Mathematical Biology and Bioinformatics最新文献_第2页

Application of Mathematical Models of the Dynamics of the Epidemic Acute Respiratory Viral Infections to Increase the Efficiency of Epidemiological Surveillance 应用流行性急性呼吸道病毒感染动态数学模型提高流行病监测效率

Mathematical Biology and Bioinformatics Pub Date : 2023-12-13 DOI: 10.17537/2023.18.517

V. Leonenko, A.I. Korzin, D.M. Danilenko

{"title":"Application of Mathematical Models of the Dynamics of the Epidemic Acute Respiratory Viral Infections to Increase the Efficiency of Epidemiological Surveillance","authors":"V. Leonenko, A.I. Korzin, D.M. Danilenko","doi":"10.17537/2023.18.517","DOIUrl":"https://doi.org/10.17537/2023.18.517","url":null,"abstract":"\u0000 Uncertainty in the calculations of forecasts of the spread of epidemic acute respiratory infections obtained using mathematical models, associated with data error and uncertainty in the choice of a model, as well as the lack of verification of modeling results by interdisciplinary teams including epidemiology specialists, prevent the correct prediction of the effectiveness of disease control measures. In this paper, we propose a solution to these problems by using a software package consisting of a family of epidemic models, methods for estimating the error of output data depending on the error of the initial morbidity data, as well as a graphical interface with the possibility of manual correction of the results of automatic calibration and generation of epidemic bulletins. The novelty of the presented study is the methodology for integrating epidemic models into software tools used by supervisory authorities, which allows to supplement weekly bulletins and annual epidemiological reports in semi-automatic mode with a quantitative interval estimation of the error of calculated indicators. The ultimate goal is to provide the supervisory authorities with informative and promptly obtained calculated data for decision-making in the field of infection control.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"204 S621","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139006275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Mathematical Analysis of Aortic Deformation in Aneurysm and Wall Dissection 动脉瘤和壁间夹层中主动脉变形的数学分析

Mathematical Biology and Bioinformatics Pub Date : 2023-12-03 DOI: 10.17537/2023.18.464

A.E. Medvedev, A.D. Erokhin

{"title":"Mathematical Analysis of Aortic Deformation in Aneurysm and Wall Dissection","authors":"A.E. Medvedev, A.D. Erokhin","doi":"10.17537/2023.18.464","DOIUrl":"https://doi.org/10.17537/2023.18.464","url":null,"abstract":"\u0000 Aortic dissection is an extremely severe pathology. From the mechanics point of view, the aorta is a multilayered anisotropic reinforced shell, which is subjected to periodic loading under the action of pulse blood pressure. The questions of mathematical modeling of aorta and large arteries dissection are considered. A review of modern mathematical models of aortic and arterial wall structure obtained on the basis of experimental data processing on biaxial stretching of samples is carried out. Mathematical models can be conditionally divided into two classes: 1) effective models, when the internal structure of the wall structure is ignored, but the mechanical parameters of the material \"averaged\" over the wall thickness are introduced; 2) structured models, when the multilayer (up to three layers) structure of the artery is taken into account with the addition of one to four families of reinforcing fibers. One of the most widely used artery models, the Holzapfel – Hasser – Ogden model, is considered in detail. This model describes a two or three-layered artery with two families of reinforcing fibers. For this model tables of design parameters are given, numerical calculations of arterial rupture and dissection are carried out. The blood vessel is subjected to pulse pressure of blood flowing through it. It is shown that rupture of the inner layer of the vessel leads to an increase in the stress on the outer wall of the vessel. Increasing the thickness and length of the rupture increases the stresses on the outer wall of the vessel. The presence of an aneurysm of the vessel increases stresses twice as much as a vessel without an aneurysm. Splitting of the inner wall of the vessel leads to an increase in stresses on the wall – stresses fall with increasing rupture width for a straight vessel and rise for a vessel with an aneurysm. Stress calculations at the “tip” of delamination showed that the maximum stress is reached at the outer wall of the rupture.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"43 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138605491","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Role of Charged Amino Acid Residues of Plastocyanin in Interaction with Cytochrome B6f Complex and Photosystem I of Higher Plants: A Study Using the Brownian Dynamics Method 质花青素带电氨基酸残基在与高等植物细胞色素 B6f 复合物和光系统 I 相互作用中的作用：布朗动力学方法研究

Mathematical Biology and Bioinformatics Pub Date : 2023-11-22 DOI: 10.17537/2023.18.434

V. Fedorov, I.A. Volkhin, S. S. Khrushchev, T.K. Antal, I.B. Kovalenko

{"title":"Role of Charged Amino Acid Residues of Plastocyanin in Interaction with Cytochrome B6f Complex and Photosystem I of Higher Plants: A Study Using the Brownian Dynamics Method","authors":"V. Fedorov, I.A. Volkhin, S. S. Khrushchev, T.K. Antal, I.B. Kovalenko","doi":"10.17537/2023.18.434","DOIUrl":"https://doi.org/10.17537/2023.18.434","url":null,"abstract":"Plastocyanin is an electron carrier protein in the electron transport chain of chloroplasts, carrying out the transfer of an electron from cytochrome f of the cytochrome b6f complex to photosystem I. Using the method of Brownian dynamics, the process of formation of the encounter complex of plastocyanin and photosystem I of higher plants was studied. The electrostatic properties of proteins were studied, and the most important amino acid residues for their interaction were identified. It was shown that plastocyanin contacts the positively charged alpha-helix protruding into the lumen of the F subunit of photosystem I with amino acid residues of both its “large” (D42, E43, D44, E45, D51) and “small” (E59, E60, D61) the negatively charged regions in 73 % of cases, and only the \"large\" region in 27 % of cases. A comparison of the study results with previously obtained data on the interaction of plastocyanin with cytochrome f made it possible to identify the role of charged amino acid residues of plastocyanin in the process of complex formation with photosystem I and cytochrome f. When interacting with cytochrome f, a positively charged region located near the small domain of cytochrome f and formed by amino acid residues K58, K65, K66, K187 and R209, attracts negatively charged amino acid residues D42, E43, D44, E45, D51 of the “large” region of plastocyanin, forming an electrostatic hinge contact around which rotation occurs when the final complex is formed. The “small” region of plastocyanin is involved in the stabilization of the final complex. Thus, both in the formation of the encounter complex with photosystem I, and in the reaction with cytochrome f the same negatively charged amino acid residues of plastocyanin are used.","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"279 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139247952","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Performance Analysis of Cross-Assembly of Metatranscriptomic Datasets in Viral Community Studies 病毒群落研究中元转录组数据集交叉组装的性能分析

Mathematical Biology and Bioinformatics Pub Date : 2023-11-20 DOI: 10.17537/2023.18.418

Yu.S. Bukin, A. N. Bondaryuk, T.V. Butina

{"title":"Performance Analysis of Cross-Assembly of Metatranscriptomic Datasets in Viral Community Studies","authors":"Yu.S. Bukin, A. N. Bondaryuk, T.V. Butina","doi":"10.17537/2023.18.418","DOIUrl":"https://doi.org/10.17537/2023.18.418","url":null,"abstract":"We conducted a comparative analysis of individual and cross-assemblies of several metatranscriptomic data sets to study viral communities using several metatranscriptomes of endemic Baikal mollusks. We have shown that, compared to individual dataset assemblies, a Hidden Markov Model-based cross-assembly procedure increases the number of viral contigs (or scaffolds) per sample, the number of virotypes identified, and the average length of scaffolds per sample. The proportion of assembled viral reads from the total number of reads in samples is higher in cross-assembly. De novo cross-genomic assemblies combined with a virus identification algorithm using Hidden Markov Model present the data in a table with the number of reads from different samples for each scaffold. The table allows comparison of samples based on the representation of all viral scaffolds, including those not taxonomically identified, i.e. those that have no analogues in the NCBI RefSeq database. Thus, cross-genomic assemblies allow for comparative analyzes taking into account the latent diversity of viruses. We propose a pipeline for metatranscriptomic data analysis using de novo cross-genomic assembly to study viral diversity.","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"27 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139256167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Exploring the Mangrove Based Phytochemicals as Potential Viral RNA Helicase Inhibitors by in silico Docking and Molecular Dynamics Simulation Methods 通过默观对接和分子动力学模拟方法探索红树林植物化学物质作为潜在病毒 RNA 螺旋酶抑制剂的可能性

Mathematical Biology and Bioinformatics Pub Date : 2023-11-19 DOI: 10.17537/2023.18.405

R. Satpathy, S. Acharya

{"title":"Exploring the Mangrove Based Phytochemicals as Potential Viral RNA Helicase Inhibitors by in silico Docking and Molecular Dynamics Simulation Methods","authors":"R. Satpathy, S. Acharya","doi":"10.17537/2023.18.405","DOIUrl":"https://doi.org/10.17537/2023.18.405","url":null,"abstract":"A variety of plant-derived molecular compounds from mangrove plants have attracted attention due to the discovery of their antiviral activity. It has been proven that herbal medicines based on them provide good protection against a number of pathogenic viruses. However, it is necessary to screen these effective antiviral compounds to select those that have fewer harmful side effects. This study aimed to screen several bioactive compounds from mangrove plants that could be used as a viral RNA helicase inhibitor. Fifty-nine compounds were selected from the literature and databases for initial study and screening according to Lipinski's rule of five. The resulting selected compounds were subjected to another round of screening through molecular docking studies with five different pathogenic virus RNA helicase enzymes using the Autodock Vina tool followed by ADMET (absorption, distribution, metabolism, excretion and toxicity) analysis. In addition, the best compound-bound helicase-RNA complexes were included in 50 ns molecular dynamics simulations using Gromacs 5.1.1 software followed by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) analysis. This comparative study predicts that the phytochemical gedunin is an excellent inhibitor of the RNA helicase enzyme of SARS-CoV-2, followed by Japanese encephalitis virus and hepatitis C virus. The results of the study may lead to the development of antiviral compounds against the RNA helicase enzymes of pathogenic viruses.","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"28 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139259878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Numerical modelling of myocardial infarction. II. Analysis of macrophage polarization mechanism as a therapeutic target 心肌梗死的数值模拟。2巨噬细胞极化作为治疗靶点的机制分析

Mathematical Biology and Bioinformatics Pub Date : 2023-10-27 DOI: 10.17537/2023.18.367

O.F. Voropaeva, Ch.A. Tsgoev

{"title":"Numerical modelling of myocardial infarction. II. Analysis of macrophage polarization mechanism as a therapeutic target","authors":"O.F. Voropaeva, Ch.A. Tsgoev","doi":"10.17537/2023.18.367","DOIUrl":"https://doi.org/10.17537/2023.18.367","url":null,"abstract":"In this study, we explore the mechanism of macrophage polarization and its significance in the development of large-scale infarction with favorable outcomes, using a minimal mathematical model of aseptic inflammation dynamics. The problem is considered in the local approximation and in the two-dimensional non-stationary formulation. The study aims to address the pertinent problem of analyzing general principles governing macrophage polarization in the context of devising therapeutic strategies and refining the \"therapeutic window\". Key trends are identified to enhance the effectiveness of macrophage polarization for therapeutic purposes, along with providing approximate estimations of optimal macrophage interventions that yield organ-preserving and regenerative effects. Our findings reveal that M1/M2 macrophage polarization results from an additive interplay of at least two mechanisms - cytokine-dependent activation and reprogramming of activated macrophages. Furthermore, our modeling data demonstrate the pivotal role of macrophage reprogramming as a direct response to microenvironmental changes, facilitating favorable disease progression and its outcomes. Moreover, we establish that the process of macrophage polarization plays a crucial role in localizing focal inflammation, leading to the formation of the infarction core within finite dimensions and quasi-stationary structure at the periphery, comprising immune cell clusters. The modeling results exhibit qualitative and quantitative agreement with the experimental data. Importantly, the computational experiments results align with the majority of laboratory and clinical studies, emphasizing the therapeutic potential of macrophage polarization management as a promising treatment strategy. The paper is a follow-up of the previously published work series, devoted to the study of spatial and temporal aspects of the inflammation and death processes development in heart muscle cells.","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"35 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136311370","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Numeric Investigation of Non-Stationary Dust-Containing Airflow and Deposition of Dust Particles in the Lower Airways 下气道非静止含尘气流及尘粒沉积的数值研究

Mathematical Biology and Bioinformatics Pub Date : 2023-10-23 DOI: 10.17537/2023.18.347

P.V. Trusov, N.V. Zaitseva, M.Yu. Tsinker, A.I. Kuchukov

{"title":"Numeric Investigation of Non-Stationary Dust-Containing Airflow and Deposition of Dust Particles in the Lower Airways","authors":"P.V. Trusov, N.V. Zaitseva, M.Yu. Tsinker, A.I. Kuchukov","doi":"10.17537/2023.18.347","DOIUrl":"https://doi.org/10.17537/2023.18.347","url":null,"abstract":"Within creation of the mathematical model to describe the human respiratory system, we accomplished numeric investigation of non-stationary dust-containing airflow as well as dust particle deposition in the lower airways with the real anatomic geometry based on CT scans. Inhaled air is considered a multi-phase mixture of a homogenous gas and solid dust particles. Motion of a basic carrier gas phase is described using the Euler approach. Solid dust particles are a dispersed carried phase, which is described with the Lagrange approach. The k-ω model is used to describe turbulence. We consider non-stationary airflow during calm inhalation. The article presents calculated flow streamlines for the velocity of particles in inhaled air in the lower airways at different moments. We quantified a share of deposited particles (SDP) with various dispersed structure (between 10 nm and 100 µm) and density (1000 kg/m3, 2000 kg/m3, 2700 kg/m3) in the lower airways; the article provides computed motion paths of particulate matter. Solid particle deposition in the airways has different efficiency depending on particle sizes and density. SDP goes down as their sizes and masses decrease. Particle density mostly influences differences in deposition of micro-sized particles (2.5–20 µm): as particle mass and density grow, SDP in the airways also increases. SDP with their diameter being less than 1 µm amounts to approximately 20 % of all the particles that reach the inlet to the trachea. According to the results obtained by numeric modeling, the greatest share of dust particles penetrates the right main bronchus, predominantly the right middle and inferior lobar bronchi. Dust particles are able to induce diseases of the lungs, pneumoconiosis included.","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"2 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135366708","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A Mathematical Model for Evolution of Human Functional Disorders Influenced by Environment Factors 环境因素影响下人类功能障碍进化的数学模型

Mathematical Biology and Bioinformatics Pub Date : 2023-10-23 DOI: 10.17537/2023.18.t73

P.V. Trusov, N.V. Zaitseva, D.A. Kiryanov, M.R. Kamaltdinov, M.Ju. Cinker, V.M. Chigvintsev, D.V. Lanin

引用次数: 0

Comparative analysis of Actinobacteria phage-plasmids and their transduction potential 放线菌噬菌体质粒及其转导潜能的比较分析

Mathematical Biology and Bioinformatics Pub Date : 2023-10-18 DOI: 10.17537/2023.18.323

N.A. Nikulin, S.S. Kiselev, V.V. Panyukov, Y. Lu, A.A. Zimin

{"title":"Comparative analysis of Actinobacteria phage-plasmids and their transduction potential","authors":"N.A. Nikulin, S.S. Kiselev, V.V. Panyukov, Y. Lu, A.A. Zimin","doi":"10.17537/2023.18.323","DOIUrl":"https://doi.org/10.17537/2023.18.323","url":null,"abstract":"The genus Streptomyces is the most extensively studied group within actinobacteria, which are widely used for the production of antibiotics and other metabolites. Streptomyces bacteriophages attract a lot of interest to study phage-host coevolution. One of the probable interactions is a bacteriophage-mediated horizontal transfer of genes encoding bacterial metabolites, which are important for humans. In this study, a search for Streptomyces bacteriophages having capacities necessary for efficient horizontal transfer was performed. Groups of bacteriophages of actinobacteria and their plasmids with relatively long GC-rich sequences containing both genes related to viral morphogenesis and plasmid-associated genes were revealed by comparative genome analysis. In one of these groups, homologs of proteins of DNA packaging into a capsid of Punavirus genus phages, that representatives are capable to perform a horizontal transfer of genes with high frequency were identified. Taking it into account, as well as the peculiarities of their genomic structure, horizontal gene transfer by this group of viruses and plasmids was assumed to occur. Considering the genome length and GC-content, it is thought that these viruses could be useful for producers construction. Moreover, some given examples showing the chimerical origin of phage-plasmids allow suggesting that recombination events between considered phages-plasmids occur at high frequency. New representatives of viruses with low similarity to known phage genomes were also detected among plasmids. A wide diversity of actinobacterial phage-plasmids that is related to their variability and a probable existence of a great number of sequences of this type of viruses in databases were found out.","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135885209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Flow in Antroduodenal Part of Digestive Tract: Mathematical Model and Some Results 消化道十二指肠流:数学模型及一些结果

Mathematical Biology and Bioinformatics Pub Date : 2023-09-05 DOI: 10.17537/2023.18.t54

P.V. Trusov, N.V. Zaitseva, M.R. Kamaltdinov

引用次数: 0