Bulletin of Mathematical Biology最新文献_第3页

When are Quarnets Sufficient to Reconstruct Semi-directed Phylogenetic Networks? 什么时候Quarnets足以重建半定向系统发育网络？

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-08-28 DOI: 10.1007/s11538-025-01510-5

Katharina T Huber, Leo van Iersel, Mark Jones, Vincent Moulton, Leonie Veenema-Nipius

{"title":"When are Quarnets Sufficient to Reconstruct Semi-directed Phylogenetic Networks?","authors":"Katharina T Huber, Leo van Iersel, Mark Jones, Vincent Moulton, Leonie Veenema-Nipius","doi":"10.1007/s11538-025-01510-5","DOIUrl":"10.1007/s11538-025-01510-5","url":null,"abstract":"Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa. They generalize phylogenetic trees since for example, unlike trees, they permit lineages to combine. Recently, there has been rising interest in semi-directed phylogenetic networks, which are mixed graphs in which certain lineage combination events are represented by directed edges coming together, whereas the remaining edges are left undirected. One reason to consider such networks is that it can be difficult to root a network using real data. In this paper, we consider the problem of when a semi-directed phylogenetic network is defined or encoded by the smaller networks that it induces on the 4-leaf subsets of its leaf set. These smaller networks are called quarnets. We prove that semi-directed binary level-2 phylogenetic networks are encoded by their quarnets, but that this is not the case for level-3. In addition, we prove that the so-called blob tree of a semi-directed binary network, a tree that gives the coarse-grained structure of the network, is always encoded by the quarnets of the network. These results are relevant for proving the statistical consistency of programs that are currently being developed for reconstructing phylogenetic networks from practical data, such as the recently developed SQUIRREL software tool.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 10","pages":"136"},"PeriodicalIF":2.2,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12394373/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144943875","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

An Asymptotic Analysis of Bivalent Monoclonal Antibody-Antigen Binding. 二价单克隆抗体-抗原结合的渐近分析。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-08-26 DOI: 10.1007/s11538-025-01520-3

Luke A Heirene, Helen M Byrne, James W T Yates, Eamonn A Gaffney

{"title":"An Asymptotic Analysis of Bivalent Monoclonal Antibody-Antigen Binding.","authors":"Luke A Heirene, Helen M Byrne, James W T Yates, Eamonn A Gaffney","doi":"10.1007/s11538-025-01520-3","DOIUrl":"10.1007/s11538-025-01520-3","url":null,"abstract":"Ligand-receptor interactions are fundamental to many biological processes. For example in antibody-based immunotherapies, the dynamics of an antibody binding with its target antigen directly influence the potency and efficacy of monoclonal antibody (mAb) therapies. In this paper, we present an asymptotic analysis of an ordinary differential equation (ODE) model of bivalent antibody-antigen binding in the context of mAb cancer therapies, highlighting the complexity associated with bivalency of the antibody. To understand what drives the complex temporal dynamics of bivalent antibody-antigen binding, we construct approximate solutions to the model equations at different timescales that are in good agreement with numerical simulations of the full model. We focus on two scenarios: one for which unbound antigens are abundant, and one for which they are scarce. We show how the dominant balance within the model equations changes between the two scenarios. Of particular importance to the potency and efficacy of mAb treatments are quantities such as antigen occupancy and bound antibody number. We use the results of our asymptotic analysis to estimate the long-time values of these quantities that could be combined with experimental data to facilitate parameter estimation.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 10","pages":"135"},"PeriodicalIF":2.2,"publicationDate":"2025-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12380953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144943864","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

Emergent Kinematics and Flow Structure of Tension Driven Pulsing Xeniid Corals. 张力驱动脉动珊瑚的涌现运动学与流动结构。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-08-22 DOI: 10.1007/s11538-025-01493-3

Matea Santiago, Alexander Hoover, Laura A Miller

{"title":"Emergent Kinematics and Flow Structure of Tension Driven Pulsing Xeniid Corals.","authors":"Matea Santiago, Alexander Hoover, Laura A Miller","doi":"10.1007/s11538-025-01493-3","DOIUrl":"https://doi.org/10.1007/s11538-025-01493-3","url":null,"abstract":"This work presents a three-dimensional fully-coupled fluid-structure interaction (FSI) model of a pulsing soft coral polyp where the movement of the tentacles is driven by a prescribed active tension during contraction with a passive expansion due to the elastic behavior of the tentacles. The resulting motion of the tentacles is emergent rather than prescribed. This approach allows one to determine how the coral's underlying morphology, mechanics, and neural activation affect its kinematics and the resulting fluid motion, which has implications for soft robotic design. More specifically, one can easily vary the maximum tension exerted by the coral, the elasticity of the model coral body, and the pulsation frequency to understand how altering neuromechanical parameters affects the flux above the coral and the energy required to pulse actively. When the parameters are tuned such that the emergent motion is similar to that measured for live coral, a large amount of upward flux is generated for a relatively low energy expenditure. Additionally, a circulation analysis reveals the generation of stopping and starting vortices with each pulse cycle, as seen in other Cnidarians such as jellyfish. We find that the relationship between kinematics, upward flux, circulation, and the polyp's active and passive material properties is highly complex. Our results suggest that the corals operate at or near an energetically favorable regime. This work further increases our understanding of how and when sessile organisms should expend energy to actively pulse to enhance nutrient exchange.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 9","pages":"133"},"PeriodicalIF":2.2,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144944027","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

Metaconcepts of Rooted Tree Balance. 树根平衡的元概念。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-08-22 DOI: 10.1007/s11538-025-01509-y

Mareike Fischer, Tom Niklas Hamann, Kristina Wicke

{"title":"Metaconcepts of Rooted Tree Balance.","authors":"Mareike Fischer, Tom Niklas Hamann, Kristina Wicke","doi":"10.1007/s11538-025-01509-y","DOIUrl":"https://doi.org/10.1007/s11538-025-01509-y","url":null,"abstract":"Measures of tree balance play an important role in many different research areas such as mathematical phylogenetics or theoretical computer science. Typically, tree balance is quantified by a single number which is assigned to the tree by a balance or imbalance index, of which several exist in the literature. Most of these indices are based on structural aspects of tree shape, such as clade sizes or leaf depths. For instance, indices like the Sackin index, total cophenetic index, and <math><mover><mi>s</mi> <mo>^</mo></mover> </math> -shape statistic all quantify tree balance through clade sizes, albeit with different definitions and properties. In this paper, we formalize the idea that many tree (im)balance indices are functions of similar underlying tree shape characteristics by introducing metaconcepts of tree balance. A metaconcept is a function <math><msub><mi>Φ</mi> <mi>f</mi></msub> </math> that depends on a function f capturing some aspect of tree shape, such as balance values, clade sizes, or leaf depths. These metaconcepts encompass existing indices but also provide new means of measuring tree balance. The versatility and generality of metaconcepts allow for the systematic study of entire families of (im)balance indices, providing deeper insights that extend beyond index-by-index analysis.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 9","pages":"134"},"PeriodicalIF":2.2,"publicationDate":"2025-08-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12373716/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144943266","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

Group-based phylogenetic models on 3-sunlet networks. 基于群的3-sunlet网络系统发育模型。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-08-18 DOI: 10.1007/s11538-025-01506-1

Shelby Cox, Elizabeth Gross, Samuel Martin

引用次数: 0

Evolutionary Dispersal of Species with Starvation-Driven Diffusion Incorporating Perceptual Constraints in Competition Models in Heterogeneous Habitats. 异质生境竞争模型中包含感知约束的饥饿驱动扩散的物种进化扩散。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-08-15 DOI: 10.1007/s11538-025-01513-2

Youngseok Chang, Wonhyung Choi, Inkyung Ahn

{"title":"Evolutionary Dispersal of Species with Starvation-Driven Diffusion Incorporating Perceptual Constraints in Competition Models in Heterogeneous Habitats.","authors":"Youngseok Chang, Wonhyung Choi, Inkyung Ahn","doi":"10.1007/s11538-025-01513-2","DOIUrl":"10.1007/s11538-025-01513-2","url":null,"abstract":"This study examines a competition model featuring nonuniform dispersal, referred to as starvation-driven-type diffusion (SDTD). This model incorporates the motility of species that adhere to a starvation-driven diffusion (SDTD). paradigm while also factoring in perceptual constraints within a spatially heterogeneous region. In the proposed model, our study aims to understand the impact of SDTD on system dynamics in a spatially heterogeneous environment. To achieve this, we consider a Lotka-Volterra-type competition model exhibiting identical population dynamics under no-flux boundary conditions. To illuminate the evolutionary implications of SDTD, this study contrasts two different models. The first model involves two species with distinct, uniform diffusion rates. In comparison, the second model features one species that adheres to a constant diffusion rate and another that operates under the principles of SDTD. This study focuses on analyzing the fitness variation of competing species based on their respective diffusion dynamics: (i) The study examines how the fitness of a species following SDTD changes compared to another species that diffuses at a constant rate. (ii) We investigate the dynamics of fitness alteration within a competitive two-species model wherein one species exhibits a constant diffusion rate while the other species alternates between constant-rate diffusion and SDTD. In addition, we examine how the shifting diffusion strategies of one species affect its fitness relative to a species with a fixed, constant diffusion rate. Our conclusions suggest that a species adhering to SDTD may enhance its fitness, consistent with the model incorporating SDD. Nonetheless, we show that certain circumstances may exist where SDTD does not result in increased fitness for a species, mainly due to the perceptual limitations of that species.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 9","pages":"131"},"PeriodicalIF":2.2,"publicationDate":"2025-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144854650","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

Insights on Influenza Control Through Vaccination for the 2023-2024 Season in the USA: Mathematical Modeling, Optimal Control, and Sensitivity Analysis. 美国2023-2024年流感季节疫苗接种控制的见解：数学建模、最优控制和敏感性分析

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-08-14 DOI: 10.1007/s11538-025-01494-2

Ana-Maria Croicu

引用次数: 0

Mathematical Modelling and Uncertainty Quantification for Analysis of Biphasic Coral Reef Recovery Patterns. 双相珊瑚礁恢复模式分析的数学模型和不确定性量化。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-08-12 DOI: 10.1007/s11538-025-01512-3

David J Warne, Kerryn Crossman, Grace E M Heron, Jesse A Sharp, Wang Jin, Paul Pao-Yen Wu, Matthew J Simpson, Kerrie Mengersen, Juan-C Ortiz

{"title":"Mathematical Modelling and Uncertainty Quantification for Analysis of Biphasic Coral Reef Recovery Patterns.","authors":"David J Warne, Kerryn Crossman, Grace E M Heron, Jesse A Sharp, Wang Jin, Paul Pao-Yen Wu, Matthew J Simpson, Kerrie Mengersen, Juan-C Ortiz","doi":"10.1007/s11538-025-01512-3","DOIUrl":"10.1007/s11538-025-01512-3","url":null,"abstract":"Coral reefs are increasingly subjected to major disturbances threatening the health of marine ecosystems. Substantial research is underway to develop intervention strategies that assist reefs in recovery from, and resistance to, inevitable future climate and weather extremes. To assess potential benefits of interventions, mechanistic understanding of coral reef recovery and resistance patterns is essential. Recent evidence suggests that more than half of the reefs surveyed across the Great Barrier Reef (GBR) exhibit deviations from standard recovery modelling assumptions when the initial coral cover is low ( <math><mrow><mo>≤</mo> <mn>10</mn></mrow> </math> %). New modelling is necessary to account for these observed patterns to better inform management strategies. We consider a new model for reef recovery at the coral cover scale that accounts for biphasic recovery patterns. The model is based on a multispecies Richards' growth model that includes a change point in the recovery patterns. Bayesian inference is applied for uncertainty quantification of key parameters for assessing reef health and recovery patterns. This analysis is applied to benthic survey data from the Australian Institute of Marine Science (AIMS). We demonstrate agreement between model predictions and data across every recorded recovery trajectory with at least two years of observations following disturbance events occurring between 1992-2020. This new approach will enable new insights into the biological, ecological and environmental factors that contribute to the duration and severity of biphasic coral recovery patterns across the GBR. These new insights will help to inform managements and monitoring practice to mitigate the impacts of climate change on coral reefs.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 9","pages":"129"},"PeriodicalIF":2.2,"publicationDate":"2025-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144820619","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

Modeling Combination Therapies and T Cell Exhaustion Dynamics in the Tumor Under Immune Checkpoint Blockade. 免疫检查点阻断下肿瘤中联合治疗和T细胞衰竭动力学的建模。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-08-11 DOI: 10.1007/s11538-025-01507-0

Xiulan Lai, Teng Yu

{"title":"Modeling Combination Therapies and T Cell Exhaustion Dynamics in the Tumor Under Immune Checkpoint Blockade.","authors":"Xiulan Lai, Teng Yu","doi":"10.1007/s11538-025-01507-0","DOIUrl":"10.1007/s11538-025-01507-0","url":null,"abstract":"Chronic antigen exposure in the tumor microenvironment drives CD <math><msup><mn>8</mn> <mo>+</mo></msup> </math> T cell exhaustion, marked by increased inhibitory receptors and diminished effector functions. Immune checkpoint blockade seeks to prevent or reverse exhaustion, but its success relies on the pre-existing state of tumor-infiltrating T cells. To investigate this, we developed a mathematical model examining: (1) how T cell exhaustion disrupts tumor-immune equilibrium, (2) anti-PD-L1 efficacy across exhaustion states, and (3) efficacy of next-generation therapies (e.g., IFN <math><mi>α</mi></math> -anti-PD-L1, PD1-IL2v). Stability analysis and simulations reveal that tumor PD-L1 expression critically influences immune dynamics, particularly the bistability of tumor-free and tumorous states. High PD-1 expression and exhaustion rates correlate with growth of tumor and impaired expansion of less-exhausted CD <math><msup><mn>8</mn> <mo>+</mo></msup> </math> T cells. While anti-PD-L1 efficacy depends on baseline exhaustion, severe exhaustion enables immune escape. Next-generation therapies enhancing cytotoxicity and sustaining less-exhausted T cell populations show improved tumor control, suggesting combination strategies may overcome resistance.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 9","pages":"128"},"PeriodicalIF":2.2,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144815782","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

Optimal Control of Immune Checkpoint Inhibitor Therapy in a Heart-Tumour Model. 免疫检查点抑制剂治疗在心脏肿瘤模型中的最优控制。

IF 2.2 4区数学

Bulletin of Mathematical Biology Pub Date : 2025-08-11 DOI: 10.1007/s11538-025-01468-4

Solveig A van der Vegt, Ruth E Baker, Sarah L Waters

{"title":"Optimal Control of Immune Checkpoint Inhibitor Therapy in a Heart-Tumour Model.","authors":"Solveig A van der Vegt, Ruth E Baker, Sarah L Waters","doi":"10.1007/s11538-025-01468-4","DOIUrl":"10.1007/s11538-025-01468-4","url":null,"abstract":"Autoimmune myocarditis, or cardiac muscle inflammation, is a rare but frequently fatal side-effect of immune checkpoint inhibitors (ICIs), a class of cancer therapies. Despite the dangers that side-effects such as these pose to patients, they are rarely, if ever, included explicitly when mechanistic mathematical modelling of cancer therapy is used for optimization of treatment. In this paper, we develop a two-compartment mathematical model which incorporates the impact of ICIs on both the heart and the tumour. Such a model can be used to inform the conditions under which autoimmune myocarditis may develop as a consequence of treatment. We use this model in an optimal control framework to design optimized dosing schedules for three types of ICI therapy that balance the positive and negative effects of treatment. We show that including the negative side-effects of ICI treatment explicitly within the mathematical framework significantly impacts the predictions for the optimized dosing schedule, thus stressing the importance of a holistic approach to optimizing cancer therapy regimens.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":"87 9","pages":"127"},"PeriodicalIF":2.2,"publicationDate":"2025-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12339619/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144815783","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