Journal of Theoretical Biology最新文献

{"title":"Unification of alpha, mu, and tau rhythms and their beta-band harmonics via eigenmodes: spectral peaks, topography, and reactivity","authors":"P.A. Robinson, Rawan Khalil El Zghir","doi":"10.1016/j.jtbi.2025.112136","DOIUrl":"10.1016/j.jtbi.2025.112136","url":null,"abstract":"<div><div><em>Objective:</em>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.</div><div><em>Methods:</em> 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.</div><div><em>Results:</em> Corticothalamic loop delays determine the basic <span><math><mrow><mo>∼</mo><mn>10</mn></mrow></math></span> Hz frequency of the alpha rhythm, the <span><math><mrow><mo>∼</mo><mn>20</mn></mrow></math></span> 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.</div><div><em>Conclusions:</em> 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.</div><div><em>Significance:</em> 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 ,&nbsp;Ben Swallow ,&nbsp;Cliff Kerr ,&nbsp;Robyn M. Stuart ,&nbsp;Jasmina Panovska-Griffiths","doi":"10.1016/j.jtbi.2025.112130","DOIUrl":"10.1016/j.jtbi.2025.112130","url":null,"abstract":"<div><div>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.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"611 ","pages":"Article 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}

{"title":"Ancestral process for infectious disease outbreaks with superspreading","authors":"Xavier Didelot ,&nbsp;David Helekal ,&nbsp;Ian Roberts","doi":"10.1016/j.jtbi.2025.112109","DOIUrl":"10.1016/j.jtbi.2025.112109","url":null,"abstract":"<div><div>When an infectious disease outbreak is of a relatively small size, describing the ancestry of a sample of infected individuals is difficult because most ancestral models assume large population sizes. Given a set of infected individuals, we show that it is possible to express exactly the probability that they have the same infector, either inclusively (so that other individuals may have the same infector too) or exclusively (so that they may not). To compute these probabilities requires knowledge of the offspring distribution, which determines how many infections each infected individual causes. We consider transmission both without and with superspreading, in the form of a Poisson and a Negative-Binomial offspring distribution, respectively. We show how our results can be incorporated into a new Lambda-coalescent model which allows multiple lineages to coalesce together. We call this new model the Omega-coalescent, we compare it with previously proposed alternatives, and advocate its use in future studies of infectious disease outbreaks.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"607 ","pages":"Article 112109"},"PeriodicalIF":1.9,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143830184","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":"What does the tree of life look like as it grows? Evolution and the multifractality of time","authors":"Kevin Hudnall ,&nbsp;Raissa M. D’Souza","doi":"10.1016/j.jtbi.2025.112121","DOIUrl":"10.1016/j.jtbi.2025.112121","url":null,"abstract":"<div><div>By unifying three foundational principles of modern biology, we develop a mathematical framework to analyze the growing tree of life. Contrary to the static case, where the analogy between phylogenetic trees and the tree that grows in soil is drawn, our framework shows that the living tree of life is analogous to a Cantor dust where each branch is a distinct fractal curve. The system as a whole is therefore multifractal in the sense that it consists of many unique fractals. The three foundational principles for the mathematical framework are that phylogeny is nested, phylogeny is dualistic (i.e., transitive between singularities and populations), and phylogeny is stochastic. Integrating these three principles, we model the dynamic (i.e., <em>living</em>) tree of life as a random iterated function system that generates unique convexly related sequences of branching random variables (visualized in <span><span><strong>Animation 1</strong></span></span>). The multifractal nature of this dynamic tree of life implies that, for any two living entities, the time interval from their last common ancestor to the present moment is a distinct fractal curve for each. Thus, the length of a time interval along each distinct branch is unique, so that time is also multifractal and not an ultrametric on the tree of life.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"607 ","pages":"Article 112121"},"PeriodicalIF":1.9,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143870413","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":"Evolution of predators and prey kills Turing patterns","authors":"Vit Piskovsky","doi":"10.1016/j.jtbi.2025.112107","DOIUrl":"10.1016/j.jtbi.2025.112107","url":null,"abstract":"<div><div>The spatiotemporal patterns of predators and their prey play a pivotal role in ecology and ecological interactions influence their formation. In particular, motility has been proposed to drive the emergence of spatiotemporal predator-prey patterns via the Turing mechanism. However, the predicted Turing patterns do not exhibit temporal changes that are common in experiments and nature. Moreover, the Turing mechanism treats motility as fixed, even though predators and prey adjust their motility in response to each other and their interactions influence their evolution. Using adaptive dynamics, I prove that the evolution of motility prevents the formation of Turing patterns and promotes the formation of dynamic patterns, such as predator-prey waves. Furthermore, I show that multiple motility phenotypes can induce predator-prey oscillations even for stabilising temporal dynamics, which extends the emergence of predator-prey cycles beyond the regimes predicted by the Lotka–Volterra or Rosenzweig–MacArthur models that require oscillatory temporal dynamics. This work unites models for predator-prey spatiotemporal patterns and evolution of motility to explain how dynamic spatiotemporal patterns of co-evolving predators and prey emerge and persist. The novel mathematical theory is general and extends to other ecological situations, such as ecological public goods games.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"607 ","pages":"Article 112107"},"PeriodicalIF":1.9,"publicationDate":"2025-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891331","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":"Arterial arcades and collaterals regress under hemodynamics-based diameter adaptation: A computational and mathematical analysis","authors":"Vivi Rottschäfer ,&nbsp;Willem G.N. Kuppers ,&nbsp;Jiao Chen ,&nbsp;Ed van Bavel","doi":"10.1016/j.jtbi.2025.112111","DOIUrl":"10.1016/j.jtbi.2025.112111","url":null,"abstract":"<div><div>Arterial networks exhibit a wide range of segment radii, largely thought to result from adaptation to wall shear stress (WSS). Segments remodel outward or inward if WSS is higher or lower than a reference value. While this mechanism seems straightforward for arterial trees, real networks contain arcades, collaterals, and loops. We investigated the stability of these looping structures under WSS control using simulation models of small networks and published coronary and cerebral artery data.</div><div>Adaptation was modeled as changes in segment radius proportional to deviations from reference WSS. A generalized model included other hemodynamic stimuli like flow and velocity. Simulations consistently predicted loop regression due to the loss of one or more segments, both for the WSS model and the generalized model, regardless of initial conditions or model parameters. This loop loss was also observed in networks with heterogeneous adaptation rates or under dynamic conditions.</div><div>A mathematical analysis confirmed that loop instability is a direct consequence of Kirchhoff’s circuit law, leading to unstable equilibria. Thus, loss of loops is an inherent outcome of arterial networks adapting to local hemodynamics. Additional mechanisms, such as communication between connected segments, may be needed to explain the presence of loops in real networks.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"607 ","pages":"Article 112111"},"PeriodicalIF":1.9,"publicationDate":"2025-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143812910","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}