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arXiv 2024年

作者： Dawood, Moez Heavner, Ben Wheeler, Marsha M. Ungar, Rachel A. LoTempio, Jonathan Wiel, Laurens Berger, Seth Bernstein, Jonathan A. Chong, Jessica X. Délot, Emmanuèle C. Eichler, Evan E. Gibbs, Richard A. Lupski, James R. Shojaie, Ali Talkowski, Michael E. Wagner, Alex H. Wei, Chia-Lin Wellington, Christopher Wheeler, Matthew T. Carvalho, Claudia M.B. Gifford, Casey A. May, Susanne Miller, Danny E. Rehm, Heidi L. Sedlazeck, Fritz J. Vilain, Eric O'Donnell-Luria, Anne Posey, Jennifer E. Chadwick, Lisa H. Bamshad, Michael J. Montgomery, Stephen B. Human Genome Sequencing Center Baylor College of Medicine HoustonTX United States Department of Molecular and Human Genetics Baylor College of Medicine HoustonTX United States Medical Scientist Training Program Baylor College of Medicine HoustonTX United States Department of Biostatistics University of Washington SeattleWA United States Department of Genetics School of Medicine Stanford University StanfordCA United States Department of Pathology School of Medicine Stanford University Stanford CA United States Stanford Center for Biomedical Ethics School of Medicine Stanford University Stanford CA United States Institute for Clinical and Translational Science University of California IrvineCA United States Division of Cardiovascular Medicine School of Medicine Stanford University Stanford CA United States Division of Genetics and Metabolism Children’s National Rare Disease Institute WashingtonDC United States Center for Genetic Medicine Research Children’s National Rare Disease Institute WashingtonDC United States Department of Genomics and Precision Medicine George Washington University WashingtonDC United States Department of Pediatrics School of Medicine Stanford University Stanford CA United States Department of Pediatrics Dvision of Genetic Medicine University of Washington SeattleWA United States Brotman Baty Institute for Precision Medicine University of Washington SeattleWA United States Department of Genome Sciences University of Washington SeattleWA United States Howard Hughes Medical Institute University of Washington SeattleWA United States Department of Pediatrics Baylor College of Medicine HoustonTX United States Center for Genomic Medicine Massachusetts General Hospital BostonMA United States Program in Medical and Population Genetics Broad Institute of MIT and Harvard BostonMA United States Department of Neurology Massachusetts General Hospital Harvard Medical School BostonMA United States Stanley Center for

Rare diseases are collectively common, affecting approximately one in twenty individuals worldwide. In recent years, rapid progress has been made in rare disease diagnostics due to advances in DNA sequencing, development of new computational and experimental approaches to prioritize genes and genetic variants, and increased global exchange of clinical and genetic data. However, more than half of individuals suspected to have a rare disease lack a genetic diagnosis. The Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium was initiated to study thousands of challenging rare disease cases and families and apply, standardize, and evaluate emerging genomics technologies and analytics to accelerate their adoption in clinical practice. Further, all data generated, currently representing ~7500 individuals from ~3000 families, is rapidly made available to researchers worldwide via the Genomic Data science Analysis, Visualization, and Informatics Lab-space (AnVIL) to catalyze global efforts to develop approaches for genetic diagnoses in rare diseases (https://***/data). The majority of these families have undergone prior clinical genetic testing but remained unsolved, with most being exome-negative. Here, we describe the collaborative research framework, datasets, and discoveries comprising GREGoR that will provide foundational resources and substrates for the future of rare disease genomics. © 2024, CC BY.

关键词： Genome

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Author Correction: Cortical astrocytes modulate dominance behavior in male mice by regulating synaptic excitatory and inhibitory balance

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Nature neuroscience 2023年第12期26卷 2250页

作者： Kyungchul Noh Woo-Hyun Cho Byung Hun Lee Dong Wook Kim Yoo Sung Kim Keebum Park Minkyu Hwang Ellane Barcelon Yoon Kyung Cho C Justin Lee Bo-Eun Yoon Se-Young Choi Hye Yoon Park Sang Beom Jun Sung Joong Lee Department of Physiology and Neuroscience Dental Research Institute Seoul National University School of Dentistry Seoul Republic of Korea. Department of Physics and Astronomy Seoul National University Seoul Republic of Korea. Department of Molecular Biology Dankook University Cheonan Republic of Korea. Department of Electronic and Electrical Engineering Ewha Womans University Seoul Republic of Korea. Center for Cognition and Sociality Institute for Basic Science (IBS) Daejeon Republic of Korea. Department of Electrical and Computer Engineering University of Minnesota Minneapolis MN USA. Graduate Program in Smart Factory Ewha Womans University Seoul Republic of Korea. Department of Brain & Cognitive Sciences Ewha Womans University Seoul Republic of Korea. Department of Physiology and Neuroscience Dental Research Institute Seoul National University School of Dentistry Seoul Republic of Korea. sjlee87@snu.ac.kr.

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RETROFITTING OF BULBOUS BOWS ON UNITED-STATES NAVY AUXILIARY AND AMPHIBIOUS WARSHIPS

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NAVAL ENGINEERS JOURNAL 1984年第6期96卷 40-51页

作者： CHUN, SK HOUGH, JJ ENGLE, AH FUNG, SC Stephen K. Chunis a graduate of the Maritime College of the State University of New York class of 1981 from which he received a B.E. degree in naval architecture and his license as a Third Assistant Engineer from the U.S. Coast Guard. Since graduation he has worked for the U.S. Navy as a naval architect with the Hull Form and Hydrodynamics Performance Division (SEA 55W3) of the Naval Sea Systems Command. Currently he is the task leader for hydrodynamic design for the DDG-51. He is also responsible for bulbous bow and appendage design for surf ace ships. Mr. Chun is a member of ASNE SNAME and ASE. Jeffrey J. Hough:is currently a naval architect with the Hull Form and Hydrodynamic Performance Division (SEA 55VV3) of the Naval Sea Systems Command (NA VSEA). In his current capacity he is a member of the Surface Ship Hydrodynamics Branch and is the divisional coordinator for computer supported design (CSD) technical director for the hull form design system (HFDS) Hull Engineering Group (SEA 55) assistant coordinator for CSD SEA 55 CSD coordinator for the DDG-51 contract design and SEA 55W3 project engineer for aircraft carrier/aviation support ship hydrodynamics. Mr. Hough received his B.S.E. degree in naval architecture and marine engineering in 1978 and his M.S.E. degree in naval architecture and marine engineering in 1979 from the University of Michigan. He began his career with the U.S. Navy in 1979 as an Engineer-in-Training in the Ship Design and Integration Directorate of NAVSEA. Prior to his current assignment Mr. Hough was the technical director responsible for the hull form and hydrodynamics energy conservation program and technical specialist for design practices for resistance and powering margins and hull form geometry. A member of ASNE since 1979 Mr. Hough is also a member of SNAME ASE and the U.S. Naval Institute. Allen H. Engleis a naval architect with the Hull Form Design and Performance Division of the Naval Sea Systems Command. He received his B.S. degree in engineering science from th

To meet energy conservation goals of the U.S. Navy, its attention has been focused on ways to reduce individual ship total resistance and powering requirements. One possible method of improving ship powering characteristics is by modifying existing individual ship hulls with the addition of bulbous bows. This paper will identify the merits of retrofitting bow bulbs on selected U.S. Navy auxiliary and amphibious warfare ships. A procedure for performing a cost-benefit analysis will be shown for candidate ship classes. An example of this technique for an amphibious warfare ship will also be provided. A brief discussion of future methods to be used for bulbous bow design such as application of systematic model test data and numerical hydrodynamic techniques will be given.

关键词： NAVAL VESSELS

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Retraction notice to "A deep learning approach based on graphs to detect plantation lines" [Heliyon Volume 10, Issue 11, 15 June 2024, e31730]

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Heliyon 2024年第23期10卷 e40689页

作者： Diogo Nunes Gonçalves José Marcato Junior Mauro Dos Santos de Arruda Vanessa Jordão Marcato Fernandes Ana Paula Marques Ramos Danielle Elis Garcia Furuya Lucas Prado Osco Hongjie He Lucio André de Castro Jorge Jonathan Li Farid Melgani Hemerson Pistori Wesley Nunes Gonçalves Faculty of Computer Science Federal University of Mato Grosso do Sul Av. Costa e Silva Campo Grande 79070-900 MS Brazil. Faculty of Engineering Architecture and Urbanism and Geography Federal University of Mato Grosso do Sul Av. Costa e Silva Campo Grande 79070-900 MS Brazil. Faculty of Agricultural Sciences Federal University of Grande Dourados Av. Costa e Silva Dourados 79070-900 MS Brazil. Faculty of Science and Technology São Paulo State University (UNESP) R. Roberto Simonsen 305 Presidente Prudente 19060-900 SP Brazil. Program of Environment and Regional Developement University of Western São Paulo Raposo Tavares km 572 Presidente Prudente 19067-175 SP Brazil. Department of Geography and Environmental Management University of Waterloo Waterloo ON N2L 3G1 Canada. National Research Center of Development of Agricultural Instrumentation Brazilian Agricultural Research Agency (EMBRAPA) 13560-970 R. XV de Novembro 1452 São Carlos SP Brazil. Department of Information Engineering and Computer Science University of Trento Trento 38122 Italy. INOVISAO Dom Bosco Catholic University Avenida Tamandaré 6000 Campo Grande 79117-900 MS Brazil.

[This retracts the article DOI: 10.1016/***.2024.e31730.].

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A deep learning approach based on graphs to detect plantation lines

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Heliyon 2024年第11期10卷 e31730页

Identifying plantation lines in aerial images of agricultural landscapes is re-quired for many automatic farming processes. Deep learning-based networks are among the most prominent methods to learn such patterns and extract this type of information from diverse imagery conditions. However, even state-of-the-art methods may stumble in complex plantation patterns. Here, we propose a deep learning approach based on graphs to detect plantation lines in UAV-based RGB imagery, presenting a challenging scenario containing spaced plants. The first module of our method extracts a feature map throughout the backbone, which consists of the initial layers of the VGG16. This feature map is used as an input to the Knowledge Estimation Module (KEM), organized in three concatenated branches for detecting 1) the plant positions, 2) the plantation lines, and 3) the displacement vectors between the plants. A graph modeling is applied considering each plant position on the image as vertices, and edges are formed between two vertices (i.e. plants). Finally, the edge is classified as pertaining to a certain plantation line based on three probabilities (higher than 0.5): i) in visual features obtained from the backbone; ii) a chance that the edge pixels belong to a line, from the KEM step; and iii) an alignment of the displacement vectors with the edge, also from the KEM step. Experiments were conducted initially in corn plantations with different growth stages and patterns with aerial RGB imagery to present the advantages of adopting each module. We assessed the generalization capability in the other two cultures (orange and eucalyptus) datasets. The proposed method was compared against state-of-the-art deep learning methods and achieved superior performance with a significant margin considering all three datasets. This approach is useful in extracting lines with spaced plantation patterns and could be implemented in scenarios where plantation gaps occur, generating lines with few-to-no

关键词： Aerial imagery Convolutional neural networks Object detection Remote sensing UAV

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Corrections to “Gastric Section Correlation Network for Gastric Precancerous Lesion Diagnosis”

IEEE Open Journal of Engineering in Medicine and Biology

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IEEE Open Journal of engineering in Medicine and Biology 2024年 6卷 68-68页

作者： Jyun-Yao Jhang Yu-Ching Tsai Tzu-Chun Hsu Chun-Rong Huang Hsiu-Chi Cheng Bor-Shyang Sheu Department of Computer Science and Engineering National Chung Hsing University Taichung Taiwan Department of Internal Medicine Tainan Hospital Ministry of Health and Welfare Tainan Taiwan Department of Internal Medicine National Cheng Kung University Hospital College of Medicine National Cheng Kung University Tainan Taiwan Cross College Elite Program and Academy of Innovative Semiconductor and Sustainable Manufacturing National Cheng Kung University Tainan Taiwan Department of Internal Medicine National Cheng Kung University Hospital Tainan Taiwan Institute of Clinical Medicine and Molecular Medicine College of Medicine National Cheng Kung University Tainan Taiwan Institute of Clinical Medicine Department of Internal Medicine College of Medicine National Cheng Kung University Hospital National Cheng Kung University Tainan Taiwan

Presents corrections to the paper, Gastric Section Correlation Network for Gastric Precancerous Lesion Diagnosis.

关键词： Correlation Lesions engineering in medicine and biology

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A Calibrated Functional Patch Clamp Assay to Enhance Clinical Variant Interpretation in KCNH2-Related Long QT Syndrome

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Heart, Lung and Circulation 2022年 31卷 S37-S37页

作者： Jiang, C. Richardson, E. Farr, J. Hill, A. Ullah, R. Kroncke, B. Harrison, S. Thomson, K. Ingles, J. Vandenberg, J. Ng, C. Mark Cowley Lidwill Research Program in Cardiac Electrophysiology Victor Chang Cardiac Research Institute Sydney NSW Australia Faculty of Medicine and Health UNSW Sydney NSW Australia Centre for Population Genomics Garvan Institute of Medical Research and UNSW Sydney Sydney NSW Australia Centre for Population Genomics Murdoch Children's Research Institute Melbourne Vic Australia School of Computer Science and Engineering UNSW Sydney Sydney NSW Australia St Vincent's Clinical School UNSW Sydney Sydney NSW Australia Vanderbilt Center for Arrhythmia Research and Therapeutics Division of Clinical Pharmacology Department of Medicine Vanderbilt University Medical Center Nashville TN USA Ambry Genetics Aliso Viejo CA USA Oxford Medical Genetics Laboratories Churchill Hospital Oxford UK

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Quantum Simulation for High-Energy Physics

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PRX Quantum 2023年第2期4卷 027001-027001页

作者： Christian W. Bauer Zohreh Davoudi A. Baha Balantekin Tanmoy Bhattacharya Marcela Carena Wibe A. de Jong Patrick Draper Aida El-Khadra Nate Gemelke Masanori Hanada Dmitri Kharzeev Henry Lamm Ying-Ying Li Junyu Liu Mikhail Lukin Yannick Meurice Christopher Monroe Benjamin Nachman Guido Pagano John Preskill Enrico Rinaldi Alessandro Roggero David I. Santiago Martin J. Savage Irfan Siddiqi George Siopsis David Van Zanten Nathan Wiebe Yukari Yamauchi Kübra Yeter-Aydeniz Silvia Zorzetti Physics Division Lawrence Berkeley National Laboratory Berkeley California 94720 USA Department of Physics Maryland Center for Fundamental Physics and the NSF Institute for Robust Quantum Simulation University of Maryland College Park Maryland 20742 USA Department of Physics University of Wisconsin Madison Wisconsin 53706 USA T-2 Los Alamos National Laboratory Los Alamos New Mexico 87545 USA Fermi National Accelerator Laboratory Batavia Illinois 60510 USA Enrico Fermi Institute University of Chicago Chicago Illinois 60637 USA Kavli Institute for Cosmological Physics University of Chicago Chicago Illinois 60637 USA Department of Physics University of Chicago Chicago Illinois 60637 USA Department of Physics and Illinois Center for the Advanced Study of the Universe and Illinois Quantum Information Science and Technology Center University of Illinois Urbana Illinois 61801 USA QuEra Computing Inc Boston Massachusetts 02135 USA Department of Mathematics University of Surrey Guildford Surrey GU2 7XH United Kingdom Center for Nuclear Theory Department of Physics and Astronomy Stony Brook University New York 11794-3800 USA Department of Physics Brookhaven National Laboratory Upton New York 11973 USA Peng Huanwu Center for Fundamental Theory Hefei Anhui 230026 China Interdisciplinary Center for Theoretical Study University of Science and Technology of China Hefei Anhui 230026 China Pritzker School of Molecular Engineering Chicago Quantum Exchange and Kadanoff Center for Theoretical Physics University of Chicago Illinois 60637 USA qBraid Co. Harper Court 5235 Chicago Illinois 60615 USA Department of Physics Harvard University Cambridge Massachusetts 02138 USA Department of Physics and Astronomy University of Iowa Iowa City Iowa 52242 USA Duke Quantum Center Duke University Durham North Carolina 27701 USA Department of Electrical and Computer Engineering Duke University Durham North Carolina 27708 USA Department of Physics Duke University

It is for the first time that quantum simulation for high-energy physics (HEP) is studied in the U.S. decadal particle-physics community planning, and in fact until recently, this was not considered a mainstream topic in the community. This fact speaks of a remarkable rate of growth of this subfield over the past few years, stimulated by the impressive advancements in quantum information sciences (QIS) and associated technologies over the past decade, and the significant investment in this area by the government and private sectors in the U.S. and other countries. High-energy physicists have quickly identified problems of importance to our understanding of nature at the most fundamental level, from tiniest distances to cosmological extents, that are intractable with classical computers but may benefit from quantum advantage. They have initiated, and continue to carry out, a vigorous program in theory, algorithm, and hardware co-design for simulations of relevance to the HEP mission. This Roadmap is an attempt to bring this exciting and yet challenging area of research to the spotlight, and to elaborate on what the promises, requirements, challenges, and potential solutions are over the next decade and beyond.

关键词： Quantum simulation

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Global priority areas for ecosystem restoration (vol 586, pg 724, 2022)

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NATURE 2022年第7926期609卷 E7-E7页

作者： Strassburg, Bernardo B. N. Iribarrem, Alvaro Beyer, Hawthorne L. Cordeiro, Carlos Leandro Crouzeilles, Renato Jakovac, Catarina C. Braga Junqueira, Andre Lacerda, Eduardo Latawiec, Agnieszka E. Balmford, Andrew Brooks, Thomas M. Butchart, Stuart H. M. Chazdon, Robin L. Erb, Karl-Heinz Brancalion, Pedro Buchanan, Graeme Cooper, David Diaz, Sandra Donald, Paul F. Kapos, Valerie Leclere, David Miles, Lera Obersteiner, Michael Plutzar, Christoph de M. Scaramuzza, Carlos Alberto Scarano, Fabio R. Visconti, Piero Rio Conservation and Sustainability Science Centre Department of Geography and the Environment Pontifical Catholic University Rio de Janeiro Brazil International Institute for Sustainability Rio de Janeiro Brazil Programa de Pós Graduacão em Ecologia Universidade Federal do Rio de Janeiro Rio de Janeiro Brazil Botanical Garden Research Institute of Rio de Janeiro Rio de Janeiro Brazil Forest Ecology and Management Group Wageningen University Wageningen The Netherlands Institut de Ciència i Tecnologia Ambientals Universitat Autònoma de Barcelona Barcelona Spain Department of Geography Fluminense Federal University Niterói Brazil Department of Production Engineering Logistics and Applied Computer Science Faculty of Production and Power Engineering University of Agriculture in Kraków Kraków Poland School of Environmental Sciences University of East Anglia Norwich UK Department of Ecology and Evolutionary Biology University of Connecticut Storrs CT USA World Resources Institute Global Restoration Initiative Washington DC USA Tropical Forests and People Research Centre University of the Sunshine Coast Sunshine Coast Queensland Australia School of Biological Sciences University of Queensland St Lucia Queensland Australia Department of Zoology University of Cambridge Cambridge UK BirdLife International Cambridge UK RSPB Centre for Conservation Science Royal Society for the Protection of Birds Edinburgh UK International Union for Conservation of Nature (IUCN) Gland Switzerland World Agroforestry Center (ICRAF) University of the Philippines Los Baños The Philippines Institute for Marine and Antarctic Studies University of Tasmania Hobart Tasmania Australia Institute of Social Ecology University of Natural Resources and Life Sciences Vienna Vienna Austria Division of Conservation Biology Vegetation Ecology and Landscape Ecology University of Vienna Vienna Austria Department of Forest Sciences ‘Luiz de Queiroz’ College of Agriculture University of São Pau

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Creation and analysis of biochemical constraint-based models: The COBRA Toolbox v3.0

arXiv

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arXiv 2017年

作者： Heirendt, Laurent Arreckx, Sylvain Pfau, Thomas Mendoza, Sebastián N. Richelle, Anne Heinken, Almut Haraldsdóttir, Hulda S. Wachowiak, Jacek Keating, Sarah M. Vlasov, Vanja Magnusdóttir, Stefania Ng, Chiam Yu Preciat, German Žagare, Alise Chan, Siu H.J. Aurich, Maike K. Clancy, Catherine M. Modamio, Jennifer Sauls, John T. Noronha, Alberto Bordbar, Aarash Cousins, Benjamin El Assal, Diana C. Valcarcel, Luis V. Apaolaza, Iñigo Ghaderi, Susan Ahookhosh, Masoud Guebila, Marouen Ben Kostromins, Andrejs Sompairac, Nicolas Le, Hoai M. Ma, Ding Sun, Yuekai Wang, Lin Yurkovich, James T. Oliveira, Miguel A.P. Vuong, Phan T. El Assal, Lemmer P. Kuperstein, Inna Zinovyev, Andrei Scott Hinton, H. Bryant, William A. Aragón Artacho, Francisco J. Planes, Francisco J. Stalidzans, Egils Maass, Alejandro Vempala, Santosh Hucka, Michael Saunders, Michael A. Maranas, Costas D. Lewis, Nathan E. Sauter, Thomas Palsson, Bernhard Ø. Thiele, Ines Fleming, Ronan M.T. Luxembourg Centre for Systems Biomedicine University of Luxembourg 6 avenue du Swing BelvauxL-4367 Luxembourg Life Sciences Research Unit University of Luxembourg 6 avenue du Swing BelvauxL-4367 Luxembourg University of Chile Blanco Encalada 2085 Santiago Chile Department of Pediatrics University of California San Diego School of Medicine San DiegoCA92093 United States Hinxton CambridgeCB10 1SD United Kingdom Department of Chemical Engineering Pennsylvania State University University University ParkPA16802 United States Department of Physics University of California San Diego 9500 Gilman Dr. San DiegoCA92093 United States Bioinformatics and Systems Biology Program University of California San Diego San DiegoCA United States Sinopia Biosciences San DiegoCA United States School of Computer Science Algorithms and Randomness Center Georgia Institute of Technology AtlantaGA United States Biomedical Engineering and Sciences Department TECNUN University of Navarra Paseo de Manuel Lardizabal 13 San Sebastian20018 Spain Institute of Microbiology and Biotechnology University of Latvia Jelgavas iela 1 RigaLV-1004 Latvia Department of Management Science and Engineering Stanford University StanfordCA94305-4026 United States Bioengineering Department University of California San Diego San DiegoCA United States Utah State University Research Foundation 1695 North Research Park Way North LoganUT84341 United States Centre for Integrative Systems Biology and Bioinformatics Department of Life Sciences Imperial College London London United Kingdom Department of Mathematics University of Alicante Spain California Institute of Technology Computing and Mathematical Sciences MC 305-16 1200 E. California Blvd. PasadenaCA91125 United States Mathomics Center for Mathematical Modeling University of Chile Beauchef 851 Santiago Chile Novo Nordisk Foundation Center for Biosustainability University of California San Diego San DiegoCA92093 Uni

COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physicochemically and biochemically feasible phenotypic states. The COBRA Toolbox is a comprehensive software suite of interoperable COBRA methods. It has found widespread applications in biology, biomedicine, and biotechnology because its functions can be flexibly combined to implement tailored COBRA protocols for any biochemical network. Version 3.0 includes new methods for quality controlled reconstruction, modelling, topological analysis, strain and experimental design, network visualisation as well as network integration of chemoinformatic, metabolomic, transcriptomic, proteomic, and thermochemical data. New multi-lingual code integration also enables an expansion in COBRA application scope via high-precision, high-performance, and nonlinear numerical optimisation solvers for multi-scale, multi-cellular and reaction kinetic modelling, respectively. This protocol can be adapted for the generation and analysis of a constraint-based model in a wide variety of molecular systems biology scenarios. This protocol is an update to the COBRA Toolbox 1.0 and 2.0. The COBRA Toolbox 3.0 provides an unparalleled depth of constraint-based reconstruction and analysis methods. Copyright © 2017, The Authors. All rights reserved.

关键词： Data integration

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