Journal of Theoretical Biology最新文献

{"title":"Effect of inosine on recurrence of tumor after radiation therapy: A mathematical investigation","authors":"K.S. Yadav ,&nbsp;Gopinath Sadhu","doi":"10.1016/j.jtbi.2025.112138","DOIUrl":"10.1016/j.jtbi.2025.112138","url":null,"abstract":"<div><div>Tumor invasion that marks the transition from localized growth to aggressive spread is critical in cancer biology. It involves the breakdown of surrounding tissues through matrix degradation enzymes, such as urokinase plasminogen activator and matrix metalloproteinases, to promote cancer cells migration. Understanding invasion pathways is crucial for developing effective therapies and improving patient outcomes. There is a significant progress in cancer treatments; however, the treatments such as radiotherapy and chemotherapy are ineffective many times in the sense that some cancer cells survive, leading to tumor recurrence. It has been observed that dead cells play a key role in cancer recurrence. The dead cells, particularly due to treatments like radiation or chemotherapy, release signals and cellular components, including nucleotides like inosine, cytokines, and growth factors. These factors influence the tumor microenvironment and promote the survival and proliferation of nearby cancer cells. In this article, a novel mathematical model is proposed to investigate the effects of inosine on tumor recurrence and invasion. The simulated results are in very good agreement with the experimental and numerical results of the literature. The model simulated the inosine generation after some time of radiotherapy treatment withdrawal, and it achieves a log-normal profile. In line of experimental observations, it is obtained that the cancer cells proliferate with usual proliferation but once inosine gets generated from the dead cells, the proliferation intensity of cancer cells is enhanced significantly.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"609 ","pages":"Article 112138"},"PeriodicalIF":1.9,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144000022","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":"Mutant emergence timing and population immunisation status impact epidemiological dynamics","authors":"Bastien Reyné ,&nbsp;Ramsès Djidjou-Demasse ,&nbsp;Mircea T. Sofonea ,&nbsp;Samuel Alizon","doi":"10.1016/j.jtbi.2025.112140","DOIUrl":"10.1016/j.jtbi.2025.112140","url":null,"abstract":"<div><div>A key question in evolutionary epidemiology is to determine differences in the conditions that may allow some mutant strains to spread in a population where a resident strain is already circulating. Evolutionary invasion analyses assume that the immunity is long-lasting for previously infected individuals making it difficult to study traits such as immune escape. We relax this last assumption and allow the environment faced by the mutant to fluctuate outside of any epidemiological equilibrium. We introduce an original two-strains non-Markovian model that accounts for realistic immunity waning and cross-immunity, inspired by the case of SARS-CoV-2 variants. We show that mutants with increased contagiousness or with some immune escape abilities are more likely to invade the population. We also show that the timing of the introduction of mutant strain in the population is key because it is associated with the population’s immunisation status. Our results underline the importance of immune waning and non-equilibrium dynamics on infectious disease evolution.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"608 ","pages":"Article 112140"},"PeriodicalIF":1.9,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143949024","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":"Biased tertiary sex ratios enhance the efficacy of sex-ratio distorting genetic techniques to control invasive species","authors":"Michael L. Jones ,&nbsp;Ronald E. Thresher ,&nbsp;Nicholas J. Bax","doi":"10.1016/j.jtbi.2025.112137","DOIUrl":"10.1016/j.jtbi.2025.112137","url":null,"abstract":"<div><div>Genetic biocontrol strategies are increasingly being developed and tested for reducing the effects of invasive species, and are highly likely to be an important tool of integrated pest management in the future. Included among such strategies are those that distort the sex ratio of the target species. Models used to forecast the efficacy of such strategies generally assume, implicitly, that the tertiary sex ratio of the target population is 50:50. We present evidence that this assumption is important, and that if the tertiary sex ratio is biased towards females, a sex-distorting construct introduced into the population that produces phenotypic males will become fixed at a level determined by the magnitude of the bias, even after further introductions cease. We show, first using a simple logistic population model, and second using a realistic simulation of an important aquatic invasive species – the sea lamprey<!--> <em>Petromyzon marinus</em> <!-->– how this effect can greatly increase the effectiveness of a sex-distorting construct at population suppression, but also increase the risk of such strategies due to reduced reversibility. We also present evidence that biased tertiary sex ratios might be present in many invasive species, particularly when their population sizes are low relative to environmental carrying capacity.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"608 ","pages":"Article 112137"},"PeriodicalIF":1.9,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143943679","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":"Quantifying the effects of intraspecific trait variation and interspecific trait correlations on interacting populations—A nonlinear averaging approach","authors":"Koen J. van Benthem ,&nbsp;Rishabh Bagawade ,&nbsp;Chantal Blüml ,&nbsp;Peter Nabutanyi ,&nbsp;Frans M. Thon ,&nbsp;Meike J. Wittmann","doi":"10.1016/j.jtbi.2025.112134","DOIUrl":"10.1016/j.jtbi.2025.112134","url":null,"abstract":"<div><div>Interactions between two species, e.g. between a predator species and a prey species, can often be described as the sum of many individual-by-individual interactions whose outcomes depend on the traits of the interacting individuals. These traits often vary substantially among individuals in each species, and individuals do not always interact randomly, e.g. due to plastic responses to a shared environmental factor in a heterogeneous landscape. Here we investigate the impact of intraspecific trait variation (ITV) and such interspecific trait correlations on species interactions via nonlinear averaging. Building on past models that integrate over an interaction kernel to obtain the impacts of ITV, we develop a theoretical framework allowing the modeling of arbitrary species interactions, with interspecific trait correlations as a novel feature. Based on two key ingredients, a joint trait distribution and a two-dimensional interaction function, the average interaction parameters (e.g. average predation rate) can be quantified numerically, approximated using an insightful Taylor approximation, and compared to cases without ITV. We highlight two applications of our framework. First, we study the quantitative and qualitative effects of ITV and trait correlations in a simple predator-prey model and show that even in the absence of evolution, variation and trait correlations among interacting individuals can make or break the coexistence between species. Second, we use simulated field data for a predator-prey system to show how the impact of ITV on an ecological interaction can be estimated from empirical data.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"609 ","pages":"Article 112134"},"PeriodicalIF":1.9,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144026825","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":"Unification of alpha, mu, and tau rhythms and their beta-band harmonics via eigenmodes: spectral peaks, topography, and reactivity","authors":"P.A. Robinson,&nbsp;Rawan Khalil El Zghir","doi":"10.1016/j.jtbi.2025.112136","DOIUrl":"10.1016/j.jtbi.2025.112136","url":null,"abstract":"&lt;div&gt;&lt;div&gt;&lt;em&gt;Objective:&lt;/em&gt;The alpha, mu, and tau rhythms all have frequencies of around 10 Hz in normal adult humans, with a range of 7–13 Hz. The beta rhythm, mu-associated activity, and tau-associated activity, are found at around twice those frequencies. The present objective is to use neural field theory (NFT) to explain the observed frequency structure and spatial topography, and to suggest a mechanism of reactivity, of all these rhythms in a unified way, and to predict other features not yet reported experimentally.&lt;/div&gt;&lt;div&gt;&lt;em&gt;Methods:&lt;/em&gt; NFT averages over the activity of large numbers of neurons to predict mean firing rates and EEG characteristics. It predicts the existence of natural modes of activity, each with characteristic spatial structure and frequencies. The lowest modes dominate large-scale activity and the first four are used here to predict spectra, topography, and reactivity of alpha, mu, and tau rhythms and their second harmonics, including split peaks.&lt;/div&gt;&lt;div&gt;&lt;em&gt;Results:&lt;/em&gt; Corticothalamic loop delays determine the basic &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mo&gt;∼&lt;/mo&gt;&lt;mn&gt;10&lt;/mn&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt; Hz frequency of the alpha rhythm, the &lt;span&gt;&lt;math&gt;&lt;mrow&gt;&lt;mo&gt;∼&lt;/mo&gt;&lt;mn&gt;20&lt;/mn&gt;&lt;/mrow&gt;&lt;/math&gt;&lt;/span&gt; Hz frequency of the beta rhythm, and explain their frequency correlations on an individual-subject level. Differential effects of cortical geometry on individual modes cause observed frequency splitting of the alpha and beta rhythms and we predict analogous splitting of mu and tau and their harmonics. Spatial topographies of alpha, mu, and tau are explained by modal structure, with amplitudes superposed rather than powers, and we predict that the harmonic of each rhythm will tend to have similar topography to its fundamental, although specific exceptions can occur. Similar results are obtained when modal eigenfrequencies differ sufficiently to give rise to split peaks. Dynamics of rotating patterns and wavefronts are also explained in terms of pairs of modes. Blocking or “desynchronization” of each rhythm can be accounted for by modest decreases in corticothalamic loop gains, magnified by proximity to a critical state, and we predict that fundamental and harmonic will tend to be blocked in tandem, an effect that has already been observed for alpha and beta. Paradoxically, modal analysis implies that blocking in one region can correlate with enhancement in another, which may account for the phenomenon of event-related synchronization.&lt;/div&gt;&lt;div&gt;&lt;em&gt;Conclusions:&lt;/em&gt; A unified explanation of alpha, mu, tau, and their harmonics is obtained in terms of just four corticothalamic eigenmodes. The results are consistent with a wide variety of experimental observations and experimentally testable predictions of new features are made.&lt;/div&gt;&lt;div&gt;&lt;em&gt;Significance:&lt;/em&gt; A century after the first observations of human EEG, this work explains and unifies alpha, the earliest detected rhythm, with its relatives and their harmonics to form a single family.","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"608 ","pages":"Article 112136"},"PeriodicalIF":1.9,"publicationDate":"2025-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143943585","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":"Probability of extinction and peak time for multi-type epidemics with application to COVID-19 variants of concern","authors":"Jacob Curran-Sebastian ,&nbsp;Louise Dyson ,&nbsp;Edward M. Hill ,&nbsp;Ian Hall ,&nbsp;Lorenzo Pellis ,&nbsp;Thomas House","doi":"10.1016/j.jtbi.2025.112135","DOIUrl":"10.1016/j.jtbi.2025.112135","url":null,"abstract":"<div><div>During the COVID-19 pandemic, the emergence of novel variants of concern (VoCs) prompted different responses from governments across the world aimed at mitigating the impacts of more transmissible or more harmful strains. We model the invasion of a novel VoC into a population with heterogeneous vaccine- and infection-acquired immunity using a multi-type branching process framework with immigration. We define the number of cases needed to be reached to ensure stochastic extinction of this strain is unlikely and, therefore, the strain has become established in the population. To estimate the first-passage time distribution to reach this number of cases we use a mixture of stochastic simulations and analytic results. The first-passage time distribution gives a time window that is useful for policymakers planning interventions aimed at suppressing or delaying the introduction of novel VoC. We apply our method to a model of COVID-19 in the United Kingdom, though our results are applicable to other pathogens and settings.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"608 ","pages":"Article 112135"},"PeriodicalIF":1.9,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143912662","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":"Can pruning improve agent-based models' calibration? An application to HPVsim.","authors":"Fabian Sturman, Ben Swallow, Cliff Kerr, Robyn Stuart, Jasmina Panovska-Griffiths","doi":"10.1016/j.jtbi.2025.112130","DOIUrl":"https://doi.org/10.1016/j.jtbi.2025.112130","url":null,"abstract":"<p><p>Agent-Based Models (ABMs) have gained popularity over the COVID-19 epidemic, but their efficient calibration remains challenging. Here we propose a novel calibration architecture by investigating the role of pruning in ABM calibration. We use a recently developed model for human papillomavirus (HPV) transmission and focus on its integrated calibration framework, Optuna. Simulating six synthetic datasets of various temporal skewness, with six pruners, we show that more aggressive pruners perform best (in terms of loss function at end of calibration) for very-back-heavy datasets, while median pruners are better for more-front-heavy datasets. For more balanced datasets most of the pruners perform similarly to no pruning. However, across all datasets pruning notably sped up calibration, in many cases without compromising on - or even improving upon - the optimal found parameter set. We validate our results through application to real-life data. Finally, we discuss approaches for improving \"bad pruners\" for balanced datasets. Our proof-of-principle study shows that pruners can improve ABMs' calibration. As ABMs are becoming more widely used in epidemiological modelling, designing the next level of pandemic preparedness strategies will need to address efficient calibration; we believe pruning is a cornerstone for this.</p>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":" ","pages":"112130"},"PeriodicalIF":1.9,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144058448","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":"Positive and negative selective assortment","authors":"Segismundo S. Izquierdo ,&nbsp;Luis R. Izquierdo ,&nbsp;Christoph Hauert","doi":"10.1016/j.jtbi.2025.112129","DOIUrl":"10.1016/j.jtbi.2025.112129","url":null,"abstract":"<div><div>In populations subject to evolutionary processes, the assortment of players with different genes or strategies can have a large impact on players’ payoffs and on the expected evolution of each strategy in the population. Here we consider assortment generated by a process of partner choice known as <em>selective assortment</em>. Under selective assortment, players looking for a mate can observe the strategies of a sample of potential mates or co-players, and select one of them to interact with. This selection mechanism can generate positive assortment (preference for players using the same strategy), or negative assortment (preference for players using a different strategy). We study the impact of selective assortment in the evolution and in the equilibria of a population, providing results for different games under different evolutionary dynamics (including the replicator dynamics).</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"608 ","pages":"Article 112129"},"PeriodicalIF":1.9,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143906333","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":"Inferring absolute cell numbers from relative proportion in stochastic models with cell plasticity","authors":"Yuman Wang ,&nbsp;Shuli Chen ,&nbsp;Zhaolian Lu ,&nbsp;Yu Liu ,&nbsp;Jie Hu ,&nbsp;Da Zhou","doi":"10.1016/j.jtbi.2025.112133","DOIUrl":"10.1016/j.jtbi.2025.112133","url":null,"abstract":"<div><div>Quantifying dynamic changes in cell populations is crucial for a comprehensive understanding of biological processes such as cell proliferation, injury repair, and disease progression. However, compared to directly measuring the absolute cell numbers of specific subpopulations, relative proportion data demonstrate greater reproducibility and yield more stable, reliable outcomes. Therefore, inferring absolute cell numbers from relative proportion data may present a novel approach for effectively predicting changes in cell population sizes. To address this, we establish two mathematical mappings between cell proportions and population sizes using moment equations derived from stochastic cell-plasticity models. Notably, our findings indicate that one of these mappings does not require prior knowledge of the initial population size, highlighting the value of incorporating variance information into cell proportion data. We evaluated the robustness of our methods from multiple perspectives and extended their application to various biological mechanisms within the context of cell plasticity models. These methods help mitigate the limitations associated with the direct measurement of absolute cell counts through experimental techniques. Moreover, they provide new insights into leveraging the stochastic dynamics of cell populations to quantify interactions between different biomasses within the system.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"608 ","pages":"Article 112133"},"PeriodicalIF":1.9,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143906334","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":"Evolutionarily stable strategies in population games: An invader’s perspective","authors":"Felipe A. Murgel ,&nbsp;Max O. Souza","doi":"10.1016/j.jtbi.2025.112108","DOIUrl":"10.1016/j.jtbi.2025.112108","url":null,"abstract":"<div><div>We revisit the various definitions of an Evolutionarily Stable Strategy (<span><math><mi>ESS</mi></math></span>) in nonlinear population games from the standpoint of barrier functions. We show the equivalence between an <span><math><mi>ESS</mi></math></span> being uniformly uninvadable and the corresponding barrier function being lower semi-continuous (LSC). Moreover, it is sufficient to check this for strategies that are near an alternative best reply lying on an opposite face. We also provide some counterexamples that show that uniform stability cannot be taken for granted in nonlinear population games; we denote such <span><math><mi>ESS</mi></math></span>s as singular <span><math><mi>ESS</mi></math></span>s. Furthermore, we obtain conditions that are equivalent to the barrier function being LSC and are typically easier to verify. As a by-product, we identify a number of instances where being an <span><math><mi>ESS</mi></math></span> is equivalent to being uniformly uninvadable: 3-player games, payoffs inducing convex incentives, or differentiable payoffs with negative definite first derivative, when considered on alternative best replies.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"607 ","pages":"Article 112108"},"PeriodicalIF":1.9,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143839761","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}