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ROLE OF SIMULATION IN RAPID PROTOTYPING FOR CONCEPT DEVELOPMENT

NAVAL ENGINEERS JOURNAL 1991年第3期103卷 204-211页

作者： KING, JF bARTON, DE J. Fred King:is the manager of the Advanced Technology Department for Unisys in Reston Virginia. He earned his Ph.D. in mathematics from the University of Houston in 1977. He has been principal investigator of research projects in knowledge engineering pattern recognition and heuristic problem-solving. Efforts include the development of a multi-temporal multispectral classifier for identifying graincrops using LANDSAT satellite imagery data for NASA. Also as a member of the research team for a NCI study with Baylor College of Medicine and NASA he helped develop techniques for detection of carcinoma using multispectral microphotometer scans of lung tissue. He established and became technical director of the AI Laboratory for Ford Aerospace where he developed expert scheduling modeling and knowledge acquisition systems for NASA. Since joining Unisys in 1985 he has led the development of object-oriented programming environments blackboard architectures data fusion techniques using neural networks and intelligent data base systems. Douglas E. Barton:is manager of Logistics Information Systems for Unisys in Reston Virginia. He earned his B.A. degree in computer science from the College of William and Mary in 1978 and did postgraduate work in London as a Drapers Company scholar. Since joining Unisys in 1981 his work has concentrated on program management and software engineering of large scale data base management systems and design and implementation of knowledge-based systems in planning and logistics. As chairman of the Logistics Data Subcommittee of the National Security Industrial Association (NSIA) he led an industry initiative which examined concepts in knowledge-based systems in military logistics. His responsibilities also include evaluation development and tailoring of software engineering standards and procedures for data base and knowledge-based systems. He is currently program manager of the Navigation Information Management System which provides support to the Fleet Ballistic Missile Progr

A valuable technique during concept development is rapid prototyping of software for key design components. This approach is particularly useful when the optimum design approach is not readily apparent or several known alternatives need to be rapidly evaluated. A problem inherent in rapid prototyping is the lack of a "target system" with which to interface. Some alternatives are to develop test driver libraries, integrate the prototype with an existing working simulator, or build one for the specific problem. This paper presents a unique approach to concept development using rapid prototyping for concept development and scenario-based simulation for concept verification. The rapid prototyping environment, derived from artificial intelligence technology, is based on a blackboard architecture. The rapid prototype simulation capability is provided through an object-oriented modeling environment. It is shown how both simulation and blackboard technologies are used collectively to rapidly gain insight into a tenacious problem. A specific example will be discussed where this approach was used to evolve the logic of a mission controller for an autonomous underwater vehicle.

关键词： Military Engineering

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A RISK-bASED APPROACH FOR MANAGING HAZARDOUS-WASTE

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GROUND WATER MONITORING AND REMEDIATION 1995年第1期15卷 79-89页

作者： CHIANG, CY PETKOVSKY, PD MCALLISTER, PM Chen Y. Chiang received his Ph.D. in environmental engineering from Rice University. He is a senior research engineer in Environmental RD&T at Shell Development Co.'s Westhollow Technology Center (3333 Hwy. 6 South Houston TX 77082 fax (713) 544–8727). He serves on the Hydrologic Science Panel of the National Science Foundation and on the Ground Water/Soil Technical Task Force of the American Petroleum Institute. He also serves on the Advisory Board of the Rutgers DARPA/ONR research program. His research interests include in situ bioremediation processes ground water/soil sampling and monitoring multiphase fluid flow phenomenon and risk/ exposure assessment. Paul Petkovsky is a senior research technician in the Groundwater Modeling Group of Environmental RD&T at Shell Development Co.'s Westhollow Technology Center. His responsibilities include site data analysis and the numerical modeling of the fate and transport of organics in ground water. He is currently pursuing a B.S. in chemical engineering with an environmental emphasis at the University of Houston. Paul McAllister received a B.S. in chemical engineering from the University of Kansas in 1987 and a Ph.D. in chemical engineering from the University of Notre Dame in 1991. He is currently an associate research engineer in Environmental RD&T at Shell Development Co.'s Westhollow Technology Center. Since joining Shell he has conducted research and provided technical support on ground water modeling and remediation issues. His research interests include in situ bioremediation of ground water and residual hydrocarbons natural attenuation of contaminants and subsurface fate and transport phenomena in the subsurface.

In 1992, the U.S. Environmental Protection Agency (EPA) proposed risk-based management of hazardous waste. A major component of the proposed rule is the determination of non-site-specific screening concentration levels from waste leachate. Ground water at a downgradient exposure point must not exceed those screening levels, or more stringent requirements would apply. The screening concentration level is determined with verified models and equations that simulate the transport and attenuation of chemicals as they travel from the source area to the exposure point. A consortium of screening levels is determined in this paper by considering varying physical, chemical, and biological conditions. In addition, a method is developed for multicomponent leaching from contaminated soils in a landfill to determine the time-dependent behavior of a finite source. Finally, this paper discusses infiltration rate through the clay liner.

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building Ramps and Pathways to data science in K-12, Minority-Serving Institutions, and Two-Year Colleges

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Scatterplot 2024年第1期1卷

作者： Rachel Saidi Helen burn ben baumer Jason black Debzani Deb Zarek Drozda a Math Statistics and Data Science Department Montgomery College – Rockville Campus Rockville MD USA b Mathematics Department Highline College Des Moines Washington Des Moines WA USA c Statistical and Data Sciences Department Smith College Northampton MA USA d School of Business and Interdisciplinary Center for Creativity and Innovation (ICCI) Florida A&M University Tallahassee FL USA e Computer Science Department Center for Applied Data Science (CADS) Winston-Salem State University Winston-Salem NC USA f Data Science 4 Everyone (DS4E) Program University of Chicago Chicago IL USA

Global demand for data scientists and analysts is on a trajectory of sustained growth, underscoring the need to expand enrollment of students in data science and data analytics courses and programs. This article explores diverse pathways to data science for various groups, including high school students, those in two-year colleges, and students in small colleges and minority-serving institutions. This article identifies opportunities and challenges associated with pursuing data science for students in these sectors, including factors such as building partnerships and awareness of the field and difficulties in establishing articulation agreements between institutions. The authors, representing various organizations participating in a panel discussion at the 2023 data science Leadership Summit of the Academic data science Alliance (ADSA), share insights into efforts to develop nontraditional pathways, serving as a resource for schools, colleges, and organizations contemplating creation of data science programs. The panelists’ combined experience spans work with a broad range of organizations including ADSA, American Mathematics Association of Two-Year Colleges, American Statistical Association, data science for Everyone, the Department of Education, HbCU data science Consortium, Mathematical Association of America, National Academies of science, Engineering, and Medicine, HbCU data science Consortium, National science Foundation, and StatPREP.

关键词： data science pathways access K-12 minority-serving institution two-year college

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OUT-OF-PRODUCTION MICRO-ELECTRONICS - AN ACHILLES HEEL OF DEFENSE SYSTEMS

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NAVAL ENGINEERS JOURNAL 1988年第5期100卷 69-72页

作者： MACKENZIE, CM WOOTTEN, R HOY, K NEELY, J KOSCO, D SMITH, W C. Malcolm Mackenzie:is the Materials and Parts Availability Control program manager at U.S. Army Laboratory Command Adelphi Md. Mr. Mackenzie has a B.S. degree in mechanical engineering from Northwestern University an M.S. degree in the same field from the University of Michigan and an M.B.A. from East Texas State University. Richard Wootten:is project officer of the U.S. Army Material Command's Materials and Parts Availability Control Information Data System Project Adelphi Md. Mr. Wootten holds an associate's degree in mechanical engineering from Northern Virginia Community College and a Bachelor of Science in Electronics Engineering from The University of Alabama. Kevin Hoy:is manager of the Microelectronics Obsolescence Management Program at the Naval Avionics Center Indianapolis. Mr. Hoy holds both bachelor and master of science degrees in mathematics from Purdue University. James Neely:is leader of the Materials Management Team Industrial Materials Division in the Directorate of Manufacturing Air Force Systems Command Dayton Ohio. Mr. Neely holds a bachelor's degree in political science from The University of Georgia and a master of science degree in public administration from The University of Missouri. Don Kosco:is an electronics engineer currently involved with introducing new technologies into weapons systems. He is in the Directorate of Reliability Maintainability and Technology Policy HQ Air Force Logistics Command Dayton Ohio. Mr. Kosco holds a bachelor of engineering degree from Widener University a master's in systems engineering from The Air Force Institute of Technology and an MBA from the University of Texas at San Antonio. William Smith:is head of the Plans Branch in the Office of Policy and Plans Defense Electronics Supply Center (DESC) Dayton Ohio. He was for many years manager ofDESC's Diminishing Manufacturing Sources (DMS) Program. Mr. Smith holds a bachelor of arts degree in political science from Indiana University.

both the timely manufacture of defense systems and their subsequent on-line operability depend upon the availability of component parts. The growing problem of microelectronic component nonavailability is casting a shadow over logistics support to these systems. This paper will discuss the causes of the problem and provide some examples of cases confronted by the DoD logistics community. It will also identify some actions which have been taken in the past to manage the issue as well as initiatives now underway. Finally it will look at what lies ahead.

关键词： Microelectronics

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Front Cover: Generation of Molecular Counterfactuals for Explainable Machine Learning based on Core-Substituent Recombination (ChemMedChem 3/2024)

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ChemMedChem 2024年第3期19卷

作者： Alec Lamens Prof. Jürgen bajorath Department of Life Science Informatics and Data Science B-IT LIMES Program Unit Chemical Biology and Medicinal Chemistry Rheinische Friedrich-Wilhelms-Universität Friedrich-Hirzebruch-Allee 5/6 53115 Bonn Germany Lamarr Institute for Machine Learning and Artificial Intelligence Rheinische Friedrich-Wilhelms-Universität Bonn Friedrich-Hirzebruch-Allee 5/6 53115 Bonn Germany

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Applying fuzzy functions and sequential coordination to optimization of machinery arrangement and pipe routing

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NAVAL ENGINEERS JOURNAL 1998年第6期110卷 43-54页

作者： Wu, bC Young, GS Schmidt, W Choppella, K Dr. Bi-Chu Wu:received a PhD in Mechanical Engineering from the University of Maryland College Park in 1991. She has worked on projects involving naval architecture design optimization solid mechanics and database development. Presently a senwr engineer with Angle Incorporated Dr Wu's research interests are in design optimization and fuzzy logic applications. Dr. Gin-Shu Young: a senior engineer with Angle Incorporated holds a PhD in Mechanical Engineering from the University of Maryland College Park. As a guest researcher with National Institute of Standards and Technologies from 1990 to 1993 he worked on vision-based navigation for autonomous vehicles. His experience also includes applications of optimization fuzzy logic neural network and genetic algorithm methods to engineering system design Mr. William Schmidt:co-founded Angle Incorporated in 1990 and has served as Vice PresidentlChiefScientist during this tame. He holds a B.Sc. in Applied Science from the Naval Acadt?my and an M.Sc. in Physics from the Naval Post Graduate School. He has cner 20 years experience in technical leadership material and personnel management. He has led the application of computer aided design (CAD) and Product Model Information Exchange to the shipbuilding industry. His experience also includes leading the amlication of model based operational analysis to support the Live Fire Test Program for DDG 51 Class Destroyers. Mr. Krishna M. Choppella:is a Sofware Engineer at Eidea Laboratories Incotporated where he works on componentbased distributed enterpvise frameworks. He has been involved in creating data analysis tools for the US Nay by integrating CAD modeis databases and graphical front ends. His work in the Masters degree program in Mechanical Engineering at the University of Texas at Austin was in di0ddase.r spectroscopy of combustion products in porous-matri burners. He received his Bachelors degree in Electrical Engineering in India. He was a Research Associate at the Centre for Laser Technology and Project Engi

Ship design is often multidisciplinary involving several design elements with various types of objectives and constraints (O/C) some easily described as mathematical formulas, others better modeled as descriptive assertions. This paper describes a method based on fuzzy functions and an integrated performance index to model O/C using descriptive assertions to be used with mathematical formulas in optimization. Another issue addressed in this paper concerns the coordination of design elements when sequentially coupled, that is, when one leads the other and the performance of the follower depends greatly on the design of the leader. based on neuro-fuzzy techniques, the method described here coordinates and optimizes sequentially coupled elements. The two methods are applied to machinery arrangement (MA) and pipe routing (PR). Preliminary models for optimization of MA and PR are described considering convenience, producibility: engine room size, interference and location as factors in the O/C set. Some test results from MA/PR applications are presented and discussed. The methods are generic and can be extended to other elements in ship design. They are mutually independent and may be used separately Two advantages of their use are an improvement in overall performance and a reduction in the need for redesign of elements.

关键词： Optimization

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Characterization of Markarian 421 during its most violent year: Multiwavelength variability and correlations

arXiv

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arXiv 2025年

作者： Abe, K. Abe, S. Abhir, J. Abhishek, A. Acciari, V.A. Aguasca-Cabot, A. Agudo, I. Aniello, T. Ansoldi, S. Antonelli, L.A. Engels, A. Arbet Arcaro, C. Asano, K. baack, D. babić, A. de Almeida, U. barres barrio, J.A. batković, I. bautista, A. baxter, J. González, J. becerra bednarek, W. bernardini, E. bernete, J. berti, A. besenrieder, J. bigongiari, C. biland, A. blanch, O. bonnoli, G. bošnjak, Ž. bronzini, E. burelli, I. Campoy-Ordaz, A. Carosi, R. Carretero-Castrillo, M. Castro-Tirado, A.J. Cerasole, D. Ceribella, G. Chai, Y. Cifuentes, A. Colombo, E. Contreras, J.L. Cortina, J. Covino, S. D’Amico, G. D’Ammando, F. D’Elia, V. Da Vela, P. Dazzi, F. De Angelis, A. De Lotto, b. de Menezes, R. Delfino, M. Delgado, J. Mendez, C. Delgado Di Pierro, F. Di Tria, R. Di Venere, L. Prester, D. Dominis Donini, A. Dorner, D. Doro, M. Eisenberger, L. Elsaesser, D. Escudero, J. Fariña, L. Fattorini, A. Foffano, L. Font, L. Fröse, S. Fukami, S. Fukazawa, Y. López, R.J. García Garczarczyk, M. Gasparyan, S. Gaug, M. Paiva, J.G. Giesbrecht Giglietto, N. Giordano, F. Gliwny, P. Godinović, N. Gradetzke, T. Grau, R. Green, D. Green, J.G. Günther, P. Hadasch, D. Hahn, A. Hassan, T. Heckmann, L. Llorente, J. Herrera Hrupec, D. Imazawa, R. Ishio, K. Martínez, I. Jiménez Jormanainen, J. Kankkunen, S. Kayanoki, T. Kerszberg, D. Kluge, G.W. Kouch, P.M. Kubo, H. Kushida, J. Láinez, M. Lamastra, A. Leone, F. Lindfors, E. Lombardi, S. Longo, F. López-Coto, R. López-Moya, M. López-Oramas, A. Loporchio, S. Lorini, A. Majumdar, P. Makariev, M. Maneva, G. Manganaro, M. Mangano, S. Mannheim, K. Mariotti, M. Martínez, M. Martínez-Chicharro, M. Mas-Aguilar, A. Mazin, D. Menchiari, S. Mender, S. Miceli, D. Miener, T. Miranda, J.M. Mirzoyan, R. González, M. Molero Molina, E. Mondal, H.A. Moralejo, A. Morcuende, D. Nakamori, T. Nanci, C. Neustroev, V. Nickel, L. Nigro, C. Nikolić, L. Nilsson, K. Nishijima, K. Ekoume, T. Njoh Noda, K. Nozaki, S. Okumura, A. Otero-Santos, J. Paiano, S. Japanese MAGIC Group Department of Physics Tokai University Kanagawa Hiratsuka259-1292 Japan The University of Tokyo Chiba Kashiwa277-8582 Japan ETH Zürich ZürichCH-8093 Switzerland Università di Siena INFN Pisa SienaI-53100 Italy Bellaterra BarcelonaE-08193 Spain Universitat de Barcelona ICCUB IEEC-UB BarcelonaE-08028 Spain Instituto de Astrofísica de Andalucía-CSIC Glorieta de la Astronomía s/n Granada18008 Spain RomeI-00136 Italy Università di Udine INFN Trieste UdineI-33100 Italy Max-Planck-Institut für Physik GarchingD-85748 Germany Università di Padova INFN PadovaI-35131 Italy Technische Universität Dortmund DortmundD-44221 Germany Zagreb10000 Croatia URCA RJ Rio de Janeiro22290-180 Brazil IPARCOS Institute EMFTEL Department Universidad Com-plutense de Madrid MadridE-28040 Spain Instituto de Astrofísica de Canarias Dpto. de Astrofísica Universidad de La Laguna La Laguna TenerifeE-38200 Spain University of Lodz Faculty of Physics and Applied Informatics Department of Astrophysics Lodz90-236 Poland Centro de Investigaciones Energéticas Medioambientales y Tecnológicas MadridE-28040 Spain Departament de Física CERES-IEEC Universitat Autònoma de Barcelona BellaterraE-08193 Spain Università di Pisa INFN Pisa PisaI-56126 Italy INFN MAGIC Group INFN Sezione di Bari Dipartimento Interateneo di Fisica dell’Università e del Politecnico di Bari BariI-70125 Italy Department for Physics and Technology University of Bergen Norway INFN MAGIC Group INFN Sezione di Torino Università degli Studi di Torino TorinoI-10125 Italy Croatian MAGIC Group University of Rijeka Faculty of Physics Rijeka51000 Croatia Universität Würzburg WürzburgD-97074 Germany Japanese MAGIC Group: Physics Program Graduate School of Advanced Science and Engineering Hiroshima University Hiroshima739-8526 Japan ZeuthenD-15738 Germany Armenian MAGIC Group: ICRANet-Armenia Yerevan0019 Armenia Split21000 Croatia Croatian MAGIC Group J

Aims. Mrk 421 was in its most active state around early 2010, which led to the highest TeV gamma-ray flux ever recorded from any active galactic nuclei (AGN). We aim to characterize the multiwavelength behavior during this exceptional year for Mrk 421, and evaluate whether it is consistent with the picture derived with data from other less exceptional years. Methods. We investigated the period from November 5, 2009, (MJD 55140) until July 3, 2010, (MJD 55380) with extensive coverage from very-high-energy (VHE;E > 100 GeV) gamma rays to radio with MAGIC, VERITAS, Fermi-LAT, RXTE, Swift, GASP-WEbT, VLbA, and a variety of additional optical and radio telescopes. We characterized the variability by deriving fractional variabilities as well as power spectral densities (PSDs). In addition, we investigated images of the jet taken with VLbA and the correlation behavior among different energy bands. Results. Mrk 421 was in widely different states of activity throughout the campaign, ranging from a low-emission state to its highest VHE flux ever recorded. We find the strongest variability in X-rays and VHE gamma rays, and PSDs compatible with power-law functions with indices around 1.5. We observe strong correlations between X-rays and VHE gamma rays at zero time lag with varying characteristics depending on the exact energy band. We also report a marginally significant (∼ 3σ) positive correlation between high-energy (HE;E > 100 MeV) gamma rays and the ultraviolet band. We detected marginally significant (∼ 3σ) correlations between the HE and VHE gamma rays, and between HE gamma rays and the X-ray, that disappear when the large flare in February 2010 is excluded from the correlation study, hence indicating the exceptionality of this flaring event in comparison with the rest of the campaign. The 2010 violent activity of Mrk421 also yielded the first ejection of features in the VLbA images of the jet of Mrk 421. Yet the large uncertainties in the ejection times of these unprece

关键词： Active Galactic Nuclei

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PRINCIPLES OF NUTRIENT UPTAKE FROM FERTILIZER bANDS .7. P32 UPTAKE bY bRACE ROOTS OF MAIZE AND ITS DISTRIbUTION WITHIN LEAVES

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AGRONOMY JOURNAL 1966年第3期58卷 293-+页

作者： RObERTSON, JA KANG, bT RAMIREZPAZ, F WERKHOVEN, CH OHLROGGE, AJ Current addresses: J. A. Robertson Department of Soil Science University of Alberta Edmonton Canada B. T. Kang Faculty of Agriculture University of Indonesion Bogar Indonesia F. Ramirez-Paz C.I.A.N.O. C. Obregon Sonora Mexico C. H. E. Werkhoven Agronomy Department University of California Davis California and A. J. Ohlrogge Professor of Agronomy Purdue University Lafayette Indiana. The authors are indebted to the following persons for contributions to this study: Wended Osborne formerly an undergraduate student in Agronomy at Purdue University for the preliminary studies with methylene blue and Ad van Egeraat a special student from Holland on a 6-month program in the Department of Agronomy Purdue University for collection of much of the 1962 data and for contributions to their interpretation.

The influence on P uptake of area of roots in the fertilized soil and the rate of fertilization was investigated using aerial brace roots of maize. Either 1 or 2 brace roots were directed into soil containing 0.62 or 3.10 g of P labeled with P32. The radioactivity of the tip and/or basal portions of all leaves was measured by wrapping one thickness of leaf around a long G-M tube. The distribution of P32 in several leaves was mapped with an end window G-M tube. The P32 accumulation measured by the in-situ technique was highly correlated with that of the standard briquet method. Phosphorus uptake varied with the rate of fertilization and the number of fed brace roots. The proportion of total P derived from the fertilizer ranged from 1-37%. The P32 distribution in the leaves depended upon their position relative to the fertilized brace roots. The leaves on the brace root side had higher P32 activity in their tip portions than in their basal portions. This distribution is explained by limited connections between vascular bundles of the stem and the diverging of the leaf veins from the midrib.

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ROCKET MOTOR DESIGN FOR UNDERWATER SHOCK

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NAVAL ENGINEERS JOURNAL 1988年第3期100卷 215-225页

作者： YAGLA, JJ The authorreceived his B.A. degree in science (physics) from the Slate College of Iowa in 1965. He received his M.S. degree in engineering mechanics in 1968 and his Ph.D. in aerospace engineering and engineering science in 1981 from Arizona State University. He has done analytical and experimental research in the field of weapons blast and dynamical response since 1965 at the Naval Surface Warfare Center in Dahlgren Virginia. As a supervisory research mechanical engineer he was previously head of the Physical Response Analysis Branch Blast Effects Branch and Ship Engineering Branch. Dr. Yagla is the test development agent and was test conductor for the gun and missile structural test firings in USSIowaclass battleships. He is a consultant to the Naval Sea Systems Command battleship combat system engineer and the Naval Air Systems Command Cruise Missile Project for blast and structural response. He has been involved in the development of Standard missile and its launching systems since 1969. He participated in the design of shock tests for the Mk 104 rocket motor and analyzed the data. He is presently analyzing shock and vibration problems for the Standard Missile Program Office.

Naval ships and equipment are designed to survive underwater shock. The underwater shock can result from a nearby explosion of a bomb or missile, or the underwater detonation of a nuclear weapon. The shock wave travels through the water and applies an impulsive pressure load to the ship. The ship responds by a sudden acceleration in a direction up and away from the explosion. The motion of the ship is imparted to its weapons and equipment. In the case of Standard missile, impulsive loads are applied to the missiles stowed in the magazines. The evolutionary design of rocket motor chambers and launch shoes for Standard missile for underwater shock is traced from the early Tartar missile to the latest version of Standard missile. As the weight of the missile has increased and the performance requirements have become more demanding, the design of the weapon for underwater shock has become more difficult. The paper explains the design approaches and techniques. Theoretical and experimental methods have been required. Finally, the paper highlights the experiences and problems in conducting underwater shock experiments with production systems in ships at sea.

关键词： WARSHIPS

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Gene set correlation enrichment analysis for interpreting and annotating gene expression profiles

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Nucleic Acids Research 2024年第3期52卷 E17页

作者： Chang, Lan-Yun Lee, Meng-Zhan Wu, Yujia Lee, Wen-Kai Ma, Chia-Liang Chang, Jun-Mao Chen, Ciao-Wen Huang, Tzu-Chun Lee, Chia-Hwa Lee, Jih-Chin Tseng, Yu-Yao Lin, Chun-Yu Institute of Bioinformatics and Systems Biology National Yang Ming Chiao Tung University Hsinchu 300 Taiwan School of Medical Laboratory Science and Biotechnology College of Medical Science and Technology Taipei Medical University New Taipei City 235 Taiwan Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B) National Yang Ming Chiao Tung University Hsinchu 300 Taiwan TMU Research Center of Cancer Translational Medicine Taipei Medical University Taipei 110 Taiwan Ph.D. Program in Medical Biotechnology College of Medical Science and Technology Taipei Medical University New Taipei City 235 Taiwan Department of Otolaryngology-Head and Neck Surgery Tri-Service General Hospital National Defense Medical Center Taipei 110 Taiwan Department of Food Science Nutrition and Nutraceutical Biotechnology Shih Chien University Taipei 104 Taiwan Department of Biological Science and Technology National Yang Ming Chiao Tung University Hsinchu 300 Taiwan Cancer and Immunology Research Center National Yang Ming Chiao Tung University Taipei 112 Taiwan Institute of Data Science and Engineering National Yang Ming Chiao Tung University Hsinchu 300 Taiwan School of Dentistry Kaohsiung Medical University Kaohsiung 807 Taiwan

Pathway analysis, including nontopology-based (non-Tb) and topology-based (Tb) methods, is widely used to interpret the biological phenomena underlying differences in expression data between two phenotypes. by considering dependencies and interactions between genes, Tb methods usually perform better than non-Tb methods in identifying pathways that include closely relevant or directly causative genes for a given phenotype. However, most Tb methods may be limited by incomplete pathway data used as the reference network or by difficulties in selecting appropriate reference networks for different research topics. Here, we propose a gene set correlation enrichment analysis method, Gscore, based on an expression dataset-derived coexpression network to examine whether a differentially expressed gene (DEG) list (or each of its DEGs) is associated with a known gene set. Gscore is better able to identify target pathways in 89 human disease expression datasets than eight other state-of-the-art methods and offers insight into how disease-wide and pathway-wide associations reflect clinical outcomes. When applied to RNA-seq data from COVID-19-related cells and patient samples, Gscore provided a means for studying how DEGs are implicated in COVID-19-related pathways. In summary, Gscore offers a powerful analytical approach for annotating individual DEGs, DEG lists, and genome-wide expression profiles based on existing biological knowledge. © 2024 Oxford University Press. All rights reserved.

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