Journal of Theoretical Biology最新文献

{"title":"Mathematical modeling of tuberculosis with two strains, seasonality, and age heterogeneity","authors":"Yang Deng ,&nbsp;Yi Zhao","doi":"10.1016/j.jtbi.2025.112313","DOIUrl":"10.1016/j.jtbi.2025.112313","url":null,"abstract":"<div><div>Tuberculosis (TB) remains a significant global health threat, particularly in the regions with diverse age-specific transmission patterns and increasing drug resistance. To address these challenges, this study establishes a dual-strain model that incorporates both drug-resistant and drug-sensitive strains to investigate how these strains contribute to the dynamics of TB transmission. By integrating age heterogeneity, social interactions, and seasonal variations, the model offers a detailed depiction of TB transmission process, highlighting its inherent complexity across various population groups. We derive the basic reproduction number of the model as the maximum of the two reproduction numbers: one for the drug-resistant strain (<span><math><msubsup><mi>R</mi><mn>0</mn><mi>r</mi></msubsup></math></span>) and one for the drug-sensitive strain (<span><math><msubsup><mi>R</mi><mn>0</mn><mi>s</mi></msubsup></math></span>). It is found that the disease-free periodic equilibrium of the system is globally asymptotically stable when <span><math><mrow><msub><mi>R</mi><mn>0</mn></msub><mo>=</mo><mi>max</mi><mrow><mo>(</mo><msubsup><mi>R</mi><mrow><mn>0</mn></mrow><mi>r</mi></msubsup><mo>,</mo><msubsup><mi>R</mi><mrow><mn>0</mn></mrow><mi>s</mi></msubsup><mo>)</mo></mrow><mo>&lt;</mo><mn>1</mn></mrow></math></span>, in the absence of reinfection. We further explore the competitive dynamics of drug-resistant and drug-sensitive strains under <span><math><mrow><msubsup><mi>R</mi><mn>0</mn><mi>r</mi></msubsup><mo>&gt;</mo><mn>1</mn><mo>&gt;</mo><msubsup><mi>R</mi><mn>0</mn><mi>s</mi></msubsup></mrow></math></span> and <span><math><mrow><msubsup><mi>R</mi><mn>0</mn><mi>s</mi></msubsup><mo>&gt;</mo><mn>1</mn><mo>&gt;</mo><msubsup><mi>R</mi><mn>0</mn><mi>r</mi></msubsup></mrow></math></span>. Using a Markov Chain Monte Carlo (MCMC) algorithm, the model is calibrated with monthly TB infection data from mainland China, enabling the reconstruction of TB transmission dynamics across eight age-specific groups. The study reveals that drug-sensitive tuberculosis strains exhibit more prominent transmission characteristics compared to drug-resistant strains. Moreover, increased vaccination coverage significantly reduces TB prevalence, particularly in younger populations, while reducing contact intensity effectively suppresses TB across all age groups. These findings highlight the role of combining age-structured modeling, strain dynamics, and behavioral interventions, offering implications for the targeted TB control strategies.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"619 ","pages":"Article 112313"},"PeriodicalIF":2.0,"publicationDate":"2025-11-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145531003","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":"Emergence of longitudinal queue behavior based on topological interaction and asynchronous dynamics","authors":"Decheng Kong,&nbsp;Kai Xue,&nbsp;Ping Wang,&nbsp;Zeyu Xu,&nbsp;Zhiqin Huang","doi":"10.1016/j.jtbi.2025.112318","DOIUrl":"10.1016/j.jtbi.2025.112318","url":null,"abstract":"<div><div>Coordinated longitudinal queue behavior in biological groups, such as migratory bird flocks, remains underexplored in classical collective motion models that focus on metric-based interactions and synchronous dynamics. This study utilizes a modified self-propelled particle model incorporating topological interactions, gliding asynchrony, and limited view angle to investigate the mechanisms driving longitudinal queue formation. Simulations reveal that interacting with only two topological neighbors is critical for stable queue emergence, with an optimal view angle range of [200°, 270°] balancing frontward tracking and lateral collision avoidance. Gliding asynchrony enhances queue formation efficiency by reducing neighbor interaction frequency, leading to higher success rates and lower interaction complexity compared to synchronous or random update mechanisms. Topological interaction networks exhibit high connectivity and stability, fundamentally supporting queue maintenance, while metric-based or Voronoi interactions fail to produce linear order. The study highlights the interplay of limited sensory perception, low neighbor connectivity, and asynchronous dynamics in self-organized migration queues, providing a theoretical guidance for understanding animal collective behavior and guiding robotic swarm design.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"618 ","pages":"Article 112318"},"PeriodicalIF":2.0,"publicationDate":"2025-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145524880","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":"Fast approximate Bayesian inference of HIV indicators using PCA adaptive Gauss-Hermite quadrature","authors":"Adam Howes ,&nbsp;Alex Stringer ,&nbsp;Seth R. Flaxman ,&nbsp;Jeffrey W. Imai–Eaton","doi":"10.1016/j.jtbi.2025.112290","DOIUrl":"10.1016/j.jtbi.2025.112290","url":null,"abstract":"<div><div>Naomi is a spatial evidence synthesis model used to produce district-level HIV epidemic indicators in sub-Saharan Africa. Multiple outcomes of policy interest, including HIV prevalence, HIV incidence, and antiretroviral therapy treatment coverage are jointly modelled using both household survey data and routinely reported health system data. The model is provided as a tool for countries to input their data to and generate estimates with during a yearly process supported by UNAIDS. Previously, inference has been conducted using empirical Bayes and a Gaussian approximation, implemented via the <span>TMB</span> <span>R</span> package. We propose a new inference method based on an extension of adaptive Gauss-Hermite quadrature to deal with more than 20 hyperparameters. Using data from Malawi, our method improves the accuracy of inferences for model parameters, while being substantially faster to run than Hamiltonian Monte Carlo with the No-U-Turn sampler. Our implementation leverages the existing <span>TMB</span> <span>C++</span> template for the model’s log-posterior, and is compatible with any model with such a template.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"618 ","pages":"Article 112290"},"PeriodicalIF":2.0,"publicationDate":"2025-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145514510","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":"Treatment of methanol toxicity through ethanol and folinic acid: A mathematical study","authors":"Sanju Sardar ,&nbsp;Priti Kumar Roy ,&nbsp;Sk Mosaraf Ahammed ,&nbsp;Tushar Ghosh ,&nbsp;David Greenhalgh","doi":"10.1016/j.jtbi.2025.112304","DOIUrl":"10.1016/j.jtbi.2025.112304","url":null,"abstract":"<div><div>Methanol poisoning is an infrequent but immensely dangerous intoxication, causing severe metabolic disturbances, neurological dysfunction, and even death, if not treated timely and properly. In this article, we formulate a mathematical model based on the chemical kinetics reaction, to analyse the effect of co-administration of the antidote ethanol and folinic acid for the treatment of methanol toxicity. The maximum concentration level of formic acid has been identified, and through a one-dimensional impulsive system, we determined the maximum dosing interval of folinic acid. Under appropriate assumptions we have demonstrated the existence and stability of the equilibrium-like periodic orbit of our system with impulsive administration of folinic acid and ethanol. The dynamical changes of toxic metabolites are illustrated numerically for different doses and dosing intervals. We performed a sensitivity analysis to identify the key parameters affecting formic acid concentration during treatment. Model results were validated by comparing them with clinical and experimental data on methanol half-life during ethanol therapy and formic acid clearance under folinic acid treatment. Based on our detailed analytical and numerical analysis, we recommend an effective dosing regimen of folinic acid and ethanol to detoxify the human body and clearly identify the conditions beyond which hemodialysis becomes essential. We verified all of our analytical outcomes through numerical simulation.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"618 ","pages":"Article 112304"},"PeriodicalIF":2.0,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145508116","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":"Rapid cell turnover to model adipocyte size distribution","authors":"Louis Fostier ,&nbsp;Aloïs Dauger ,&nbsp;Romain Yvinec ,&nbsp;Magali Ribot ,&nbsp;Chloe Audebert ,&nbsp;Hedi Soula","doi":"10.1016/j.jtbi.2025.112311","DOIUrl":"10.1016/j.jtbi.2025.112311","url":null,"abstract":"<div><div>White adipose tissue, composed of adipocyte cells, primarily stores energy as lipid droplets. The size of adipocytes varies significantly within the tissue according to the amount of stored lipids. A striking observation is that the adipocyte size distribution is bimodal, and thus, this tissue is lacking a characteristic size.</div><div>We propose a novel dynamical model, based on a partial differential equation, to represent the adipocyte size distribution. The model assumes continuous adipocyte growth, with a velocity dependent on cell radius and extracellular lipid availability, together with constant rates of cell recruitment and death.</div><div>We prove the existence and local stability of a unique stationary solution for a broad range of growth velocity functions. Choosing a parcimonious formulation, we show that only three parameters are enough to describe adipocyte size distributions measurements in rats. These parameters are robustly estimated through approximate Bayesian computation, and the model demonstrates excellent agreement with experimental data. This mechanistic, three-parameter framework offers a new and interpretable approach to characterizing adipocyte size distributions.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"618 ","pages":"Article 112311"},"PeriodicalIF":2.0,"publicationDate":"2025-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145508140","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 modelling of tumor-immune interactions in breast cancer","authors":"Haifeng Zhang ,&nbsp;Chenghang Li","doi":"10.1016/j.jtbi.2025.112310","DOIUrl":"10.1016/j.jtbi.2025.112310","url":null,"abstract":"<div><div>The dynamic interplay between tumors and immune system is pivotal to the progression of breast cancer. To systematically investigate how interactions between tumor cells and immune cells shape breast cancer evolution, we developed a mathematical model that incorporates tumor cells, dendritic cells (DCs), natural killer (NK) cells, regulatory T cells (Tregs) and CD8+ T cells. We first established analytical conditions for the local stability of the tumor-free equilibrium, identifying key constraints on tumor growth imposed by immune activity. The existence of a positive equilibrium solution further suggests the potential coexistence of tumor and immune cells. Numerical simulations demonstrate that effective tumor control is achieved under a high baseline level of CD8+ T cell precursors coupled with a low level of regulatory T cell precursors. These results highlight the important role of balancing immunostimulatory and immunosuppressive forces within the tumor microenvironment. Through bifurcation analysis, we identified regimes of bistability in which both high-tumor and low-tumor equilibria coexist with dynamic features that may underlie divergent clinical outcomes and present a critical challenge for clinical therapeutic intervention. Moreover, simulations of tumor-immune dynamics in virtual cohorts reveal that tumor control hinges on CD8+ T cell infiltration, whereas regulatory T cell abundance is a potent predictor of immune escape. Finally, we formulated an optimal control framework to design adaptive CD8+ T cell injection protocols. Numerical solutions demonstrate that such optimized strategies achieve superior tumor reduction compared with constant dosing, despite using the same total injection dose of CD8+ T cells and identical treatment intervals. Collectively, our findings provide a mechanistic understanding of breast cancer progression and establish a theoretical foundation for developing personalized therapeutic strategies to optimize clinical outcomes.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"618 ","pages":"Article 112310"},"PeriodicalIF":2.0,"publicationDate":"2025-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145490872","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":"Direct reciprocity in multi-action repeated games","authors":"Feipeng Zhang ,&nbsp;Lei Zhou ,&nbsp;Guofeng Zhang ,&nbsp;Long Wang","doi":"10.1016/j.jtbi.2025.112312","DOIUrl":"10.1016/j.jtbi.2025.112312","url":null,"abstract":"<div><div>Direct reciprocity is a fundamental mechanism for sustaining cooperation in repeated interactions, where individuals adjust their behavior based on past experiences. Most previous models have focused on the prisoner’s dilemma, in which individuals face a strict choice between full cooperation and complete defection. However, this dichotomy oversimplifies the complexity of real-world reciprocal interactions. To address this, we introduce additional actions between these extremes, thereby increasing action diversity. Our analysis demonstrates that a broader range of available actions fosters cooperation more effectively than a binary choice. Through evolutionary analysis, we identify which types of intermediate actions promote cooperation. Moreover, equilibrium analysis establishes the theoretical conditions underlying this effect. While the increased computational complexity makes it infeasible to simulate scenarios with an arbitrarily large number of actions, our theoretical analysis remains applicable to settings with more actions, offering broader insights into the role of action diversity in promoting cooperation. These findings deepen our understanding of direct reciprocity and highlight the importance of action diversity in shaping cooperative behavior.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"618 ","pages":"Article 112312"},"PeriodicalIF":2.0,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145477155","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":"Network reciprocity turns cheap talk into a force for cooperation","authors":"Zhao Song ,&nbsp;Chen Shen ,&nbsp;The Anh Han","doi":"10.1016/j.jtbi.2025.112303","DOIUrl":"10.1016/j.jtbi.2025.112303","url":null,"abstract":"<div><div>Non-binding communication is common in daily life and crucial for fostering cooperation, even though it has no direct payoff consequences. However, despite robust empirical evidence, its evolutionary basis remains poorly understood. Here, we develop a game-theoretic model in which individuals can signal an intention to cooperate before playing a Donation game. Strategies differ in how they respond to these signals, ranging from unconditional to conditional types, with the latter incurring a cognitive cost for deliberation. Through evolutionary analysis, we show that non-binding communication alone cannot sustain cooperation in well-mixed, anonymous populations, consistent with empirical observations. In contrast, structured populations support the emergence of cooperation, with conditional cooperators acting as catalysts that protect unconditional cooperators through context-dependent patterns of cyclic dominance. These findings offer an evolutionary explanation for how non-binding communication promotes cooperation and provide a modelling framework for exploring its effects in diverse social settings.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"617 ","pages":"Article 112303"},"PeriodicalIF":2.0,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145474952","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":"Stability and threshold analysis of a class of epidemic models in a multi-patch environment","authors":"Linhe Zhu ,&nbsp;Le He ,&nbsp;Haoyan Sha ,&nbsp;Shuling Shen","doi":"10.1016/j.jtbi.2025.112285","DOIUrl":"10.1016/j.jtbi.2025.112285","url":null,"abstract":"<div><div>Spatial heterogeneity and population migration may affect transmission threshold and the asymptotic behavior of epidemic transmission near the steady state. To investigate this issue, an epidemic transmission model with nonlinear natural growth mechanism and linear migration mechanism based on multi-patch structure is established. First, we study the findings related to the equilibrium state of the system and the transmission threshold, proving the uniqueness and the existence of epidemic-free equilibrium points, the existence of positive equilibrium points under certain conditions and the non-existence of mixed equilibrium points. Meanwhile, we discuss the asymptotic behavior of various types of equilibrium points and define the global basic reproduction number and the local basic reproduction number, demonstrating some of their unequal relationships. Further, we also consider the impact of the blocking mechanism on the patch model, illustrating that the epidemic disappears or persists in single patch under certain conditions. Finally, we carry out the numerical simulation analysis of our system. The results suggest that the epidemic may form a certain oscillatory pattern in space and there are multiple positive equilibrium points for the system. At the same time, the blocking mechanism may lead to different types of equilibrium states in different patches, but it is not effective in reducing the total number of infected individuals and the convergence time of the system.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"618 ","pages":"Article 112285"},"PeriodicalIF":2.0,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145477166","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":"Evaluating the impact of NPC1 single nucleotide polymorphisms on entry efficiency of filoviruses in vitro: Agent-based model approach","authors":"Juseong Kim ,&nbsp;Kwang Su Kim ,&nbsp;Ayato Takada ,&nbsp;Yusuke Asai ,&nbsp;Shingo Iwami ,&nbsp;Seung-Woo Son ,&nbsp;Mi Jin Lee","doi":"10.1016/j.jtbi.2025.112315","DOIUrl":"10.1016/j.jtbi.2025.112315","url":null,"abstract":"<div><div>Ebola and Marburg viruses are highly pathogenic filoviruses that cause severe hemorrhagic fever in humans, with case fatality rates reaching approximately 50 %. These viruses pose significant public health challenges owing to their potential for large-scale outbreaks. A key step in their infection process is the interaction between the Niemann-Pick C1 (NPC1) protein on host cells and the viral glycoprotein (GP), which is responsible for viral entry into cells. Genetic variations in NPC1 caused by single nucleotide polymorphisms (SNPs) can lead to amino acid substitutions, potentially altering the efficiency of viral entry. To better understand this process, we developed an agent-based model (ABM) to simulate viral plaque growth with spatial resolution beyond traditional models. By applying this model, we quantified how naturally occurring SNPs at GP-binding interface of NPC1, such as D508N, P424A, and S425L, reduced entry efficiency of both Ebola and Marburg viruses. Notably, the P424A substitution led to a 53 % reduction in Ebola virus entry efficiency compared to the wild-type. Our findings highlight the potential of computational modeling to uncover the impact of genetic variations on viral infections and provide insights that may inform therapeutic strategies against these deadly viruses.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"618 ","pages":"Article 112315"},"PeriodicalIF":2.0,"publicationDate":"2025-11-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145483539","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}