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TransMut: a program to predict HLA-I peptide binding and optimize mutated peptides for vaccine design by the Transformer-derived self-attention model

Research Square

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Research Square 2021年

作者： Chu, Yanyi Zhang, Yan Wang, Qiankun Zhang, Lingfeng Wang, Xuhong Wang, Yanjing Wang, Jianmin Jiang, Xue Salahub, Dennis Russell Xiong, Yi Wei, Dong-Qing State Key Laboratory of Microbial Metabolism Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances Joint International Research Laboratory of Metabolic & Developmental Sciences School of Life Sciences and Biotechnology Shanghai Jiao Tong University Shanghai200030 China Department of Chemistry CMS - Centre for Molecular Simulation IQST - Institute for Quantum Science and Technology University of Calgary 2500 University Drive NW CalgaryABT2N 1N4 Canada Department of Clinical Oncology The University of Hong Kong-Shenzhen Hospital Shenzhen China School of Electrical Engineering and Computer Science University of Ottawa 75 Laurier Ave. OttawaONK1N 6N5 Canada The Ministry of Education Key Laboratory of System control and information processing Department of Automation School of Electronic Information and Electrical Engineering Shanghai Jiao Tong University Shanghai200030 China Integrative Biotechnology & Translational Medicine Yonsei University Incheon21983 Korea Republic of Peng Cheng Laboratory Vanke Cloud City Phase I Building 8 Xili Street Nanshan District Guangdong Shenzhen518055 China

Computational prediction of the interaction between human leukocyte antigen (HLA) and peptide (pHLA) can speed up epitope screening and vaccine design. Here, we develop the TransMut framework composed of TransPHLA for pHLA binding prediction and AOMP for mutated peptide optimization, which can be generalized to any binding and mutation task of biomolecules. Firstly, TransPHLA is developed by using a Transformer-derived self-attention model to predict pHLA binding, which is significantly superior to 11 previous methods on pHLA binding prediction, neoantigen and human papilloma virus vaccine identification. For vaccine design, the AOMP program is then developed to automatically optimize mutated peptides to search for mutant peptides with higher affinity to the target HLA and with high homology to the source peptide. Among 3660 non-binding pHLAs, 3630 were successfully mutated. Of these, 94% were verified by the IEDB recommended method, and 88% have homology higher than 80% to the source peptide. © 2021, CC BY.

关键词： Peptides

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An approach to the direct analysis of transient stability

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European Transactions on Electrical Power 1993年第3期3卷 241-248页

作者： Djukanovic, M.B. Sobajic, D.J. Pao, Y.‐H. Miodrag B. Djukanovic (1959) received his B.S. M.Sc. and Ph.D. degrees in Electrical Engineering from the University of Belgrade/Yugoslavia in 1982 1985 and 1992 respectively specializing in electric power systems. In 1984 he joined the Electrical Engineering Institute “Nikola Tesla” in Belgrade where he was working on the scientific studies in the field of power systems planning operation and control. In 1985 and 1990 he was appointed as a research scholar at the Royal Institute of Technology Stockholm and Case Western Reserve University Cleveland Ohio. His major in- terests are in the area of power system analysis steady-state and dynamic security and application of neural networks in electric power systems. (Electrical Engineering Institute “Nicola Tesla” ul. Koste Glavinica 8A YU-11000 Belgrad T +3811/2351-619 Fax + 3811/2351-823) Dejan J. Sobajic (1949) received the B.S.E.E. and the M.S.E.E. degrees from the University of Belgrade/Yugoslavia in 1972 and 1976 respectively and the Ph.D. degree from Case Western Reserve University Cleveland Ohio in 1988. At present he is with the Department of Electrical Engineering and Applied Physics Case Western Reserve University Cleveland. He is also the Engineering Manager of A1 WARE Inc. Cleveland. His current research interests include power system operation and control neuralnet systems and adaptive control. He is a member of the IEEE Task Force on Neural-Network Applications in Power Systems and of the IEEE Intelligent Controls Committee. He is the Chairman of the International Neural-Networks Society Special Interest Group on Power Engineering. (Case Western Reserve University Department of Electrial Engineering and Computer Sciences Glennan Building Ohio 44 106 USA T + 1216/421-2380 Fax +1216/368-8776) Yoh-Han Pao (1922) has been a Professor of Electrical Engineering and Computer Science at Case Westem Reserve University (CWRU) Cleveland Ohio since 1967. He has served as chairman of the University's Electrical Engineering Department

The Transient Energy Function (TEF) method has been intensely investigated over the last decade as a reliable and accurate tool for transient stability assessment of multimachine power systems. In this paper we propose the Potential Energy Boundary Surface (PEBS) based method for direct analysis of transient stability. The critical value of transient energy and the Critical Clearing Time (T_CCT) are evaluated without the need for successive calculation and memorization of the system kinetic and potential energy values along the sustained fault trajectory. The method is used for determination of output features in the training phase of the neural‐net based transient security assessment. The proposed approach is tested on the well‐known ten‐generator New England test system demonstrating the validity and accuracy of obtained results. Copyright © 1993 John Wiley & Sons, Ltd.

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Preconditioning for the integration of a spatiotemporal pharmacodynamic system

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PAMM 2023年第1期22卷

作者： Jurjen Duintjer Tebbens Martin Lanzendörfer Ctirad Matonoha Štěpán Papáček Department of Computational Mathematics Institute of Computer Science of the Czech Academy of Sciences Pod Vodárenskou věží 271/2 Praha - Libeň 182 07 Czech Republic Department of Biophysics and Physical Chemistry Faculty of Pharmacy in Hradec Kralove Charles University Heyrovského 1203 Hradec Králové 500 05 Czech Republic Department of Computational Mathematics Institute of Computer Science of the Czech Academy of Sciences Pod Vodárenskou věží 271/2 Praha - Libeň 182 07 Czech Republic Department of Biophysics and Physical Chemistry Faculty of Pharmacy in Hradec Kralove Charles University Heyrovského 1203 Hradec Králové 500 05 Czech Republic Institute of Hydrogeology Engineering Geology and Applied Geophysics Faculty of Science Charles University Albertov 6 128 43 Praha 2 Czech Republic Department of Control Theory Institute of Information Theory and Automation of the Czech Academy of Sciences Pod Vodárenskou věží 4 Praha - Libeň 182 00 Czech Republic

We address efficient modeling of the intracellular action of a drug binding to the nuclear pregnane X receptor. The binded complex enters the cell nucleus and acts on DNA, resulting in enhanced production of an enzyme which metabolizes, among others, co-administered drugs. Pharmacodynamic modeling is traditionally based on a compartmental approach, which simplifies the complex processes in the human body through the definition of a small number of compartments representing organs, tissues, cells, cytoplasm or abstract units. Inside a compartment, the concentrations of all substances are assumed to be distributed homogeneously, i.e. there is no spatial dependence. They lead to a system of ODEs for the time-dependence of the concentrations of the active substances. We will present an extension of a model from the literature for the action of the tuberculose-drug Rifampicin. The extension consists of a first attempt to add spatial resolution for substances that are active in the cytoplasm. Spatial resolution can be benecifial to analyze important issues like, among others, local exceeding of toxic drug levels, delay of transport and drug-drug interactions. We address efficient solution of the linear systems arising when numerically integrating the resulting PDE's and consider some preconditioning techniques based on properties of the underlying biochemical network.

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MODELING AND control OF ELEVATORS BY STATECHARTS

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Asian Journal of control 2008年第2期6卷

作者： Yi-Sheng Huang Sheng-Luen Chung Mu-Der Jeng Department of Aeronautical Engineering Chung Cheng Institute of Technology National Defense University Tashi Taoyuan 335 Taiwan R.O.C. Department of Electrical Engineering National Taiwan University of Science and Technology Taipei 106 Taiwan R.O.C. Department of Electrical Engineering National Taiwan Ocean University Kellung 202 Taiwan R.O.C. MuDer Jeng received the Ph.D. degree in computer and systems engineering from Rensselaer Polytechnic Institute Troy NY in 1992. Since August 1992 Dr. Jeng has been with National Taiwan Ocean University Keelung Taiwan where he is currently a full Professor at the Department of Electrical Engineering. His current research interests include Petri nets discrete event systems computer integrated manufacturing semiconductor factory automation embedded systems. Dr. Jeng is the author/co-author of over 120 book chapters journal papers and conference papers. Dr. Jeng received the Franklin V. Taylor Outstanding Paper Award from the IEEE Systems Man and Cybernetics Society in 1993. He was granted the Research Award by the National Science Council of Taiwan annually from 1994 to 2000. He is an Associate Editor for IEEE Transactions on Systems Man and Cybernetics-Part A IEEE Transactions on Robotics and Automation IEEE Transactions on Robotics and serves on the Editorial Board of International Journal of Computer Integrated Manufacturing. He has been a Guest Editor for eight leading journals. Dr. Jeng is the Chair of the Technical Committee on Discrete Event Systems of the IEEE SMC Society and the Founding Chair of the Technical Committee on Semiconductor Factory Automation of the IEEE Robotics and Automation Society. He served as the Exhibitions Chair of 2003 IEEE International Conference on Robotics and Automation and the Special Sessions Chair of 2004 IEEE International Conference on Networking Sensing and Control. He serves as a Program Co-Chair of 2005 IEEE International Conference on Networking Sensing and Control and the Organization Commit

Statechart has been utilized as a visual formalism for the modeling of complex and interactive systems for its illuminating features on describing properties of causality, concurrency, and synchronization. This paper presents the application of satechart to the modeling, design and implementation of an elevator system, whose system behavior involves aggregating complexity of state descriptions, and imposition of underlying control policy. Based on the operational flow of an elevator, we derive the associated statechart model by looking into the inherent hierarchical structure of the elevator. The advantage of the proposed approach is the clear presentation of system behavior in terms of conditions and events that cause the transitions in system dynamics. Implementation of the controlled elevator based on the modeled statechart is also presented.

关键词： Statechart interactive systems elevator

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SHIPBOARD MAIN BOILER AND FEED PUMP control-SYSTEM ONLINE ALIGNMENT VERIFICATION

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NAVAL ENGINEERS JOURNAL 1982年第6期94卷 39-46页

作者： BANHAM, JW ADAM, DJ James W. Banham:holds positions both as Director of the Machinery Automation Systems Department of the Naval Ship Systems Engineering Station and as Assistant Chairman of the Mechanical and Industrial Engineering Department of Drexel University's Evening College where he holds the rank of Adjunct Associate Professor. He is the author of a text on Numerical Methods Applications in Engineering. In addition to numerous technical papers he is also the author of the ISA film on Boiler Feedwater Control Systems. A registered professional engineer in the state of Pennsylvania Mr. Banham is co-author of a forthcoming handbook on preparing for the Professional Engineering Examination in mechanical engineering. Mr. Banham holds a bachelor of science degree in mechanical engineering from the Pennsylvania State University his graduate studies were taken at the University of Pennsylvania. He is currently a member of the American Society for Engineering Education and the Instrument Society of America. He served as a member of the ISA Education Committee from 1964 through 1973 and as a member of the ISA Power Plant Dynamics Committee since 1969. His service on the latter committee includes terms as Executive Secretary Vice-Chairman and Chairman. Among other honors Mr. Banham was the winner of the Naval Ship Engineering Center's first Technical Achievement Award (1963) Technical Publication Award (1974) and Equal Employment Opportunity Award (1978). He was also the recipient of Drexel University's Laura S. Campbell Award for Excellence in Teaching (1978). He has taught undergraduate courses in classical control theory numerical methods computer programming systems design and analysis and instrumentation. He also teaches systems theory and computer science in an EIT Review and heat transfer in a PE Review conducted by the Drexel University Department of Continuing Professional Education. Mr. David J. Adam:is a Project Engineer in the Naval Sea Systems Command (PMS301) Steam Propulsion Plant Improvement Program where he i

One of the most serious problems encountered in Naval steam plants following World War II was the unreliable performance of boiler and main feedpump pneumatic control systems. In addition to control component and system design deficiencies, these control systems suffered from inadequate methods to measure and adjust system alignment. This paper describes the development of a set of procedures for on-line alignment verification (OLV) of pneumatic main boiler and feedpump control systems. The procedures are designed for use by N avy control system technicians and, in addition to on-line alignment verification, provide guidance for troubleshooting and for performing system alignment. Procedure static checks measure steady state steaming performance and OLV procedure dynamic checks measure the ability of the boiler and control systems to respond to load changes. The paper describes typical control system characteristics that influence OLV procedure content and the supporting analysis that was used to establish alignment criteria ranges that satisfy both steady state and transient performance requirements. Also described is the alignment criteria tolerance analysis along with the steps involved in a typical OLV check procedure development. Descriptions of the various OLV checks, troubleshooting procedures and alignment procedures are provided. Typical shipboard implementation requirements are described and experience to date with the procedures is provided along with a status report on OLV procedure implementations.

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The Twenty‐first Century Enterprise, Agile Manufacturing and Something Called CALS

World Class Design to Manufacture

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World Class Design to Manufacture 1994年第3期1卷

作者： Eric M. Ross The Vice‐President of ProActive Resources Inc. a Rhode Island‐based industrial improvement consulting and training firm. He also serves as the Chair Commercial Application Task Group of the all‐volunteer US CALS/CE Industry Steering Group. Previously he was Director CALS at Intergraph Corporation a worldwide supplier of interactive computer graphic CAD/CAE/CAM systems and Program Director Strategic Enterprise Modernization at BDM International Inc. Mr Ross also served in various technical management and leadership positions in United States Air Force internal and contractor industrial base improvement programmes. He is a member of the American Society for Quality Control the American Production and Inventory Control Society the Automation Forum and the Computer and Automated Systems Association of the Society of Manufacturing Engineers. He holds a BS and an MS degree from Rensselaer Polytechnic Institute and the State University of New York College of Ceramics respectively. He can be contacted at ProActive Resources Inc. Tel/Fax: 401 421 4072 or 10733 Basket Oak Ct. Burke VA 22015 USA.

Success in the twenty‐first century will require many manufacturingenterprises to have the innovative flexibility to respond rapidly tomarket desires, to produce top quality products, to deliver almostinstantaneously, and to provide superb service. Built on leanmanufacturing, the agile manufacturing paradigm is an evolutionary step,partially based on a combination of flexible manufacturing, integratedproduct development and stratgic partnering. An agile manufactuingenterprice is a dynamically reconfigurable organization of independentcompanies which forms individual companies optimized for the specificsof each market opportunity. Key to the success of such a paradigm is theability (for often geographically dispersed functions) to share fullythe technical information required and used for product design,development, validation, production and service. Argues that CALS, astandardized approach to integrated product data management, has thestrategies, approaches, technologies and neutral data formats as well asthe growing international commitment to enable this data sharing.

关键词： Agile production computer‐aided acquisition and logistic support Co‐operation Flexible organizations Information exchange Manufacturing industry Partnering Product development

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Corrigendum: Dielectric cross-shaped-resonator-based metasurface for vortex beam generation at mid-IR and THz wavelengths (Nanophotonics (2019) 8:7 (1263–1270) DOI: 10.1515/nanoph-2019-0112)

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Nanophotonics 2019年

作者： Dharmavarapu, Raghu Izumi, Ken-ichi Katayama, Ikufumi Ng, Soon Hock Vongsvivut, Jitraporn Tobin, Mark J. Kuchmizhak, Aleksandr Nishijima, Yoshiaki Bhattacharya, Shanti Juodkazis, Saulius Centre for NEMS and Nanophotonics (CNNP) Department of Electrical Engineering Indian Institute of Technology Madras Chennai 600036 India Centre for Micro-Photonics Faculty of Science Engineering and Technology Swinburne University of Technology Hawthorn VIC 3122 Australia Melbourne Centre for Nanofabrication ANFF 151 Wellington Road Clayton VIC 3168 Australia Physics Department Yokohama National University 79-5 Tokiwadai Hodogaya-ku Yokohama 240-8501 Japan Infrared Microspectroscopy Beamline Australian Synchrotron Clayton VIC 3168 Australia Institute of Automation and Control Processes Far Eastern Branch Russian Academy of Sciences Vladivostok 690041 Russia Far Eastern Federal University Vladivostok 690090 Russia Department of Electrical and Computer Engineering Graduate School of Engineering Yokohama National University 79-5 Tokiwadai Hodogaya-ku Yokohama 240-8501 Japan Institute of Advanced Sciences Yokohama National University 79-5 Tokiwadai Hodogaya-ku Yokohama 240-8501 Japan Tokyo Tech World Research Hub Initiative (WRHI) School of Materials and Chemical Technology Tokyo Institute of Technology 2-12-1 Ookayama Meguro-ku Tokyo 152-8550 Japan

There was a mistake in the grant number used in the recently published paper (DOI: https://***/10.1515/ nanoph-2019-0112. Published Online: 2019-07-09). The text should read: A.K. is grateful for support via the Russian Science Foundation (grant no. 17-19-01325), and R.D. thanks the IIT Madras-Swinburne joint PhD program. © 2019 De Gruyter. All rights reserved.

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A Study On Iterative Learning control With Adjustment Of Learning Interval For Monotone Convergence In The Sense Of Sup-Norm

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Asian Journal of control 2008年第1期4卷

作者： Kwang-Hyun Park Zeungnam Bien Division of EE Department of EECS Korea Advanced Institute of Science and Technology 373–1 Kusong-dong Yusong-gu Taejon 305–701 Korea. Zeungname Bien:received the B.S. degree in electronics engineering from Seoul National University Seoul Korea in 1969 and the M.S. and Ph.D. degrees in electrical engineering from the University of Iowa Iowa City Iowa U.S.A. in 1972 and 1975 respectively. During 1976–1977 academic years he taught as assistant professor at the Department of Electrical Engineering University of Iowa. Then Dr. Bien joined Korea Advanced Institute of Science and Technology summer 1977 and is now Professor of Control Engineering at the Department of Electrical Engineering and Computer Science KAIST. Dr. Bien was the president of the Korea Fuzzy Logic and Intelligent Systems Society during 1990–1995 and also the general chair of IFSA World Congress 1993 and for FUZZ-IEEE99 respectively. He is currently co-Editor-in-Chief for International Journal of Fuzzy Systems (IJFS) Associate Editor for IEEE Transactions on Fuzzy Systems and a regional editor for the International Journal of Intelligent Automation and Soft Computing. He has been serving as Vice President for IFSA since 1997 and is now Chief Chairman of Institute of Electronics Engineers of Korea and Director of Humanfriendly Welfare Robot System Research Center. His current research interests include intelligent control methods with emphasis on fuzzy logic systems service robotics and rehabilitation engineering and large-scale industrial control systems. Kwang-Hyun Park:received the B.S. M.S. and Ph.D. degrees in electrical engineering and computer science from KAIST Korea in 1994 19997 and 2001 respectively. He is now a researcher at Human-friendly Welfare Robot System Research Center. His research interests include learning control machine learning human-friendly interfaces and service robotics.

It has been found that some huge overshoot in the sense of sup-norm may be observed when typical iterative learning control (ILC) algorithms are applied to LTI systems, even though monotone convergence in the sense of λ-norm is guaranteed. In this paper, a new ILC algorithm with adjustment of learning interval is proposed to resolve such an undesirable phenomenon, and it is shown that the output error can be monotonically converged to zero in the sense of sup-norm when the proposed ILC algorithm is applied. A numerical example is given to show the effectiveness of the proposed algorithm.

关键词： Iterative learning control monotone convergence learning interval sup-norm

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TRACKING control IN THE PRESENCE OF NONLINEAR DYNAMIC FRICTIONAL EFFECTS: ROBOT EXTENSION

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Asian Journal of control 2008年第3期1卷

作者： M. Feemster D.M. Dawson A. Behal W. Dixon Matthew Feemster received the B.S degree in Electrical Engineering from Clemson University Clemson South Carolina in December 1994. Upon graduation he remained at Clemson University and received the M.S. degree in Electrical Engineering in 1997. During this time he also served as a research/teaching assistant. His research work focused on the design and implementation of various nonlinear control algorithms with emphasis on the induction motor and mechanical systems with friction present. He is currently working toward his Ph.D. degree in Electrical Engineering at Clemson University. Darren M. Dawson was born in 1962 in Macon Georgia. He received an Associate Degree in Mathematics from Macon Junior College in 1982 and a B.S. Degree in Electrical Engineering from the Georgia Institute of Technology in 1984. He then worked for Westinghouse as a control engineer from 1985 to 1987. In 1987 he returned to the Georgia Institute of Technology where he received the Ph.D. Degree in Electrical Engineering in March 1990. During this time he also served as a research/teaching assistant. In July 1990 he joined the Electrical and Computer Engineering Department and the Center for Advanced Manufacturing (CAM) at Clemson University where he currently holds the position of Professor. Under the CAM director's supervision he currently leads the Robotics and Manufacturing Automation Laboratory which is jointly operated by the Electrical and Mechanical Engineering departments. His main research interests are in the fields of nonlinear based robust adaptive and learning control with application to electro-mechanical systems including robot manipulators motor drives magnetic bearings flexible cables flexible beams and high-speed transport systems. Aman Behal was born in India in 1973. He received his Masters Degree in Electrical Engineering from Indian Institute of Technology Bombay in 1996. He is currently working towards a Ph.D in Controls and Robotics at Clemson University. His research focuses on the control of no

In this paper, we extend the observer/control strategies previously published in [25] to an n -link, serially connected, direct drive, rigid link, revolute robot operating in the presence of nonlinear friction effects modeled by the Lu-Gre model. In addition, we also present a new adaptive control technique for compensating for the nonlinear parameterizable Stribeck effects. Specifically, an adaptive observer/controller scheme is developed which contains a feedforward approximation of the Stribeck effects. This feedforward approximation is used in a composite controller/observer strategy which forces the average square integral of the position tracking error to an arbitrarily small value. Experimental results are included to illustrate the performance of the proposed controllers.

关键词： Friction compensation nonlinear control

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