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The molecular epidemiology of multiple zoonotic origins of SARS-CoV-2

四川生理科学杂志 2022年第7期44卷 1299-1299页

作者： Jonathan E Pekar Bioinformatics and Systems Biology Graduate Program University of California San Diego La Jolla CA 92093 USA Department of Biomedical Informatics University of California San Diego La Jolla CA 92093 USA Department of Human Genetics David Geffen School of Medicine University of California Los Angeles Los Angeles CA 90095 USA Department of Immunology and Microbiology The Scripps Research Institute La Jolla CA 92037 USA Department of Computer Science and Engineering University of California San Diego La Jolla CA 92093 USA Department of Mathematics University of California San Diego La Jolla CA 92093 USA Department of Ecology and Evolutionary Biology University of Arizona Tucson AZ 85721 USA W. Harry Feinstone Department of Molecular Microbiology and Immunology Johns Hopkins Bloomberg School of Public Health Baltimore MD 21205 USA New York City Public Health Laboratory New York City Department of Health and Mental Hygiene New York NY 11101 USA Department of Microbiology Institute for Viral Diseases Biosafety Center College of Medicine Korea University Seoul South Korea BK21 Graduate Program Department of Biomedical Sciences Korea University College of Medicine Seoul 02841 Republic of Korea National Public Health Laboratory National Centre for Infectious Diseases Singapore Malaysia Genome and Vaccine Institute Jalan Bangi 43000 Kajang Selangor Malaysia Department of Medicine University of California San Diego La Jolla CA 92093 USA Department of Microbiology and Immunology School of Medicine Tulane University New Orleans LA 70112 USA Zalgen Labs Frederick MD 21703 USA Global Virus Network (GVN) Baltimore MD 21201 USA Sydney Institute for Infectious Diseases School of Life and Environmental Sciences and School of Medical Sciences The University of Sydney Sydney NSW 2006 Australia Institute of Evolutionary Biology University of Edinburgh King’s Buildings Edinburgh EH9 3FL UK Department of Biomathematics David Geffen School of Medicine Un

Understanding the circumstances that lead to pandemics is important for their prevention. Here, we analyze the genomic diversity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) early in the coronavirus disease 2019 (COVID-19) pandemic. We show that SARS-CoV-2 genomic diversity before February 2020 likely comprised only two distinct viral lineages, denoted A and B. Phylodynamic rooting methods, coupled with epidemic simulations, reveal that these lineages were the result of at least two separate cross-species transmission events into humans. The first zoonotic transmission likely involved lineage B viruses around 18 November 2019 (23 October-8 December), while the separate introduction of lineage A likely occurred within weeks of this event.

关键词： epidemiology likely acute

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Author Correction: The high-dimensional space of human diseases built from diagnosis records and mapped to genetic loci

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Nature computational science 2023年第7期3卷 658页

作者： Gengjie Jia Yu Li Xue Zhong Kanix Wang Milton Pividori Rabab Alomairy Aniello Esposito Hatem Ltaief Chikashi Terao Masato Akiyama Koichi Matsuda David E Keyes Hae Kyung Im Takashi Gojobori Yoichiro Kamatani Michiaki Kubo Nancy J Cox James Evans Xin Gao Andrey Rzhetsky Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen China. jiagengjie@***. Computational Bioscience Research Center King Abdullah University of Science and Technology Thuwal Saudi Arabia. Computer Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal Saudi Arabia. Department of Computer Science and Engineering The Chinese University of Hong Kong Hong Kong People's Republic of China. Department of Medicine and Vanderbilt Genetics Institute Vanderbilt University Medical Center Nashville TN US. Department of Medicine Institute of Genomics and Systems Biology Committee on Genomics Genetics and Systems Biology University of Chicago Chicago IL US. Department of Operations Business Analytics and Information Systems University of Cincinnati Cincinnati OH US. Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine University of Pennsylvania Philadelphia PA US. Extreme Computing Research Center Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal Saudi Arabia. College of Computer Science and Engineering University of Jeddah Jeddah Saudi Arabia. HPE HPC/AI EMEA Research Laboratory Bristol UK. RIKEN Center for Integrative Medical Sciences Yokohama Japan. Clinical Research Center Shizuoka General Hospital Shizuoka Japan. Department of Applied Genetics The School of Pharmaceutical Sciences University of Shizuoka Shizuoka Japan. Department of Ophthalmology Graduate School of Medical Sciences Kyushu University Fukuoka Japan. Department of Computational Biology and Medical Sciences Graduate School of Frontier Sciences The University of Tokyo Tokyo Japan. Biological and Environmenta

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Development and validation of a novel combinational index of liquid biopsy biomarker for longitudinal lung cancer patient management

The journal of liquid biopsy

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The journal of liquid biopsy 2024年 6卷 100167页

作者： Min-Yi Liao Yun-Jie Hao Ching-Shan Luo Ching-Mei Chen Po-Hao Feng Hsin-Yu Yang Da-Jeng Yao Kang-Yun Lee Fan-Gang Tseng Department of Power Mechanical Engineering National Tsing Hua University Hsinchu 30013 Taiwan. Department of Engineering and System Science National Tsing Hua University Hsinchu 30013 Taiwan. International Ph.D. Program in Cell Therapy and Regeneration Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan. Division of Pulmonary Medicine Department of Internal Medicine Shuang Ho Hospital Taipei Medical University New Taipei City 23561 Taiwan. TMU Research Center of Thoracic Medicine Taipei Medical University Taipei 11031 Taiwan. Division of Pulmonary Medicine Department of Internal Medicine School of Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan. Nano Science and Technology Program National Tsing Hua University Hsinchu 30013 Taiwan. Institute of Nano Engineering and Micro Systems (NEMS) National Tsing Hua University Hsinchu 30013 Taiwan. Graduate Institute of Clinical Medicine College of Medicine Taipei Medical University Taipei 11031 Taiwan. Frontier Research Center on Fundamental and Applied Sciences of Matters National Tsing Hua University Hsinchu 30013 Taiwan.

Objectives:Many cancer biomarkers such as the circulating tumor cells/microemboli (CTCs/CTM) have been reported significant associations with clinical outcomes. However, different biomarkers have different sensitivities and specificities for cancer types and cohort patients, and synergistic effects between certain biomarkers have also been observed, leading to the inaccurate, fluctuating, and even controversial results when multiple biomarkers are analyzed together. In this paper, a novel combinational index, P-score, was developed for monitoring and predicting the disease condition of lung cancer patients during follow-up visits. Materials and methods:There were totally 13 return patients with 54 blood samples involved in this study to examine the number of CTC and CTM. Information from one group of 7 patients including 27 blood samples with published clinical data was employed to develop while those from another group of 4 patients containing 14 blood samples with unpublished clinical data were used to validate the P score in prediction. Enumerations were based on immunofluorescent staining images. Distributions of CTC/CTM and their frequencies in stratified patients were carefully examined and analyzed the ROC curve and AUC value to develop the P score and P score-based prediction model. Results and conclusion:We found that the predictive power of P-score was not only comparable to the traditional cancer marker, in comparison with individual CTC/CTM, more false positives could be corrected by using P-score, thereby to improve the accuracy of analysis. From our preliminary validation tests, the prognosis and disease progression monitored longitudinally by P-score were further confirmed by clinical outcome data from physicians and its sensitivity was even better than those from individual biomarkers. We believe that this novel combinational indicator could be a promising tool to interpret clinical outcomes more accurately from multiple factors, particularly useful

关键词： Circulating tumor cells/microemboli Combinational index Disease monitoring and prognosis Drug screening Lung cancer

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THE UNITED STATES NAVY'S “DESIGN WORK STUDY” APPROACH TO THE DEVELOPMENT OF SHIPBOARD CONTROL systems

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Naval Engineers Journal 1976年第6期88卷 62-74页

作者： PLATO, ARTIS I. GAMBREL, WILLIAM DAVID Artis I. Plato:is Head of the Design Work Study/ Shipboard Manning/Human Factors Engineering Section Systems Engineering and Analysis Branch Naval Ship Engineering Center (NAVSEC). He graduated from the City College of New York in 1956 receiving his Bachelor of Mechanical Engineering degree. Following this he started work at the New York Naval Shipyard in the Internal Combustion Engine and Cargo Elevator Section. During 1957 and 1958 he was called up for active duty with the U.S. Army Corps of Engineers and served in Europe with a Construction Engineer Battalion. After release from active duty he returned to the shipyard where he remained until 1961 when he transferred to the Naval Supply Research and Development Facility Bayonne New Jersey. Initially he was in charge of an Engineering Support Test Group and the drafting services for the whole Facility. Later he became a Project Engineer in the Food Services Facilities Branch with duties that included planning and designing new afloat and ashore messing facilities for the Navy. In 1966 he transferred to NAVSEC as a Project Engineer in the Design Work Study Section and in this capacity worked on selected projects and manning problems for new construction and also developed a computer program (Manpower Determination Model) that makes accurate crew predictions for feasibility studies. In 1969 he became Head of the Section. He has been active in the U.S. Army Reserve since his release from active duty and his duties have included command of an Engineer Company various Staff positions and his present assignment as Operations Officer for a Civil Affairs Group. He has completed the U. S. A rmy Corps of Engineers Career Course and the Civil Affairs Career Course and is presently enrolled in the U.S. Army Command and General Staff College non-resident course. Additionally he completed graduate studies at American University Washington D.C in 1972 receiving his MSTM degree in Technology of Management and is a member of ASE ASME CAA U. S. Naval Instit

The purpose of this paper is to discuss a system analysis technique called “Design Work Study”, that is used by the U.S. Navy for the development of improved ship control systems. The Design Work Study approach is one which brings about the most efficient and cost effective man‐machine combination for the ship control functions. Adherence to this process insures that the advantages of automation are balanced against incurred operational and maintenance expense. At present, U.S. Navy doctrine requires that certain ship operating stations, such as steering and propulsion control, be manned at specified ship conditions of readiness. Therefore, if personnel are needed to fulfill these combat environment obligations, excessive automation may only result in unnecessary additional acquisition costs and increased personnel skill requirements. The Design Work Study process can be applied to establish the required fine balance between the degree of built‐in automation and the shipboard manpower levels. In order to explain the techniques that are used for this process, the Authors will present a brief summary of the Design Work Study approach for optimizing shipboard control systems, including an explanation of the formal procedural tools that are applicable. In addition, a practical case study of ship control system design for one of the latest classes of Navy destroyers will be presented. This example will illustrate the resultant savings and benefits that can be realized by a judicious application of this technique. © 1976 American Society of Naval Engineers

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Control of ship fouling in U.S. Navy

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Naval Engineers Journal 1967年第n 1期v 79卷 p77-85页

作者： Birnbaum, L.S. Bukzin, E.A. Saroyan, J.R. Leon S. Birnbaum holds a B.S. degree in Chemistry from City College of New York. He has completed graduate work in Chemistry at the University of Maryland and Temple University and in Technology and Management at American University. He has been with the Navy Department Washington since 1949 and is currently Head of the Coatings and Chemistry Branch of the Materials Development and Application Office of the Naval Ship Engineering Center. Responsibilities of this Branch include such items as coatings corrosion control techniques insulation chemical cleaning water treatment toxicology and detection and decontamination of biological and chemical warfare agents. Prior to this Mr. Birnbaum was employed in the Industrial Test Laboratory Philadelphia Naval Shipyard from 1938 to 1949. Work during this period included supervision of a section which inspected paints and allied materials and petroleum products to determine their suitability for Naval use and direction of research in fire retardant treatments. He is a member of the American Chemical Society Washington Paint Technical Group. National Association of Corrosion Engineers and the American Society of Naval Engineers. Mr. Bukzin is a research and development program manager in the Naval Ship Systems Command of the Department of the Navy in the fields of non-metallic materials fuels lubricants cold weather operations and several other areas. He is a graduate chemical engineer from New York University with additional training in naval architecture and management which culminated in his participation in the Senior Development Program at Cornell University during the summer of 1960. He has been employed by the Command and its predecessor for the past 2b years and has been in his present position of R&D planning and programming for the past six years. Prior to that his major technical responsibilities were in the field of elastomers and their applications. He received several awards and published a number of papers during those years. Mr. Bukzin is a me

Report on paints used on surface ships and submarines for protection against corrosion and prevention of fouling, and on work connected with development and evaluation of such coatings;experiences with "hot plastic", "cold plastic" and vinyl paints;hazards in use of vinyl paints and safety precautions;test techniques;new toxics (which are only kind so far satisfactory antifouling formulations) under test.

关键词： Ships

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WHAT IS A NUCLEAR REACTOR?

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Journal of the American Society for Naval Engineers 1958年第2期70卷 311-326页

作者： CARRISON, D.A. SMITH, C.O. Donald A. Carrison received a B. S. degree from the University of Illinois and did graduate work in Physics Mathematics and Engineering at the University of California at Los Angeles. He was a Staff Member in Training at the Oak Ridge School of Reactor Technology prior to joining the Director's Division at the Oak Ridge National Laboratory as a Senior Physicist with a group investigating an advanced reactor concept. Since May of 1957 he has been a member of the senior staff of Aeronutronic Systems Inc. a Ford Motor Co. subsidiary in Glendale Calif. Charles O. Smith received a B.S. in Mech. Eng. from Worcester Polytechnic Institute a S. M. in Mech. Eng. from Massachusetts Institute of Technology and a Sc.D. in Metallurgy from Massachusetts Institute of Technology. He served in the Navy during World War II in aviation maintenance. He currently holds the rank of Lieutenant Commander USNR and is active in the reserve program of the Office of Naval Research. He has seven years teaching experience at WPI and MIT and was associated with Alcoa Research Laboratories for three and one-half years as a Research Engineer. He currently is Lecturer in Reactor Materials at the Oak Ridge School of Reactor Technology at the Oak Ridge National Laboratory.

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The U.S. Navy Diving program

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Naval Engineers Journal 1974年第4期86卷 17-28页

作者： COLEMAN, JAMES J. USN The author is a graduate of the U.S. Navy Academy Class of 1957. Prior to pursuing an advanced degree at Webb Institute of Naval Architecture he spent two years in destroyers and four years in submarines. Designated an Engineering Duty Officer (EDO) in 1966 he attended the Deep Sea Diving School and proceeded to Hunters Point Division of the San Francisco Naval Shipyard. Here he was responsible for the production efforts in the Deep Dive System MK 2 and the SEALAB III Program. While at Hunters Point he was also the 12th Naval District Salvage Officer and the Salvage Master during the raising of the nuclear submarine USS Guitarro which sank at Mare Island Naval Shipyard in May 1969. Following a tour on the Staff Commander Service Force U.S. Atlantic Fleet as the Fleet Salvage Officer he assumed command of the Experimental Diving Unit Washington D.C. in 1971 with additional duty at the Naval Ship Systems Command as the Supervisor of Diving. During this tour the Experimental Diving Unit conducted a world record 1600 foot wet hyperbaric dive. Relieved of this command on 1 October 1973 he presently remains as the Supervisor of Diving.

The office of the Supervisor of Diving, Naval Ship systems Command, is responsible for the development and testing of swimmer and diver equipment. The goal of the Navy Diving program is to enable the diver to work safely, efficiently, and in comfort at 1,000 feet today;1,500 feet in the near future;and 2,500 feet in the far term. This program is divided into three areas of concern: a) Surface Supported Diving;b) Integrated Diving System;and c) Man‐in‐the‐Sea Deep Ocean. The paper focuses on the aforementioned areas by relating to existing equipments, their problems, and what programs are currently being proved to resolve these problems. © 1974 American Society of Naval Engineers

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Author Correction: Single-cell transcriptomics uncovers EGFR signaling-mediated gastric progenitor cell differentiation in stomach homeostasis

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Nature communications 2023年第1期14卷 6540页

作者： Hitomi Takada Yohei Sasagawa Mika Yoshimura Kaori Tanaka Yoshimi Iwayama Tetsutaro Hayashi Ayako Isomura-Matoba Itoshi Nikaido Akira Kurisaki Laboratory of Stem Cell Technologies Graduate School of Science and Technology Nara Institute of Science and Technology Takayama-cho Ikoma Nara Japan. Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research Wako Saitama Japan. Department of Functional Genome Informatics Biological Data Science Medical Research Institute Tokyo Medical and Dental University Bunkyo Tokyo Japan. Laboratory for Bioinformatics Research RIKEN Center for Biosystems Dynamics Research Wako Saitama Japan. itoshi.nikaido@riken.jp. Department of Functional Genome Informatics Biological Data Science Medical Research Institute Tokyo Medical and Dental University Bunkyo Tokyo Japan. itoshi.nikaido@riken.jp. Master's/Doctoral Program in Life Science Innovation (Bioinformatics) Degree Programs in Systems and Information Engineering Graduate School of Science and Technology University of Tsukuba Tsukuba Ibaraki Japan. itoshi.nikaido@riken.jp. Laboratory of Stem Cell Technologies Graduate School of Science and Technology Nara Institute of Science and Technology Takayama-cho Ikoma Nara Japan. akikuri@bs.naist.jp.

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Corrigendum to: Spatial Topography of Individual-Specific Cortical Networks Predicts Human Cognition, Personality and Emotion

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Cerebral cortex (New York, N.Y. : 1991) 2021年第8期31卷 3974页

作者： Ru Kong Jingwei Li Csaba Orban Mert R Sabuncu Hesheng Liu Alexander Schaefer Nanbo Sun Xi-Nian Zuo Avram J Holmes Simon B Eickhoff B T Thomas Yeo Department of Electrical and Computer Engineering ASTAR-NUS Clinical Imaging Research Centre Singapore Institute for Neurotechnology and Memory Networks Program National University of Singapore Singapore. School of Electrical and Computer Engineering Cornell University Ithaca NY USA. Martinos Center for Biomedical Imaging Massachusetts General Hospital Charlestown MA USA. CAS Key Laboratory of Behavioral Sciences and Research Center for Lifespan Development of Brain and Mind (CLIMB) Institute of Psychology Beijing China. University of Chinese Academy of Sciences Beijing China. Department of Psychology Yale University New Haven CT USA. Institute for Systems Neuroscience Medical Faculty Heinrich-Heine University Düsseldorf Düsseldorf Germany. Institute of Neuroscience and Medicine Brain & Behaviour (INM-7) Research Center Jülich Jülich Germany. Centre for Cognitive Neuroscience DukeNUS Medical School Singapore. NUS Graduate School for Integrative Sciences and Engineering National University of Singapore Singapore.

In the originally published version of this manuscript, there was an error in the legends in figures S1 and S2 in the supplementary material. The colours of two labels (Limbic A and Limbic B) were mistakenly swapped. Limbic A should refer to brain regions in the temporal lobes shown in the brighter colour, while Limbic B should refer to regions in the orbitofrontal cortex shown in the darker colour. The colours for Limbic A and Limbic B in the figure legends have now been corrected. No changes are required in the text and none of the conclusions of the study are affected.

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Proceedings of the 16th Annual UT-KBRIN Bioinformatics Summit 2016: bioinformatics

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BMC Bioinformatics 2017年第9期18卷 1-9页

作者： Eric C. Rouchka Juw Won Park Julia H. Chariker David A. Tieri Shreedharkumar Rajurkar Vikas Singh Nishchal K. Verma Yan Cui Mark Farman Bradford Condon Jolanta Jaromczyk Neil Moore Jerzy Jaromczyk Daniel Harris Patrick Calie Eun Kyong Shin Robert L. Davis Arash Shaban-Nejad Joshua M. Mitchell Hunter N. B. Moseley Robert M. Flight Qing Jun Wang Richard M. Higashi Teresa W-M Fan Andrew N. Lane Liangqun Lu Bernie J Daigle Jr. Xi Chen Andrey Smelter Jerzy W. Jaromczyk Bailey K. Phan Nathaniel J. Serpico Ethan G. Toney Li Chen Caroline E. Melton Jennifer R. Mandel Bernie J. Daigle Jr. Hao Chen Kazi I. Zaman Ramin Homayouni Patrick J. Trainor Andrew P. DeFilippis Samantha M. Carlisle Shesh N. Rai Department of Computer Engineering and Computer Science University of Louisville Duthie Center for Engineering Louisville KY 40292 USA Kentucky Biomedical Research Infrastructure (KBRIN) Bioinformatics Core 522 East Gray Street Louisville KY 40292 USA Department of Psychological and Brain Sciences University of Louisville Louisville KY 40292 USA Department of Anatomical Sciences and Neurobiology University of Louisville Louisville KY 40292 USA Department of Electrical Engineering IIT Kanpur India Department of Microbiology Immunology and Biochemistry University of Tennessee Health Science Center Memphis TN 38103 USA Center for Integrative and Translational Genomics University of Tennessee Health Science Center Memphis TN 38103 USA Department of Plant Pathology University of Kentucky Lexington KY 40546 USA UK Healthcare Genomics University of Kentucky Lexington KY 40536 USA Department of Entomology & Plant Pathology University of Tennessee Knoxville TN 37996 USA Department of Forestry University of Kentucky Lexington KY 40506 USA Department of Computer Science University of Kentucky Lexington KY 40506 USA Department of Computer Science University of Kentucky Lexington KY 40508 USA Department of Biological Sciences Eastern Kentucky University Richmond KY 40475 USA University of Tennessee Health Science Center – Oak-Ridge National Lab (UTHSC-ORNL) Center for Biomedical Informatics Department of Pediatrics Memphis TN 38103 USA Department of Molecular & Cellular Biochemistry University of Kentucky Lexington KY 40536 USA Markey Cancer Center University of Kentucky Lexington KY 40536 USA Center for Environmental and Systems Biochemistry University of Kentucky Lexington KY 40536 USA Institute for Biomedical Informatics University of Kentucky Lexington KY 40536 USA Department of Molecular and Cellular Biochemistry University of Kentucky Lexington KY 40536 USA Department of Statistics University of Kentucky Louisville KY

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