Mathematical Biology and Bioinformatics最新文献_第9页

Modeling of Hemodynamics in a Vascular Bioprosthesis 血管生物假体的血流动力学建模

Mathematical Biology and Bioinformatics Pub Date : 2021-02-09 DOI: 10.17537/2021.16.15

P. Onishchenko, Yu. N. Zakharov, V. Borisov, K. Klyshnikov, E. Ovcharenko, Yu. Kudravceva, Y. Shokin

引用次数: 1

Study of the Perception of Written Speech Using Functional Tomography Based On Electroencephalography Data 基于脑电图数据的功能断层扫描研究书面语言感知

Mathematical Biology and Bioinformatics Pub Date : 2021-01-11 DOI: 10.17537/2021.16.1

M. Ustinin, S. Rykunov, A. Boyko, E. Tarasov, I. V. Zhuravlev, M. Polikarpov, T. A. Ryabov, I. A. Filatov, A. Yurenya, V. Panchenko

{"title":"Study of the Perception of Written Speech Using Functional Tomography Based On Electroencephalography Data","authors":"M. Ustinin, S. Rykunov, A. Boyko, E. Tarasov, I. V. Zhuravlev, M. Polikarpov, T. A. Ryabov, I. A. Filatov, A. Yurenya, V. Panchenko","doi":"10.17537/2021.16.1","DOIUrl":"https://doi.org/10.17537/2021.16.1","url":null,"abstract":"\u0000The spectral and spatial characteristics of the electroencephalograms recorded during the perception of written speech were studied. For the experimental study, four groups were formed, each containing 100 words: words with a positive emotional rating, words with a negative emotional rating, words with concrete meanings, and words with abstract meanings. A separate experiment was conducted for each group with the subjects. Words were represented by white text on a black background, each word was presented for 1000 ms, after the presentation of the stimulus there was a pause of 500 ms. Brain activity was recorded using an electroencephalograph with 19 leads, arranged according to the 10–20 scheme. For detailed quantitative analysis of this activity, method of functional tomography of the brain, based on electroencephalography data, was used. This method is based on the Fourier transform of multichannel encephalographic data and the localization of individual spectral components. The method makes it possible to single out and stably localize in space various spectral features of the brain activity studied in experiments on speech research. The frequency band from 8 to 30 Hz was analyzed; for all spectral components in this band, the inverse problem was solved in the approximation of an equivalent current dipole in a single-layer spherical conductor, without any restrictions on the position of the source. As a result, three-dimensional maps of activity were built - the functional structures of the brain. The presentation of these functional structures on magnetic resonance imaging allows one to study the frequency and spatial characteristics of responses to various speech stimuli.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"63 4 1","pages":"1-14"},"PeriodicalIF":0.0,"publicationDate":"2021-01-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77584593","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

Correlation of the Brain Compartments in the Attention Deficit and Hyperactivity Disorder Calculated by the Method of Virtual Electrodes from Magnetic Encephalography Data 利用脑磁图数据的虚拟电极计算注意缺陷与多动障碍脑区相关性

Mathematical Biology and Bioinformatics Pub Date : 2020-12-31 DOI: 10.17537/2020.15.471

M. Ustinin, A. Boyko, S. Rykunov

{"title":"Correlation of the Brain Compartments in the Attention Deficit and Hyperactivity Disorder Calculated by the Method of Virtual Electrodes from Magnetic Encephalography Data","authors":"M. Ustinin, A. Boyko, S. Rykunov","doi":"10.17537/2020.15.471","DOIUrl":"https://doi.org/10.17537/2020.15.471","url":null,"abstract":"\u0000New method to study the correlation of the human brain compartments based on the magnetic encephalography data analysis was proposed. The time series for the correlation analysis are generated by the method of virtual electrodes. First, the multichannel time series of the subject with confirmed attention deficit and hyperactivity disorder are transformed into the functional tomogram - spatial distribution of the magnetic field sources structure on the discrete grid. This structure is provided by the inverse problem solution for all elementary oscillations, found by the Fourier transform. Each frequency produces the elementary current dipole located in the node of the 3D grid. The virtual electrode includes the part of space, producing the activity under study. The time series for this activity is obtained by the summation of the spectral power of all sources, covered by the virtual electrode. To test the method, in this article we selected ten basic compartments of the brain, including frontal lobe, parietal lobe, occipital lobe and others. Each compartment was included in the virtual electrode, obtained from the subjects' MRI. We studied the correlation between compartments in the frequency bands, corresponding to four brain rhythms: theta, alpha, beta, and gamma. The time series for each electrode were calculated for the period of 300 seconds. The correlation coefficient between power series was calculated on the 1 second epoch and then averaged. The results were represented as matrices. The method can be used to study correlations of the arbitrary parts of the brain in any spectral band.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"119 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79417099","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

RDBMS and NOSQL Based Hybrid Technology for Transcriptome Data Structuring and Processing 基于RDBMS和NOSQL的转录组数据结构和处理混合技术

Mathematical Biology and Bioinformatics Pub Date : 2020-12-28 DOI: 10.17537/2020.15.455

A. M. Mukhin, M. Genaev, D. Rasskazov, S. Lashin, D. Afonnikov

引用次数: 1

Coding Structure for the ORF1ab, S, M and N Coronavirus Genes ORF1ab、S、M和N冠状病毒基因的编码结构

Mathematical Biology and Bioinformatics Pub Date : 2020-12-25 DOI: 10.17537/2020.15.441

M. Chaley, Zh.S. Tyulko, V. Kutyrkin

{"title":"Coding Structure for the ORF1ab, S, M and N Coronavirus Genes","authors":"M. Chaley, Zh.S. Tyulko, V. Kutyrkin","doi":"10.17537/2020.15.441","DOIUrl":"https://doi.org/10.17537/2020.15.441","url":null,"abstract":"\u0000Spectral-statistical approach was applied to comparative analysis of coronavirus genomes from the four genus Alphacoronavirus, Betacoronavirus (including new SARS-CoV-2 virus), Gammacoronavirus and Deltacoronavirus. This analysis was done from the point of view of 3-regularity and latent triplet profile periodicity existence in the coding sequences of four structural genes: ORF1ab encoding transcriptase; S-gene of glycoprotein forming spikes; M-gene of membrane protein; N-gene of nucleoprotein. A whole number of the genomes analyzed was equal to 3410. Gene numbers in each of the four groups in the study respectively were the same. In the result, practically, in the CDSs of all analyzed genes of ORF1ab, S and N the latent profile triplet periodicity was revealed and high value of 3-regularity index, being a quality estimate of coding triplet structure conservation, was determined. On the contrary, for coding structure of M-genes a tendency was revealed to diffuse up to homogeneity for 60 % of the genes in the genomes of alphacoronaviruses analyzed and for 67 % of the genes of the gammacoronaviruses. Tendency of the such structure diffusion, being accompanied by decrease of 3-regularity index average value in comparison with other genes, while the triplet profile periodicity remains saved, was also noted for M-genes of SARS-CoV-2 viruses. Probably, this tendency reflects a significance of M-genes variability in coronavirus adaptation to the novel hosts of genus. Analysis of 3-profile periodicity matrices of the four groups of SARS-CoV-2 genes considered in the work, for the viruses isolated in Europe, Asia and USA, did not revealed their significant difference, that is allowing to propose a single source of this virus propagation. \u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75217721","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: 1

Conserved Peptides Recognition by Ensemble of Neural Networks for Mining Protein Data – LPMO Case Study 基于集成神经网络的蛋白质数据挖掘中的保守肽识别- LPMO案例研究

Mathematical Biology and Bioinformatics Pub Date : 2020-12-22 DOI: 10.17537/2020.15.429

G. Dotsenko, A. Dotsenko

{"title":"Conserved Peptides Recognition by Ensemble of Neural Networks for Mining Protein Data – LPMO Case Study","authors":"G. Dotsenko, A. Dotsenko","doi":"10.17537/2020.15.429","DOIUrl":"https://doi.org/10.17537/2020.15.429","url":null,"abstract":"\u0000Mining protein data is a recent promising area of modern bioinformatics. In this work, we suggested a novel approach for mining protein data – conserved peptides recognition by ensemble of neural networks (CPRENN). This approach was applied for mining lytic polysaccharide monooxygenases (LPMOs) in 19 ascomycete, 18 basidiomycete, and 18 bacterial proteomes. LPMOs are recently discovered enzymes and their mining is of high relevance for biotechnology of lignocellulosic materials. CPRENN was compared with two conventional bioinformatic methods for mining protein data – profile hidden Markov models (HMMs) search (HMMER program) and peptide pattern recognition (PPR program combined with Hotpep application). The maximum number of hypothetical LPMO amino acid sequences was discovered by HMMER. Profile HMMs search proved to be more sensitive method for mining LPMOs than conserved peptides recognition. Totally, CPRENN found 76 %, 67 %, and 65 % of hypothetical ascomycete, basidiomycete, and bacterial LPMOs discovered by HMMER, respectively. For AA9, AA10, and AA11 families which contain the major part of all LPMOs in the carbohydrate-active enzymes database (CAZy), CPRENN and PPR + Hotpep found 69–98 % and 62–95 % of amino acid sequences discovered by HMMER, respectively. In contrast with PPR + Hotpep, CPRENN possessed perfect precision and provided more complete mining of basidiomycete and bacterial LPMOs.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"11 1","pages":"429-440"},"PeriodicalIF":0.0,"publicationDate":"2020-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86661026","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

Assessing Diagnostic Accuracy of Quantitative Data in Biomedical Studies Using Descriptive Statistics and Standardized Mean Difference 使用描述性统计和标准化平均差评估生物医学研究中定量数据的诊断准确性

Mathematical Biology and Bioinformatics Pub Date : 2020-12-17 DOI: 10.17537/2020.15.416

A. A. Glazkov, D. Kulikov, P. Glazkova

{"title":"Assessing Diagnostic Accuracy of Quantitative Data in Biomedical Studies Using Descriptive Statistics and Standardized Mean Difference","authors":"A. A. Glazkov, D. Kulikov, P. Glazkova","doi":"10.17537/2020.15.416","DOIUrl":"https://doi.org/10.17537/2020.15.416","url":null,"abstract":"\u0000ROC analysis is the most used method for analyzing the diagnostic accuracy of quantitative data in biomedical research. ROC analysis generates a curve describing the frequencies of true positive and false positive results for different degrees of the analyzed variable. However, in many publications devoted to the application of quantitative diagnostic methods, this analysis is not carried out: researchers report only analysis of statistical significance for the groups difference. In meta-analyses, the estimated parameter is the effect size expressed through standardized mean difference. The article describes the approach, which allows performing ROC analysis using cumulative normal distribution functions for studied and controlling groups. The proposed approach can be used to evaluate the diagnostic accuracy of quantitative variables on the base of one of the sets of descriptive statistics (mean and standard deviation, or median and quartiles) or the value of standardized mean difference. Examples of application of the proposed approach on model data, on data from literature sources, as well as on the authors' own observations are given as an example of assessment of diagnostic accuracy of quantitative variables analyzed in the microcirculation studies in various diseases. The results presented in the article can be used by medical and biological specialists to assess the diagnostic accuracy of various quantitative variables without access to primary data.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"232 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81257930","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: 1

Rational Design of Potential Bcr-Abl Tyrosine Kinase Inhibitors by the Methods of Molecular Modeling 基于分子模拟的Bcr-Abl酪氨酸激酶抑制剂合理设计

Mathematical Biology and Bioinformatics Pub Date : 2020-12-09 DOI: 10.17537/2020.15.396

A. M. Anrdrianov, Yuri V. Kornoushenko, A. D. Karpenko, I. P. Bosko, Zh. V. Ignatovich, E. Koroleva

{"title":"Rational Design of Potential Bcr-Abl Tyrosine Kinase Inhibitors by the Methods of Molecular Modeling","authors":"A. M. Anrdrianov, Yuri V. Kornoushenko, A. D. Karpenko, I. P. Bosko, Zh. V. Ignatovich, E. Koroleva","doi":"10.17537/2020.15.396","DOIUrl":"https://doi.org/10.17537/2020.15.396","url":null,"abstract":"\u0000 Discovery of the nature of inhibiting cancer processes by small organic molecules has changed the principles of the development of drug compounds for antitumor therapy. Recent achievements in this area are associated with the design of small-molecule protein kinase inhibitors, organic compounds exhibiting directed pathogenetic action. In this study, in silico design of 38 potential anti-cancer compounds with multikinase profile was carried out based on the derivatives of 2-arylaminopyrimidine. Evaluation of inhibitory activity potential of these compounds against the native and mutant (T315I) forms of Bcr-Abl tyrosine kinase, an enzyme that plays a key role in the pathogenesis of chronic myeloid leukemia characterized by uncontrolled growth myeloid cells in peripheral blood and bone marrow, was performed using molecular modeling tools. As a result, 5 top-ranking compounds that exhibit, according to the calculated data, a high-affinity binding to the native and mutant Bcr-Abl tyrosine kinase were identified. The designed compounds were shown to form good scaffolds for the development of novel potent antitumor drugs.\u0000","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"9 1","pages":"396-415"},"PeriodicalIF":0.0,"publicationDate":"2020-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77245884","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: 1

Application of Molecular Dynamics and Monte-Carlo Methods near the Critical Points 分子动力学和蒙特卡罗方法在临界点附近的应用

Mathematical Biology and Bioinformatics Pub Date : 2020-12-09 DOI: 10.17537/2020.15.394

N. Balabaev, V. Lakhno

引用次数: 1

Transmission of Acute Respiratory Infections in a City: Agent-Based Approach 城市急性呼吸道感染的传播:基于主体的方法

Mathematical Biology and Bioinformatics Pub Date : 2020-12-08 DOI: 10.17537/2020.15.338

A. Vlad, T. E. Sannikova, A. Romanyukha

{"title":"Transmission of Acute Respiratory Infections in a City: Agent-Based Approach","authors":"A. Vlad, T. E. Sannikova, A. Romanyukha","doi":"10.17537/2020.15.338","DOIUrl":"https://doi.org/10.17537/2020.15.338","url":null,"abstract":"An incidence curve of acute respiratory infections in Moscow hasthree picks between September and April and reaches its maximum in January-February The emergence of new strains of influenza A could account for onlyone pick a year The most cases of common cold are caused by ubiquitous lowpathogenic viruses In order to simulate weekly fluctuation of incidence rate ofacute respiratory illnesses we developed an agent-based model It contains 10 millions agents with such attributes as sex, age, social status, levels of specific immune memory and lists of contacts Each agent can contact with members of its household, colleagues or classmates Through such contacts susceptible agent can be infected with one of seven circulating respiratory viruses Viruses differ in their immunologic properties and assume to present influenza A virus, influenza B virus, parainfluenza, adenovirus, coronavirus, rhinovirus and respiratory syncytial virus The rate of transmission depends on duration of contact, vulnerability of susceptible agent, infectivity of infected agent and air temperature Proposed network of social interactions proved to be sufficiently detailed as it provided good fitting for observed incidence rate including periods of school holidays and winter public holidays Additionally, the estimates of basic reproductive rate for the viruses confirm that all these viruses except new strains of influenza A are relatively harmless and unable to cause significant growth of acute respiratory infections morbidity © 2020 All Rights Reserved","PeriodicalId":53525,"journal":{"name":"Mathematical Biology and Bioinformatics","volume":"4 1","pages":"338-356"},"PeriodicalIF":0.0,"publicationDate":"2020-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85325595","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: 10