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arXiv 2022年

作者： Lobentanzer, Sebastian Aloy, Patrick Baumbach, Jan Bohar, Balazs Charoentong, Pornpimol Danhauser, Katharina Doğan, Tunca Dreo, Johann Dunham, Ian Fernandez-Torras, Adrià Gyori, Benjamin M. Hartung, Michael Hoyt, Charles Tapley Klein, Christoph Korcsmaros, Tamas Maier, Andreas Mann, Matthias Ochoa, David Pareja-Lorente, Elena Popp, Ferdinand Preusse, Martin Probul, Niklas Schwikowski, Benno Sen, Bünyamin Strauss, Maximilian T. Turei, Denes Ulusoy, Erva Heidrun Wodke, Judith Andrea Saez-Rodriguez, Julio Heidelberg University Faculty of Medicine Heidelberg University Hospital Institute for Computational Biomedicine Bioquant Heidelberg Germany The Barcelona Institute of Science and Technology Catalonia Barcelona Spain Catalonia Barcelona Spain Institute for Computational Systems Biology University of Hamburg Germany Earlham Institute Norwich United Kingdom Biological Research Centre Szeged Hungary Heidelberg University Im Neuenheimer Feld 267 Heidelberg69120 Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Department of Pediatrics Dr. von Hauner Children’s Hospital University Hospital LMU Munich Germany Biological Data Science Lab Department of Computer Engineering Hacettepe University Ankara Turkey Department of Bioinformatics Graduate School of Health Sciences Hacettepe University Ankara Turkey Computational Systems Biomedicine Lab Department of Computational Biology Institut Pasteur Université Paris Cité Paris France Bioinformatics and Biostatistics Hub Institut Pasteur Université Paris Cité Paris France Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Open Targets Wellcome Genome Campus Cambridgeshire HinxtonCB10 1SD United Kingdom Laboratory of Systems Pharmacology Harvard Medical School Boston United States Imperial College London London United Kingdom Quadram Institute Bioscience Norwich United Kingdom Proteomics Program Novo Nordisk Foundation Centre for Protein Research University of Copenhagen Copenhagen Denmark Department of Proteomics and Signal Transduction Max Planck Institute of Biochemistry Martinsried Germany Im Neuenheimer Feld 460 Heidelberg69120 Germany Neuherberg Germany Medical Informatics Laboratory University Medicine Greifswald Germany

Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to nonspecialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://***) frees up valuable developer time;we encourage further development and usage by the community. © 2022, CC BY-NC-ND.

关键词： Ontology

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scTenifoldXct: A semi-supervised method for predicting cell-cell interactions and mapping cellular communication graphs

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Cell systems 2023年第4期14卷 302-311.e4页

作者： Yongjian Yang Guanxun Li Yan Zhong Qian Xu Yu-Te Lin Cristhian Roman-Vicharra Robert S Chapkin James J Cai Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA. Department of Statistics Texas A&M University College Station TX 77843 USA. Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE School of Statistics East China Normal University 3663 North Zhongshan Road Shanghai 200062 China. Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA. Graduate Institute of Biomedical Electronics and Bioinformatics National Taiwan University Taipei Taiwan. Department of Nutrition and the Program in Integrative Nutrition & Complex Diseases Texas A&M University College Station TX 77843 USA. Electronic address: r-chapkin@tamu.edu. Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843 USA Department of Veterinary Integrative Biosciences Texas A&M University College Station TX 77843 USA Interdisciplinary Program of Genetics Texas A&M University College Station TX 77843 USA. Electronic address: jcai@tamu.edu.

We present scTenifoldXct, a semi-supervised computational tool for detecting ligand-receptor (LR)-mediated cell-cell interactions and mapping cellular communication graphs. Our method is based on manifold alignment, using LR pairs as inter-data correspondences to embed ligand and receptor genes expressed in interacting cells into a unified latent space. Neural networks are employed to minimize the distance between corresponding genes while preserving the structure of gene regression networks. We apply scTenifoldXct to real datasets for testing and demonstrate that our method detects interactions with high consistency compared with other methods. More importantly, scTenifoldXct uncovers weak but biologically relevant interactions overlooked by other methods. We also demonstrate how scTenifoldXct can be used to compare different samples, such as healthy vs. diseased and wild type vs. knockout, to identify differential interactions, thereby revealing functional implications associated with changes in cellular communication status.

关键词： cell-cell interaction cellular communication gene regression network machine learning manifold alignment neural networks scRNA-seq single-cell RNA sequencing

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Design of Decision Support System Determination of Inventory Inventory Using Single Exponential Smoothing Forecasting Method

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Journal of Physics: Conference Series 2018年第1期1114卷

作者： Muhammad Iqbal Dahlan Abdullah H Hartono Cut Ita Erliana S Sriadhi Nurmawati M Adhi Prasnowo Abdurrozzaq Hasibuan Akbar Iskandar Kundharu Saddhono Abdussakir Hastuti Musa Muhammad Ikhsan Setiawan Youmeni Sagala Rumiris Siahaan Eka Mayastika Sinaga Anggraini Syahputri Feby Milanie Henry Aspan Muammar Khaddafi Department of Computer System Universitas Pembangunan Panca Budi Medan Indonesia Department of Informatics Universitas Malikussaleh Aceh Indonesia Department of Computer Science STMIK IBBI Medan Indonesia Department of Industrial Engineering Universitas Malikussaleh Aceh Indonesia Department of Electrical Engineering Universitas Negeri Medan Indonesia Faculty of Industry Technique University of 45 Surabaya Indonesia Department of Industrial Engineering Universitas Maarif Hasyim Latif Sidoarjo Indonesia Faculty of Engineering Universitas Islam Sumatera UtaraMedan-Indonesia Informatics Engineering STMIK AKBA Makassar Indonesia Graduate Program Universitas Sebelas Maret Surakarta Indonesia Department of Mathematics Education State Islamic University of Malang Malang Indonesia Department of Mathematics Universitas Muhammadiyah Parepare Indonesia Department of Civil Engineering Narotama University Surabaya Indonesia STIE Bina Karya Tebing Tinggi Indonesia Universitas Pembangunan Panca Budi Medan Indonesia Department of Accounting Universitas Malikussaleh Aceh Indonesia

The development of information and communication technology at this time has touched all sides of life. Almost no side of human life is not touched by this information technology, which is more synonymous with the world of computerization. No exception also with the computerization that is popular in the corporate environment and government agencies. If in ancient times everything was still done manually. However, at this time all leaders and management have realized the importance of this information technology products that can facilitate them in carrying out the day-to-day corporate functions. Decision Making System of goods purchasing is one of the determinants of the accumulation of goods. If the decision is taken right then stockpiling of goods can be avoided. In this thesis the authors designed a web-based system that helps Management in making the decision of the purchase amount of goods. the system was developed by using Microsoft Visual Studio 2010 and using SQL Server database processing applications. The end result of system design is expected to help minimize the accumulation of goods.

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Retraction: Design of Decision Support System Determination of Inventory Inventory Using Single Exponential Smoothing Forecasting Method (J. Phys.: Conf. Ser. 1114 012082)

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Journal of Physics: Conference Series 2018年第1期1114卷

This paper was retracted by IOP Publishing on 12 December 2018. This paper was published due to a technical error and was not intended to be included in this journal. Retraction published: 8 February 2019

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Global Wheat Head Dataset 2021: more diversity to improve the benchmarking of wheat head localization methods.

arXiv

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arXiv 2021年

作者： David, Etienne Serouart, Mario Smith, Daniel Madec, Simon Velumani, Kaaviya Liu, Shouyang Wang, Xu Pinto, Francisco Shafiee, Shahameh Tahir, Izzat S.A. Tsujimoto, Hisashi Nasuda, Shuhei Zheng, Bangyou Kichgessner, Norbert Aasen, Helge Hund, Andreas Sadhegi-Tehran, Pouria Nagasawa, Koichi Ishikawa, Goro Dandrifosse, Sébastien Carlier, Alexis Dumont, Benjamin Mercatoris, Benoit Evers, Byron Kuroki, Ken Wang, Haozhou Ishii, Masanori Badhon, Minhajul A. Pozniak, Curtis LeBauer, David Shaner Lillemo, Morten Poland, Jesse Chapman, Scott de Solan, Benoit Baret, Frédéric Stavness, Ian Guo, Wei Arvalis Institut du végétal 3 Rue Joseph et Marie Hackin Paris75116 France UMR1114 EMMAH INRAE Centre PACA Bâtiment Climat Domaine Saint-Paul 228 Route de l’Aérodrome CS 40509 Avignon Cedex84914 France School of Food and Agricultural Sciences The University of Queensland GattonQLD4343 Australia Hiphen SAS Agroparc Bâtiment Technicité 120 rue Jean Dausset Avignon84140 France Plant Phenomics Research Center Nanjing Agricultural University Nanjing China Wheat Genetics Resource Center Dep. of Plant Pathology Kansas State Univ. 4024 Throckmorton Plant Sciences Center ManhattanKS United States Mexico D.F. Mexico Norwegian University of Life Sciences Faculty of Biosciences P.O. Box 5003 ÅsNO-1432 Norway Agricultural Research Corporation Wheat Research Program P.O. Box 126 Wad Medani Sudan Arid Land Research Center Tottori University Tottori680-0001 Japan Laboratories of Plant Genetics and Plant Breeding Graduate School of Agriculture Kyoto University Japan CSIRO Agriculture and Food Queensland Biosciences Precinct 306 Carmody Road St LuciaQLD4067 Australia Institute of Agricultural Sciences ETH Zurich Universitätstrasse 2 Zurich8092 Switzerland Plant Sciences Department Rothamsted Research Harpenden United Kingdom Institute of Crop Science National Agriculture and Food Research Organization Japan Hokkaido Agricultural Research Center National Agriculture and Food Research Organization Japan Biosystems Dynamics and Exchanges TERRA Teaching and Research Center Gembloux Agro-Bio Tech University of Liège Gembloux5030 Belgium Plant Sciences TERRA Teaching and Research Center Gembloux Agro-Bio Tech University of Liège Gembloux5030 Belgium Graduate School of Agricultural and Life Sciences The University of Tokyo 1-1-1 Midori-cho Nishitokyo City Tokyo Japan Department of Computer Science University of Saskatchewan Canada Department of Plant Sciences University of Saskatchewan Canada College of Agriculture and Life Sciences University o

The Global Wheat Head Detection (GWHD) dataset was created in 2020 and has assembled 193,634 labelled wheat heads from 4,700 RGB images acquired from various acquisition platforms and 7 countries/institutions. With an associated competition hosted in Kaggle, GWHD has successfully attracted attention from both the computer vision and agricultural science communities. From this first experience in 2020, a few avenues for improvements have been identified, especially from the perspective of data size, head diversity and label reliability. To address these issues, the 2020 dataset has been reexamined, relabeled, and augmented by adding 1,722 images from 5 additional countries, allowing for 81,553 additional wheat heads to be added. We now release a new version of the Global Wheat Head Detection (GWHD) dataset in 2021, which is bigger, more diverse, and less noisy than the 2020 version. The GWHD 2021 is now publicly available at http://***/ and a new data challenge has been organized on AIcrowd to make use of this updated dataset. © 2021, CC BY.

关键词： Object detection

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Genomic Surveillance of SARS-CoV-2 in Taiwan: A Perspective on Evolutionary Data Interpretation and Sequencing Issues

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Biomedical journal 2024年 100820页

作者： Yu-Nong Gong Nai-Yu Kuo Ting-Syuan Yeh Shin-Ru Shih Guang-Wu Chen Research Center for Emerging Viral Infections College of Medicine Chang Gung University Taoyuan Taiwan International Master Degree Program for Molecular Medicine in Emerging Viral Infections College of Medicine Chang Gung University Taoyuan Taiwan Department of Laboratory Medicine Linkou Chang Gung Memorial Hospital Taoyuan Taiwan. Medical Education Department Linkou Chang Gung Memorial Hospital Taoyuan Taiwan. National Institute of Infectious Diseases and Vaccinology National Health Research Institutes Taiwan. Department of Laboratory Medicine Linkou Chang Gung Memorial Hospital Taoyuan Taiwan Department of Medical Biotechnology and Laboratory Science College of Medicine Chang Gung University Taoyuan Taiwan Research Center for Chinese Herbal Medicine Research Center for Food and Cosmetic Safety and Graduate Institute of Health Industry Technology College of Human Ecology Chang Gung University of Science and Technology Taoyuan Taiwan. Department of Computer Science and Information Engineering College of Engineering Chang Gung University Taoyuan Taiwan. Electronic address: gwchen@mail.cgu.edu.tw.

This review presents a comprehensive perspective on the genomic surveillance of SARS-CoV-2 in Taiwan, with a focus on next-generation sequencing and phylogenetic interpretation. This article aimed to explore how Taiwan has utilized genomic sequencing technologies and surveillance to monitor and mitigate the spread of COVID-19. We examined databases and sources of genomic sequences and highlighted the role of data science methodologies in the explanation and analyses of evolutionary data. This review addressed the challenges and limitations inherent in genomic surveillance, such as concerns regarding data quality and the necessity for interdisciplinary expertise for accurate data interpretation. Special attention was given to the unique challenges faced by Taiwan, including its high population density and major transit destination for international travelers. We underscored the far-reaching implications of genomic surveillance data for public health policy, particularly in influencing decisions regarding travel restrictions, vaccine administration, and public health decision-making. Studies were examined to demonstrate the effectiveness of using genomic data to implement public health measures. Future research should prioritize the integration of methodologies and technologies in evolutionary data science, particularly focusing on phylodynamic analytics. This integration is crucial to enhance the precision and applicability of genomic data. Overall, we have provided an overview of the significance of genomic surveillance in tracking SARS-CoV-2 variants globally and the pivotal role of data science methodologies in interpreting these data for effective public health interventions.

关键词： SARS-CoV-2 data science genomic surveillance next-generation sequencing phylodynamics

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CENTML CONTROL SYSTEM TRAINING THROUGH STA TIC AND DYNAMIC SIMULATION

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Naval Engineers Journal 1980年第2期92卷 196-206页

作者： HALL, EDWIN E. MOSS, DONALD G. NORRIS, CLIFFORD S. PETERSON, HAROLD D. Mr. Edwin E. Hall received his Bachelor's degree in Electronics from Oklahoma City University. He also is a certified College-Level Instructor in the state of Florida and has done graduate work in Computer Science at the University of Florida. As the Technical Publications and Training Manager Simulation and Control Systems Department. General Electric Company Daytona Beach Fla. he currently is responsible for the costing. planning performance scheduling and timely completion of the Department's Technical Manuals and Technical Training Programs. These Training and Manual contracts cover Ship Systems Programs. Simulation Programs. and Communications Programs for the Armed Services and commercial customers. Mr. Hall has over twenty-years experience as a Technical Writer and Instructor and for the past seventeen years has been at the General Electric Company's Daytona Beach Facility. His experience ranges from teaching Basic Electronics and Radar Circuitry as a civilian instructor for the U.S. Army to writing Manuals Proposals Reports Specifications and Brochures for General Electric's product lines. Mr. Donald G. MOSS is a graduate of Kansas State University from which he received both his B.S. degree in Business Administration and his M.S. degree in Electrical Engineering. He is presently a Senior Systems Engineer for Control Systems in the Simulation and Control Systems Department at the General Electric Company's Daytona Beach Facility. He has been employed by General Electric for 23 years — the first seven as an Engineer and Program Manager on the Fire Control Systems for the Fleet Ballistics Missile Program the next six managing the design of control and checkout equipment on the APOLLO Program and the last ten years working on control equipment for the machinery plants of new Navy ships. Over the span of years at General Electric he has worked on propulsion control for the DD-963 propulsion electric plant and auxiliary control for the FFG-7: propulsion boiler burner electric auxiliary and car

Dynamic Simulation is defined as the hardware and software required to present to the student operator visual and audible cues and responses that are the same as those encountered when operating the Control Consoles aborad ship. This type of simulation is considered essential to the development of operator skills for critical tasks. Less critical tasks can be practiced using static simulation devices. This paper discusses the utilization of these types of training devices to train Navy crews. An overview of the Machinery Control Systems of the FFG 7 and AO 177 Class ships is discussed to provide an understanding of state‐of‐the‐art equipment development. The training programs for these two ship Classes are then reviewed to show how simulation devices are currently used by the Training Community, and this is followed by a brief discussion of the additional benefits that also are derived. © 1980 by the American Society of Naval Engineers, Inc.

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Percutaneous Coronary Intervention With a Drug-Eluting Stent Versus Coronary Artery Bypass Grafting in Patients Receiving Dialysis: A National Study From Taiwan

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Kidney medicine 2024年第2期6卷 100768页

作者： Szu-Yu Pan Ju-Yeh Yang Nai-Chi Teng Yun-Yi Chen Shi-Heng Wang Chien-Lin Lee Kang-Lung Chen Yen-Ling Chiu Shih-Ping Hsu Yu-Sen Peng Yung-Ming Chen Shuei-Liong Lin Likwang Chen Department of Integrated Diagnostics and Therapeutics National Taiwan University Hospital Taipei Taiwan. Division of Nephrology Department of Internal Medicine National Taiwan University Hospital Taipei Taiwan. Division of Nephrology Department of Internal Medicine Far Eastern Memorial Hospital New Taipei City Taiwan. Institute of Health Policy and Management College of Public Health National Taiwan University Taipei Taiwan. Institute of Population Health Sciences National Health Research Institutes Zhunan Taiwan. Department of Research Shin-Kong Wu Ho-Su Memorial Hospital Taipei Taiwan. Institute of Hospital and Health Care Administration National Yang Ming Chiao Tung University Taipei Taiwan. National Center for Geriatrics and Welfare Research National Health Research Institutes Yunlin Taiwan. Department of Cardiology Far Eastern Memorial Hospital New Taipei City Taiwan. Department of Cardiovascular Surgery Far Eastern Memorial Hospital New Taipei City Taiwan. Graduate Program in Biomedical Informatics Department of Computer Science and Engineering College of Informatics Yuan Ze University Taoyuan Taiwan. Graduate Institute of Clinical Medicine National Taiwan University College of Medicine Taipei Taiwan. Graduate Institute of Physiology College of Medicine National Taiwan University Taipei Taiwan.

Rationale & Objective:We aimed to study the comparative effectiveness of percutaneous coronary intervention with drug-eluting stent and coronary artery bypass grafting in patients receiving dialysis. Study Design:This was a retrospective observational cohort study. Setting & Participants:This population-based study identified patients receiving dialysis hospitalized for coronary revascularization between January 1, 2009 and December 31, 2015, in the Taiwan National Health Insurance Research Database. Exposures:Patients received percutaneous coronary intervention with drug-eluting stent versus coronary artery bypass grafting. Outcomes:The study outcomes were all-cause mortality, in-hospital mortality, and repeat revascularization. Analytical Approach:Propensity scores were used to match patients. Cox proportional hazards models and logistic regression models were constructed to examine associations between revascularization strategies and mortality. Interval Cox models were fitted to estimate time-varying hazards during different periods. Results:A total of 1,840 propensity score-matched patients receiving dialysis were analyzed. Coronary artery bypass grafting was associated with higher in-hospital mortality (coronary artery bypass grafting vs percutaneous coronary intervention with drug-eluting stent; crude mortality rate 12.5% vs 3.3%; adjusted OR, 5.22; 95% CI, 3.42-7.97; < 0.001) and longer hospitalization duration (median [IQR], 20 [14-30] days vs 3 [2-8] days; < 0.001). After discharge, repeat revascularization, acute coronary syndrome, and repeat hospitalization all occurred more frequently in the percutaneous coronary intervention with drug-eluting stent group. Importantly, with a median follow-up of 2.8 years, coronary artery bypass grafting was significantly associated with a higher risk of all-cause overall mortality (adjusted HR, 1.19; 95% CI, 1.05-1.35; = 0.006) in the multivariable Cox proportional hazard model. Sensitivity and subgroup analyses yie

关键词： Coronary artery bypass grafting coronary revascularization dialysis drug-eluting stent end-stage kidney disease mortality percutaneous coronary intervention survival

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Erratum to 'Relation Between Mitral Valve Prolapse and Erectile Dysfunction (from a Nationwide Case-Control Study)': The American Journal of Cardiology 2019 Nov 15;124(10):1590-1593./ doi: 10.1016/***.2019.08.010

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The American journal of cardiology 2021年 142卷 161页

作者： Shiu-Dong Chung Ju-Chi Liu Tsai-Ning Lou Ben-Chang Shia Herng-Ching Lin Li-Ting Kao Division of Urology Department of Surgery Far Eastern Memorial Hospital Taipei Taiwan Department of Computer Science and Engineering and Graduate Program in Biomedical Informatics College of Informatics Yuan-Ze University Chung-Li Taiwan Sleep Research Center Taipei Medical University Hospital Taipei Taiwan. Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei Taiwan Division of Cardiovascular Medicine Department of Medicine Medical University Hospital-Shuang Ho Hospital TaipeiTaiwan. School of Health Care Administration Taipei Medical University Taipei Taiwan. Big Data Research Center Taipei Medical University Taipei Taiwan. Sleep Research Center Taipei Medical University Hospital Taipei Taiwan School of Health Care Administration Taipei Medical University Taipei Taiwan Graduate Institute of Life Sciences National Defense Medical Center Taipei Taiwan Department of Pharmacy Practice Tri-Service General Hospital Taipei Taiwan School of Pharmacy National Defense Medical Center Taipei Taiwan.. Electronic address: kaoliting@***.

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Abstracts

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JOURNAL OF SPINAL CORD MEDICINE 2021年第SUPPL 1期44卷 S278-S324页

作者： [Anonymous] Department of Medicine Division of Physical Medicine and Rehabilitation University of Toronto Toronto ON CA KITE - Toronto Rehabilitation Institute University Health Network Toronto ON CA Institute for Health Policy Management and Evaluation University of Toronto Toronto ON CA Rehabilitation Sciences Institute University of Toronto Toronto ON CA Institute of Medical Sciences University of Toronto Toronto ON CA. Rehabilitation Sciences Institute University of Toronto ON CA KITE Research Institute-Toronto Rehab-University Health Network Toronto ON CA Physical Therapy Department University of Toronto ON CA Praxis Spinal Cord Institute Vancouver BC Université de Montréal (École de réadaptation) Montreal QC CA Institut de réadaptation Gingras-Linsay-de-Montréal Montreal QC CA Division of Physical Medicine & Rehabilitation Department of Medicine Faculty of Medicine & Dentistry University of Alberta Edmonton AB CA University of Calgary Calgary AB CA Alberta Health Services Centre for Family Medicine Kitchener ON CA McMaster University Department of Family Medicine Hamilton ON CA Dept. of Physical Therapy University of Toronto Toronto ON CA KITE-University Health Network Toronto ON CA Praxis Spinal Cord Institute Vancouver BC CA Center for Interdisciplinary Research in Rehabilitation and Social Integration (CIRRIS) Quebec City QC CA Dept. of Rehabilitation Laval University Quebec City QC CA Institute of Health Policy Management and Evaluation University of Toronto Toronto ON CA School of Rehabilitation Science University of Saskatchewan Saskatoon SK CA Ontario Neurotrauma Foundation Toronto ON CA Canadian Spinal Research Organization Toronto ON CA CIUSSS du Centre-Sud-de-l ‘Île-de-Montréal (Installation Gingras-Lindsay) Montréal QC CA École de réadaptation Université de Montréal Montréal QC CA First Steps Wellness Centre Regina SK CA Stan Cassidy Centre for Rehabilitation Horizon Health Network Fredericton NB CA Departmen

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