Bulletin of Mathematical Biology最新文献_第4页

Variational Supertrees for Bayesian Phylogenetics. 贝叶斯系统进化论的变异超树

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-05 DOI: 10.1007/s11538-024-01338-5

Michael D Karcher, Cheng Zhang, Frederic A Matsen

引用次数: 0

Cost Optimisation of Individual-Based Institutional Reward Incentives for Promoting Cooperation in Finite Populations. 促进有限人群合作的基于个人的制度奖励激励的成本优化。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-05 DOI: 10.1007/s11538-024-01344-7

M H Duong, C M Durbac, T A Han

{"title":"Cost Optimisation of Individual-Based Institutional Reward Incentives for Promoting Cooperation in Finite Populations.","authors":"M H Duong, C M Durbac, T A Han","doi":"10.1007/s11538-024-01344-7","DOIUrl":"10.1007/s11538-024-01344-7","url":null,"abstract":"In this paper, we study the problem of cost optimisation of individual-based institutional incentives (reward, punishment, and hybrid) for guaranteeing a certain minimal level of cooperative behaviour in a well-mixed, finite population. In this scheme, the individuals in the population interact via cooperation dilemmas (Donation Game or Public Goods Game) in which institutional reward is carried out only if cooperation is not abundant enough (i.e., the number of cooperators is below a threshold <math><mrow><mn>1</mn> <mo>≤</mo> <mi>t</mi> <mo>≤</mo> <mi>N</mi> <mo>-</mo> <mn>1</mn></mrow> </math> , where N is the population size); and similarly, institutional punishment is carried out only when defection is too abundant. We study analytically the cases <math><mrow><mi>t</mi> <mo>=</mo> <mn>1</mn></mrow> </math> for the reward incentive under the small mutation limit assumption and two different initial states, showing that the cost function is always non-decreasing. We derive the neutral drift and strong selection limits when the intensity of selection tends to zero and infinity, respectively. We numerically investigate the problem for other values of t and for population dynamics with arbitrary mutation rates.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11300551/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141888537","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

Relaxation and Noise-Driven Oscillations in a Model of Mitotic Spindle Dynamics 有丝分裂纺锤体动力学模型中的弛豫和噪声驱动振荡

IF 3.5 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-03 DOI: 10.1007/s11538-024-01341-w

Dionn Hargreaves, Sarah Woolner, Oliver E. Jensen

{"title":"Relaxation and Noise-Driven Oscillations in a Model of Mitotic Spindle Dynamics","authors":"Dionn Hargreaves, Sarah Woolner, Oliver E. Jensen","doi":"10.1007/s11538-024-01341-w","DOIUrl":"https://doi.org/10.1007/s11538-024-01341-w","url":null,"abstract":"During cell division, the mitotic spindle moves dynamically through the cell to position the chromosomes and determine the ultimate spatial position of the two daughter cells. These movements have been attributed to the action of cortical force generators which pull on the astral microtubules to position the spindle, as well as pushing events by these same microtubules against the cell cortex and plasma membrane. Attachment and detachment of cortical force generators working antagonistically against centring forces of microtubules have been modelled previously (Grill et al. in Phys Rev Lett 94:108104, 2005) via stochastic simulations and mean-field Fokker–Planck equations (describing random motion of force generators) to predict oscillations of a spindle pole in one spatial dimension. Using systematic asymptotic methods, we reduce the Fokker–Planck system to a set of ordinary differential equations (ODEs), consistent with a set proposed by Grill et al., which can provide accurate predictions of the conditions for the Fokker–Planck system to exhibit oscillations. In the limit of small restoring forces, we derive an algebraic prediction of the amplitude of spindle-pole oscillations and demonstrate the relaxation structure of nonlinear oscillations. We also show how noise-induced oscillations can arise in stochastic simulations for conditions in which the mean-field Fokker–Planck system predicts stability, but for which the period can be estimated directly by the ODE model and the amplitude by a related stochastic differential equation that incorporates random binding kinetics.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141885519","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

Blood Lipoproteins Shape the Phenotype and Lipid Content of Early Atherosclerotic Lesion Macrophages: A Dual-Structured Mathematical Model. 血脂蛋白塑造早期动脉粥样硬化病变巨噬细胞的表型和脂质含量：双重结构数学模型

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-08-02 DOI: 10.1007/s11538-024-01342-9

Keith L Chambers, Mary R Myerscough, Michael G Watson, Helen M Byrne

{"title":"Blood Lipoproteins Shape the Phenotype and Lipid Content of Early Atherosclerotic Lesion Macrophages: A Dual-Structured Mathematical Model.","authors":"Keith L Chambers, Mary R Myerscough, Michael G Watson, Helen M Byrne","doi":"10.1007/s11538-024-01342-9","DOIUrl":"10.1007/s11538-024-01342-9","url":null,"abstract":"Macrophages in atherosclerotic lesions exhibit a spectrum of behaviours or phenotypes. The phenotypic distribution of monocyte-derived macrophages (MDMs), its correlation with MDM lipid content, and relation to blood lipoprotein densities are not well understood. Of particular interest is the balance between low density lipoproteins (LDL) and high density lipoproteins (HDL), which carry bad and good cholesterol respectively. To address these issues, we have developed a mathematical model for early atherosclerosis in which the MDM population is structured by phenotype and lipid content. The model admits a simpler, closed subsystem whose analysis shows how lesion composition becomes more pathological as the blood density of LDL increases relative to the HDL capacity. We use asymptotic analysis to derive a power-law relationship between MDM phenotype and lipid content at steady-state. This relationship enables us to understand why, for example, lipid-laden MDMs have a more inflammatory phenotype than lipid-poor MDMs when blood LDL lipid density greatly exceeds HDL capacity. We show further that the MDM phenotype distribution always attains a local maximum, while the lipid content distribution may be unimodal, adopt a quasi-uniform profile or decrease monotonically. Pathological lesions exhibit a local maximum in both the phenotype and lipid content MDM distributions, with the maximum at an inflammatory phenotype and near the lipid content capacity respectively. These results illustrate how macrophage heterogeneity arises in early atherosclerosis and provide a framework for future model validation through comparison with single-cell RNA sequencing data.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11297092/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141874253","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

The Distance Between: An Algorithmic Approach to Comparing Stochastic Models to Time-Series Data. 之间的距离：将随机模型与时间序列数据进行比较的算法方法。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-26 DOI: 10.1007/s11538-024-01331-y

Brock D Sherlock, Marko A A Boon, Maria Vlasiou, Adelle C F Coster

{"title":"The Distance Between: An Algorithmic Approach to Comparing Stochastic Models to Time-Series Data.","authors":"Brock D Sherlock, Marko A A Boon, Maria Vlasiou, Adelle C F Coster","doi":"10.1007/s11538-024-01331-y","DOIUrl":"10.1007/s11538-024-01331-y","url":null,"abstract":"While mean-field models of cellular operations have identified dominant processes at the macroscopic scale, stochastic models may provide further insight into mechanisms at the molecular scale. In order to identify plausible stochastic models, quantitative comparisons between the models and the experimental data are required. The data for these systems have small sample sizes and time-evolving distributions. The aim of this study is to identify appropriate distance metrics for the quantitative comparison of stochastic model outputs and time-evolving stochastic measurements of a system. We identify distance metrics with features suitable for driving parameter inference, model comparison, and model validation, constrained by data from multiple experimental protocols. In this study, stochastic model outputs are compared to synthetic data across three scales: that of the data at the points the system is sampled during the time course of each type of experiment; a combined distance across the time course of each experiment; and a combined distance across all the experiments. Two broad categories of comparators at each point were considered, based on the empirical cumulative distribution function (ECDF) of the data and of the model outputs: discrete based measures such as the Kolmogorov-Smirnov distance, and integrated measures such as the Wasserstein-1 distance between the ECDFs. It was found that the discrete based measures were highly sensitive to parameter changes near the synthetic data parameters, but were largely insensitive otherwise, whereas the integrated distances had smoother transitions as the parameters approached the true values. The integrated measures were also found to be robust to noise added to the synthetic data, replicating experimental error. The characteristics of the identified distances provides the basis for the design of an algorithm suitable for fitting stochastic models to real world stochastic data.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11282162/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141765546","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

Identifiability of Level-1 Species Networks from Gene Tree Quartets. 从基因树四元组识别一级物种网络的可识别性

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-25 DOI: 10.1007/s11538-024-01339-4

Elizabeth S Allman, Hector Baños, Marina Garrote-Lopez, John A Rhodes

引用次数: 0

Fitting Epidemic Models to Data: A Tutorial in Memory of Fred Brauer. 根据数据拟合流行病模型：纪念弗雷德-布劳尔教程》。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-25 DOI: 10.1007/s11538-024-01326-9

David J D Earn, Sang Woo Park, Benjamin M Bolker

引用次数: 0

A Mathematical Model for Fibrous Dysplasia: The Role of the Flow of Mutant Cells. 纤维发育不良的数学模型：突变细胞流的作用

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-15 DOI: 10.1007/s11538-024-01336-7

Mariia Soloviova, Juan C Beltrán-Vargas, Luis Fernandez de Castro, Juan Belmonte-Beitia, Víctor M Pérez-García, Magdalena Caballero

引用次数: 0

Modelling Role of Protective and Nonprotective HLA Allele Inducing Different HIV Infection Outcomes. 模拟保护性和非保护性 HLA 等位基因诱发不同 HIV 感染结果的作用。

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-13 DOI: 10.1007/s11538-024-01334-9

Shilian Xu

{"title":"Modelling Role of Protective and Nonprotective HLA Allele Inducing Different HIV Infection Outcomes.","authors":"Shilian Xu","doi":"10.1007/s11538-024-01334-9","DOIUrl":"10.1007/s11538-024-01334-9","url":null,"abstract":"Human immunodeficiency virus (HIV) infects CD4+ cells and causes progressive immune function failure, and CD8+ cells lyse infected CD4+ cell via recognising peptide presented by human leukocyte antigens (HLA). Variations in HLA allele lead to observed different HIV infection outcomes. Within-host HIV dynamics involves virus replication within infected cells and lysing of infected cells by CD8+ cells, but how variations in HLA alleles determine different infection outcomes was far from clear. Here, we used mathematical modelling and parameter inference with a new analysis of published virus inhibition assay data to estimate CD8+ cell lysing efficiency, and found that lysing efficiency fall in the gap between low bound (0.1-0.2 day-1 (Elemans et al. in PLoS Comput Biol 8(2):e1002381, 2012)) and upper boundary (6.5-8.4 day-1 (Wick et al. in J Virol 79(21):13579-13586, 2005)). Our outcomes indicate that both lysing efficiency and viral inoculum size jointly determine observed different infection outcomes. Low lysing rate associated with non-protective HLA alleles leads to monostable viral kinetic to high viral titre and oscillatory viral kinetics. High lysing rate associated with protective HLA alleles leads monostable viral kinetic to low viral titre and bistable viral kinetics; at a specific interval of CD8+ cell counts, small viral inoculum sizes are inhibited but not large viral inoculum sizes remain infectious. Further, with CD8+ cell recruitment, HIV kinetics always exhibit oscillatory kinetics, but lysing rate is negatively correlated with range of CD8+ cell count. Our finding highlights role of HLA allele determining different infection outcomes, thereby providing a potential mechanistic explanation for observed good and bad HIV infection outcomes induced by protective HLA allele.","PeriodicalId":9372,"journal":{"name":"Bulletin of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":2.0,"publicationDate":"2024-07-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11246342/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141603305","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

Maximum Likelihood Estimation for Unrooted 3-Leaf Trees: An Analytic Solution for the CFN Model. 无根三叶树的最大似然估计：CFN 模型的解析解

IF 2 4区数学

Bulletin of Mathematical Biology Pub Date : 2024-07-12 DOI: 10.1007/s11538-024-01340-x

Max Hill, Sebastien Roch, Jose Israel Rodriguez

引用次数: 0