Journal of Theoretical Biology最新文献

{"title":"Resource budget model with Duffing oscillator for dynamics of synchronized biennial-bearing olives in the Levant","authors":"Eileen Joan Magero ,&nbsp;Koichi Unami ,&nbsp;Osama Mohawesh ,&nbsp;Marie Sato","doi":"10.1016/j.jtbi.2024.111973","DOIUrl":"10.1016/j.jtbi.2024.111973","url":null,"abstract":"<div><div>We develop and analyze a temporally continuous spatially lumped resource budget model to explain the dynamics of synchronized biennial-bearing olives in the Levant, specifically focusing on Syria, the region’s foremost olive-producing country. The model is a time-continuous counterpart of the celebrated resource budget model. It consists of a Duffing oscillator coupled with a dynamical model of pollination with an external force propelling olive growth by photosynthesis. The reference data are obtained from statistical databases of international organizations and our own observation systems in Jordan, a country neighboring Syria, providing a wealth of information to refine the model structure. An intensive review of Syria’s modern history involving significant shifts in agricultural policy and social stability leads to a conclusion that the model should comprehend the anomaly of olive yield interacting with socio-political factors as an autonomous behavior. The conventional mathematical methodology analyzes the model’s characteristics, such as solutions’ non-negativity, boundedness, and stability. The system is stable during pollination off-season but may become unstable and unbounded during pollination on-season, which is a property that the time-discrete resource budget model cannot reproduce. A significant finding is that coupling individual fruit trees by anemophily is not essential in synchronization, overturning earlier studies in the literature. The values of model parameters that best fit the historical data of olive yield in Syria result in bounded chaos. With alternative parameter values, the model could exhibit periodic oscillation, instability, or blowing up, as clearly shown in bifurcation diagrams.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111973"},"PeriodicalIF":1.9,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Use of 3D chaos game representation to quantify DNA sequence similarity with applications for hierarchical clustering","authors":"Stephanie Young ,&nbsp;Jérôme Gilles","doi":"10.1016/j.jtbi.2024.111972","DOIUrl":"10.1016/j.jtbi.2024.111972","url":null,"abstract":"<div><div>A 3D chaos game is shown to be a useful way for encoding DNA sequences. Since matching subsequences in DNA converge in space in 3D chaos game encoding, a DNA sequence’s 3D chaos game representation can be used to compare DNA sequences without prior alignment and without truncating or padding any of the sequences. Two proposed methods inspired by shape-similarity comparison techniques show that this form of encoding can perform as well as alignment-based techniques for building phylogenetic trees. The first method uses the volume overlap of intersecting spheres and the second uses shape signatures by summarizing the coordinates, oriented angles, and oriented distances of the 3D chaos game trajectory. The methods are tested using: (1) the first exon of the beta-globin gene for 11 species, (2) mitochondrial DNA from four groups of primates, and (3) a set of synthetic DNA sequences. Simulations show that the proposed methods produce distances that reflect the number of mutation events; additionally, on average, distances resulting from deletion mutations are comparable to those produced by substitution mutations.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111972"},"PeriodicalIF":1.9,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481172","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mathematical model of repressive response to collective action and protest waves","authors":"V. Volpert","doi":"10.1016/j.jtbi.2024.111970","DOIUrl":"10.1016/j.jtbi.2024.111970","url":null,"abstract":"<div><div>The intricate interplay between the state and society may foster opposition and prompt collective action as a mode of protest. When the state responds repressively to such collective action, it aims to undermine it escalating its costs. A mathematical model relating the repressive response to collective action, articulated through differential equations, facilitates a thorough analysis of their dynamic interaction. Modelling outcomes indicate that repressive regimes may exhibit sustained persistence, oscillatory patterns, or destabilization, potentially transitioning into alternative regimes. This modelling framework offers a means to discern the impact of diverse factors on the dynamics of repressive regimes and to provide modelling insight on the emergence of cycles of protest observed in different countries during certain periods of their history.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111970"},"PeriodicalIF":1.9,"publicationDate":"2024-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481169","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"JTB Editorial for Professor Denise Kirschner","authors":"Mark Chaplain (Journal of Theoretical Biology co-Chief Editor),&nbsp;Akira Sasaki (Journal of Theoretical Biology co-Chief Editor),&nbsp;Joshua Weitz (Journal of Theoretical Biology co-Chief Editor)","doi":"10.1016/j.jtbi.2024.111976","DOIUrl":"10.1016/j.jtbi.2024.111976","url":null,"abstract":"","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111976"},"PeriodicalIF":1.9,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Probabilistic analysis of tumor growth inhibition models to Support trial design","authors":"Marcus Baaz ,&nbsp;Tim Cardilin ,&nbsp;Torbjörn Lundh ,&nbsp;Mats Jirstrand","doi":"10.1016/j.jtbi.2024.111969","DOIUrl":"10.1016/j.jtbi.2024.111969","url":null,"abstract":"<div><div>A large enough sample size of patients is required to statistically show that one treatment is better than another. However, too large a sample size is expensive and can also result in findings that are statistically significant, but not clinically relevant. How sample sizes should be chosen is a well-studied problem in classical statistics and analytical expressions can be derived from the appropriate test statistic. However, these expressions require information regarding the efficacy of the treatment, which may not be available, particularly for newly developed drugs. Tumor growth inhibition (TGI) models are frequently used to quantify the efficacy of newly developed anticancer drugs. In these models, the tumor growth dynamics are commonly described by a set of ordinary differential equations containing parameters that must be estimated using experimental data.</div><div>One widely used endpoint in clinical trials is the proportion of patients in different response categories determined using the Response Evaluation Criteria In Solid Tumors (RECIST) framework. From the TGI model, we derive analytical expressions for the probability of patient response to combination therapy. The probabilistic expressions are used together with classical statistics to derive a parametric model for the sample size required to achieve a certain significance level and test power when comparing two treatments.</div><div>Furthermore, the probabilistic expressions are used to generalize the Tumor Static Exposure concept to be more suitable for predicting clinical response. The derivatives of the probabilistic expressions are used to derive two additional expressions characterizing the exposure and its sensitivity. Finally, our results are illustrated using parameters obtained from calibrating the model to preclinical data.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111969"},"PeriodicalIF":1.9,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481170","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A bulk-surface mechanobiochemical modelling approach for single cell migration in two-space dimensions","authors":"David Hernandez-Aristizabal ,&nbsp;Diego-Alexander Garzon-Alvarado ,&nbsp;Carlos-Alberto Duque-Daza ,&nbsp;Anotida Madzvamuse","doi":"10.1016/j.jtbi.2024.111966","DOIUrl":"10.1016/j.jtbi.2024.111966","url":null,"abstract":"<div><div>In this work, we present a mechanobiochemical model for two-dimensional cell migration which couples mechanical properties of the cell cytosol with biochemical processes taking place near or on the cell plasma membrane. The modelling approach is based on a recently developed mathematical formalism of evolving bulk-surface partial differential equations of reaction–diffusion type. We solve these equations using finite element methods within a moving-mesh framework derived from the weak formulation of the evolving bulk-surface PDEs. In the present work, the cell cytosol interior (bulk) dynamics are coupled to the cell membrane (surface) dynamics through non-homogeneous Dirichlet boundary conditions. The modelling approach exhibits both directed cell migration in response to chemical cues as well as spontaneous migration in the absence of such cues. As a by-product, the approach shows fundamental characteristics associated with single cell migration such as: (i) cytosolic and membrane polarisation, (ii) actin dependent protrusions, and (iii) continuous shape deformation of the cell during migration.</div><div>Cell migration is an ubiquitous process in life that is mainly triggered by the dynamics of the actin cytoskeleton and therefore is driven by both mechanical and biochemical processes. It is a multistep process essential for mammalian organisms and is closely linked to a vast diversity of processes; from embryonic development to cancer invasion. Experimental, theoretical and computational studies have been key to elucidate the mechanisms underlying cell migration. On one hand, rapid advances in experimental techniques allow for detailed experimental measurements of cell migration pathways, while, on the other, computational approaches allow for the modelling, analysis and understanding of such observations. The bulk-surface mechanobiochemical modelling approach presented in this work, set premises to study single cell migration through complex non-isotropic environments in two- and three-space dimensions.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111966"},"PeriodicalIF":1.9,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481167","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bayesian parameter inference for epithelial mechanics","authors":"Xin Yan ,&nbsp;Goshi Ogita ,&nbsp;Shuji Ishihara ,&nbsp;Kaoru Sugimura","doi":"10.1016/j.jtbi.2024.111960","DOIUrl":"10.1016/j.jtbi.2024.111960","url":null,"abstract":"<div><div>Cell-based mechanical models, such as the Cell Vertex Model (CVM), have proven useful for studying the mechanical control of epithelial tissue dynamics. We recently developed a statistical method called image-based parameter inference for formulating CVM model functions and estimating their parameters from image data of epithelial tissues. In this study, we employed Bayesian statistics to improve the utility and flexibility of image-based parameter inference. Tests on synthetic data confirmed that both our non-hierarchical and hierarchical Bayesian models provide accurate estimates of model parameters. By applying this method to <em>Drosophila</em> wings, we demonstrated that the reliability of parameter estimation is closely linked to the mechanical anisotropies present in the tissue. Moreover, we revealed that the cortical elasticity term is dispensable for explaining force-shape correlations <em>in vivo</em>. We anticipate that the flexibility of the Bayesian statistical framework will facilitate the integration of various types of information, thereby contributing to the quantitative dissection of the mechanical control of tissue dynamics.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111960"},"PeriodicalIF":1.9,"publicationDate":"2024-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142481173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Choice of landscape discretisation method affects the inferred rate of spread in wildlife disease spread models","authors":"Mossa Merhi Reimert,&nbsp;Maya Katrin Gussmann,&nbsp;Anette Ella Boklund,&nbsp;Matt Denwood","doi":"10.1016/j.jtbi.2024.111963","DOIUrl":"10.1016/j.jtbi.2024.111963","url":null,"abstract":"<div><div>Disease modelling at the livestock-wildlife interface is an important topic for which discrete-space models are used for the wildlife component. One prominent example is African Swine Fever, where wild boar play an influential role as reservoirs of disease spillover into domestic pig farms. In this paper, we present a simulation study that demonstrates the impact of seemingly arbitrary choices of landscape discretisation method on the inferred rate of spread within the model. We use an ordinary differential equation model to implement a simplified model of disease transmission between discrete groups of wild boar with spillover into domestic pig farms contained within a homogeneous landscape. We examine a range of scenarios whereby the landscape is discretised into wild boar patches of varying size and shape, and compare the rate of spread between domestic pig farms placed at fixed points on the landscape. Our results demonstrate a non-monotonic relationship between patch size and rate of spread, which is particularly unstable and unpredictable for square and triangular shaped patches. Discretisation of the landscape into hexagons appears to produce a more stable relationship between patch size and rate of spread for the three types of transmission kernel we investigated. Although the rate of disease spread does converge to a stable value, this occurs at patch sizes that are much smaller than would be used in practice for wild boar. We conclude that outputs of disease models containing a wildlife component should not be considered to be robust to arbitrary choices for patch size and placement, but rather as a source of uncertainty to be examined using sensitivity analysis. Furthermore, we strongly recommend the use of hexagons rather than squares or right triangles for landscape discretisation.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"596 ","pages":"Article 111963"},"PeriodicalIF":1.9,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142402022","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"An immuno-epidemiological model with non-exponentially distributed disease stage on complex networks","authors":"Junyuan Yang ,&nbsp;Xinyi Duan ,&nbsp;Guiquan Sun","doi":"10.1016/j.jtbi.2024.111964","DOIUrl":"10.1016/j.jtbi.2024.111964","url":null,"abstract":"<div><div>Most of epidemic models assume that duration of the disease phase is distributed exponentially for the simplification of model formulation and analysis. Actually, the exponentially distributed assumption on the description of disease stages is hard to accurately approximate the interplay of drug concentration and viral load within host. In this article, we formulate an immuno-epidemiological epidemic model on complex networks, which is composed of ordinary differential equations and integral equations. The linkage of within- and between-host is connected by setting that the death caused by the disease is an increasing function in viral load within host. Mathematical analysis of the model includes the existence of the solution to the epidemiological model on complex networks, the existence and stability of equilibrium, which are completely determined by the basic reproduction number of the between-host system. Numerical analysis are shown that the non-exponentially distributions and the topology of networks have significant roles in the prediction of epidemic patterns.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111964"},"PeriodicalIF":1.9,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142401942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A model for transcription-dependent R-loop formation at double-stranded DNA breaks: Implications for their detection and biological effects","authors":"Boris P. Belotserkovskii,&nbsp;Philip C. Hanawalt","doi":"10.1016/j.jtbi.2024.111962","DOIUrl":"10.1016/j.jtbi.2024.111962","url":null,"abstract":"<div><div>R-loops are structures containing an RNA-DNA duplex and an unpaired DNA strand. During R-loop formation an RNA strand invades the DNA duplex, displacing the homologous DNA strand and binding the complementary DNA strand. Here we analyze a model for transcription-dependent R-loop formation at double-stranded DNA breaks (DSBs). In this model, R-loop formation is preceded by detachment of the non-template DNA strand from the RNA polymerase (RNAP). Then, strand exchange is initiated between the nascent RNA and the non-template DNA strand. During that strand exchange the length of the R-loop could either increase, or decrease in a biased random-walk fashion, in which the bias would depend upon the DNA sequence. Eventually, the restoration of the DNA duplex would completely displace the RNA. However, as long as the RNAP remains bound to the template DNA strand it prevents that displacement. Thus, according to the model, RNAPs stalled at DSBs can increase the lifespan of R-loops, increasing their detectability in experiments, and perhaps enhancing their biological effects.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111962"},"PeriodicalIF":1.9,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142395390","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"数学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}