Journal of Mathematical Biology最新文献

{"title":"Phylogenetic network classes through the lens of expanding covers","authors":"Andrew Francis, Daniele Marchei, Mike Steel","doi":"10.1007/s00285-024-02075-y","DOIUrl":"https://doi.org/10.1007/s00285-024-02075-y","url":null,"abstract":"<p>It was recently shown that a large class of phylogenetic networks, the ‘labellable’ networks, is in bijection with the set of ‘expanding’ covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks can be characterised purely in terms of properties of their associated covers. These classes include the tree-based, tree-child, orchard, tree-sibling, and normal networks. In the opposite direction, we give an example of how a restriction on the set of expanding covers can define a new class of networks, which we call ‘spinal’ phylogenetic networks.</p>","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140600844","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":"The role of memory-based movements in the formation of animal home ranges","authors":"Nathan Ranc, John W. Cain, Francesca Cagnacci, Paul R. Moorcroft","doi":"10.1007/s00285-024-02055-2","DOIUrl":"https://doi.org/10.1007/s00285-024-02055-2","url":null,"abstract":"<p>Most animals live in spatially-constrained home ranges. The prevalence of this space-use pattern in nature suggests that general biological mechanisms are likely to be responsible for their occurrence. Individual-based models of animal movement in both theoretical and empirical settings have demonstrated that the revisitation of familiar areas through memory can lead to the formation of stable home ranges. Here, we formulate a deterministic, mechanistic home range model that includes the interplay between a bi-component memory and resource preference, and evaluate resulting patterns of space-use. We show that a bi-component memory process can lead to the formation of stable home ranges and control its size, with greater spatial memory capabilities being associated with larger home range size. The interplay between memory and resource preferences gives rise to a continuum of space-use patterns–from spatially-restricted movements into a home range that is influenced by local resource heterogeneity, to diffusive-like movements dependent on larger-scale resource distributions, such as in nomadism. Future work could take advantage of this model formulation to evaluate the role of memory in shaping individual performance in response to varying spatio-temporal resource patterns.</p>","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140600843","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":"Memory effects in disease modelling through kernel estimates with oscillatory time history","authors":"Adam Mielke, Mads Peter Sørensen, John Wyller","doi":"10.1007/s00285-024-02080-1","DOIUrl":"https://doi.org/10.1007/s00285-024-02080-1","url":null,"abstract":"<p>We design a linear chain trick algorithm for dynamical systems for which we have oscillatory time histories in the distributed time delay. We make use of this algorithmic framework to analyse memory effects in disease evolution in a population. The modelling is based on a susceptible-infected-recovered SIR—model and on a susceptible-exposed-infected-recovered SEIR—model through a kernel that dampens the activity based on the recent history of infectious individuals. This corresponds to adaptive behavior in the population or through governmental non-pharmaceutical interventions. We use the linear chain trick to show that such a model may be written in a Markovian way, and we analyze the stability of the system. We find that the adaptive behavior gives rise to either a stable equilibrium point or a stable limit cycle for a close to constant number of susceptibles, i.e. locally in time. We also show that the attack rate for this model is lower than it would be without the dampening, although the adaptive behavior disappears as time goes to infinity and the number of infected goes to zero.</p>","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140600999","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":"Hopf bifurcation in an age-structured predator–prey system with Beddington–DeAngelis functional response and constant harvesting","authors":"San-Xing Wu, Zhi-Cheng Wang, Shigui Ruan","doi":"10.1007/s00285-024-02070-3","DOIUrl":"https://doi.org/10.1007/s00285-024-02070-3","url":null,"abstract":"<p>In this paper, an age-structured predator–prey system with Beddington–DeAngelis (B–D) type functional response, prey refuge and harvesting is investigated, where the predator fertility function <i>f</i>(<i>a</i>) and the maturation function <span>(beta (a))</span> are assumed to be piecewise functions related to their maturation period <span>(tau )</span>. Firstly, we rewrite the original system as a non-densely defined abstract Cauchy problem and show the existence of solutions. In particular, we discuss the existence and uniqueness of a positive equilibrium of the system. Secondly, we consider the maturation period <span>(tau )</span> as a bifurcation parameter and show the existence of Hopf bifurcation at the positive equilibrium by applying the integrated semigroup theory and Hopf bifurcation theorem. Moreover, the direction of Hopf bifurcation and the stability of bifurcating periodic solutions are studied by applying the center manifold theorem and normal form theory. Finally, some numerical simulations are given to illustrate of the theoretical results and a brief discussion is presented.</p>","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140600998","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":"Modelling non-local cell-cell adhesion: a multiscale approach","authors":"Anna Zhigun, Mabel Lizzy Rajendran","doi":"10.1007/s00285-024-02079-8","DOIUrl":"https://doi.org/10.1007/s00285-024-02079-8","url":null,"abstract":"<p>Cell-cell adhesion plays a vital role in the development and maintenance of multicellular organisms. One of its functions is regulation of cell migration, such as occurs, e.g. during embryogenesis or in cancer. In this work, we develop a versatile multiscale approach to modelling a moving self-adhesive cell population that combines a careful microscopic description of a deterministic adhesion-driven motion component with an efficient mesoscopic representation of a stochastic velocity-jump process. This approach gives rise to mesoscopic models in the form of kinetic transport equations featuring multiple non-localities. Subsequent parabolic and hyperbolic scalings produce general classes of equations with non-local adhesion and myopic diffusion, a special case being the classical macroscopic model proposed in Armstrong et al. (J Theoret Biol 243(1): 98–113, 2006). Our simulations show how the combination of the two motion effects can unfold. Cell-cell adhesion relies on the subcellular cell adhesion molecule binding. Our approach lends itself conveniently to capturing this microscopic effect. On the macroscale, this results in an additional non-linear integral equation of a novel type that is coupled to the cell density equation.</p>","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140600760","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":"Back to the fundamentals: a reply to Basener and Sanford 2018","authors":"Zachary B. Hancock, Daniel Stern Cardinale","doi":"10.1007/s00285-024-02077-w","DOIUrl":"https://doi.org/10.1007/s00285-024-02077-w","url":null,"abstract":"<p>Fisher’s fundamental theorem of natural selection has haunted theoretical population genetic literature since it was proposed in 1930, leading to numerous interpretations. Most of the confusion stemmed from Fisher’s own obscure presentation. By the 1970s, a clearer view of Fisher’s theorem had been achieved and it was found that, regardless of its utility or significance, it represents a general theorem of evolutionary biology. Basener and Sanford (J Math Biol 76:1589–1622, 2018) writing in <i>JOMB</i>, however, paint a different picture of the fundamental theorem as one hindered by its assumptions and incomplete due to its failure to explicitly incorporate mutational effects. They argue that Fisher saw his theorem as a “mathematical proof of Darwinian evolution”. In this reply, we show that, contrary to Basener and Sanford, Fisher’s theorem is a general theorem that applies to any evolving population, and that, far from their assertion that it needed to be expanded, the theorem already implicitly incorporates ancestor–descendant variation. We also show that their numerical simulations produce unrealistic results. Lastly, we argue that Basener and Sanford’s motivations were in undermining not merely Fisher’s theorem, but the concept of universal common descent itself.</p>","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140600588","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":"Global analysis of an age-structured tuberculosis model with an application to Jiangsu, China.","authors":"Shuanglin Jing, Ling Xue, Hao Wang, Zhihang Peng","doi":"10.1007/s00285-024-02066-z","DOIUrl":"10.1007/s00285-024-02066-z","url":null,"abstract":"<p><p>Diagnostic delay for TB infected individuals and the lack of TB vaccines for adults are the main challenges to achieve the goals of WHO by 2050. In order to evaluate the impacts of diagnostic delay and vaccination for adults on prevalence of TB, we propose an age-structured model with latent age and infection age, and we incorporate Mycobacterium TB in the environment and vaccination into the model. Diagnostic delay is indicated by the age of infection before receiving treatment. The threshold dynamics are established in terms of the basic reproduction number <math><msub><mi>R</mi> <mn>0</mn></msub> </math> . When <math> <mrow><msub><mi>R</mi> <mn>0</mn></msub> <mo><</mo> <mn>1</mn></mrow> </math> , the disease-free equilibrium is globally asymptotically stable, which means that TB epidemic will die out; When <math> <mrow><msub><mi>R</mi> <mn>0</mn></msub> <mo>=</mo> <mn>1</mn></mrow> </math> , the disease-free equilibrium is globally attractive; there exists a unique endemic equilibrium and the endemic equilibrium is globally attractive when <math> <mrow><msub><mi>R</mi> <mn>0</mn></msub> <mo>></mo> <mn>1</mn></mrow> </math> . We estimate that the basic reproduction number <math> <mrow><msub><mi>R</mi> <mn>0</mn></msub> <mo>=</mo> <mn>0.5320</mn></mrow> </math> (95% CI (0.3060, 0.7556)) in Jiangsu Province, which means that TB epidemic will die out. However, we find that the annual number of new TB cases by 2050 is 1,151 (95%CI: (138, 8,014)), which means that it is challenging to achieve the goal of WHO by 2050. To this end, we evaluate the possibility of achieving the goals of WHO if we start vaccinating adults and reduce diagnostic delay in 2025. Our results demonstrate that when the diagnostic delay is reduced from longer than four months to four months, or 20% adults are vaccinated, the goal of WHO in 2050 can be achieved, and 73,137 (95%CI: (23,906, 234,086)) and 54,828 (95%CI: (15,811, 206,468)) individuals will be prevented from being infected from 2025 to 2050, respectively. The modeling approaches and simulation results used in this work can help policymakers design control measures to reduce the prevalence of TB.</p>","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140337477","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":"The effects of spatially-constrained treatment regions upon a model of wombat mange","authors":"Ivy J. Hindle, Lawrence K. Forbes, Stephen J. Walters, Scott Carver","doi":"10.1007/s00285-024-02078-9","DOIUrl":"https://doi.org/10.1007/s00285-024-02078-9","url":null,"abstract":"<p>The use of therapeutic agents is a critical option to manage wildlife disease, but their implementation is usually spatially constrained. We seek to expand knowledge around the effectiveness of management of environmentally-transmitted <i>Sarcoptes scabiei</i> on a host population, by studying the effect of a spatially constrained treatment regime on disease dynamics in the bare-nosed wombat <i>Vombatus ursinus</i>. A host population of wombats is modelled using a system of non-linear partial differential equations, a spatially-varying treatment regime is applied to this population and the dynamics are studied over a period of several years. Treatment could result in mite decrease within the treatment region, extending to a lesser degree outside, with significant increases in wombat population. However, the benefits of targeted treatment regions within an environment are shown to be dependent on conditions at the start (endemic vs. disease free), as well as on the locations of these special regions (centre of the wombat population or against a geographical boundary). This research demonstrates the importance of understanding the state of the environment and populations before treatment commences, the effects of re-treatment schedules within the treatment region, and the transient large-scale changes in mite numbers that can be brought about by sudden changes to the environment. It also demonstrates that, with good knowledge of the host-pathogen dynamics and the spatial terrain, it is possible to achieve substantial reduction in mite numbers within the target region, with increases in wombat numbers throughout the environment.\u0000</p>","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140600582","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":"Exact p-values for global network alignments via combinatorial analysis of shared GO terms","authors":"Wayne B. Hayes","doi":"10.1007/s00285-024-02058-z","DOIUrl":"https://doi.org/10.1007/s00285-024-02058-z","url":null,"abstract":"<p>Network alignment aims to uncover topologically similar regions in the protein–protein interaction (PPI) networks of two or more species under the assumption that topologically similar regions tend to perform similar functions. Although there exist a plethora of both network alignment algorithms and measures of topological similarity, currently no “gold standard” exists for evaluating how well either is able to uncover functionally similar regions. Here we propose a formal, mathematically and statistically rigorous method for evaluating the statistical significance of shared GO terms in a global, 1-to-1 alignment between two PPI networks. Given an alignment in which <i>k</i> aligned protein pairs share a particular GO term <i>g</i>, we use a combinatorial argument to precisely quantify the <i>p</i>-value of that alignment with respect to <i>g</i> compared to a random alignment. The <i>p</i>-value of the alignment with respect to <i>all</i> GO terms, including their inter-relationships, is approximated using the <i>Empirical Brown’s Method</i>. We note that, just as with BLAST’s <i>p</i>-values, this method is <i>not</i> designed to guide an alignment algorithm towards a solution; instead, just as with BLAST, an alignment is guided by a <i>scoring matrix or function</i>; the <i>p</i>-values herein are computed <i>after the fact</i>, providing independent feedback to the user on the <i>biological</i> quality of the alignment that was generated by optimizing the scoring function. Importantly, we demonstrate that among all GO-based measures of network alignments, ours is the only one that correlates with the precision of GO annotation <i>predictions</i>, paving the way for network alignment-based protein function prediction.</p>","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140323868","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":"Final epidemic size of a two-community SIR model with asymmetric coupling.","authors":"Zhimin Han, Yi Wang, Shan Gao, Guiquan Sun, Hao Wang","doi":"10.1007/s00285-024-02073-0","DOIUrl":"10.1007/s00285-024-02073-0","url":null,"abstract":"<p><p>Communities are commonly not isolated but interact asymmetrically with each other, allowing the propagation of infectious diseases within the same community and between different communities. To reveal the impact of asymmetrical interactions and contact heterogeneity on disease transmission, we formulate a two-community SIR epidemic model, in which each community has its contact structure while communication between communities occurs through temporary commuters. We derive an explicit formula for the basic reproduction number <math><msub><mi>R</mi> <mn>0</mn></msub> </math> , give an implicit equation for the final epidemic size z, and analyze the relationship between them. Unlike the typical positive correlation between <math><msub><mi>R</mi> <mn>0</mn></msub> </math> and z in the classic SIR model, we find a negatively correlated relationship between counterparts of our model deviating from homogeneous populations. Moreover, we investigate the impact of asymmetric coupling mechanisms on <math><msub><mi>R</mi> <mn>0</mn></msub> </math> . The results suggest that, in scenarios with restricted movement of susceptible individuals within a community, <math><msub><mi>R</mi> <mn>0</mn></msub> </math> does not follow a simple monotonous relationship, indicating that an unbending decrease in the movement of susceptible individuals may increase <math><msub><mi>R</mi> <mn>0</mn></msub> </math> . We further demonstrate that network contacts within communities have a greater effect on <math><msub><mi>R</mi> <mn>0</mn></msub> </math> than casual contacts between communities. Finally, we develop an epidemic model without restriction on the movement of susceptible individuals, and the numerical simulations suggest that the increase in human flow between communities leads to a larger <math><msub><mi>R</mi> <mn>0</mn></msub> </math> .</p>","PeriodicalId":50148,"journal":{"name":"Journal of Mathematical Biology","volume":null,"pages":null},"PeriodicalIF":1.9,"publicationDate":"2024-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140319751","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}