Theoretical Biology and Medical Modelling最新文献

{"title":"Relational grounding facilitates development of scientifically useful multiscale models.","authors":"C Anthony Hunt,&nbsp;Glen E P Ropella,&nbsp;Tai ning Lam,&nbsp;Andrew D Gewitz","doi":"10.1186/1742-4682-8-35","DOIUrl":"https://doi.org/10.1186/1742-4682-8-35","url":null,"abstract":"<p><p>We review grounding issues that influence the scientific usefulness of any biomedical multiscale model (MSM). Groundings are the collection of units, dimensions, and/or objects to which a variable or model constituent refers. To date, models that primarily use continuous mathematics rely heavily on absolute grounding, whereas those that primarily use discrete software paradigms (e.g., object-oriented, agent-based, actor) typically employ relational grounding. We review grounding issues and identify strategies to address them. We maintain that grounding issues should be addressed at the start of any MSM project and should be reevaluated throughout the model development process. We make the following points. Grounding decisions influence model flexibility, adaptability, and thus reusability. Grounding choices should be influenced by measures, uncertainty, system information, and the nature of available validation data. Absolute grounding complicates the process of combining models to form larger models unless all are grounded absolutely. Relational grounding facilitates referent knowledge embodiment within computational mechanisms but requires separate model-to-referent mappings. Absolute grounding can simplify integration by forcing common units and, hence, a common integration target, but context change may require model reengineering. Relational grounding enables synthesis of large, composite (multi-module) models that can be robust to context changes. Because biological components have varying degrees of autonomy, corresponding components in MSMs need to do the same. Relational grounding facilitates achieving such autonomy. Biomimetic analogues designed to facilitate translational research and development must have long lifecycles. Exploring mechanisms of normal-to-disease transition requires model components that are grounded relationally. Multi-paradigm modeling requires both hyperspatial and relational grounding.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"35"},"PeriodicalIF":0.0,"publicationDate":"2011-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-35","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30169492","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":"A reaction-diffusion model of the receptor-toxin-antibody interaction.","authors":"Vladas Skakauskas,&nbsp;Pranas Katauskis,&nbsp;Alex Skvortsov","doi":"10.1186/1742-4682-8-32","DOIUrl":"https://doi.org/10.1186/1742-4682-8-32","url":null,"abstract":"<p><strong>Background: </strong>It was recently shown that the treatment effect of an antibody can be described by a consolidated parameter which includes the reaction rates of the receptor-toxin-antibody kinetics and the relative concentration of reacting species. As a result, any given value of this parameter determines an associated range of antibody kinetic properties and its relative concentration in order to achieve a desirable therapeutic effect. In the current study we generalize the existing kinetic model by explicitly taking into account the diffusion fluxes of the species.</p><p><strong>Results: </strong>A refined model of receptor-toxin-antibody (RTA) interaction is studied numerically. The protective properties of an antibody against a given toxin are evaluated for a spherical cell placed into a toxin-antibody solution. The selection of parameters for numerical simulation approximately corresponds to the practically relevant values reported in the literature with the significant ranges in variation to allow demonstration of different regimes of intracellular transport.</p><p><strong>Conclusions: </strong>The proposed refinement of the RTA model may become important for the consistent evaluation of protective potential of an antibody and for the estimation of the time period during which the application of this antibody becomes the most effective. It can be a useful tool for in vitro selection of potential protective antibodies for progression to in vivo evaluation.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"32"},"PeriodicalIF":0.0,"publicationDate":"2011-09-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-32","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30124191","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":"Mathematical model insights into arsenic detoxification.","authors":"Sean D Lawley,&nbsp;Molly Cinderella,&nbsp;Megan N Hall,&nbsp;Mary V Gamble,&nbsp;H Frederik Nijhout,&nbsp;Michael C Reed","doi":"10.1186/1742-4682-8-31","DOIUrl":"https://doi.org/10.1186/1742-4682-8-31","url":null,"abstract":"<p><strong>Background: </strong>Arsenic in drinking water, a major health hazard to millions of people in South and East Asia and in other parts of the world, is ingested primarily as trivalent inorganic arsenic (iAs), which then undergoes hepatic methylation to methylarsonic acid (MMAs) and a second methylation to dimethylarsinic acid (DMAs). Although MMAs and DMAs are also known to be toxic, DMAs is more easily excreted in the urine and therefore methylation has generally been considered a detoxification pathway. A collaborative modeling project between epidemiologists, biologists, and mathematicians has the purpose of explaining existing data on methylation in human studies in Bangladesh and also testing, by mathematical modeling, effects of nutritional supplements that could increase As methylation.</p><p><strong>Methods: </strong>We develop a whole body mathematical model of arsenic metabolism including arsenic absorption, storage, methylation, and excretion. The parameters for arsenic methylation in the liver were taken from the biochemical literature. The transport parameters between compartments are largely unknown, so we adjust them so that the model accurately predicts the urine excretion rates of time for the iAs, MMAs, and DMAs in single dose experiments on human subjects.</p><p><strong>Results: </strong>We test the model by showing that, with no changes in parameters, it predicts accurately the time courses of urinary excretion in mutiple dose experiments conducted on human subjects. Our main purpose is to use the model to study and interpret the data on the effects of folate supplementation on arsenic methylation and excretion in clinical trials in Bangladesh. Folate supplementation of folate-deficient individuals resulted in a 14% decrease in arsenicals in the blood. This is confirmed by the model and the model predicts that arsenicals in the liver will decrease by 19% and arsenicals in other body stores by 26% in these same individuals. In addition, the model predicts that arsenic methyltransferase has been upregulated by a factor of two in this population. Finally, we also show that a modification of the model gives excellent fits to the data on arsenic metabolism in human cultured hepatocytes.</p><p><strong>Conclusions: </strong>The analysis of the Bangladesh data using the model suggests that folate supplementation may be more effective at reducing whole body arsenic than previously expected. There is almost no data on the upregulation of arsenic methyltransferase in populations chronically exposed to arsenic. Our model predicts upregulation by a factor of two in the Bangladesh population studied. This prediction should be verified since it could have important public health consequences both for treatment strategies and for setting appropriate limits on arsenic in drinking water. Our model has compartments for the binding of arsenicals to proteins inside of cells and we show that these comparments are necessary to obtain good ","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"31"},"PeriodicalIF":0.0,"publicationDate":"2011-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-31","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30102483","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":"Cancer as a dynamical phase transition.","authors":"Paul Cw Davies,&nbsp;Lloyd Demetrius,&nbsp;Jack A Tuszynski","doi":"10.1186/1742-4682-8-30","DOIUrl":"https://doi.org/10.1186/1742-4682-8-30","url":null,"abstract":"<p><p>This paper discusses the properties of cancer cells from a new perspective based on an analogy with phase transitions in physical systems. Similarities in terms of instabilities and attractor states are outlined and differences discussed. While physical phase transitions typically occur at or near thermodynamic equilibrium, a normal-to-cancer (NTC) transition is a dynamical non-equilibrium phenomenon, which depends on both metabolic energy supply and local physiological conditions. A number of implications for preventative and therapeutic strategies are outlined.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"30"},"PeriodicalIF":0.0,"publicationDate":"2011-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-30","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30100107","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":"Defining the buffering process by a triprotic acid without relying on Stewart-electroneutrality considerations.","authors":"Minhtri K Nguyen,&nbsp;Liyo Kao,&nbsp;Ira Kurtz","doi":"10.1186/1742-4682-8-29","DOIUrl":"https://doi.org/10.1186/1742-4682-8-29","url":null,"abstract":"<p><p>Upon the addition of protons to an aqueous solution, a component of the H+ load will be bound i.e. buffered. In an aqueous solution containing a triprotic acid, H+ can be bound to three different states of the acid as well as to OH- ions that are derived from the auto-ionization of H2O. In quantifying the buffering process of a triprotic acid, one must define the partitioning of H+ among the three states of the acid and also the OH- ions in solution in order to predict the equilibrium pH value. However, previous quantitative approaches that model triprotic acid titration behaviour and used to predict the equilibrium pH rely on the mathematical convenience of electroneutrality/charge balance considerations. This fact has caused confusion in the literature, and has led to the assumption that charge balance/electroneutrality is a causal factor in modulating proton buffering (Stewart formulation). However, as we have previously shown, although charge balance can be used mathematically as a convenient tool in deriving various formulae, electroneutrality per se is not a fundamental physicochemical parameter that is mechanistically involved in the underlying buffering and proton transfer reactions. The lack of distinction between a mathematical tool, and a fundamental physicochemical parameter is in part a reason for the current debate regarding the Stewart formulation of acid-base analysis. We therefore posed the following question: Is it possible to generate an equation that defines and predicts the buffering of a triprotic acid that is based only on H+ partitioning without incorporating electroneutrality in the derivation? Towards this goal, we derived our new equation utilizing: 1) partitioning of H+ buffering; 2) conservation of mass; and 3) acid-base equilibria. In validating this model, we compared the predicted equilibrium pH with the measured pH of an aqueous solution consisting of Na2HPO4 to which HCl was added. The measured pH values were in excellent agreement with the predictions of our equation. Our results provide further important evidence that one can mathematically model the chemistry of acid-base phenomenology without relying on electroneutrality (Stewart formulation) considerations.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"29"},"PeriodicalIF":0.0,"publicationDate":"2011-08-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-29","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29938312","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":"Site-specific dose-response relationships for cancer induction from the combined Japanese A-bomb and Hodgkin cohorts for doses relevant to radiotherapy.","authors":"Uwe Schneider,&nbsp;Marcin Sumila,&nbsp;Judith Robotka","doi":"10.1186/1742-4682-8-27","DOIUrl":"https://doi.org/10.1186/1742-4682-8-27","url":null,"abstract":"<p><strong>Background and purpose: </strong>Most information on the dose-response of radiation-induced cancer is derived from data on the A-bomb survivors. Since, for radiation protection purposes, the dose span of main interest is between zero and one Gy, the analysis of the A-bomb survivors is usually focused on this range. However, estimates of cancer risk for doses larger than one Gy are becoming more important for radiotherapy patients. Therefore in this work, emphasis is placed on doses relevant for radiotherapy with respect to radiation induced solid cancer.</p><p><strong>Materials and methods: </strong>For various organs and tissues the analysis of cancer induction was extended by an attempted combination of the linear-no-threshold model from the A-bomb survivors in the low dose range and the cancer risk data of patients receiving radiotherapy for Hodgkin's disease in the high dose range. The data were fitted using organ equivalent dose (OED) calculated for a group of different dose-response models including a linear model, a model including fractionation, a bell-shaped model and a plateau-dose-response relationship.</p><p><strong>Results: </strong>The quality of the applied fits shows that the linear model fits best colon, cervix and skin. All other organs are best fitted by the model including fractionation indicating that the repopulation/repair ability of tissue is neither 0 nor 100% but somewhere in between. Bone and soft tissue sarcoma were fitted well by all the models. In the low dose range beyond 1 Gy sarcoma risk is negligible. For increasing dose, sarcoma risk increases rapidly and reaches a plateau at around 30 Gy.</p><p><strong>Conclusions: </strong>In this work OED for various organs was calculated for a linear, a bell-shaped, a plateau and a mixture between a bell-shaped and plateau dose-response relationship for typical treatment plans of Hodgkin's disease patients. The model parameters (α and R) were obtained by a fit of the dose-response relationships to these OED data and to the A-bomb survivors. For any three-dimensional inhomogenous dose distribution, cancer risk can be compared by computing OED using the coefficients obtained in this work.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"27"},"PeriodicalIF":0.0,"publicationDate":"2011-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-27","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30033543","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":"Optimizing automated characterization of liver fibrosis histological images by investigating color spaces at different resolutions.","authors":"Doaa Mahmoud-Ghoneim","doi":"10.1186/1742-4682-8-25","DOIUrl":"https://doi.org/10.1186/1742-4682-8-25","url":null,"abstract":"<p><p>Texture analysis (TA) of histological images has recently received attention as an automated method of characterizing liver fibrosis. The colored staining methods used to identify different tissue components reveal various patterns that contribute in different ways to the digital texture of the image. A histological digital image can be represented with various color spaces. The approximation processes of pixel values that are carried out while converting between different color spaces can affect image texture and subsequently could influence the performance of TA. Conventional TA is carried out on grey scale images, which are a luminance approximation to the original RGB (Red, Green, and Blue) space. Currently, grey scale is considered sufficient for characterization of fibrosis but this may not be the case for sophisticated assessment of fibrosis or when resolution conditions vary. This paper investigates the accuracy of TA results on three color spaces, conventional grey scale, RGB, and Hue-Saturation-Intensity (HSI), at different resolutions. The results demonstrate that RGB is the most accurate in texture classification of liver images, producing better results, most notably at low resolution. Furthermore, the green channel, which is dominated by collagen fiber deposition, appears to provide most of the features for characterizing fibrosis images. The HSI space demonstrated a high percentage error for the majority of texture methods at all resolutions, suggesting that this space is insufficient for fibrosis characterization. The grey scale space produced good results at high resolution; however, errors increased as resolution decreased.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"25"},"PeriodicalIF":0.0,"publicationDate":"2011-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-25","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30006045","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":"A biochemical hypothesis on the formation of fingerprints using a turing patterns approach.","authors":"Diego A Garzón-Alvarado,&nbsp;Angelica M Ramírez Martinez","doi":"10.1186/1742-4682-8-24","DOIUrl":"https://doi.org/10.1186/1742-4682-8-24","url":null,"abstract":"<p><strong>Background: </strong>Fingerprints represent a particular characteristic for each individual. Characteristic patterns are also formed on the palms of the hands and soles of the feet. Their origin and development is still unknown but it is believed to have a strong genetic component, although it is not the only thing determining its formation. Each fingerprint is a papillary drawing composed by papillae and rete ridges (crests). This paper proposes a phenomenological model describing fingerprint pattern formation using reaction diffusion equations with Turing space parameters.</p><p><strong>Results: </strong>Several numerical examples were solved regarding simplified finger geometries to study pattern formation. The finite element method was used for numerical solution, in conjunction with the Newton-Raphson method to approximate nonlinear partial differential equations.</p><p><strong>Conclusions: </strong>The numerical examples showed that the model could represent the formation of different types of fingerprint characteristics in each individual.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"24"},"PeriodicalIF":0.0,"publicationDate":"2011-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-24","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29969145","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":"A nucleotide binding rectification Brownian ratchet model for translocation of Y-family DNA polymerases.","authors":"Ping Xie","doi":"10.1186/1742-4682-8-22","DOIUrl":"https://doi.org/10.1186/1742-4682-8-22","url":null,"abstract":"<p><p>Y-family DNA polymerases are characterized by low-fidelity synthesis on undamaged DNA and ability to catalyze translesion synthesis over the damaged DNA. Their translocation along the DNA template is an important event during processive DNA synthesis. In this work we present a Brownian ratchet model for this translocation, where the directed translocation is rectified by the nucleotide binding to the polymerase. Using the model, different features of the available structures for Dpo4, Dbh and polymerase ι in binary and ternary forms can be easily explained. Other dynamic properties of the Y-family polymerases such as the fast translocation event upon dNTP binding for Dpo4 and the considerable variations of the processivity among the polymerases can also be well explained by using the model. In addition, some predicted results of the DNA synthesis rate versus the external force acting on Dpo4 and Dbh polymerases are presented. Moreover, we compare the effect of the external force on the DNA synthesis rate of the Y-family polymerase with that of the replicative DNA polymerase.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"22"},"PeriodicalIF":0.0,"publicationDate":"2011-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-22","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29959740","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":"Review and application of group theory to molecular systems biology.","authors":"Edward A Rietman,&nbsp;Robert L Karp,&nbsp;Jack A Tuszynski","doi":"10.1186/1742-4682-8-21","DOIUrl":"https://doi.org/10.1186/1742-4682-8-21","url":null,"abstract":"<p><p>In this paper we provide a review of selected mathematical ideas that can help us better understand the boundary between living and non-living systems. We focus on group theory and abstract algebra applied to molecular systems biology. Throughout this paper we briefly describe possible open problems. In connection with the genetic code we propose that it may be possible to use perturbation theory to explore the adjacent possibilities in the 64-dimensional space-time manifold of the evolving genome. With regards to algebraic graph theory, there are several minor open problems we discuss. In relation to network dynamics and groupoid formalism we suggest that the network graph might not be the main focus for understanding the phenotype but rather the phase space of the network dynamics. We show a simple case of a C6 network and its phase space network. We envision that the molecular network of a cell is actually a complex network of hypercycles and feedback circuits that could be better represented in a higher-dimensional space. We conjecture that targeting nodes in the molecular network that have key roles in the phase space, as revealed by analysis of the automorphism decomposition, might be a better way to drug discovery and treatment of cancer.</p>","PeriodicalId":51195,"journal":{"name":"Theoretical Biology and Medical Modelling","volume":" ","pages":"21"},"PeriodicalIF":0.0,"publicationDate":"2011-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/1742-4682-8-21","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29956838","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}