Mathematical Biology and Bioinformatics最新文献

{"title":"Changes in the Hippocampal Genes Transcriptome in Depression Model Mice upon Intranasal Exposure to M2 Macrophage Secretome Factors","authors":"E. Shevela, E. Markova, M. Knyazheva, A. Proskurina, Y. Efremov, V. Molodtsov, I. Seledtsov, A. Ostanin, S. Bogachev, N. Kolchanov, E. Chernykh","doi":"10.17537/2020.15.357","DOIUrl":"https://doi.org/10.17537/2020.15.357","url":null,"abstract":"\u0000 In the current report, the effect of bioactive compounds of the M2 macrophage secretome on transcription of hippocampal genes in mice with a depression-like condition caused by social stress has been investigated. Surgically resected hippocampus was used for mRNA isolation with following RNA sequencing procedures. Comparative analysis of transcriptomes from the control depressive mice treated with physiological saline solution and mice after intranasal administration of M2 macrophages-conditioned medium revealed that remission of the depressive-like state is associated with a significant up- and downregulation of a number of genes, which were found to participate in restoration/regulation of ATP/Adenosine balance. Among the events associated with positive changes in behavioral pattern of depressive mice, the switch of microglial environment from a pro-inflammatory phenotype to an anti-inflammatory one, and subsequent restoration of compromised cannabinoid and glutamatergic transmitter pathways has been predicted.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"17 1","pages":"357-393"},"PeriodicalIF":0.0,"publicationDate":"2020-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82779838","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":"The complexity of DNA sequences. Different approaches and definitions","authors":"V. Gusev, L. A. Miroshnichenko","doi":"10.17537/2020.15.313","DOIUrl":"https://doi.org/10.17537/2020.15.313","url":null,"abstract":"\u0000An important quantitative characteristic of symbolic sequence (texts, strings) is complexity, which reflects at the intuitive level the degree of their \"non-randomness\". A.N. Kolmogorov formulated the most general definition of complexity. He proposed measuring the complexity of an object (symbolic sequence) by the length of the shortest descriptions by which this object can be uniquely reconstructed. Since there is no program guaranteed to search for the shortest description, in practice, various algorithmic approximations considered in this paper are used for this purpose. Along with definitions of complexity, suggesting the possibility of reconstruction a sequence from its \"description\", a number of measures are considered that do not imply such restoration. They are based on the calculation of some quantitative characteristics. Of interest is not only a quantitative assessment of complexity, but also the identification and classification of structural regularities that determine its specific value. In one form or another, they are expressed in the demonstration of repetition in the broadest sense. The considered measures of complexity are conventionally divided into statistical ones that take into account the frequency of occurrence of symbols or short “words” in the text, “dictionary” ones that estimate the number of different “subwords” and “structural” ones based on the identification of long repeating fragments of text and the determination of relationships between them.\u0000Most of the methods are designed for sequences of an arbitrary linguistic nature. The special attention paid to DNA sequences, reflected in the title of the article, is due to the importance of the object, manifestations of repetition of different types, and numerous examples of using the concept of complexity in solving problems of classification and evolution of various biological objects. Local structural features found in the sliding window mode in DNA sequences are of considerable interest, since zones of low complexity in the genomes of various organisms are often associated with the regulation of basic genetic processes.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"306 1","pages":"313-337"},"PeriodicalIF":0.0,"publicationDate":"2020-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79841100","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":"Analytical Study of Non-Newtonian Reiner–Rivlin Model for Blood flow through Tapered Stenotic Artery","authors":"N. Dash, Sarita Singh","doi":"10.17537/2020.15.295","DOIUrl":"https://doi.org/10.17537/2020.15.295","url":null,"abstract":"Аbstract. Stenosis, the abnormal narrowing of artery, significantly affects dynamics of blood flow due to increasing resistance to flow of blood. Velocity of blood flow, arterial pressure distribution, wall shear stress and resistance impedance factors are altered at different degree of stenosis. Prior knowledge of flow parameters such as velocity, flow rate, pressure drop in diseased artery is acknowledged to be crucial for preventive and curative medical intervention. The present paper develops the solution of Navier – Stokes equations for conservation of mass and momentum for axis-symmetric steady state case considering constitutive relation for Reiner – Rivlin fluid. Reiner – Rivlin constitutive relation renders the conservation equations nonlinear partial differential equations. Few semi-analytical and numerical solutions are found to be reported in literature but no analytical solution. This has motivated the present research to obtain a closed-form solution considering Reiner – Rivlin constitutive relation. Solution yields an expression for axial velocity, which is utilized to obtain pressure gradient, resistance impedance and wall shear stress by considering volumetric flow rate as initial condition. The effect of viscosity, cross viscosity, flow rate, taper angle of artery and degree of stenosis on axial velocity, resistance impedance and wall shear stress are studied.","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"494 1","pages":"295-312"},"PeriodicalIF":0.0,"publicationDate":"2020-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85604324","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":"Modeling of Insect-Pathogen Dynamics with Biological Control","authors":"Sangeeta Saha, G. Samanta","doi":"10.17537/2020.15.268","DOIUrl":"https://doi.org/10.17537/2020.15.268","url":null,"abstract":"In this work, amodel is proposed to analyze the effect of wild plant species on biologically-based technologies for pest control. It is assumed that the pest species have a second food source (wild host plants) except crops. Analytical results prove that the model is well-posed as the system variables are non-negative and uniformly bounded. The permanence of the system has been verified. Equilibrium points and corresponding stability analysis have also been performed. Numerical figures have supported the fact that the interior steady state if it exists, remains stable for any transmission rate. Henceforth biological control has a stabilizing effect. Furthermore, the results prove that biological control is beneficial not only for wild plants but for crops too.","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"55 5 1","pages":"268-294"},"PeriodicalIF":0.0,"publicationDate":"2020-11-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77097696","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":"DNA Transformation, Cell Epigenetic Landscape and Open Complex Dynamics in Cancer Development","authors":"O. Naimark, Y. Bayandin, Y. Beloglazova, O. N. Gagarskich, V. Grishko, A. Nikitiuk, A. Voronina","doi":"10.17537/2020.15.251","DOIUrl":"https://doi.org/10.17537/2020.15.251","url":null,"abstract":"\u0000Statistical thermodynamics allowed the formulation of mesoscopic approach of DNA transformation in course of the excitation of collective distortion modes (denaturation bubbles) associated with hydrogen bond breaking between the base pairs. Intermediate (non-continual limit) of DNA modeling (the Peyrard-Bishop model) is combined with the field description (generalized Ginzburg-Landau approach) to analyze the dynamics of collective open complex modes associated with mesodefects in the DNA ensemble. Collective modes dynamics describes different scenario of gene expression according to statistically predicted form of out-of-equilibrium potential (epigenetic landscape) reflecting specific type criticality of “soft matter” with mesodefects (open complexes) – the structural-scaling transition. Principal difference of thermodynamics of non-continual and continual models is thermalization conditions related to thermal fluctuations responsible for the DNA breathing (localized excitation with breather dynamics) and structural-scaling parameter responsible for spinodal decomposition of out-of-equilibrium potential metastability due to generation of open complex collective modes. Open complex collective modes have the nature of self-similar solutions (breathers, auto-solitary and blow-up modes) of open complex evolution equation accounting qualitative different types of potential metastabilities. Sub-sets of collective modes represent the phase variables of attractors associated with different scenario of expression dynamics, which allows the interpretation of multistability of the epigenetic landscape and the Huang diagram of gene expression. It was shown different epigenetic pathway in attractors phase space corresponding to normal and cancer expression scenario. These scenarios were supported by laser interference microscopy of living normal and cancer cells illustrating multi- and monofractal dynamics. \u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"37 1","pages":"251-267"},"PeriodicalIF":0.0,"publicationDate":"2020-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74941130","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":"Discrete-Time Model of Seasonal Plankton Bloom","authors":"G. P. Neverova, O. Zhdanova, A. Abakumov","doi":"10.17537/2020.15.235","DOIUrl":"https://doi.org/10.17537/2020.15.235","url":null,"abstract":"\u0000 The most interesting results in modeling phytoplankton bloom were obtained based on a modification of the classical system of phytoplankton and zooplankton interaction. The modifications using delayed equations, as well as piecewise continuous functions with a delayed response to intoxication processes, made it possible to obtain adequate phytoplankton dynamics like in nature.\u0000This work develops a dynamic model of phytoplankton-zooplankton community consisting of two equations with discrete time. We use recurrent equations, which allows to describe delay in response naturally. The proposed model takes into account the phytoplankton toxicity and zooplankton response associated with phytoplankton toxicity. We use a discrete analogue of the Verhulst model to describe the dynamics of each of the species in the community under autoregulation processes. We use Holling-II type response function taking into account predator saturation to describe decrease in phytoplankton density due to its consumption by zooplankton. Growth and survival rates of zooplankton also depend on its feeding. Zooplankton mortality, caused by an increase in the toxic substances concentration with high density of zooplankton, is included in the limiting processes.\u0000An analytical and numerical study of the model proposed is made. The analysis shows that the stability loss of nontrivial fixed point corresponding to the coexistence of phytoplankton and zooplankton can occur through a cascade of period doubling bifurcations and according to the Neimark-Saker scenario leading to the appearance of quasiperiodic fluctuations as well. The proposed dynamic model of the phytoplankton and zooplankton community allows observing long-period oscillations, which is consistent with the results of field experiments. As well, the model have multistability areas, where a variation in initial conditions with the unchanged values of all model parameters can result in a shift of the current dynamic mode.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"467 1","pages":"235-250"},"PeriodicalIF":0.0,"publicationDate":"2020-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77484533","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":"Determination of the Structure of Biological Macromolecular Particles Using X-Ray Lasers. Achievements and Prospects","authors":"T. Petrova, V. Lunin","doi":"10.17537/2020.15.195","DOIUrl":"https://doi.org/10.17537/2020.15.195","url":null,"abstract":"\u0000 X-ray diffraction analysis is the main experimental approach to determining the atomic structure of biological macromolecules and their complexes. The most serious limitation of its applicability, to date, is the need to prepare a sample of the object under study in the form of a single crystal, which is caused by the extremely low intensity of rays scattered by a single molecule. The commissioning of X-ray Free-Electron Lasers with their super-powerful (by many orders of magnitude exceeding the brightness of modern synchrotrons) and ultra-short (less than 100 fs) pulse is an experimental breakthrough that allows us to expect to obtain diffraction patterns from individual biological particles and then determine their structure. The first experimental results demonstrate the fundamental possibility of such an approach and are accompanied by the publication of a significant number of articles on various aspects of the development of the method. The purpose of this article is to discuss the current state of art in this area, evaluate the results achieved and discuss the prospects for further development of the method based on the analysis of publications in the world scientific literature of recent years and the experience of work carried out by the review authors and their colleagues.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81610313","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":"Skin Lesion Classification Using Deep Learning Methods","authors":"E. Shchetinin, A. V. Demidova, D. Kulyabov, L. A. Sevastyanov","doi":"10.17537/2020.15.180","DOIUrl":"https://doi.org/10.17537/2020.15.180","url":null,"abstract":"\u0000 In this paper, we propose an approach to solving the problem of recognizing skin lesions, namely melanoma, based on the analysis of dermoscopic images using deep learning methods. For this purpose, the architecture of a deep convolutional neural network was developed, which was applied to the processing of dermoscopic images of various skin lesions contained in the HAM10000 data set. The data under study were preprocessed to eliminate noise, contamination, and change the size and format of images. In addition, since the disease classes are unbalanced, a number of transformations were performed to balance them. The data obtained in this way were divided into two classes: Melanoma and Benign. Computer experiments using the built deep neural network based on the data obtained in this way have shown that the proposed approach provides 94% accuracy on the test sample, which exceeds similar results obtained by other algorithms.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"94 1","pages":"180-194"},"PeriodicalIF":0.0,"publicationDate":"2020-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83564631","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":"The Reaction Path of Product Release in NO Detoxification at the Active Site of Truncated Hemoglobin N in MCSCF Approach","authors":"K. Simon, A. V. Tulub","doi":"10.17537/2020.15.172","DOIUrl":"https://doi.org/10.17537/2020.15.172","url":null,"abstract":"\u0000 The Multi-Configurational Self-Consistent Field approach with the geometry optimization was applied to the calculation of electronic properties of active site of heme core of truncated hemoglobin N, with the inclusion of [ONOO] functional group and two water molecules. The localized molecular orbitals are employed as a starting set. Two subspaces of full interaction have been used by the construction of MCSCF wavefunction. The first one includes 3d orbitals of iron atom, and the second contains bonding and antibonding molecular orbitals of peroxynitrite with one unshared electronic pair of the O2 fragment. The reaction is characterized by two transition states; the products are nitrate anion and one unbound water molecule. There arise an evidence of NO2 and NO radicals as the reaction products.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"42 1","pages":"172-179"},"PeriodicalIF":0.0,"publicationDate":"2020-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85115584","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":"Modeling Of Chlorophyll a Content in Microalgae Cultures","authors":"A. Lelekov, R. P. Trenkenshu","doi":"10.17537/2020.15.158","DOIUrl":"https://doi.org/10.17537/2020.15.158","url":null,"abstract":"\u0000 The work focuses on mathematical modeling of light influence mechanisms on chlorophyll a content in microalgae biomass. The well-known qualitative models are based on concepts \u0000 of synthesis and photodestructive oxidation of chlorophyll a, however the later for some microalgae species seems doubtful. We proposed an alternative approach \u0000 to modeling the light-dependent chlorophyll a content in microalgae biomass. The basic model is based on generally accepted two-stage photoautotrophic growth \u0000 of microalgae. At the first stage, during photosynthesis a reserve part of biomass is formed, from which the biosynthesis of cell structures occurs at \u0000 the second stage. Three partial solutions of the basic system of equations describing the dependence of chlorophyll a content on the external light \u0000 intensity are considered for various limiting conditions. Due to the equality of specific growth rates of formation of reserve and structural forms \u0000 of biomass, the equations obtained can be used only for turbidostat cultures. Verification of the obtained equations for Arthrospira platensis \u0000 allows us to estimate kinetic coefficients, the values of which are generally in good agreement with theoretically calculated ones. For approximate \u0000 calculations, a simple equation is proposed that shows a good agreement with experimental data for Tetraselmis viridis \u0000 (R2 = 0.98), Dunaliella tertiolecta (R2 = 0.92) and describes the results for Sceletonema costatum \u0000 and Chlorella vulgaris (R2 = 0.8) quite well. Chlorophyll a refers to structural forms of biomass. \u0000 The proportion of chlorophyll a in the structural biomass is about 2.5–3.5 %, it is a species-specific parameter.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"12 1","pages":"158-171"},"PeriodicalIF":0.0,"publicationDate":"2020-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90484021","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}