Theoretical Biology and Medical Modelling最新文献

{"title":"An outbreak vector-host epidemic model with spatial structure: the 2015-2016 Zika outbreak in Rio De Janeiro.","authors":"W E Fitzgibbon,&nbsp;J J Morgan,&nbsp;G F Webb","doi":"10.1186/s12976-017-0051-z","DOIUrl":"https://doi.org/10.1186/s12976-017-0051-z","url":null,"abstract":"<p><strong>Background: </strong>A deterministic model is developed for the spatial spread of an epidemic disease in a geographical setting. The disease is borne by vectors to susceptible hosts through criss-cross dynamics. The model is focused on an outbreak that arises from a small number of infected hosts imported into a subregion of the geographical setting. The goal is to understand how spatial heterogeneity of the vector and host populations influences the dynamics of the outbreak, in both the geographical spread and the final size of the epidemic.</p><p><strong>Methods: </strong>Partial differential equations are formulated to describe the spatial interaction of the hosts and vectors. The partial differential equations have reaction-diffusion terms to describe the criss-cross interactions of hosts and vectors. The partial differential equations of the model are analyzed and proven to be well-posed. A local basic reproduction number for the epidemic is analyzed.</p><p><strong>Results: </strong>The epidemic outcomes of the model are correlated to the spatially dependent parameters and initial conditions of the model. The partial differential equations of the model are adapted to seasonality of the vector population, and applied to the 2015-2016 Zika seasonal outbreak in Rio de Janeiro Municipality in Brazil.</p><p><strong>Conclusions: </strong>The results for the model simulations of the 2015-2016 Zika seasonal outbreak in Rio de Janeiro Municipality indicate that the spatial distribution and final size of the epidemic at the end of the season are strongly dependent on the location and magnitude of local outbreaks at the beginning of the season. The application of the model to the Rio de Janeiro Municipality Zika 2015-2016 outbreak is limited by incompleteness of the epidemic data and by uncertainties in the parametric assumptions of the model.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-017-0051-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34859373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling multi-mutation and drug resistance: analysis of some case studies.","authors":"Mitra Shojania Feizabadi","doi":"10.1186/s12976-017-0052-y","DOIUrl":"https://doi.org/10.1186/s12976-017-0052-y","url":null,"abstract":"<p><strong>Background: </strong>Drug-induced resistance is one the major obstacles that may lead to therapeutic failure during cancer treatment. Different genetic alterations occur when tumor cells divide. Among new generations of tumor cells, some may express intrinsic resistance to a specific chemotherapeutic agent. Also, some tumor cells may carry a gene that can develop resistance induced by the therapeutic drug. The methods by which the therapeutic approaches need to be revised in the occurrence of drug induced resistance is still being explored. Previously, we introduced a model that expresses only intrinsic drug resistance in a conjoint normal-tumor cell setting. The focus of this work is to expand our previously reported model to include terms that can express both intrinsic drug resistance and drug-induced resistance. Additionally, we assess the response of the cell population as a function of time under different treatment strategies and discuss the outcomes.</p><p><strong>Methods: </strong>The model introduced is expressed in the format of coupled differential equations which describe the growth pattern of the cells. The dynamic of the cell populations is simulated under different treatment cases. All computational simulations were executed using Mathematica v7.0.</p><p><strong>Results: </strong>The outcome of the simulations clearly demonstrates that while some therapeutic strategies can overcome or control the intrinsic drug resistance, they may not be effective, and are even to some extent damaging, if the administered drug creates resistance by itself.</p><p><strong>Conclusion: </strong>In the present study, the evolution of the cells in a conjoint setting, when the system expresses both intrinsic and induced resistance, is mathematically modeled. Followed by a set of computer simulations, the different growing patterns that can be created based on choices of therapy were examined. The model can still be improved by considering other factors including, but not limited to, the nature of the cancer growth, the level of toxicity that the body can tolerate, or the strength of the patient's immune system.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-017-0052-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34842254","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"High resolution hemodynamic profiling of murine arteriovenous fistula using magnetic resonance imaging and computational fluid dynamics.","authors":"Daniel Pike,&nbsp;Yan-Ting Shiu,&nbsp;Maheshika Somarathna,&nbsp;Lingling Guo,&nbsp;Tatyana Isayeva,&nbsp;John Totenhagen,&nbsp;Timmy Lee","doi":"10.1186/s12976-017-0053-x","DOIUrl":"https://doi.org/10.1186/s12976-017-0053-x","url":null,"abstract":"<p><strong>Background: </strong>Arteriovenous fistula (AVF) maturation failure remains a major cause of morbidity and mortality in hemodialysis patients. The two major etiologies of AVF maturation failure are early neointimal hyperplasia development and persistent inadequate outward remodeling. Although hemodynamic changes following AVF creation may impact AVF remodeling and contribute to neointimal hyperplasia development and impaired outward remodeling, detailed AVF hemodynamics are not yet fully known. Since murine AVF models are valuable tools for investigating the pathophysiology of AVF maturation failure, there is a need for a new approach that allows the hemodynamic characterization of murine AVF at high resolutions.</p><p><strong>Methods: </strong>This methods paper presents a magnetic resonance imaging (MRI)-based computational fluid dynamic (CFD) method that we developed to rigorously quantify the evolving hemodynamic environment in murine AVF. The lumen geometry of the entire murine AVF was reconstructed from high resolution, non-contrast 2D T2-weighted fast spin echo MRI sequence, and the flow rates of the AVF inflow and outflow were extracted from a gradient echo velocity mapping sequence. Using these MRI-obtained lumen geometry and inflow information, CFD modeling was performed and used to calculate blood flow velocity and hemodynamic factors at high resolutions (on the order of 0.5 μm spatially and 0.1 ms temporally) throughout the entire AVF lumen. We investigated both the wall properties (including wall shear stress (WSS), wall shear stress spatial gradient, and oscillatory shear index (OSI)) and the volumetric properties (including vorticity, helicity, and Q-criterion).</p><p><strong>Results: </strong>Our results demonstrate increases in AVF flow velocity, WSS, spatial WSS gradient, and OSI within 3 weeks post-AVF creation when compared to pre-surgery. We also observed post-operative increases in flow disturbances and vortices, as indicated by increased vorticity, helicity, and Q-criterion.</p><p><strong>Conclusions: </strong>This novel protocol will enable us to undertake future mechanistic studies to delineate the relationship between hemodynamics and AVF development and characterize biological mechanisms that regulate local hemodynamic factors in transgenic murine AVF models.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-017-0053-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34835363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Method for generating multiple risky barcodes of complex diseases using ant colony algorithm","authors":"Xiong Li, Wen Jiang","doi":"10.1186/s12976-017-0050-0","DOIUrl":"https://doi.org/10.1186/s12976-017-0050-0","url":null,"abstract":"","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87589452","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 role of mobility and health disparities on the transmission dynamics of Tuberculosis","authors":"Victor M. Moreno, B. Espinoza, K. Barley, Marlio Paredes, Derdei Bichara, A. Mubayi, C. Castillo-Chavez","doi":"10.1186/s12976-017-0049-6","DOIUrl":"https://doi.org/10.1186/s12976-017-0049-6","url":null,"abstract":"","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-017-0049-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65719652","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":"Thermodynamic considerations in renal separation processes.","authors":"Robert H Louw, David M Rubin, David Glasser, Robyn F R Letts, Diane Hildebrandt","doi":"10.1186/s12976-017-0048-7","DOIUrl":"10.1186/s12976-017-0048-7","url":null,"abstract":"<p><strong>Background: </strong>Urine production in the kidney is generally thought to be an energy-intensive process requiring large amounts of metabolic activity to power active transport mechanisms. This study uses a thermodynamic analysis to evaluate the minimum work requirements for urine production in the human kidney and provide a new perspective on the energy costs of urine production. In this study, black-box models are used to compare the Gibbs energy inflow and outflow of the overall kidney and physiologically-based subsections in the kidney, to calculate the work of separation for urine production.</p><p><strong>Results: </strong>The results describe the work done during urine production broadly and for specific scenarios. Firstly, it shows glomerular filtration in both kidneys requires work to be done at a rate of 5 mW under typical conditions in the kidney. Thereafter, less than 54 mW is sufficient to concentrate the filtrate into urine, even in the extreme cases considered. We have also related separation work in the kidney with the excretion rates of individual substances, including sodium, potassium, urea and water. Lastly, the thermodynamic calculations indicate that plasma dilution significantly reduces the energy cost of separating urine from blood.</p><p><strong>Conclusions: </strong>A comparison of these thermodynamic results with physiological reference points, elucidates how various factors affect the energy cost of the process. Surprisingly little energy is required to produce human urine, seeing that double the amount of work can theoretically be done with all the energy provided through pressure drop of blood flow through the kidneys, while the metabolic energy consumption of the kidneys could possibly drive almost one hundred times more separation work. Nonetheless, the model's outputs, which are summarised graphically, show the separation work's nuances, which can be further analysed in the context of more empirical evidence.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2017-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-017-0048-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85508758","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Estimating the subcritical transmissibility of the Zika outbreak in the State of Florida, USA, 2016","authors":"Linh Dinh, G. Chowell, K. Mizumoto, H. Nishiura","doi":"10.1186/s12976-016-0046-1","DOIUrl":"https://doi.org/10.1186/s12976-016-0046-1","url":null,"abstract":"","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-016-0046-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"65719600","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":"Erratum to: 'Comparison of calculated and experimental power in maximal lactate-steady state during cycling'.","authors":"Thomas Hauser,&nbsp;Jennifer Adam,&nbsp;Henry Schulz","doi":"10.1186/s12976-016-0044-3","DOIUrl":"https://doi.org/10.1186/s12976-016-0044-3","url":null,"abstract":"","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-016-0044-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34428456","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Feed-forward neural network model for hunger and satiety related VAS score prediction.","authors":"Shaji Krishnan,&nbsp;Henk F J Hendriks,&nbsp;Merete L Hartvigsen,&nbsp;Albert A de Graaf","doi":"10.1186/s12976-016-0043-4","DOIUrl":"https://doi.org/10.1186/s12976-016-0043-4","url":null,"abstract":"<p><strong>Background: </strong>An artificial neural network approach was chosen to model the outcome of the complex signaling pathways in the gastro-intestinal tract and other peripheral organs that eventually produce the satiety feeling in the brain upon feeding.</p><p><strong>Methods: </strong>A multilayer feed-forward neural network was trained with sets of experimental data relating concentration-time courses of plasma satiety hormones to Visual Analog Scales (VAS) scores. The network successfully predicted VAS responses from sets of satiety hormone data obtained in experiments using different food compositions.</p><p><strong>Results: </strong>The correlation coefficients for the predicted VAS responses for test sets having i) a full set of three satiety hormones, ii) a set of only two satiety hormones, and iii) a set of only one satiety hormone were 0.96, 0.96, and 0.89, respectively. The predicted VAS responses discriminated the satiety effects of high satiating food types from less satiating food types both in orally fed and ileal infused forms.</p><p><strong>Conclusions: </strong>From this application of artificial neural networks, one may conclude that neural network models are very suitable to describe situations where behavior is complex and incompletely understood. However, training data sets that fit the experimental conditions need to be available.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-07-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s12976-016-0043-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34644246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Long range physical cell-to-cell signalling via mitochondria inside membrane nanotubes: a hypothesis.","authors":"Felix Scholkmann","doi":"10.1186/s12976-016-0042-5","DOIUrl":"10.1186/s12976-016-0042-5","url":null,"abstract":"<p><p>Coordinated interaction of single cells by cell-to-cell communication (signalling) enables complex behaviour necessary for the functioning of multicellular organisms. A quite newly discovered cell-to-cell signalling mechanism relies on nanotubular cell-co-cell connections, termed \"membrane nanotubes\" (MNTs). The present paper presents the hypothesis that mitochondria inside MNTs can form a connected structure (mitochondrial network) which enables the exchange of energy and signals between cells. It is proposed that two modes of energy and signal transmission may occur: electrical/electrochemical and electromagnetic (optical). Experimental work supporting the hypothesis is reviewed, and suggestions for future research regarding the discussed topic are given.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-06-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4896004/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34616164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}