Mathematical Biology and Bioinformatics最新文献

{"title":"The Incipient Formation of the Internal Dynamics of a Uniformly Moving Polaron in a Polynucleotide Chain Subjected To a Constant Electric Field","authors":"A. N. Korshunova, V. Lakhno","doi":"10.17537/2022.17.452","DOIUrl":"https://doi.org/10.17537/2022.17.452","url":null,"abstract":"\u0000In this paper we consider the incipient formation of the internal dynamics of a uniformly moving polaron in a polynucleotide chain subjected to a constant electric field. The calculations performed show that Bloch oscillations arising in the course of the polaron oscillatory motion along the chain do not completely disappear when the polaron's motion along the chain becomes uniform. When the polaron moves uniformly along the chain, Bloch oscillations are also observed, although in a slightly different form. It is shown that the shape of the electron density distribution in a polaron during its stationary motion in a constant electric field takes an explicit structure. In this case, such characteristics of Bloch oscillations as the period of Bloch oscillations and the maximum Bloch amplitude demonstrate low-density components of the polaron.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73586323","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}

{"title":"Structure and features of amino acid sequences of Π-modules in OB-folds","authors":"E. Brazhnikov, A. V. Efimov","doi":"10.17537/2022.17.441","DOIUrl":"https://doi.org/10.17537/2022.17.441","url":null,"abstract":"\u0000 Stereochemical analysis has been performed for П-modules from the large set of non-homologous protein structures containing the OB-fold. That module consists of two β-strands connected by a loop and placed in different sheets in such a way which looks as Greek letter П. Total 70 non-homologous proteins at resolution not less than 2.5Å have been selected for the analysis from 265 suitable structures belonging to sixteen OB-fold super families. We have disclosed two types of П-modules: the fist with the connecting loop containing α-helix, and second one without helix. Entrance of protein chain into second β-sheet is carried out by the same arch with conformation βββαLβp. In most cases, 85 % of total, α-positions are occupied by glycine residue, while at entrance in the loop such residues are absent. Occupancy frequency of П-modules has been obtained in dependence on the loop length. Spatial pathway of structures of all modules are superimposed very well. Structural alignment of amino acid for П-module sequences allows us to determine the key positions of the hydrophobic, hydrophilic, and glycine residues. \u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"192 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76950964","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}

{"title":"Extracting Factual Information about the Pandemic from Open Internet Sources","authors":"E. Akulinina, A. Karmanov, N. A. Teplykh, V. Vlasov, V. Baluta, S. S. Varykhanov, A. Karandeev, V. Osipov, Y. Rykov, B. Chetverushkin","doi":"10.17537/2022.17.423","DOIUrl":"https://doi.org/10.17537/2022.17.423","url":null,"abstract":"\u0000 A large number of different source data is needed for multi-agent models of the spread of infectious diseases. Most of them are not directly accessible. Therefore, one of the key problems to design such models is the development of tools for obtaining data from various sources. This article presents approaches that allow to extract the values of the parameters of the functioning of the simulated society and statistical data on the development of the pandemic from text messages published in the Internet. The proposed method and software implementation provide intelligent search of open source information in the Internet and process of unstructured data. The data collected this way used to set up parameters of mathematical model, which provides ability to study various scenarios and predict progress of the epidemic in concrete regions. The emphasis of the proposed approach is placed on two main technologies. The first is the use of regular expressions. The second is analysis using machine learning methods. The use of the regular expression method allows for high-speed text processing, but its applicability is limited by a strong dependence on the context. Machine learning allows to adapt the information context of the message, but at the same time there is a relatively large amount of time spent on analysis. To improve the accuracy of the analysis and to level the shortcomings of each of these approaches, ways of combining these technologies are proposed. The article presents the obtained results of optimization of algorithms for obtaining the necessary data.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"49 10","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-12-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72405573","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}

{"title":"Two Approaches to Modeling Phytoplankton Biomass Dynamics Based on the Droop Model","authors":"A. Abakumov, S. Pak","doi":"10.17537/2022.17.401","DOIUrl":"https://doi.org/10.17537/2022.17.401","url":null,"abstract":"\u0000 This work continues the study of the Droop model based on the concept of cell quota. Description of the photosynthetic processes in phytoplankton includes in the model structure. The concept of chlorophyll quota is used. It is the proportion of photosynthetic substances in plant cells. In addition to the chlorophyll quota, the photosynthetic activity of phytoplankton is determined by external conditions, primarily by the level of photosynthetically active radiation (PAR). The model is based on separating the dependence of phytoplankton reproduction on external conditions according to the stages of photosynthesis. The light stage is largely determined by the PAR, and the dark stage is limited by the nutrient resource under the controlling influence of the temperature of the aquatic environment. In order to develop the model, the storage of energy in the light stage of photosynthesis is described in detail. Energy is stored in the form of energy-intensive substances in macroergic molecules (macroergs). The most common cell macroerg is adenosine triphosphate (ATP). The proportion of ATP in phytoplankton varies depending on the light regime and on the energy amount stored in the dark stage. The model includes the Droop kinetics and equations for the dynamics of the chlorophyll quota and the ATP pool. The conditions for the existence and stability of equilibrium solutions are compared for the same values of parameters common to both models. The greatest influence on the dynamic modes of the minimum value of the cell quota has been established. The proportion of biomass associated with the light period of photosynthesis is also significant. For the first model that is the biomass produced during daylight hours. And in terms of the second model, it is the biomass formed due to the energy of ATP stored in the light phase. The influence of the structure of dynamic models on the daily and annual dynamics of phytoplankton was revealed. Scenarios of behavior of models under various lighting conditions, including constant and periodically changing lighting, have been studied.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"91 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91258452","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}

{"title":"Problems of Quantum-Classical Modeling Of the Primary Photoreaction in Rhodopsin","authors":"A. S. Shigaev, I. V. Lihachev, V. Lakhno","doi":"10.17537/2022.17.360","DOIUrl":"https://doi.org/10.17537/2022.17.360","url":null,"abstract":"\u0000 A modified model of the primary photoreaction in rhodopsin, cis-trans photoisomerization of the chromophore (retinal), is studied. The quantum subsystem of the model includes three vibronic states: the ground state, the excited state, and the ground state of the primary photoproduct. These states correspond to three point masses in the classical subsystem. The modification consists in the exponential dependence of the electronic-vibrational coupling constant on the displacement of point masses. The properties of the optimal loci of the multiparameter space, which characterized by the best agreement with the experimental data, are studied. A rather small “multidimensional volume” of these loci shown in all ranges of the used values of the model parameters. Several ways to optimize the quantum-classical model of rhodopsin photoisomerization have been proposed.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"126 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81329481","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}

{"title":"Estimation of Oxygen and Glucose Concentration Distribution in the Rat Brain Arterial System","authors":"V. Kopylova, S. Boronovskiy, Y. Nartsissov","doi":"10.17537/2022.17.386","DOIUrl":"https://doi.org/10.17537/2022.17.386","url":null,"abstract":"\u0000 Glucose and oxygen concentration gradients are the key indicators that form the trophic tissue supply in mammalian brain. To describe them in detail it is essential to combine the solution of both hemodynamics and the convection-diffusion-reaction problems in the tissue. Visualization of spatio-temporal distributions of the metabolites noted above can be carried out both using the gradients themselves and the corresponding probability density functions. In the case of considering large parts of the brain, as well as the entire organ as a whole, the second method for metabolite heterogeneity description is of greater interest for practical purposes. This paper presents an approach to obtain a probability density functions based on structural segmentation of the diffusion region using Delaunay triangulation and the spherical source diffusion field method. It is shown that the average values of the estimated distributions deviate by 8 % from the experimentally obtained results and it corresponds to the best match during the validation by the finite element method in the triangulation simplices of basic topology. Given the relatively low computational complexity of both the segmentation process and the estimation of concentration in a single segment, the proposed method to obtain integral distributions of various compounds, in particular glucose and oxygen, can be used as an affordable alternative to precise calculation of the concentration gradients in the whole brain and its distinct anatomical structures.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"23 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83706223","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}

{"title":"Identification of Novel miRNAs Involved in Cancer Progression and Metastasis in Clear Cell Renal Cell Carcinoma","authors":"R. H. Hamoode, T. A. Rafaa, R. H. Abduljaleel, A. Suleiman","doi":"10.17537/2022.17.338","DOIUrl":"https://doi.org/10.17537/2022.17.338","url":null,"abstract":"\u0000 MicroRNAs are non-coding molecules 21–23 nucleotides long that are involved in post-transcriptional regulation of gene expression by mRNA silencing. There is evidence that miRNA activity is associated with various types of human cancer, such as breast cancer, colorectal cancer, ovarian cancer and hepatocellular carcinoma, as well as with clear cell renal cell carcinoma. In 2020, the incidence of kidney cancer worldwide was 319,016. Clear cell renal cell carcinoma is associated with loss or mutation of the VHL gene. The aim of this study was to identify miRNAs that are expressed differently in samples of normal kidney tissue and tissue affected by clear cell renal cell carcinoma. For this study, a public miRNA dataset from ArrayExpress was obtained and post-processed. Mapping, identification of known and new microRNAs, and quantification were performed using the miRDeep2 computer program from the DESeq R/Bioconductor package. We performed target identification and functional load analysis using GeneCodis4. A total of 2656 miRNAs were found to be differentially expressed, of which 229 miRNAs were overexpressed and 302 were underexpressed. In this study, we identified five miRNAs that were already known from the literature to be significantly associated with clear cell renal cell carcinoma. In addition, we found a set of five microRNAs that had not previously associated with clear cell renal cell carcinoma.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91047498","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}

{"title":"Linkage Disequilibrium in Targeted Sequencing","authors":"D. Romanov, N. Skoblikow","doi":"10.17537/2022.17.325","DOIUrl":"https://doi.org/10.17537/2022.17.325","url":null,"abstract":"\u0000 We propose an approach for optimizing the development of gene diagnostic panels, which is based on the construction of non-equilibrium linkage maps. In the process of gene selection we essentially use genome-wide association analysis (GWAS). Whole-genome analysis of associations makes it possible to reveal the relationship of genomic variants with the studied phenotype. However, the nucleotide variants that showed the highest degree of association can only be statistically associated with the phenotype, not being the true cause of the phenotype. In this case, they may be in the block of linked inheritance with nucleotide variants that really affect the manifestation of the phenotype. The construction of maps of non-equilibrium linkage of nucleotides makes it possible to optimally determine the boundaries of linkage blocks, in which the desired variants fall. The aim of this study was to optimize the demarcation of genomic loci to create targeted panels aimed at predicting susceptibility to SARS-CoV-2 and the severity of COVID-19. The proposed method for selecting loci for a target panel, taking into account nonequilibrium linkage, makes it possible to use the phenomenon of nonequilibrium linkage in order to maximally cover the regions involved in the development of the phenotype, while simultaneously minimizing the length of these regions, and, at the same time, the cost of sequencing.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84964081","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}

{"title":"Construction of Complex Three-Dimensional Structures of the Aorta of a Particular Patient Using Finite Analytical Formulas","authors":"A. Medvedev","doi":"10.17537/2022.17.312","DOIUrl":"https://doi.org/10.17537/2022.17.312","url":null,"abstract":"\u0000 We have developed a method for constructing the geometry of a morphologically realistic human aorta, including the aortic root (Valsalva sinus), thoracic aorta, aortic arch with branches, abdominal aorta with bifurcation vessels. The creation of a three-dimensional model of the human aorta is necessary when planning surgical interventions, when performing numerical modeling of blood flow in the aorta. The anatomical structure of the aorta differs in different patients, especially in the presence of various pathologies (aneurysms, stenoses, aortic dissection). Creation of an individual human aorta model based on MRI, CT images requires time-consuming manual work of a highly computer skilled specialist. Presented is a simple method of building a 3D model of the human aorta. Initially, a 3D model of the aorta (or selected section of the aorta) of one patient is created. For this purpose, an analytical 3D model of this aorta is constructed from the raw model of the aorta. To build such an analytical aorta, it is necessary to divide the aorta into characteristic sections and specify defining parameters for each section. To build a model of another patient's aorta, a base model is taken and adjusted based on the individual features of the patient's aorta structure. At that, areas of pathology (stenoses and aneurysms) are added if necessary. Correction of the basic model requires much less time and effort than creating an aortic model of a particular patient from scratch. One of the key features of the technique is ease of use, eliminating the monotonous manual labor of building an individual patient's aorta. The resulting three-dimensional model of the aorta is fully ready for 3D modeling and printing on a 3D printer. Sections of the aorta are docked with the second order of smoothness (continuous second derivative between sections of the constructed aorta).\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"18 12 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84616570","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}

{"title":"On Classification and Taxonomy of Coronaviruses (Riboviria, Nidovirales, Coronaviridae) with Special Focus on Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV-2)","authors":"E. Mavrodiev, M. Tursky, N. E. Mavrodiev, L. Schroder, A. Laktionov, M. Ebach, D. Williams","doi":"10.17537/2022.17.289","DOIUrl":"https://doi.org/10.17537/2022.17.289","url":null,"abstract":"\u0000 Coronaviruses are highly virulent and therefore important human and veterinary pathogens worldwide. This study presents the first natural hierarchical classification of Coronaviridae. We also demonstrate a “one-step” solution to incorporate the principles of binomial (binary) nomenclature into taxonomy of Coronaviridae. We strongly support the complete rejection of the non-taxonomic category “virus” in any future taxonomic study in virology. This will aid future recognition of numerous virus species, particularly in the currently monotypic subgenus Sarbecovirus. Commenting on the nature of SARS-CoV-2, the authors emphasize that no member of the Sarbecovirus clade is an ancestor of this virus, and humans are the only natural known host. \u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73979195","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}