Bulletin of Mathematical Biology最新文献

A Framework for Parameter Estimation and Uncertainty Quantification in Systems Biology Using Quantile Regression and Physics-Informed Neural Networks.

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-03-28 DOI: 10.1007/s11538-025-01439-9

Haoran Hu, Qianru Cheng, Shuli Guo, Huifang Wen, Jing Zhang, Yongqi Song, Kaiqun Wang, Di Huang, Hui Zhang, Chaofeng Zhang, Yanhu Shan

{"title":"A Framework for Parameter Estimation and Uncertainty Quantification in Systems Biology Using Quantile Regression and Physics-Informed Neural Networks.","authors":"Haoran Hu, Qianru Cheng, Shuli Guo, Huifang Wen, Jing Zhang, Yongqi Song, Kaiqun Wang, Di Huang, Hui Zhang, Chaofeng Zhang, Yanhu Shan","doi":"10.1007/s11538-025-01439-9","DOIUrl":"https://doi.org/10.1007/s11538-025-01439-9","url":null,"abstract":"A framework for parameter estimation and uncertainty quantification is crucial for understanding the mechanisms of biological interactions within complex systems and exploring their dynamic behaviors beyond what can be experimentally observed. Despite recent advances, challenges remain in achieving the high accuracy of parameter estimation and uncertainty quantification at moderate computational costs. To tackle these challenges, we developed a novel approach that integrates the quantile method with Physics-Informed Neural Networks (PINNs). This method utilizes a network architecture with multiple parallel outputs, each corresponding to a distinct quantile, facilitating a comprehensive characterization of parameter estimation and its associated uncertainty. The effectiveness of the proposed approach was validated across three study cases, where it was compared to the Monte Carlo dropout (MCD) and the Bayesian methods. Furthermore, a larger-scale model was employed to further demonstrate the excellent performance of the proposed approach. Our approach exhibited significantly superior efficacy in parameter estimation and uncertainty quantification. This highlights its great promise to broaden the scope of applications in system biology modeling.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 5","pages":"60"},"PeriodicalIF":2.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735553","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}

引用次数: 0

How Missed Doses of Antibiotics Affect Bacteria Growth Dynamics.

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-03-28 DOI: 10.1007/s11538-025-01430-4

Hwai-Ray Tung, Sean D Lawley

引用次数: 0

Understanding How Chromatin Folding and Enzyme Competition Affect Rugged Epigenetic Landscapes. 了解染色质折叠和酶竞争如何影响崎岖的表观遗传景观

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-03-28 DOI: 10.1007/s11538-025-01434-0

Daria Stepanova, Meritxell Brunet Guasch, Helen M Byrne, Tomás Alarcón

{"title":"Understanding How Chromatin Folding and Enzyme Competition Affect Rugged Epigenetic Landscapes.","authors":"Daria Stepanova, Meritxell Brunet Guasch, Helen M Byrne, Tomás Alarcón","doi":"10.1007/s11538-025-01434-0","DOIUrl":"https://doi.org/10.1007/s11538-025-01434-0","url":null,"abstract":"Epigenetics plays a key role in cellular differentiation and maintaining cell identity, enabling cells to regulate their genetic activity without altering the DNA sequence. Epigenetic regulation occurs within the context of hierarchically folded chromatin, yet the interplay between the dynamics of epigenetic modifications and chromatin architecture remains poorly understood. In addition, it remains unclear what mechanisms drive the formation of rugged epigenetic patterns, characterised by alternating genomic regions enriched in activating and repressive marks. In this study, we focus on post-translational modifications of histone H3 tails, particularly H3K27me3, H3K4me3, and H3K27ac. We introduce a mesoscopic stochastic model that incorporates chromatin architecture and competition of histone-modifying enzymes into the dynamics of epigenetic modifications in small genomic loci comprising several nucleosomes. Our approach enables us to investigate the mechanisms by which epigenetic patterns form on larger scales of chromatin organisation, such as loops and domains. Through bifurcation analysis and stochastic simulations, we demonstrate that the model can reproduce uniform chromatin states (open, closed, and bivalent) and generate previously unexplored rugged profiles. Our results suggest that enzyme competition and chromatin conformations with high-frequency interactions between distant genomic loci can drive the emergence of rugged epigenetic landscapes. Additionally, we hypothesise that bivalent chromatin can act as an intermediate state, facilitating transitions between uniform and rugged landscapes. This work offers a powerful mathematical framework for understanding the dynamic interactions between chromatin architecture and epigenetic regulation, providing new insights into the formation of complex epigenetic patterns.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 5","pages":"59"},"PeriodicalIF":2.0,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143735557","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}

引用次数: 0

Approximate Solutions of a General Stochastic Velocity-Jump Model Subject to Discrete-Time Noisy Observations.

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-03-25 DOI: 10.1007/s11538-025-01437-x

Arianna Ceccarelli, Alexander P Browning, Ruth E Baker

{"title":"Approximate Solutions of a General Stochastic Velocity-Jump Model Subject to Discrete-Time Noisy Observations.","authors":"Arianna Ceccarelli, Alexander P Browning, Ruth E Baker","doi":"10.1007/s11538-025-01437-x","DOIUrl":"10.1007/s11538-025-01437-x","url":null,"abstract":"Advances in experimental techniques allow the collection of high-resolution spatio-temporal data that track individual motile entities over time. These tracking data motivate the use of mathematical models to characterise the motion observed. In this paper, we aim to describe the solutions of velocity-jump models for single-agent motion in one spatial dimension, characterised by successive Markovian transitions within a finite network of n states, each with a specified velocity and a fixed rate of switching to every other state. In particular, we focus on obtaining the solutions of the model subject to noisy, discrete-time, observations, with no direct access to the agent state. The lack of direct observation of the hidden state makes the problem of finding the exact distributions generally intractable. Therefore, we derive a series of approximations for the data distributions. We verify the accuracy of these approximations by comparing them to the empirical distributions generated through simulations of four example model structures. These comparisons confirm that the approximations are accurate given sufficiently infrequent state switching relative to the imaging frequency. The approximate distributions computed can be used to obtain fast forwards predictions, to give guidelines on experimental design, and as likelihoods for inference and model selection.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 5","pages":"57"},"PeriodicalIF":2.0,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11937228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143708630","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}

引用次数: 0

Correction: Stochastic Models of Zoonotic Avian Influenza with Multiple Hosts, Environmental Transmission, and Migration in the Natural Reservoir.

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-03-24 DOI: 10.1007/s11538-025-01428-y

Rowan L Hassman, Iona M H McCabe, Kaia M Smith, Linda J S Allen

引用次数: 0

Vaccination and Collective Action Under Social Norms.

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-03-24 DOI: 10.1007/s11538-025-01436-y

Bryce Morsky

{"title":"Vaccination and Collective Action Under Social Norms.","authors":"Bryce Morsky","doi":"10.1007/s11538-025-01436-y","DOIUrl":"https://doi.org/10.1007/s11538-025-01436-y","url":null,"abstract":"Social dynamics are an integral part of the spread of disease affecting contact rates as well as the adoption of pharmaceutical and non-pharmaceutical interventions. When vaccines provide waning immunity, efficient and timely uptake of boosters is required to maintain protection and reduce infections. How then do social dynamics affect the timely uptake of vaccines and thereby the course of an epidemic? This paper explores this scenario through a behavioural-epidemiological model. It features a tipping-point dynamic for the uptake of vaccines that combines the risk of infection, perceived morbidity risk of the vaccine, and social payoffs for deviating from the vaccination decision-making of others. The social payoffs are derived from a social norm of conformity, and they create a collective action problem. A key finding driven by this dilemma is that waves of vaccine uptake and infections can occur due to inefficient and delayed uptake of boosters. This results in a nonlinear response of the infection load to the transmission rate: an intermediate transmission rate can result in greater prevalence of disease relative to more or less transmissible diseases. Further, global information about the prevalence of the disease and vaccine uptake can increase the infection load and peak relative to information restricted to individuals' contact networks. Thus, decisions driven by local information can mitigate the collective action problem across the population. Finally, the optimal public policy program to promote boosters is shown to be one that focuses on overcoming the social inertia to vaccinate at the start of an epidemic.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 5","pages":"55"},"PeriodicalIF":2.0,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143699768","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}

引用次数: 0

Mathematical Modelling of the First HIV/ZIKV Co-infection Cases in Colombia and Brazil.

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-03-21 DOI: 10.1007/s11538-025-01429-x

Jhoana P Romero-Leiton, Idriss Sekkak, Julien Arino, Iain Moyles, Bouchra Nasri

{"title":"Mathematical Modelling of the First HIV/ZIKV Co-infection Cases in Colombia and Brazil.","authors":"Jhoana P Romero-Leiton, Idriss Sekkak, Julien Arino, Iain Moyles, Bouchra Nasri","doi":"10.1007/s11538-025-01429-x","DOIUrl":"https://doi.org/10.1007/s11538-025-01429-x","url":null,"abstract":"This paper presents a mathematical model to investigate the co-infection with human immunodeficiency virus (HIV) and Zika virus (ZIKV) in Colombia and Brazil, where the first cases were reported in 2015. The model considers the sexual transmission dynamics of both viruses and vector-host interactions. We begin by exploring the qualitative behaviour of each model separately. We then analyze the dynamics of the co-infection model using the thresholds and results defined separately for each model. The model also considers the impact of intervention strategies, such as personal protection, antiretroviral therapy (ART), and sexual protection (condom use). Using available and assumed parameter values for Colombia and Brazil, the model is calibrated to investigate the long-term co-infection dynamics, the influence of specific parameters, and the potential effect of implementing these intervention strategies on co-infection spread. The study's results revealed that the duration of Zika infection is a critical factor influencing the burden of co-infection cases. Additionally, bed nets and use of condoms are essential for disease control, while ART is less emphasized due to the cost-effectiveness of condom use.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 5","pages":"54"},"PeriodicalIF":2.0,"publicationDate":"2025-03-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143673386","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}

引用次数: 0

A Mathematical Exploration of SDH-b Loss in Chromaffin Cells.

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-03-13 DOI: 10.1007/s11538-025-01427-z

Elías Vera-Sigüenza, Himani Rana, Ramin Nashebi, Ielyaas Cloete, Katarína Kl'uvčková, Fabian Spill, Daniel A Tennant

{"title":"A Mathematical Exploration of SDH-b Loss in Chromaffin Cells.","authors":"Elías Vera-Sigüenza, Himani Rana, Ramin Nashebi, Ielyaas Cloete, Katarína Kl'uvčková, Fabian Spill, Daniel A Tennant","doi":"10.1007/s11538-025-01427-z","DOIUrl":"10.1007/s11538-025-01427-z","url":null,"abstract":"The succinate dehydrogenase (SDH) is a four-subunit enzyme complex (SDH-a, SDH-b, SDH-c, and SDH-d) central to cell carbon metabolism. The SDH bridges the tricarboxylic acid cycle to the electron transport chain. A pathological loss of the SDH-b subunit leads to a cell-wide signalling cascade that shifts the cell's metabolism into a pseudo-hypoxic state akin to the so-called Warburg effect (or aerobic glycolysis). This trait is a hallmark of phaeochromocytomas, a rare tumour arising from chromaffin cells; a type of cell that lies in the medulla of the adrenal gland. In this study, we leverage the insights from a mathematical model constructed to underpin the metabolic implications of SDH-b dysfunction in phaeochromocytomas. We specifically investigate why chromaffin cells seemingly have the ability to maintain electron transport chain's Complex I function when confronted with the loss of the SDH-b subunit while other cells do not. Our simulations indicate that retention of Complex I is associated with cofactor oxidation, which enables cells to manage mitochondrial swelling and limit the reversal of the adenosine triphosphate synthase, supporting cell fitness, without undergoing lysis. These results support previous hypotheses that point to mitochondrial proton leaks as a critical factor of future research. Moreover, the model asserts that control of the proton gradient across the mitochondrial inner membrane is rate-limiting upon fitness management of SDH-b deficient cells.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 4","pages":"53"},"PeriodicalIF":2.0,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11906556/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623523","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}

引用次数: 0

Characterization of the Long-distance Dispersal Kernel of White-Tailed Deer and Evaluating its Impact on Chronic Wasting Disease Spread in Wisconsin. 白尾鹿长距离传播内核的特征及其对威斯康星州慢性消耗性疾病传播的影响评估。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-03-13 DOI: 10.1007/s11538-024-01394-x

Mennatallah Gouda, Jim Powell, W Jacob McClure, Daniel P Walsh, Daniel Storm

{"title":"Characterization of the Long-distance Dispersal Kernel of White-Tailed Deer and Evaluating its Impact on Chronic Wasting Disease Spread in Wisconsin.","authors":"Mennatallah Gouda, Jim Powell, W Jacob McClure, Daniel P Walsh, Daniel Storm","doi":"10.1007/s11538-024-01394-x","DOIUrl":"10.1007/s11538-024-01394-x","url":null,"abstract":"Chronic wasting disease (CWD) is a fatal neurodegenerative disease infecting cervids. It is highly contagious and caused by misfolded prions that propagate via templated conformational conversion of the cervid's normal prion protein. Prevalence of CWD in free-ranging deer in North America is mostly low, but in some regions local prevalence has reached 80%. CWD prions can be transmitted via direct contact with infected individuals or indirectly through the environment. Infected individuals shed prions through feces, urine, saliva or carcasses, and prions have long environmental persistence. Long-distance dispersal of infected deer poses a significant risk for CWD spread. We propose an integrodifference equation (IDE) model to capture CWD dynamics and the consequences of long-distance dispersal behavior in white-tailed deer (WTD, Odocoileus virginianus). A diffusion-settling model characterizes long-distance dispersal kernels, accommodating hypothetical dispersal behaviors through time-dependent settling rate functions. Three new closed-form dispersal kernels are approximated using Laplace's method and parameterized with GPS location data collected from WTD in Wisconsin, USA. Settling rates reflecting ongoing sensitivity to stimuli which prompt deer to disperse from their natal home range give the most supported long-distance dispersal kernel. Impact of long-distance dispersal on CWD spread is quantified using the IDE model. At high population densities, long-distance dispersal can magnify CWD spread by a factor of four. At lower population densities single infected individuals cannot initiate an outbreak, but CWD may still spread due to the accumulation of environmental hazard from prions behind the wave of invasion, possibly presenting substantial management challenges.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 4","pages":"52"},"PeriodicalIF":2.0,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143623671","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}

引用次数: 0

Exploring the Evolution of Altruistic Punishment with a PDE Model of Cultural Multilevel Selection.

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-03-12 DOI: 10.1007/s11538-025-01422-4

Daniel B Cooney

{"title":"Exploring the Evolution of Altruistic Punishment with a PDE Model of Cultural Multilevel Selection.","authors":"Daniel B Cooney","doi":"10.1007/s11538-025-01422-4","DOIUrl":"10.1007/s11538-025-01422-4","url":null,"abstract":"Two mechanisms that have been used to study the evolution of cooperative behavior are altruistic punishment, in which cooperative individuals pay additional costs to punish defection, and multilevel selection, in which competition between groups can help to counteract individual-level incentives to cheat. Boyd, Gintis, Bowles, and Richerson have used simulation models of cultural evolution to suggest that altruistic punishment and pairwise group-level competition can work in concert to promote cooperation, even when neither mechanism can do so on its own. In this paper, we formulate a PDE model for multilevel selection motivated by the approach of Boyd and coauthors, modeling individual-level birth-death competition with a replicator equation based on individual payoffs and describing group-level competition with pairwise conflicts based on differences in the average payoffs of the competing groups. Building off of existing PDE models for multilevel selection with frequency-independent group-level competition, we use analytical and numerical techniques to understand how the forms of individual and average payoffs can impact the long-time ability to sustain altruistic punishment in group-structured populations. We find several interesting differences between the behavior of our new PDE model with pairwise group-level competition and existing multilevel PDE models, including the observation that our new model can feature a non-monotonic dependence of the long-time collective payoff on the strength of altruistic punishment. Going forward, our PDE framework can serve as a way to connect and compare disparate approaches for understanding multilevel selection across the literature in evolutionary biology and anthropology.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 4","pages":"51"},"PeriodicalIF":2.0,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143613490","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}

引用次数: 0