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Proof Method for correctness of refinements of algebraic specification in abstract sequential machine style

systems AND computerS IN JAPAN 1996年第5期27卷 25-38页

作者： Okano, K Higashino, T Taniguchi, K Member Faculty of Engineering Science Osaka University Toyonaka Japan 560 Teruo Hipshino received his B.E. M.E.and Ph.D. degrees in Information and Computer Sciences from Osaka University Osaka Japan in 1R9 1981 and 1984 respectively. He joined the Faculty of Osaka University in 1984. Since 1991 he has been an Associate Professor in the Department of Information and Computer Sciences at Osaka University. In 1990 he was a Visiting Researcher of Dept. I.R.O. at University of Montreal Canada. His current research interests include design and analysis of distributed systems specification and verification of communication protocols and formal approach of program design. He is a member of IEEE-CS ACM IEICE of Japan and IPS of Japan.

In this paper, new methods for providing the correctness of refinement among abstract sequential machine style programs are described. The programs are described in algebraic language ASL using some useful notions, i.e., the extended projection and the valid reachability condition for each transition function. These notions allow a designer to refine a given text (program or specification) to a concrete text more freely than the text that does not use such notions. These notions can also enhance the expressive power of the text. On the other hand, these advantages would have lost half their values, if useful methods to prove the correctness of refinement among the texts using them are not found. Thus new methods for proving the correctness of the texts are proposed, and they do not require much proof loads. First, the correctness of refinement among the ASL texts with the extended projection is defined. Second, a method is proposed for proving the correctness of refinement among such texts. Also proposed is a definition of the correctness of refinement among the texts with the valid reachability conditions and a method to prove their correctness. These methods do not require more proof loads than the usual methods for the texts that do not use such notions in the abstract sequential machine style. Therefore, these methods are useful.

关键词： abstract sequential machine ASL language proof algebraic specification

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A computer-MODEL FOR SHIPBOARD ENERGY ANALYSIS

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NAVAL ENGINEERS JOURNAL 1984年第5期96卷 33-45页

作者： DETOLLA, JP FLEMING, JR Joseph DeTolla:is a ship systems engineer in the Ship Systems Engineering Division SEA 56D5 at the Naval Sea Systems Command. His career with the Navy started in 1965 at the Philadelphia Naval Shipyard Design Division. In 1971 he transferred to the Naval Ship Engineering Center. He has held positions as a fluid systems design engineer and auxiliary systems design integration engineer. Mr. DeTolla has worked extensively in the synthesis and analysis of total energy systems notably the design development of the FFG-7 class waste heat recovery system. He is NA VSEA's machinery group computer supported design project coordinator and is managing the development of a machinery systems data base load forecasting algorithms and design analysis computer programs. Mr. DeTolla has a bachelor of science degree in mechanical engineering from Drexel University and a master of engineering administration degree from George Washington University. He is a registered professional engineer in the District of Columbia and has written several technical papers on waste heat recovery and energy conservation. Jeffrey Fleming:is a senior project engineer in the Energy R&D Office at the David Taylor Naval Ship R&D Center. In his current position as group leader for the future fleet energy conservation portion of the Navy's energy R&D program he is responsible for the identification and development of advanced components and subsystems which will lead to reductions in the fossil fuel consumption of future ships. Over the past several years he has also directed the development and application of total energy computer analysis techniques for the assessment of conventional and advanced shipboard machinery concepts. Mr. Fleming is a 1971 graduate electrical engineer of Virginia Polytechnic Institute and received his MS in electrical engineering from Johns Hopkins University in 1975. Mr. Fleming has authored various technical publications and was the recipient of the Severn Technical Society's “Best Technical Paper of the Year” award in 1

In support of the Navy's efforts to improve the energy usage of future ships and thereby to reduce fleet operating costs, a large scale computer model has been developed by the David Taylor Naval Ship Research and Development Center (DTNSRDC) to analyze the performance of shipboard energy systems for applications other than nuclear or oil-fired steam propulsion plants. This paper discusses the applications and utility of this computer program as a performance analysis tool for design of ship machinery systems. The program is a simulation model that performs a complete thermodynamic analysis of a user-specified energy system. It offers considerable flexibility in analyzing a variety of propulsion, electrical, and auxiliary plant configurations through a component building block structure. Component subroutines that model the performance of shipboard equipment such as engines, boilers, generators, and compressors are available from the program library. Component subroutines are selected and linked in the program to model the desired machinery plant functional configurations. The operation of the defined shipboard energy system may then be simulated over a user-specified scenario of temperature, time, and load profiles. The program output furnishes information on component operating characteristics and fuel demands, which allows evaluation of the total system performance.

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Hamiltonian Hopping for Efficient Chiral Mode Switching in Encircling Exceptional Points

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Physical Review Letters 2020年第18期125卷 187403-187403页

作者： Aodong Li Jianji Dong Jian Wang Ziwei Cheng John S. Ho Dawei Zhang Jing Wen Xu-Lin Zhang C. T. Chan Andrea Alù Cheng-Wei Qiu Lin Chen Wuhan National Laboratory for Optoelectronics Huazhong University of Science and Technology Wuhan 430074 China Department of Electrical and Computer Engineering National University of Singapore Singapore 117583 Singapore Engineering Research Center of Optical Instrument and Systems Ministry of Education and Shanghai Key Lab of Modern Optical System University of Shanghai for Science and Technology No. 516 Jungong Road Shanghai 200093 China State Key Laboratory of Integrated Optoelectronics College of Electronic Science and Engineering Jilin University Changchun 130012 China Department of Physics The Hong Kong University of Science and Technology Clear Water Bay Hong Kong 999077 China Photonics Initiative Advanced Science Research Center City University of New York New York New York 10031 USA Physics Program Graduate Center City University of New York New York New York 10016 USA

Dynamically encircling exceptional points (EPs) can lead to chiral mode switching as the system parameters are varied along a path that encircles EP. However, conventional encircling protocols result in low transmittance due to path-dependent losses. Here, we present a paradigm to encircle EPs that includes fast Hamiltonian variations on the parameter boundaries, termed Hamiltonian hopping, enabling ultrahigh-efficiency chiral mode switching. This protocol avoids path-dependent loss and allows us to experimentally demonstrate nearly 90% efficiency at 1550 nm in the clockwise direction, overcoming a long-standing challenge of non-Hermitian optical systems and powering up new opportunities for EP physics.

关键词： Open quantum systems & decoherence PT-symmetric quantum mechanics Photonics Waveguides

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Human systems integration and advanced technology in engineering department workload and manpower reduction

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NAVAL ENGINEERS JOURNAL 2003年第1期115卷 57-65页

作者： Lively, KA Seman, AJ Kirkpatrick, M KENNETH A. LIVELY graduated from the University of Colorado with a BS in applied mathematics and an MS in mathematics in 1976 and from the Massachusetts Institute of Technology with an MS in electrical engineering and the degree ocean engineer in naval architecture and marine engineering in 1984. He retired from the U.S. Navy in 1989 after 23 years of service. Assignments included electrical officer on the USS Constellation (CV 64) project engineer for the DDG 51 machinery control system (NAVSEA) and DDG 51 Technical Director (NAVSEA). He was vice president of the PDI Division of Bird-Johnson Company from July 1989 to November 1998 where he managed various gas turbine and machinery controls related development projects. He joined Anteon Corporation's Systems Engineering Group as senior controls engineer in December 1998 where he provided technical support to the integrated power systems program (NAVSEA PMS 510) and managed the Office of Naval Research Afloat Laboratory. DR. MARK KIRKPATRICK is currently an independent consultant in human factors and work-load/manning analysis and modeling. He holds a Ph.D. degree in experimental psychology from The Ohio State University and has 34 years of experience in applied human factors. From 1982 through 2000 Dr. Kirkpatrick served as the senior vice president of Carlow International. Prior to joining Carlow in 1982 Dr. Kirkpatrick served as a member of the technical staff at North American Rockwell's Missiles Division and as a project director and vice president for Essex Corporation. His areas of expertise include workload simulation task analysis operator-in-the-loop simulation human performance experimentation statistical analysis and human factors T&E. He has directed and/or participated in human factors projects for the U.S. Navy U.S. Army NASA Department of Transportation the U.S. Nuclear Regulatory Commission and private industry. ANTHONY J. SEMAN III is the technical manager for the reduced ship's crew by virtual presence (RSVP) advanced technology d

Aboard current ships, such as the DDG 51, engineering control and damage control activities are manpower intensive. It is anticipated that, for future combatants, the workload demand arising from operation of systems under conditions of normal steaming and during casualty response will need to be markedly reduced via automated monitoring, autonomous control, and other technology initiatives. Current DDG 51 class ships can be considered as a manpower baseline and under Condition III typical engineering control involves seven to eight watchstanders at manned stations in the Central Control Station, the engine rooms and other machinery spaces. In contrast to this manning level, initiatives such as DD 21 and the integrated engineering plant (IEP) envision a partnership between the operator and the automation system, with more and more of the operator's functions being shifted to the automation system as manning levels decrease. This paper describes some human systems integration studies of workload demand reduction and, consequently, manning reduction that can be achieved due to application of several advanced technology concepts. Advanced system concept studies in relation to workload demand are described and reviewed including. Piecemeal applications of diverse automation and remote control technology concepts to selected high driver tasks in current DDG 51 activities. Development of the reduced ship's crew by virtual presence system that will provide automated monitoring and display to operators of machinery health, compartment conditions, and personnel health. The IEP envisions the machinery control system as a provider of resources that are used by various consumers around the ship. Resource needs and consumer priorities are at all times dependent upon the ship's current mission and the availability of equipment pawnbrokers.

关键词： Naval warfare

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computer-SYSTEM ARCHITECTURE CONCEPTS FOR FUTURE COMBAT systems

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NAVAL ENGINEERS JOURNAL 1990年第3期102卷 43-62页

作者： ZITZMAN, LH FALATKO, SM PAPACH, JL Dr. Lewis H. Zitzman:is the group supervisor of the Advanced Systems Design Group Fleet Systems Department The Johns Hopkins University Applied Physics Laboratory (JHU/APL). He has been employed at JHU/APL since 1972 performing applied research in computer science and in investigating and applying advanced computer technologies to Navy shipboard systems. He is currently chairman of Aegis Computer Architecture Data Bus and Fiber Optics Working Group from which many concepts for this paper were generated. Dr. Zitzman received his B.S. degree in physics from Brigham Young University in 1963 and his M.S. and Ph.D. degrees in physics from the University of Illinois in 1967 and 1972 respectively. Stephen M. Falatko:was a senior engineering analyst in the Combat Systems Engineering Department Comptek Research Incorporated for the majority of this effort. He is currently employed at ManTech Services Corporation. During his eight-year career first at The Johns Hopkins University Applied Physics Laboratory and currently with ManTech Mr. Falatko's work has centered around the development of requirements and specifications for future Navy systems and the application of advanced technology to Navy command and control systems. He is a member of both the Computer Architecture Fiber Optics and Data Bus Working Group and the Aegis Fiber Optics Working Group. Mr. Falatko received his B.S. degree in aerospace engineering with high distinction from the University of Virginia in 1982 and his M.S. degree in applied physics from The Johns Hopkins University in 1985. Mr. Falatko is a member of Tau Beta Pi Sigma Gamma Tau the American Society of Naval Engineers and the U.S. Naval Institute. Janet L. Papach:is a section leader and senior engineering analyst in the Combat Systems Engineering Department Comptek Research Incorporated. She has ten years' experience as an analyst supporting NavSea Spa War and the U.S. Department of State. She currently participates in working group efforts under Aegis Combat System Doctrin

This paper sets forth computer systems architecture concepts for the combat system of the 2010–2030 timeframe that satisfy the needs of the next generation of surface combatants. It builds upon the current Aegis computer systems architecture, expanding that architecture while preserving, and adhering to, the Aegis fundamental principle of thorough systems engineering, dedicated to maintaining a well integrated, highly reliable, and easily operable combat system. The implementation of these proposed computer systems concepts in a coherent architecture would support the future battle force capable combat system and allow the expansion necessary to accommodate evolutionary changes in both the threat environment and the technology then available to effectively counter that threat. Changes to the current Aegis computer architecture must be carefully and effectively managed such that the fleet will retain its combat readiness capability at all times. This paper describes a possible transition approach for evolving the current Aegis computer architecture to a general architecture for the future. The proposed computer systems architecture concepts encompass the use of combinations of physically distributed, microprocessor-based computers, collocated with the equipment they support or embedded within the equipment itself. They draw heavily on widely used and available industry standards, including instruction set architectures (ISAs), backplane busses, microprocessors, computer programming languages and development environments, and local area networks (LANs). In this proposal, LANs, based on fiber optics, will provide the interconnection to support system expandability, redundancy, and higher data throughput rates. A system of cross connected LANs will support a high level of combat system integration, spanning the major warfare areas, and will facilitate the coordination and development of a coherent multi-warfare tactical picture supporting the future combatant command st

关键词： computer Architecture

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Computational Methods for Single-Cell RNA Sequencing

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Biomedical Data Science 1000年第1期3卷 339-364页

作者： Brian Hie Joshua Peters Sarah K. Nyquist Alex K. Shalek Bonnie Berger Bryan D. Bryson 1Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA email: bab@mit.edu 3Ragon Institute of MGH MIT and Harvard Cambridge Massachusetts 02139 USA 2Department of Biological Engineering Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA email: bryand@mit.edu 4Program in Computational and Systems Biology Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA 5Department of Chemistry Institute for Medical Engineering & Science (IMES) and Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA 6Department of Mathematics Massachusetts Institute of Technology Cambridge Massachusetts 02139 USA

Single-cell RNA sequencing (scRNA-seq) has provided a high-dimensional catalog of millions of cells across species and diseases. These data have spurred the development of hundreds of computational tools to derive novel biological insights. Here, we outline the components of scRNA-seq analytical pipelines and the computational methods that underlie these steps. We describe available methods, highlight well-executed benchmarking studies, and identify opportunities for additional benchmarking studies and computational methods. As the biochemical approaches for single-cell omics advance, we propose coupled development of robust analytical pipelines suited for the challenges that new data present and principled selection of analytical methods that are suited for the biological questions to be addressed.

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Finding shortest and nearly shortest path nodes in large substantially incomplete networks

arXiv

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arXiv 2022年

作者： Kitsak, Maksim Ganin, Alexander Elmokashfi, Ahmed Cui, Hongzhu Eisenberg, Daniel A. Alderson, David L. Korkin, Dmitry Linkov, Igor Faculty of Electrical Engineering Mathematics and Computer Science Delft University of Technology Delft Netherlands Network Science Institute Northeastern University BostonMA02115 United States Department of Systems and Information Engineering University of Virginia CharlottesvilleVA22904 United States U.S. Army Engineer Research and Development Center Contractor Concord MA01742 United States Simula Metropolitan Center for Digital Engineering Oslo Norway Bioinformatics and Computational Biology Program Worcester Polytechnic Institute WorcesterMA01609 United States Institute for Genomic Medicine Columbia University Medical Center New YorkNY United States Operations Research Department Naval Postgraduate School MontereyCA93943 United States Data Science Program Worcester Polytechnic Institute WorcesterMA01609 United States Computer Science Department Worcester Polytechnic Institute WorcesterMA01609 United States U.S. Army Engineer Research and Development Center Environmental Laboratory Concord MA01742 United States

Dynamic processes on networks, be it information transfer in the Internet, contagious spreading in a social network, or neural signaling, take place along shortest or nearly shortest paths. Unfortunately, our maps of most large networks are substantially incomplete due to either the highly dynamic nature of networks, or high cost of network measurements, or both, rendering traditional path finding methods inefficient. We find that shortest paths in large real networks, such as the network of protein-protein interactions (PPI) and the Internet at the autonomous system (AS) level, are not random but are organized according to latent-geometric rules. If nodes of these networks are mapped to points in latent hyperbolic spaces, shortest paths in them align along geodesic curves connecting endpoint nodes. We find that this alignment is sufficiently strong to allow for the identification of shortest path nodes even in the case of substantially incomplete networks. We demonstrate the utility of latent-geometric path finding in problems of cellular pathway reconstruction and communication security. Copyright © 2022, The Authors. All rights reserved.

关键词： Proteins

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Accelerating Real-Time Imaging for Radiotherapy: Leveraging Multi-GPU Training with PyTorch

Accelerating Real-Time Imaging for Radiotherapy: Leveraging ...

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International Conference on Machine Learning and Applications (ICMLA)

作者： Ruth Obe Brandt Kaufmann Kaelen Baird Sam Kadel Yasmin Soltani Mostafa Cham Matthias K. Gobbert Carlos A. Barajas Zhuoran Jiang Vijay R. Sharma Lei Ren Stephen W. Peterson Jerimy C. PoIf Dept. of Computer Science and of Software Engineering U. of Houston-Clear Lake USA Dept. of Mathematics and Statistics U. of San Francisco USA Dept. of Computer Science and of Mathematics Skidmore College USA Dept. of Computer Science and of Psychology Mount Holyoke College USA Dept. of Biomedical Engineering U. of Houston USA Dept. of Information Systems U. of Maryland Baltimore County Dept. of Mathematics and Statistics U. of Maryland Baltimore County Medical Physics Graduate Program Duke University USA Dept. of Radiation Oncology U. of Maryland School of Medicine USA Department of Radiation Oncology U. of Maryland School of Medicine USA Dept. of Physics U. of Cape Town South Africa H3D Inc. USA

Proton beam therapy is an advanced form of cancer radiotherapy that uses high-energy proton beams to deliver precise and targeted radiation to tumors. This helps to mit-igate unnecessary radiation exposure in healthy tissues. Real-time imaging of prompt gamma rays with Compton cameras has been suggested to improve therapy efficacy. However, the camera's non-zero time resolution leads to incorrect interaction classifications and noisy images that are insufficient for accurately assessing proton delivery in patients. To address the challenges posed by the Compton camera's image quality, machine learning techniques are employed to classify and refine the generated data. These machine-learning techniques include recurrent and feedforward neural networks. A PyTorch model was designed to improve the data captured by the Compton camera. This decision was driven by PyTorch's flexibility, powerful capabilities in handling sequential data, and enhanced G PU usage. This accelerates the model's computations on large-scale radiotherapy data. Through hyperparameter tuning, the validation accuracy of our PyTorch model has been improved from an initial 7 % to over 60 %. Moreover, the PyTorch Distributed Data Parallelism strategy was used to train the RNN models on multiple G PU s, which significantly reduced the training time with a minor impact on model accuracy.

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INNOVATIONS IN computer-AIDED-DESIGN OF MARINE TURBINES USING INTERACTIVE GRAPHICS

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NAVAL ENGINEERS JOURNAL 1980年第2期92卷 207-217页

作者： GINGRICH, JK WINTER, RL Mr. John K. Gingrich joined the General Electric Company after his graduation from Lafayette College in 1948. His early assignments were with the General Engineering Laboratory and the Knolls Atomic Power Laboratory in Schenectady. N. Y. He joined the Marine Turbine and Gear Department in 1968 as Manager Engineering Administration. and assumed his present assignment as Manager Engineering Resource Planning & Administration in 1976. Mr. Gingrich was instrumental in procuring the Interactive Graphics System for the Medium Steam Department. having headed up the Study Team and is now responsible for the Interactive Graphics Systems management including new procurements. He is a member of the American Institute of Design Drafting and is currently the Chairman of the Computer-Aided Drafting Committee in that organization. Mr. Reinhold L. Winter is a graduate of the General Electric Apprentice Program and Salem State College from which he received his B.S. degree in Business Administration. He has nineteen years experience with the General Electric Company including eight years in Business Systems and Programming two years in Computer Operations Management and six years in his present position as Manager Engineering Business Systems. He was a member of the original Study Team that investigated and selected the present Applicon Interactive Graphics (IAG) equipment and currently is responsible for the management of software and hardware support for the ZAG Facility.

This paper discusses the Interactive Graphics System used by the General Electric Company, Medium Steam Turbine Department (engineering & Manufacturing) for designing, drafting, and manufacturing applications. A brief overview of the hardware malting up the system is described, followed by a more detailed description of the actual applications. Two-dimensional applications described include a Heat Balance Analysis, Flow Diagrams, and Electrical Schematics. A more fruitful area for increased productivity gains is described in the three-dimensional or mechanical applications including turbine design & layout and bucket design. coordination of the design with manufacturing for numerical control tape generation is described through CAM and Plate Frame Cutting applications. Finally, a short review of the engineering design work using Interactive Graphics is discussed. Productivity gains of 2.6 to 1 are being realized, and the overall savings to the Medium Steam Department are outlined.

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Enriching and Characterizing T-Cell Repertoires from 3' Barcoded Single-Cell Whole Transcriptome Amplification Products

arXiv

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arXiv 2022年

作者： Jivanjee, Tasneem Ibrahim, Samira Nyquist, Sarah K. James Gatter, G. Bromley, Joshua D. Jaiswal, Swati Berger, Bonnie Behar, Samuel M. Christopher Love, J. Shalek, Alex K. Institute for Medical Engineering & Science Department of Chemistry Massachusetts Institute of Technology CambridgeMA United States Koch Institute for Integrative Cancer Research Massachusetts Institute of Technology CambridgeMA United States Ragon Institute of MGH MIT and Harvard CambridgeMA United States Broad Institute of MIT and Harvard CambridgeMA United States Massachusetts Institute of Technology CambridgeMA United States Program in Computational and Systems Biology Massachusetts Institute of Technology CambridgeMA United States Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology CambridgeMA United States Microbiology Graduate Program Massachusetts Institute of Technology CambridgeMA02139 United States Department of Microbiology and Physiological Systems University of Massachusetts Medical School WorcesterMA United States Department of Mathematics Massachusetts Institute of Technology CambridgeMA United States Department of Chemical Engineering Massachusetts Institute of Technology CambridgeMA United States

Antigen-specific T cells play an essential role in immunoregulation and many diseases such as cancer. Characterizing the T cell receptor (TCR) sequences that encode T cell specificity is critical for elucidating the antigenic determinants of immunological diseases and designing therapeutic remedies. However, methods of obtaining single-cell TCR sequencing data are labor and cost intensive, typically requiring both cell sorting and full length single-cell RNA-sequencing (scRNA-seq). New high-throughput 3' cell-barcoding scRNA-seq methods can simplify and scale this process;however, they do not routinely capture TCR sequences during library preparation and sequencing. While 5' cell-barcoding scRNA-seq methods can be used to examine TCR repertoire at single-cell resolution, doing so requires specialized reagents which cannot be applied to samples previously processed using 3' cell-barcoding methods. Here, we outline a method for sequencing TCRα and TCRβ transcripts from samples already processed using 3' cell-barcoding scRNA-seq platforms, ensuring TCR recovery at a single-cell resolution. In short, a fraction of the 3' barcoded whole transcriptome amplification (WTA) product typically used to generate a massively parallel 3' scRNA-seq library is enriched for TCR transcripts using biotinylated probes, and further amplified using the same universal primer sequence from WTA. Primer extension using TCR V-region primers and targeted PCR amplification using a second universal primer results in a 3' barcoded single-cell CDR3-enriched library that can be sequenced with custom sequencing primers. Coupled with 3' scRNA-seq of the same WTA, this method enables simultaneous analysis of single-cell transcriptomes and TCR sequences which can help interpret inherent heterogeneity among antigen-specific T cells and salient disease biology. The method presented here can also be adapted readily to enrich and sequence other transcripts of interest from both 3' and 5' barcoded scRNA-seq

关键词： RNA

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