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Bio-Inspired computational methods for the Polio Virus Epidemic Model

Computers, Materials & Continua 2022年第8期72卷 2357-2374页

作者： Fatimah Abdulrahman Alrawajeh F.M.Allehiany Ali Raza Shaimaa A.M.Abdelmohsen Tahir Nawaz Cheema Muhammad Rafiq Muhammad Mohsin Department of Mathematics Faculty of Science CollegeImam Abdulrahman Bin Faisal University(IAU)Dammam31441Saudi Arabia Department of Mathematical Sciences College of Applied SciencesUmm Al-Qura UniversityP.O.Box 715Makkah21955Saudi Arabia Department of Mathematics Govt.Maulana Zafar Ali Khan Graduate College Wazirabad52000Punjab Higher Education Department(PHED)Lahore54000Pakistan Department of Physics College of SciencePrincess Nourah bint Abdulrahman UniversityRiyadh 11671Saudi Arabia Department of Mathematics University of GujratGujrat50700Pakistan Department of Mathematics Faculty of SciencesUniversity of Central PunjabLahore54600Pakistan Department of Mathematics Technische Universitat Chemnitz6209111Germany

In 2021,most of the developing countries are fighting polio,and parents are concerned with the disabling of their *** transmits from person to person,which can infect the spinal cord,and paralyzes the parts of the body within a matter of *** to the World Health Organization(WHO),18 million currently healthy people could have been paralyzed by the virus during 1988–*** all countries but Pakistan,Afghanistan,and a fewmore have been declared *** mathematical modeling of poliovirus is studied in the population by categorizing it as susceptible individuals(S),exposed individuals(E),infected individuals(I),and recovered individuals(R).In this study,we study the fundamental properties such as positivity and boundedness of the *** also rigorously study the model’s stability and equilibria with or without *** numerical study,we design the Euler,Runge–Kutta,and nonstandard finite difference ***,the standard techniques are time-dependent and fail to present the results for an extended *** nonstandard finite difference method works well to study disease dynamics for a long time without any ***,the results of different methods are compared to prove their effectiveness.

关键词： Poliovirus modeling stability results computational methods

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SURVEY OF INFRARED MEASUREMENT TECHNIQUES AND computational methods IN RADIANT HEAT TRANSFER

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JOURNAL OF SPACECRAFT AND ROCKETS 1966年第7期3卷 961-+页

作者： DUNN, ST RICHMOND, JC PARMER, JF National Bureau of Standards Washington D. C. University of West Virginia Morgantown W. Va.

Stuart Thomas Dunn is a Mechanical Engineer with a B.S. from the University of Missouri at Rolla in 1962;an M.S. in 1963 and Ph.D. in 1965, both from Oklahoma State University. He was employed in the Photometry and Colorimetry Section of the National Bureau of Standards from May 1964 through December 1965, where he completed his Ph.D. thesis in the field of infrared reflectance. He is now president of Dunn Associates Inc., of Silver Spring, Md. Dr. Dunn has several publications in the general area of thermal radiation measurements. Jerome F. Parmer is a Mechanical Engineer with a B.S. from the University of Notre Dame in 1957, an M.S. from West Virginia University in 1960, and a Ph.D. from Oklahoma State University in 1965. At West Virginia University, he was an Instructor from 1957-1960, an Assistant Professor of Mechanical Engineering from 1960-1962, and has been Associate Professor of Mechanical Engineering and Assistant Director of the Engineering Experiment Station since 1965. Dr. Parmer has several publications dealing with spacecraft thermal control. Joseph C. Richmond is a Ceramics Engineer with a B.S. from the Slate University of New York, College of Ceramics, in 1935;a B.S. with a major in mathematics from Alfred University in 1935;and an M.S. from North Carolina State University in 1939. He has been employed at the National Bureau of Standards since 1939, and is currently Leader of the Thermal Radiation Group of the Photometry and Colorimetry Section. He was Editor of the book Measurement of Thermal Radiation Properties of Solids (NASA SP-31), and General Chairman of the Symposium on Thermal Radiation of Solids held in San Francisco in March 1964. He is currently a member of the Thermophysics Committee of AI AA, and Vice-Chairman elect of the American Society for testing materials (ASTM) Committee E-21 on Space Simulation. Air. Richmond has over 60 publications, mostly in the areas of procelain enamels and high-temperature ceramic coatings for metals, and

关键词： Heat Transfer Analysis computational methods Thermal Radiation Radiation Properties Radiators Thermocouples Stefan Boltzmann Constant Bidirectional Reflectance Pyrometer Thermal Conductivity

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Heterocycles 33: Lipophilicity of a New Class of Thioethers Estimated by Reversed-Phase Thin-Layer Chromatography and Different computational methods

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JOURNAL OF CHROMATOGRAPHIC SCIENCE 2014年第10期52卷 1302-1307页

作者： Toma, Alexandra Hapau, Denisa Casoni, Dorina Zaharia, Valentin Iuliu Hatieganu Univ Med & Pharm Dept Organ Chem RO-400012 Cluj Napoca Romania Univ Babes Bolyai Fac Chem & Chem Engn Dept Analyt Chem RO-400028 Cluj Napoca Romania

The retention behavior for a series of new polyheterocyclic compounds containing azolic rings (1,3-thiazole, 1,2,4-triazole, 1,3,4-oxadiazole, 1,3,4-thiadiazole) has been investigated using reversed-phase thin-layer chromatography. Different approaches and computational methods were employed to evaluate their lipophilicity indices derived from chromatographic parameters. The obtained experimental results were correlated with various lipophilicity indices estimated via different computer software and internet websites. A strong correlation between experimental and computed results was observed. Furthermore, the lipophilicity parameters obtained by applying principal component analysis divided the investigated compounds into four groups according to their structural similarities.

关键词： Thioethers Estimated Reversed-Phase computer software thin layer chromatography computational methods REVERSE PHASE New classes Reversed phase thin layer chromatography Thioethers Lipophilicity

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Recent Advances in Predicting Functional Impact of Single Amino Acid Polymorphisms: A Review of Useful Features, computational methods and Available Tools

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CURRENT BIOINFORMATICS 2013年第2期8卷 161-176页

作者： Wang, Mingjun Sun, Zhongwei Akutsu, Tatsuya Song, Jiangning Chinese Acad Sci Tianjin Inst Ind Biotechnol Natl Engn Lab Ind Enzymes Tianjin 300308 Peoples R China Chinese Acad Sci Tianjin Inst Ind Biotechnol Key Lab Syst Microbial Biotechnol Tianjin 300308 Peoples R China Suzhou Int Dev Venture Capital Holding Co Ltd Suzhou 215128 Peoples R China Kyoto Univ Inst Chem Res Bioinformat Ctr Uji Kyoto 6110011 Japan Monash Univ Dept Biochem & Mol Biol Fac Med Melbourne Vic 3800 Australia

Owing to the biological significance of single amino acid polymorphism (SAP), there has been an increasing interest in understanding how certain amino acid substitutions give rise to functional change and consequent disease association, while others remain neutral polymorphisms. With the increasing availability of biological data, our knowledge regarding functional elements of the proteome continues to expand. As experimental approaches to characterize specific genetic variants are expensive and time-consuming, it is greatly desirable to develop effective computational methods that are capable of accurately predicting the functional impact of SAPs. In this review, we summarize 22 in silico tools that were previously developed and also discuss the related work of the functional impact prediction of SAPs that did not specifically develop webservers/tools. Procedures regarding how to extract annotations of SAPs and select the relevant useful features, as well as how to choose appropriate algorithms are also described in this review. In the end, a case study is given as an illustration to assess the predictive ability of available tools for predicting the functional consequence of SAPs. It is our hope that this review could serve as a useful guidance for developing next-generation in silico approaches for identification of the functional impacts of SAPs in the future.

关键词： Bioinformatics computational methods feature selection in silico tool machine learning sequence analysis single amino acid polymorphism (SAP)

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ROLE OF MAGGI EQUATIONS IN computational methods FOR CONSTRAINED MULTIBODY SYSTEMS

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JOURNAL OF GUIDANCE CONTROL AND DYNAMICS 1990年第1期13卷 113-120页

作者： KURDILA, A PAPASTAVRIDIS, JG KAMAT, MP GEORGIA INST TECHNOL ENGN SCI & MECH GRPATLANTAGA 30332 GEORGIA INST TECHNOL ENGN SCI & MECH GRPATLANTAGA 30332 GEORGIA INST TECHNOL SCH MECH ENGNATLANTAGA 30332 GEORGIA INST TECHNOL SCH AEROSP ENGNATLANTAGA 30332

This paper presents a unified theoretical basis for a class of methods that generate the governing equations of constrained dynamical systems by eliminating the constraints. By using Maggi's equations in conjunction with a common projective theory from numerical analysis, it is shown that members of the class are precisely characterized by the basis they choose for the null-space of the variational form of the constraints. For each method considered, the specific basis chosen for the null-space of the variational constraints is derived, as well as a dual basis for the orthogonal complement. The latter basis is of particular interest since it is shown that its knowledge theoretically enables one to generalize certain methods of the class to calculate constraint forces and torques. Practical approaches based on orthogonal transformations to effect this strategy are also outlined. In addition, since the theory presented herein stresses a common, fundamental structure to the various methods, it is especially useful as a means of comparing and evaluating individual numerical algorithms. The theory presented makes clear the relationship between certain numerical instabilities that have been noted in some methods that eliminate a priori constraint contributions to the governing equations by selecting an independent subset of unknowns. It is also briefly indicated how this formalism can be extended, in principle, to the wider class of nonlinear nonholonomic constraints. © 1990 American Institute of Aeronautics and Astronautics, Inc., All rights reserved.

关键词： computational methods Multibody System Numerical Algorithms Singular Value Decomposition Mechanism Dynamics Newton's Second Law Large Space Structures Holonomic Constraints Numerical Simulation Digital Computers

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Mapping nucleosome and chromatin architectures: A survey of computational methods

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computational AND STRUCTURAL BIOTECHNOLOGY JOURNAL 2022年 20卷 3955-3962页

作者： Fang, Kun Wang, Junbai Liu, Lu Jin, Victor X. Med Coll Wisconsin MCW Canc Ctr Inst Hlth & Equ Milwaukee WI 53226 USA Med Coll Wisconsin Mellowes Ctr Genome Sci & Precis Med Milwaukee WI 53226 USA Univ Oslo Dept Clin Mol Biol Lorenskog Norway Akershus Univ Hosp Lorenskog Norway North Dakota State Univ Dept Comp Sci Fargo ND USA

With ever-growing genomic sequencing data, the data variabilities and the underlying biases of the sequencing technologies pose significant computational challenges ranging from the need for accurately detecting the nucleosome positioning or chromatin interaction to the need for developing normalization methods to eliminate systematic biases. This review mainly surveys the computational methods for mapping the higher-resolution nucleosome and higher-order chromatin architectures. While a detailed discussion of the underlying algorithms is beyond the scope of our survey, we have discussed the methods and tools that can detect the nucleosomes in the genome, then demonstrated the computational methods for identifying 3D chromatin domains and interactions. We further illustrated computational approaches for integrating multi-omics data with Hi-C data and the advance of single-cell (sc)Hi-C data analysis. Our survey provides a comprehensive and valuable resource for biomedical scientists interested in studying nucleosome organization and chromatin structures as well as for computational scientists who are interested in improving upon them. (c) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of computational and Structural Biotechnology.

关键词： computational methods Nucleosome Chromatin architectures

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Dynamical analysis and design of computational methods for nonlinear stochastic leprosy epidemic model

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ALEXANDRIA ENGINEERING JOURNAL 2022年第10期61卷 8097-8111页

作者： Raza, Ali Awrejcewicz, Jan Rafiq, Muhammad Ahmed, Nauman Ehsan, Muhammad Sarwar Mohsin, Muhammad Govt Maulana Zafar Ali Khan Grad Coll Wazirabad Punjab Higher Educ Dept PHED Dept Math Lahore 52000 Pakistan Lodz Univ Technol Dept Automat Biomech & Mechatron 1-15 Stefanowskiego St PL-90924 Lodz Poland Univ Cent Punjab Fac Sci Dept Math Lahore Pakistan Univ Lahore Dept Math & Stat Lahore Pakistan Univ Cent Punjab Lahore Fac Engn Lahore Pakistan Tech Univ Chemnitz Dept Math Chemnitz Germany

This article presents the dynamical analysis of the stochastic leprosy epidemic model. Positivity and boundedness are the criteria used in the deterministic model. A primary technique is known as the Euler Maruyama used in the solution of the said model. The standard computational methods will evaluate the design stability and efficiency based on the chosen criteria. The traditional computational methods like the stochastic Euler and the stochastic Runge Kutta fail to restore the essential features of biological problems. However, our proposed approach, the stochastic non-standard finite difference (NSFD), is used and found to be efficient, cost-effective, and accommodates all the desired feasible properties. Our method achieves all-time convergence against the backdrop of other classical techniques that perform conditionally or fail over a long period. In the end, a comparison between this scheme and the existing ones reviews the novelty of our approach.(c) 2022 THE AUTHORS. Published by Elsevier BV on behalf of Faculty of Engineering, Alexandria University This is an open access article under the CC BY-NC-ND license (http://***/ licenses/by-nc-nd/4.0/).

关键词： Leprosy disease Stochastic model computational methods Stability analysis

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Whisper: Sensitivity/Uncertainty-Based computational methods and Software for Determining Baseline Upper Subcritical Limits

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NUCLEAR SCIENCE AND ENGINEERING 2015年第1期181卷 17-47页

作者： Kiedrowski, Brian C. Brown, Forrest B. Conlin, Jeremy L. Favorite, Jeffrey A. Kahler, Albert C. Kersting, Alyssa R. Parsons, D. Kent Walker, Jessie L. Univ Michigan Dept Nucl Engn & Radiol Sci Ann Arbor MI 48109 USA Los Alamos Natl Lab Los Alamos NM 87545 USA

Nuclear criticality safety analysis using computational methods such as a Monte Carlo method must establish, for a defined area of applicability, an upper subcritical limit (USL), which is a calculated multiplication factor k that can be treated as actually subcritical and is derived from a calculational margin (combination of bias and bias uncertainty) and a margin of subcriticality. Whisper, a nonparametric, extreme-value method based on sensitivity/uncertainty techniques and the associated software are presented. Whisper uses benchmark critical experiments, nuclear data sensitivities from the continuous-energy Monte Carlo transport software MCNP, and nuclear covariance data to set a baseline USL. Comparisons with a traditional parametric approach for validation, which requires benchmark data to be normally distributed, show that Whisper typically obtains similar or more conservative calculational margins;comparisons with a rank-order nonparametric approach show that Whisper obtains less stringent cakulational margins.

关键词： computational methods

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Molecular electronic spectroscopy: from often neglected fundamental principles to limitations of state-of-the-art computational methods

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COLORATION TECHNOLOGY 2015年第1期131卷 9-26页

作者： Mustroph, Heinz Ernst, Steffen Senns, Bianca Towns, Andrew D. FEW Chem GmbH D-06756 Bitterfeld Germany Vivimed Labs Europe Ltd Huddersfield HD1 6BU W Yorkshire England

The creation of the first synthetic dyes not only stimulated the hunt for new colorants but also drove the search for rules correlating the constitution of organic compounds with their colour. Dye chemistry additionally facilitated the development of molecular electronic spectroscopy as well as theories of molecular electronic structure and electronic transitions. Powerful quantum chemical computational tools are now available for the prediction of the electronic structure and spectroscopic characteristics of organic compounds. Such methods are thus useful in designing new functional colorants and aiding interpretation of their properties. However, without a deep appreciation of the principles and assumptions behind the calculations, one runs the risk of misunderstanding what can be achieved as well as becoming confused about how the outputted electronic and vibronic transition data correspond to observed absorption spectra. This review therefore aims to cover fundamentals of electronic spectroscopy that are often overlooked and enable the dye chemist using modern computational methods to comprehend the subtle differences in the types of transition energy value that such software can generate. In addition, the limitations of these methods in predicting absorption maxima and intensities of real-world colorants will be discussed in the context of physical influences on absorption band position and shape, for example from the perspective of different forms of the Franck-Condon principle. In essence, the goal of this review is to clarify, in terms that practical dye chemists will understand, what computational methods can predict and how valid these predictions are compared with reality.

关键词： computational methods

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Databases and computational methods for the identification of piRNA-related molecules: A survey

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computational AND STRUCTURAL BIOTECHNOLOGY JOURNAL 2024年 23卷 813-833页

作者： Guo, Chang Wang, Xiaoli Ren, Han Guangdong Univ Foreign Studies Lab Language Engn & Comp Guangzhou 510420 Peoples R China Huazhong Univ Sci & Technol Inst Reprod Hlth Tongji Med Coll Wuhan 430030 Peoples R China Guangdong Univ Foreign Studies Lab Language & Artificial Intelligence Guangzhou 510420 Peoples R China

Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs (ncRNAs) that plays important roles in many biological processes and major cancer diagnosis and treatment, thus becoming a hot research topic. This study aims to provide an in-depth review of computational piRNA-related research, including databases and computational models. Herein, we perform literature analysis and use comparative evaluation methods to summarize and analyze three aspects of computational piRNA-related research: (i) computational models for piRNA-related molecular identification tasks, (ii) computational models for piRNA-disease association prediction tasks, and (iii) computational resources and evaluation metrics for these tasks. This study shows that computational piRNA-related research has significantly progressed, exhibiting promising performance in recent years, whereas they also suffer from the emerging challenges of inconsistent naming systems and the lack of data. Different from other reviews on piRNA-related identification tasks that focus on the organization of datasets and computational methods, we pay more attention to the analysis of computational models, algorithms, and performances that aim to provide valuable references for computational piRNA-related identification tasks. This study will benefit the theoretical development and practical application of piRNAs by better understanding computational models and resources to investigate the biological functions and clinical implications of piRNA.

关键词： piRNA Machine learning Deep learning computational methods piRNA -disease association prediction

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