative proportions of carbohydrates. Conclusions Eating a diet with at least 40% of its energy from fats relative to carbohydrates can achieve the largest reductions in total calories consumed and late-night snacking each day compared to consuming higher proportions of carbohydrates, with even further reductions as more fat is added to the diet, when considering the physiological responses to dietary intake alone. Future research should layer in other strong contributing factors to eating such as stress, social context, palatability, physical activity, types of macronutrients, etc. and also repr

关键词： Precision nutrition computational modeling Systems science Dietary intake Hunger Satiety CCK Cholecystokinin GI Gastrointestinal GLP-1 Glucagon-like Peptide 1 NIH National institutes of Health PYY Peptide Tyrosine Tyrosine

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

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NATURE 2023年第7948期614卷 E37-E37页

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

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Cover Image, Volume 5, Number 3, March 2023

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Carbon Energy 2023年第3期5卷

作者： Jun Yang Xing Li Ke Qu Yixian Wang Kangqi Shen Changhuan Jiang Bo Yu Pan Luo Zhuangzhi Li Mingyang Chen Bingshu Guo Mingshan Wang Junchen Chen Zhiyuan Ma Yun Huang Zhenzhong Yang Pengcheng Liu Rong Huang Xiaodi Ren David Mitlin School of New Energy and Materials Southwest Petroleum University Chengdu China Energy Storage Research Institute Southwest Petroleum University Chengdu China Ke Qu Shenzhen Key Laboratory of Nanobiomechanics Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen 518055 China. China Key Laboratory of Polar Materials and Devices (MOE) and Department of Electronics East China Normal University Shanghai 200062 China. Mingyang Chen Beijing Computational Science Research Center Beijing 100193 China. Center for Green Innovation School of Materials Science and Engineering University of Science and Technology Beijing Beijing 100083 China. Rong Huang China Key Laboratory of Polar Materials and Devices (MOE) and Department of Electronics East China Normal University Shanghai 200062 China. Xiaodi Ren Hefei National Research Center for Physical Sciences at the Microscale Department of Materials Science and Engineering University of Science and Technology of China Hefei Anhui 230026 China. David Mitlin Materials Science Program and Texas Materials Institute The University of Texas at Austin Austin Texas 78712-1591 USA. Shenzhen Key Laboratory of Nanobiomechanics Shenzhen Institutes of Advanced Technology Chinese Academy of Sciences Shenzhen China China Key Laboratory of Polar Materials and Devices (MOE) Department of Electronics East China Normal University Shanghai China Xing Li School of New Energy and Materials Southwest Petroleum University Chengdu China. Materials Science Program and Texas Materials Institute The University of Texas at Austin Austin Texas USA Beijing Computational Science Research Center Beijing China School of Materials Science and Engineering Center for Green Innovation University of Science and Technology Beijing Beijing China Department of Materials Science and Engineering Hefei National Research Center for Physical Sciences at the Microscale University of Science and Technology of China Hefei Anhui China

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Multiwavelength study of GRB 201216C using the sub-TeV emission detected by MAGIC 38

Multiwavelength study of GRB 201216C using the sub-TeV emiss...

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38th International Cosmic Ray Conference, ICRC 2023

作者： Fukami, Satoshi Berti, Alessio Loporchio, Serena Nava, Lara Suda, Yusuke Noda, Koji Asano, Katsuaki Bošnjak, Željka Longo, Francesco Jordana-Mitjans, Nuria Melandri, Andrea Mundell, Carole Shrestha, Manisha Steele, Iain Abe, H. Abe, S. Abhir, J. Acciari, V.A. Agudo, I. Aniello, T. Ansoldi, S. Antonelli, L.A. Arbet Engels, A. Arcaro, C. Artero, M. Asano, K. Baack, D. Babić, A. Baquero, A. Barres de Almeida, U. Barrio, J.A. Batković, I. Baxter, J. Becerra González, J. Bednarek, W. Bernardini, E. Bernardos, M. Bernete, J. Berti, A. Besenrieder, J. Bigongiari, C. Biland, A. Blanch, O. Bonnoli, G. Bošnjak, Ž. Burelli, I. Busetto, G. Campoy-Ordaz, A. Carosi, A. Carosi, R. Carretero-Castrillo, M. Castro-Tirado, A.J. Ceribella, G. Chai, Y. Chilingarian, A. Cifuentes, A. Cikota, S. Colombo, E. Contreras, J.L. Cortina, J. Covino, S. D’Amico, G. D’Elia, V. Da Vela, P. Dazzi, F. De Angelis, A. De Lotto, B. Del Popolo, A. Delfino, M. Delgado, J. Delgado Mendez, C. Depaoli, D. Di Pierro, F. Di Venere, L. Dominis Prester, D. Donini, A. Dorner, D. Doro, M. Elsaesser, D. Emery, G. Escudero, J. Fariña, L. Fattorini, A. Foffano, L. Font, L. Fröse, S. Fukami, S. Fukazawa, Y. García López, R.J. Garczarczyk, M. Gasparyan, S. Gaug, M. Giesbrecht Paiva, J.G. Giglietto, N. Giordano, F. Gliwny, P. Godinović, N. Grau, R. Green, D. Green, J.G. Hadasch, D. Hahn, A. Hassan, T. Heckmann, L. Herrera, J. Hrupec, D. Hütten, M. Imazawa, R. Inada, T. Iotov, R. Ishio, K. Jiménez Martínez, I. Jormanainen, J. Kerszberg, D. Kluge, G.W. Kobayashi, Y. Kouch, P.M. Kubo, H. Kushida, J. Láinez Lezáun, M. Lamastra, A. Lelas, D. Leone, F. Lindfors, E. Linhoff, L. Lombardi, S. Longo, F. López-Coto, R. López-Moya, M. López-Oramas, A. Loporchio, S. Lorini, A. Lyard, E. Machado de Oliveira Fraga, B. Majumdar, P. Makariev, M. Maneva, G. Mang, N. Manganaro, M. Mangano, S. Mannheim, K. Mariotti, M. Martínez, M. Martínez-Chicharro, M. Mas-Aguilar, A. Mazin, D. Menchiari, S. Mender, S. Institute for Particle Physics and Astrophysics ETH Zürich Otto-Stern-Weg 5 Zürich8093 Switzerland Institute for Cosmic Ray Research The University of Tokyo Kashiwanoha 5-1-5 Kashiwa Japan Max Planck Institut for Physics Föhringer Ring 6 Munich Germany INFN MAGIC Group INFN Sezione di Bari Dipartimento Interateneo di Fisica Università e del Politecnico di Bari BariI-70125 Italy RomeI-00136 Italy Physics Program Graduate School of Advanced Science and Engineering Hiroshima University Hiroshima739-8526 Japan Faculty of Electrical Engineering and Computing University of Zagreb Zagreb Croatia INFN Sezione di Trieste via Valerio 2 Trieste Italy Department of Physics University of Bath Claverton Down BathBA2 7AY United Kingdom INAF-Osservatorio Astronomico di Brera Via E. Bianchi 46 LC MerateI-23807 Italy European Space Agency European Space Astronomy Centre Villanueva de la Canñada Madrid28692 Spain Astrophysics Research Institute Liverpool John Moores University Liverpool Science Park IC2 146 Brownlow HillL3 5RF United Kingdom Steward Observatory University of Arizona 933 North Cherry Avenue TucsonAZ85721-0065 United States The University of Tokyo Chiba Kashiwa277-8582 Japan ETH Zürich ZürichCH-8093 Switzerland Instituto de Astrofísica de Canarias Dpto. de Astrofísica Universidad de La Laguna Tenerife La LagunaE-38200 Spain Instituto de Astrofísica de Andalucía-CSIC Glorieta de la Astronomía s/n Granada18008 Spain Università di Udine INFN Trieste UdineI-33100 Italy Max-Planck-Institut für Physik MünchenD-80805 Germany Università di Padova INFN PadovaI-35131 Italy Bellaterra BarcelonaE-08193 Spain Technische Universität Dortmund DortmundD-44221 Germany Zagreb10000 Croatia IPARCOS Institute EMFTEL Department Universidad Complutense de Madrid MadridE-28040 Spain URCA RJ Rio de Janeiro22290-180 Brazil University of Lodz Faculty of Physics and Applied Informatics Department of Astrophysics Lodz90-236 Pola

Recently, several gamma-ray bursts (GRBs) have been detected in the very-high-energy (VHE) gamma-ray energy range by ground-based gamma-ray experiments such as MAGIC, H.E.S.S., and LHASSO. For some GRBs, the VHE emission is consistent with synchrotron self-Compton (SSC) emission from high-energy electrons accelerated in the forward shock of the relativistic jet. However, more statistics are needed to further constrain the emission models. GRB 201216C is a long bright GRB detected in a broad energy range from radio to VHE. The redshift is estimated to be 1.1, making the GRB the most distant source detected in the VHE energy range. MAGIC started the observation 56 seconds after the GRB was triggered by the Swift-BAT telescope. We performed a detailed analysis and detected the signal with about 6 sigma in the first 20 minutes. MAGIC continued the observation for 2.2 hours on the same night and 4 hours on the next night. No signal was detected later than 40 minutes after the GRB trigger. We have performed modelling of the multi-wavelength emission using the MAGIC data. We analysed simultaneous optical data from Liverpool Telescope with MAGIC and included the results in the modelling. The sub-TeV emission is consistent with the single-zone SSC model in the forward shock. In this presentation, we show the final results of the MAGIC data analysis of GRB 201216C and discuss the emission mechanism of the multi-wavelength data. © Copyright owned by the author(s) under the terms of the Creative Commons.

关键词： Gamma rays

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Benchmarking Emergency Department Triage Prediction Models with Machine Learning and Large Public Electronic Health Records

arXiv

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arXiv 2021年

作者： Xie, Feng Zhou, Jun Lee, Jin Wee Tan, Mingrui Li, Siqi Rajnthern, Logasan S.O. Chee, Marcel Lucas Chakraborty, Bibhas Wong, An-Kwok Ian Dagan, Alon Ong, Marcus Eng Hock Gao, Fei Liu, Nan Centre for Quantitative Medicine and Programme in Health Services and Systems Research Duke-NUS Medical School Singapore Singapore Singapore Singapore School of Electrical and Electronic Engineering Nanyang Technological University Singapore Singapore Faculty of Medicine Nursing and Health Sciences Monash University VIC Australia Department of Statistics and Data Science National University of Singapore Singapore Singapore Department of Biostatistics and Bioinformatics Duke University DurhamNC United States Division of Pulmonary Allergy and Critical Care Medicine Duke University DurhamNC United States Department of Emergency Medicine Beth Israel Deaconess Medical Center Harvard Medical School BostonMA United States MIT Critical Data Laboratory for Computational Physiology Institute for Medical Engineering and Science Massachusetts Institute of Technology CambridgeMA United States Department of Emergency Medicine Singapore General Hospital Singapore Singapore SingHealth AI Health Program Singapore Health Services Singapore Singapore Institute of Data Science National University of Singapore Singapore Singapore

The demand for emergency department (ED) services is increasing across the globe, particularly during the current COVID-19 pandemic. Clinical triage and risk assessment have become increasingly challenging due to the shortage of medical resources and the strain on hospital infrastructure caused by the pandemic. As a result of the widespread use of electronic health records (EHRs), we now have access to a vast amount of clinical data, which allows us to develop predictive models and decision support systems to address these challenges. To date, however, there are no widely accepted benchmark ED triage prediction models based on large-scale public EHR data. An open-source benchmarking platform would streamline research workflows by eliminating cumbersome data preprocessing, and facilitate comparisons among different studies and methodologies. In this paper, based on the Medical Information Mart for Intensive Care IV Emergency Department (MIMIC-IV-ED) database, we developed a publicly available benchmark suite for ED triage predictive models and created a benchmark dataset that contains over 400,000 ED visits from 2011 to 2019. We introduced three ED-based outcomes (hospitalization, critical outcomes, and 72-hour ED reattendance) and implemented a variety of popular methodologies, ranging from machine learning methods to clinical scoring systems. We evaluated and compared the performance of these methods against benchmark tasks. Our codes are open-source, allowing anyone with MIMIC-IV-ED data access to perform the same steps in data processing, benchmark model building, and experiments. This study provides future researchers with insights, suggestions, and protocols for managing raw data and developing risk triaging tools for emergency care. © 2021, CC BY.

关键词： Learning systems

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Efficient architecture-aware acceleration of BWA-MEM for multicore systems

arXiv

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arXiv 2019年

作者： Md, Vasimuddin Misra, Sanchit Li, Heng Aluru, Srinivas Parallel Computing Lab Intel Corporation Bangalore India Department of Biostatistics and Computational Biology Dana-Farber Cancer Institute Boston United States Department of Biomedical Informatics Harvard Medical School Boston United States School of Computational Science and Engineering Georgia Institute of Technology Atlanta United States

Innovations in Next-Generation Sequencing are enabling generation of DNA sequence data at ever faster rates and at very low cost. For example, the Illumina NovaSeq 6000 sequencer can generate 6 Terabases of data in less than two days, sequencing nearly 20 Billion short DNA fragments called reads at the low cost of $1000 per human genome. Large sequencing centers typically employ hundreds of such systems. Such high-throughput and low-cost generation of data underscores the need for commensurate acceleration in downstream computational analysis of the sequencing data. A fundamental step in downstream analysis is mapping of the reads to a long reference DNA sequence, such as a reference human genome. Sequence mapping is a compute-intensive step that accounts for more than 30% of the overall time of the GATK (Genome Analysis ToolKit) best practices workflow. BWA-MEM is one of the most widely used tools for sequence mapping and has tens of thousands of users. Copyright © 2019, The Authors. All rights reserved.

关键词： Costs

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An Early Stage Researcher's Primer on Systems Medicine Terminology

Network and Systems Medicine

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Network and Systems Medicine 2021年第1期4卷 2-50页

作者： Zanin, Massimiliano Aitya, Nadim A.A. Basilio, José Baumbach, Jan Benis, Arriel Behera, Chandan K. Bucholc, Magda Castiglione, Filippo Chouvarda, Ioanna Comte, Blandine Dao, Tien-Tuan Ding, Xuemei Pujos-Guillot, Estelle Filipovic, Nenad Finn, David P. Glass, David H. Harel, Nissim Iesmantas, Tomas Ivanoska, Ilinka Joshi, Alok Boudjeltia, Karim Zouaoui Kaoui, Badr Kaur, Daman Maguire, Liam P. McClean, Paula L. McCombe, Niamh De Miranda, João Luís Moisescu, Mihnea Alexandru Pappalardo, Francesco Polster, Annikka Prasad, Girijesh Rozman, Damjana Sacala, Ioan Sanchez-Bornot, Jose M. Schmid, Johannes A. Sharp, Trevor Solé-Casals, Jordi Spiwok, Vojtěch Spyrou, George M. Stalidzans, Egils Stres, Blaa Sustersic, Tijana Symeonidis, Ioannis Tieri, Paolo Todd, Stephen Van Steen, Kristel Veneva, Milena Wang, Da-Hui Wang, Haiying Wang, Hui Watterson, Steven Wong-Lin, Kongfatt Yang, Su Zou, Xin Schmidt, Harald H.H.W. Centro de Tecnología Biomédica Universidad Politécnica de Madrid Madrid Spain Intelligent Systems Research Centre School of Computing Engineering and Intelligent Systems Ulster University Ulster United Kingdom Center for Physiology and Pharmacology Institute of Vascular Biology and Thrombosis Research Medical University of Vienna Vienna Austria TUM School of Life Sciences Weihenstephan Technical University of Munich Freising Germany Holon Israel CNR National Research Council IAC Institute for Applied Computing Rome Italy Lab of Computing Medical Informatics and Biomedical Imaging Technologies School of Medicine Aristotle University of Thessaloniki Thessaloniki Greece Université Clermont Auvergne INRAE UNH Plateforme d'Exploration du Métabolisme MetaboHUB Clermont Clermont-Ferrand France Université de Technologie de Compiègne Compiègne France Labex MS2T Control of Technological Systems-of-Systems CNRS and Université de Technologie de Compiègne Compiègne France Faculty of Engineering University of Kragujevac Kragujevac Serbia Kragujevac Serbia Steinbeis Advanced Risk Technologies Institute Doo Kragujevac Kragujevac Serbia Pharmacology and Therapeutics School of Medicine Galway Neuroscience Centre National University of Ireland Galway Ireland School of Computing Ulster University Ulster United Kingdom Holon Israel Department of Mathematics and Natural Sciences Kaunas University of Technology Kaunas Lithuania Faculty of Computer Science and Engineering Ss. Cyril and Methodius University Skopje Macedonia Medicine Faculty Université Libre de Bruxelles CHU de Charleroi Charleroi Belgium Northern Ireland Centre for Stratified Medicine Biomedical Sciences Research Institute Ulster University Ulster United Kingdom Escola Superior de Tecnologia e Gestão Instituto Politécnico de Portalegre Portalegre Portugal Instituto Superior Técnico Universidade de Lisboa Lisboa Portugal Faculty of Automatic Control and Computers University Politehnica of B

Background: Systems Medicine is a novel approach to medicine, that is, an interdisciplinary field that considers the human body as a system, composed of multiple parts and of complex relationships at multiple levels, and further integrated into an environment. Exploring Systems Medicine implies understanding and combining concepts coming from diametral different fields, including medicine, biology, statistics, modeling and simulation, and data science. Such heterogeneity leads to semantic issues, which may slow down implementation and fruitful interaction between these highly diverse fields. Methods: In this review, we collect and explain more than100 terms related to Systems Medicine. These include both modeling and data science terms and basic systems medicine terms, along with some synthetic definitions, examples of applications, and lists of relevant references. Results: This glossary aims at being a first aid kit for the Systems Medicine researcher facing an unfamiliar term, where he/she can get a first understanding of them, and, more importantly, examples and references for digging into the topic. © Massimiliano Zanin et al., 2021;Published by Mary Ann Liebert, Inc. 2021.

关键词： Semantics

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SARS-CoV-2 Wastewater Genomic Surveillance: Approaches, Challenges, and Opportunities

arXiv

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arXiv 2023年

作者： Munteanu, Viorel Saldana, Michael A. Dreifuss, David Ouyang, Wenhao O. Ferdous, Jannatul Mohebbi, Fatemeh Schlueter, Jessica Ciorba, Dumitru Bostan, Viorel Gordeev, Victor Su, Justin Maine Kasianchuk, Nadiia Sharma, Nitesh Kumar Knyazev, Sergey Aßmann, Eva Lobiuc, Andrei Covasa, Mihai Crandall, Keith A. Wu, Nicholas C. Mason, Christopher E. Tierney, Braden T. Lucaci, Alexander G. Ophoff, Roel A. Gibas, Cynthia Rzymski, Piotr Skums, Pavel Solo-Gabriele, Helena Niko, Beerenwinkel Zelikovsky, Alex Hölzer, Martin Smith, Adam Mangul, Serghei Department of Computers Informatics and Microelectronics Technical University of Moldova Chisinau2045 Moldova Department of Biological and Morphofunctional Sciences College of Medicine and Biological Sciences Stefan cel Mare University of Suceava Suceava720229 Romania Astani Department of Civil and Environmental Engineering University of Southern California 3620 South Vermont Avenue Los AngelesCA90089 United States Department of Biosystems Science and Engineering ETH Zurich Basel Switzerland SIB Swiss Institute of Bioinformatics Lausanne Switzerland Department of Biochemistry University of Illinois at Urbana-Champaign UrbanaIL61801 United States Department of Bioinformatics and Genomics University of North Carolina Charlotte United States Department of Clinical Pharmacy School of Pharmacy University of Southern California 1540 Alcazar Street Los AngelesCA90033 United States Department of Computers Informatics and Microelectronics Technical University of Moldova Chisinau2045 Moldova Titus Family Department of Clinical Pharmacy USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences University of Southern California Los AngelesCA90089 United States Faculty of Biology Adam Mickiewicz University Poznan61-712 Poland Faculty of Pharmacy Bogomolets National University Kyiv01601 Ukraine Kyiv School of Economics Kyiv02000 Ukraine Titus Family Department of Clinical Pharmacy USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences University of Southern California 1540 Alcazar Street Los AngelesCA90033 United States Department of Pathology and Laboratory Medicine David Geffen School of Medicine University of California Los Angeles Los AngelesCA United States Method Development and Research Infrastructure Robert Koch Institute Berlin13353 Germany Robert Koch Institute Berlin13353 Germany College of Medicine and Biological Sciences University of Suceava Suceava720229 Romania College of Osteopathic Medicine of the Pacific

During the SARS-CoV-2 pandemic, wastewater-based genomic surveillance (WWGS) emerged as an efficient virus surveillance tool capable of accounting for asymptomatic cases, identifying known and novel mutations, and assigning them to lineages and sublineages of the virus. WWGS also offers the potential to uncover novel or cryptic lineages, although identifying and defining these lineages solely from wastewater presents challenges. Besides the significant advantages of WWGS for monitoring SARS-CoV-2 viral spread, technical challenges remain, including coverage dropouts and poor quality of wastewater sequencing (WWS) data due to viral RNA fragmentation and degradation. Subsequently, WWGS analysis requires advanced computational tools that are yet to be developed and benchmarked. The existing bioinformatics tools used to analyze WWS data are often based on previously developed computational methods for variant calling, de-novo assembly, or quantifying the expression of transcripts. Those methods were not specifically developed for WWS data and must be optimized to address unique challenges associated with wastewater analysis. While specialized tools for analyzing WWS data have also been developed recently, it remains to be seen how they will perform given the ongoing evolution of SARS-CoV-2 and the decline in testing and patient-based genomic surveillance. Here, we explore opportunities and challenges associated with WWGS, including aspects such as sample preparation, sequencing technology, and bioinformatics methods. We also highlight its potential role in monitoring infectious diseases and informing public health responses by complementing other surveillance systems. We also critically examine the practical applications and ethical considerations of WWGS, emphasizing the need for a robust framework and its translation into sustainable wastewater surveillance programs to fully realize its potential for public health. © 2023, CC BY.

关键词： Coronavirus

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Benchmarking the CoW with the TopCoW Challenge: Topology-Aware Anatomical Segmentation of the Circle of Willis for CTA and MRA

arXiv

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arXiv 2023年

作者： Yang, Kaiyuan Musio, Fabio Ma, Yihui Juchler, Norman Paetzold, Johannes C. Al-Maskari, Rami Höher, Luciano Li, Hongwei Bran Hamamci, Ibrahim Ethem Sekuboyina, Anjany Shit, Suprosanna Huang, Houjing Prabhakar, Chinmay de la Rosa, Ezequiel Waldmannstetter, Diana Kofler, Florian Navarro, Fernando Menten, Martin Ezhov, Ivan Rueckert, Daniel Vos, Iris Ruigrok, Ynte Velthuis, Birgitta Kuijf, Hugo Hämmerli, Julien Wurster, Catherine Bijlenga, Philippe Westphal, Laura Bisschop, Jeroen Colombo, Elisa Baazaoui, Hakim Makmur, Andrew Hallinan, James Wiestler, Bene Kirschke, Jan S. Wiest, Roland Montagnon, Emmanuel Letourneau-Guillon, Laurent Galdran, Adrian Galati, Francesco Falcetta, Daniele Zuluaga, Maria A. Lin, Chaolong Zhao, Haoran Zhang, Zehan Ra, Sinyoung Hwang, Jongyun Park, Hyunjin Chen, Junqiang Wodzinski, Marek Müller, Henning Shi, Pengcheng Liu, Wei Ma, Ting Yalçin, Cansu Hamadache, Rachika E. Salvi, Joaquim Llado, Xavier Estrada, Uma Maria Lal-Trehan Abramova, Valeriia Giancardo, Luca Oliver, Arnau Liu, Jialu Huang, Haibin Cui, Yue Lin, Zehang Liu, Yusheng Zhu, Shunzhi Patel, Tatsat R. Tutino, Vincent M. Orouskhani, Maysam Wang, Huayu Mossa-Basha, Mahmud Zhu, Chengcheng Rokuss, Maximilian R. Kirchhoff, Yannick Disch, Nico Holzschuh, Julius Isensee, Fabian Maier-Hein, Klaus Sato, Yuki Hirsch, Sven Wegener, Susanne Menze, Bjoern Department of Quantitative Biomedicine University of Zurich Zurich Switzerland Center for Computational Health Zurich University of Applied Sciences Zurich Switzerland Department of Neuroradiology University Hospital of Zurich Zurich Switzerland Department of Neurosurgery Zhongnan Hospital of Wuhan University Wuhan China Department of Computing Imperial College London London United Kingdom Helmholtz Center Munich Germany Athinoula A. Martinos Center for Biomedical Imaging Harvard Medical School Boston United States School of Medicine Technical University of Munich Munich Germany Department of Informatics Technical University of Munich Munich Germany Helmholtz AI Helmholtz Munich Munich Germany Image Sciences Institute UMC Utrecht Utrecht Netherlands Department of Neurology UMC Utrecht Utrecht Netherlands Department of Radiology UMC Utrecht Utrecht Netherlands Department of Clinical Neurosciences Division of Neurosurgery Geneva University Hospitals Geneva Switzerland Department of Neurology University Hospital of Zurich Zurich Switzerland Department of Physiology University of Toronto Toronto Canada Department of Neurosurgery University Hospital of Zurich Zurich Switzerland Department of Diagnostic Imaging National University Hospital Singapore Department of Diagnostic and Interventional Neuroradiology University Hospital Berne University of Berne Berne Switzerland Montreal Canada Universitat Pompeu Fabra Barcelona Spain EURECOM Biot France Institute of Medical Technology Peking University Health Science Center Beijing China Hangzhou Genlight Medtech Co. Ltd. Hangzhou China Department of Artificial Intelligence Sungkyunkwan University Seoul Korea Republic of Department of Electrical and Computer Engineering Sungkyunkwan University Seoul Korea Republic of Shanghai MediWorks Precision Instruments Co. Ltd. Shanghai China Institute of Informatics HES-SO Valais-Wallis Switzerland Department of Measurement and Electronics AGH University

The Circle of Willis (CoW) is an important network of arteries connecting major circulations of the brain. Its vascular architecture is believed to affect the risk, severity, and clinical outcome of serious neuro-vascular diseases. However, characterizing the highly variable CoW anatomy is still a manual and time-consuming expert task. The CoW is usually imaged by two angiographic imaging modalities, magnetic resonance angiography (MRA) and computed tomography angiography (CTA), but there exist limited public datasets with annotations on CoW anatomy, especially for CTA. Therefore we organized the TopCoW Challenge in 2023 with the release of an annotated CoW dataset. The TopCoW dataset was the first public dataset with voxel-level annotations for thirteen possible CoW vessel components, enabled by virtual-reality (VR) technology. It was also the first large dataset with paired MRA and CTA from the same patients. TopCoW challenge formalized the CoW characterization problem as a multiclass anatomical segmentation task with an emphasis on topological metrics. We invited submissions worldwide for the CoW segmentation task, which attracted over 140 registered participants from four continents. The top performing teams managed to segment many CoW components to Dice scores around 90%, but with lower scores for communicating arteries and rare variants. There were also topological mistakes for predictions with high Dice scores. Additional topological analysis revealed further areas for improvement in detecting certain CoW components and matching CoW variant topology accurately. TopCoW represented a first attempt at benchmarking the CoW anatomical segmentation task for MRA and CTA, both morphologically and topologically. © 2023, CC BY-NC-ND.

关键词： Large datasets

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Training of Physical Neural Networks

arXiv

引用

arXiv 2024年

作者： Momeni, Ali Rahmani, Babak Scellier, Benjamin Wright, Logan G. McMahon, Peter L. Wanjura, Clara C. Li, Yuhang Skalli, Anas Berloff, Natalia G. Onodera, Tatsuhiro Oguz, Ilker Morichetti, Francesco del Hougne, Philipp Le Gallo, Manuel Sebastian, Abu Mirhoseini, Azalia Zhang, Cheng Marković, Danijela Brunner, Daniel Moser, Christophe Gigan, Sylvain Marquardt, Florian Ozcan, Aydogan Grollier, Julie Liu, Andrea J. Psaltis, Demetri Alù, Andrea Fleury, Romain Lausanne Switzerland Microsoft Research 198 Cambridge Science Park CambridgeCB4 0AB United Kingdom Rain AI San Francisco United States Department of Applied Physics Yale University CT United States School of Applied and Engineering Physics Cornell University IthacaNY14853 United States Max Planck Institute for the Science of Light Staudtstraße 2 Erlangen91058 Germany Department of Electrical and Computer Engineering University of California Los AngelesCA90095 United States FEMTO-ST Institute Optics Department CNRS University Bourgogne Franche-Comté Besançon25030 Cedex France Department of Applied Mathematics and Theoretical Physics University of Cambridge Cambridge United Kingdom NTT Physics and Informatics Laboratories NTT Research Inc. Sunnyvale United States Lausanne Switzerland Dipartimento di Elettronica Informazione e Bioingegneria Politecnico di Milano Milan Italy Univ Rennes CNRS IETR UMR 6164 RennesF-35000 France IBM Research Europe– Zurich Rüschlikon8803 Switzerland Department of Computer Science Stanford University United States Google DeepMind 1600 Amphitheatre Parkway Mountain ViewCA94043 United States Unité Mixte de Physique CNRS/Thales CNRS Thales Université Paris-Saclay Palaiseau France Laboratoire Kastler Brossel Sorbonne Université École Normale Supérieure Collège de France CNRS UMR 8552 Paris France Laboratoire Albert Fert CNRS Thales UniversitéParis-Saclay Palaiseau91767 France Department of Physics and Astronomy University of Pennsylvania PhiladelphiaPA19104 United States Lausanne Switzerland Photonics Initiative Advanced Science Research Center City University of New York New YorkNY10031 United States Physics Program Graduate Center City University of New York New YorkNY10016 United States

Physical neural networks (PNNs) are a class of neural-like networks that leverage the properties of physical systems to perform computation. While PNNs are so far a niche research area with small-scale laboratory demonstrations, they are arguably one of the most underappreciated important opportunities in modern artificial intelligence (AI). Could we train AI models 1000x larger than current ones? Could we do this and also have them perform inference locally and privately on edge devices, such as smartphones or sensors? Research over the past few years has shown that the answer to all these questions is likely "textityes, with enough research": PNNs could one day radically change what is possible and practical for AI systems. To do this will however require rethinking both how AI models work, and how they are trained – primarily by considering the problems through the constraints of the underlying hardware physics. To train PNNs at large scale, many methods including backpropagation-based and backpropagation-free approaches are now being explored. These methods have various trade-offs, and so far no method has been shown to scale to the same scale and performance as the backpropagation algorithm widely used in deep learning today. However, this is rapidly changing, and a diverse ecosystem of training techniques provides clues for how PNNs may one day be utilized to create both more efficient realizations of current-scale AI models, and to enable unprecedented-scale models. Copyright © 2024, The Authors. All rights reserved.

关键词： Deep learning

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