Journal of Theoretical Biology最新文献_第9页

Optimal control of combination immunotherapy for a virtual murine cohort in a glioblastoma-immune dynamics model 胶质母细胞瘤-免疫动力学模型中虚拟小鼠队列的联合免疫疗法优化控制。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-20 DOI: 10.1016/j.jtbi.2024.111951

Hannah G. Anderson , Gregory P. Takacs , Jeffrey K. Harrison , Libin Rong , Tracy L. Stepien

{"title":"Optimal control of combination immunotherapy for a virtual murine cohort in a glioblastoma-immune dynamics model","authors":"Hannah G. Anderson , Gregory P. Takacs , Jeffrey K. Harrison , Libin Rong , Tracy L. Stepien","doi":"10.1016/j.jtbi.2024.111951","DOIUrl":"10.1016/j.jtbi.2024.111951","url":null,"abstract":"<div><div>The immune checkpoint inhibitor anti-PD-1, commonly used in cancer immunotherapy, has not been successful as a monotherapy for the highly aggressive brain cancer glioblastoma. However, when used in conjunction with a CC-chemokine receptor-2 (CCR2) antagonist, anti-PD-1 has shown efficacy in preclinical studies. In this paper, we aim to optimize treatment regimens for this combination immunotherapy using optimal control theory. We extend a treatment-free glioblastoma-immune dynamics ODE model to include interventions with anti-PD-1 and the CCR2 antagonist. An optimized regimen increases the survival of an average mouse from 32 days post-tumor implantation without treatment to 111 days with treatment. We scale this approach to a virtual murine cohort to evaluate mortality and quality of life concerns during treatment, and predict survival, tumor recurrence, or death after treatment. A parameter identifiability analysis identifies five parameters suitable for personalizing treatment within the virtual cohort. Sampling from these five practically identifiable parameters for the virtual murine cohort reveals that personalized, optimized regimens enhance survival: 84% of the virtual mice survive to day 100, compared to 60% survival in a previously studied experimental regimen. Subjects with high tumor growth rates and low T cell kill rates are identified as more likely to die during and after treatment due to their compromised immune systems and more aggressive tumors. Notably, the MDSC death rate emerges as a long-term predictor of either disease-free survival or death.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111951"},"PeriodicalIF":1.9,"publicationDate":"2024-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301240","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 consideration of massive estimation of dissociation rate constant for genotype–phenotype linking molecules bound to targets through washing/selection and next-generation sequencing 对通过洗涤/选择和新一代测序与靶标结合的基因型-表型连接分子的解离率常数进行大规模估算的数学考虑。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-19 DOI: 10.1016/j.jtbi.2024.111944

Takuyo Aita , Naoto Nemoto

{"title":"Mathematical consideration of massive estimation of dissociation rate constant for genotype–phenotype linking molecules bound to targets through washing/selection and next-generation sequencing","authors":"Takuyo Aita , Naoto Nemoto","doi":"10.1016/j.jtbi.2024.111944","DOIUrl":"10.1016/j.jtbi.2024.111944","url":null,"abstract":"<div><div>As one of methods for <em>in vitro</em> selection, a flow reactor type washing/selection system seems to be effective, where a ligand library is composed of “genotype–phenotype linking molecules”. In this system, high affinity ligands are selected by their respective “residual ratio” given by <span><math><mrow><mo>exp</mo><mrow><mo>(</mo><mo>−</mo><msub><mrow><mi>k</mi></mrow><mrow><mi>off</mi></mrow></msub><mo>×</mo><mi>t</mi><mo>)</mo></mrow></mrow></math></span>, where <span><math><msub><mrow><mi>k</mi></mrow><mrow><mi>off</mi></mrow></msub></math></span> is the dissociation rate constant and <span><math><mi>t</mi></math></span> is the washing time. In this paper, we mathematically considered the following possibility. When the washing/selection dynamics obeys the residual ratio <span><math><mrow><mo>exp</mo><mrow><mo>(</mo><mo>−</mo><msub><mrow><mi>k</mi></mrow><mrow><mi>off</mi></mrow></msub><mo>×</mo><mi>t</mi><mo>)</mo></mrow></mrow></math></span> deterministically and mole fraction measurement for sampled sequences by next-generation sequencing (NGS) is performed ideally, the “relative value” of <span><math><msub><mrow><mi>k</mi></mrow><mrow><mi>off</mi></mrow></msub></math></span> for each of high-ranking sequences can be estimated simultaneously. In addition to these, when the residual ratio for the whole ligand population is measured correctly, the “absolute value” for each sequence can be estimated. We deduced formulas to present the relative and absolute estimates, and mathematically analyzed the effect of fluctuations in the number of NGS reads on the estimates in details. These were confirmed by numerical simulations.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111944"},"PeriodicalIF":1.9,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301238","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

The evolution of fear-acquisition strategies under predation 捕食下恐惧获取策略的进化

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-19 DOI: 10.1016/j.jtbi.2024.111949

Megan E. Bishop, Maria R. Servedio, Brian A. Lerch

{"title":"The evolution of fear-acquisition strategies under predation","authors":"Megan E. Bishop, Maria R. Servedio, Brian A. Lerch","doi":"10.1016/j.jtbi.2024.111949","DOIUrl":"10.1016/j.jtbi.2024.111949","url":null,"abstract":"<div><div>Fear is a taxonomically widespread behavioral response that functions to keep individuals out of danger. Empirical research has demonstrated that a diverse set of strategies are used in order to acquire a fear response across animals. Animals often use a mixed strategy: fear is acquired both innately and through learning. Despite the ubiquity of the fear response, and its established importance for shaping predator–prey interactions, little is known about why different fear acquisition strategies evolve or why mixed strategies appear common. Here, we model the evolution of fear acquisition (learning versus innate) under predation. We assume a tradeoff where individuals that learn fear are at higher risk from predators initially, but eventually obtain a lower risk as they survive predation attempts. We find that frequent predator encounters, predators that are not very dangerous, and effective learning favor the evolution of learned fear. Only pure strategies of fear acquisition evolve unless individuals suffer from either a cost to fear or, especially, a cost to learning, either of which can lead to the evolution of mixed strategies. Our results thus shed light onto the evolution of mixed fear acquisition strategies and open the door to further research on the evolution of fear acquisition.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111949"},"PeriodicalIF":1.9,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301242","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

Convergence of reputations under indirect reciprocity 间接互惠下的声誉趋同。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-18 DOI: 10.1016/j.jtbi.2024.111947

Bryce Morsky , Joshua B. Plotkin , Erol Akçay

引用次数: 0

Temperature variability regulates the interactive effects of warming and pharmaceutical on aquatic ecosystem dynamics 温度变化调节着气候变暖和制药对水生生态系统动态的交互影响。

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-17 DOI: 10.1016/j.jtbi.2024.111948

Guangjing Qian , Dan Wu , Lai Zhang , Susanne Kortsch

{"title":"Temperature variability regulates the interactive effects of warming and pharmaceutical on aquatic ecosystem dynamics","authors":"Guangjing Qian , Dan Wu , Lai Zhang , Susanne Kortsch","doi":"10.1016/j.jtbi.2024.111948","DOIUrl":"10.1016/j.jtbi.2024.111948","url":null,"abstract":"<div><div>Climate warming and pharmaceutical contaminants have profound impacts on population dynamics and ecological community structure, yet the consequences of their interactive effects remain poorly understood. Here, we explore how climate warming interacts with pharmaceutical-induced boldness change to affect aquatic ecosystems, built on an empirically well-informed food-chain model, consisting of a size-structured fish consumer, a zooplankton prey, and a fish predator. Climate warming is characterized by both daily mean temperature (DMT) and diurnal temperature range (DTR) in our model. Results show that DMT and high levels of species’ boldness are the primary drivers of community instability. However, their interactive effects can lead to diverse outcomes: from predator collapse to coexistence with seasonality-driven cycles and coexistence with population interaction-driven cycles. The interactive effects are significantly modulated by daily temperature variability, where moderate DTR counteracts the destabilizing interactive effects by increasing consumer reproduction, while large temperature variability considerably reduces consumer biomass<em>,</em> destabilizing the community at high mean temperatures. Our analyses disentangle the respective roles of DMT, DTR and boldness in mediating the response of aquatic ecosystems to the impacts from pharmaceutical contaminants in the context of climate warming. The interactive effects of the environmental stressors reported here underscore the pressing need for studies aimed at quantifying the cumulative impacts of multiple environmental stressors on aquatic ecosystems.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111948"},"PeriodicalIF":1.9,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301241","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

New insights into the combined effect of dispersal and local dynamics in a two-patch population model 对双斑块种群模型中扩散和局部动态综合效应的新认识

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-17 DOI: 10.1016/j.jtbi.2024.111942

Daniel Franco , Juan Perán , Juan Segura

引用次数: 0

Delayed loss of stability of periodic travelling waves: Insights from the analysis of essential spectra 周期性行波的延迟失稳：本质光谱分析的启示

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-16 DOI: 10.1016/j.jtbi.2024.111945

Lukas Eigentler , Mattia Sensi

{"title":"Delayed loss of stability of periodic travelling waves: Insights from the analysis of essential spectra","authors":"Lukas Eigentler , Mattia Sensi","doi":"10.1016/j.jtbi.2024.111945","DOIUrl":"10.1016/j.jtbi.2024.111945","url":null,"abstract":"<div><div>Periodic travelling waves (PTW) are a common solution type of partial differential equations. Such models exhibit multistability of PTWs, typically visualised through the Busse balloon, and parameter changes typically lead to a cascade of wavelength changes through the Busse balloon. In the past, the stability boundaries of the Busse balloon have been used to predict such wavelength changes. Here, motivated by anecdotal evidence from previous work, we provide compelling evidence that the Busse balloon provides insufficient information to predict wavelength changes due to a delayed loss of stability phenomenon. Using two different reaction–advection–diffusion systems, we relate the delay that occurs between the crossing of a stability boundary in the Busse balloon and the occurrence of a wavelength change to features of the essential spectrum of the destabilised PTW. This leads to a predictive framework that can estimate the order of magnitude of such a time delay, which provides a novel “early warning sign” for pattern destabilisation. We illustrate the implementation of the predictive framework to predict under what conditions a wavelength change of a PTW occurs.</div></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111945"},"PeriodicalIF":1.9,"publicationDate":"2024-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022519324002303/pdfft?md5=3013d4efdcdbd16448a87c3fd0061653&pid=1-s2.0-S0022519324002303-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142301237","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

Persistent biological invasions alter ecological network topology, impacting disease transmission during community assembly 持续性生物入侵改变生态网络拓扑结构，影响群落集结过程中的疾病传播

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-15 DOI: 10.1016/j.jtbi.2024.111950

Min Su , Xiaowei Chen , Cang Hui

{"title":"Persistent biological invasions alter ecological network topology, impacting disease transmission during community assembly","authors":"Min Su , Xiaowei Chen , Cang Hui","doi":"10.1016/j.jtbi.2024.111950","DOIUrl":"10.1016/j.jtbi.2024.111950","url":null,"abstract":"<div><p>Ecological networks experiencing persistent biological invasions may exhibit distinct topological properties, complicating the understanding of how network topology affects disease transmission during invasion-driven community assembly. We developed a trait-based network model to assess the impact of network topology on disease transmission, measured as community- and species-level disease prevalence. We found that trait-based feeding interactions between host species determine the frequency distribution of the niche of co-occurring species in steady-state communities, being either bimodal or multimodal. The width of the growth kernel influences the degree-biomass relationship of species, being either weakly positive or strongly negative. When this relationship is weakly positive, species-level disease prevalence is primarily correlated with biomass. However, when the degree-biomass relationship is strongly negative, species-level disease prevalence is determined by the difference between a host species’ in-degree and out-degree closeness centrality. At the community level, disease prevalence is generally amplified by increasing host richness, community biomass, and the standard deviation of interaction generality, while it is diluted by higher network connectance. Our framework verifies the amplification effects of host richness during invasion-driven community assembly and offers valuable insights for estimating disease prevalence based on host network topology.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111950"},"PeriodicalIF":1.9,"publicationDate":"2024-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142242601","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

Genomic compliance with Chargaff’s second parity rule may have originated non-adaptively, but stem-loops now function adaptively 基因组遵守查尔加夫的第二条奇偶性规则可能是非适应性的，但茎环现在的功能是适应性的

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-12 DOI: 10.1016/j.jtbi.2024.111943

Donald R. Forsdyke

{"title":"Genomic compliance with Chargaff’s second parity rule may have originated non-adaptively, but stem-loops now function adaptively","authors":"Donald R. Forsdyke","doi":"10.1016/j.jtbi.2024.111943","DOIUrl":"10.1016/j.jtbi.2024.111943","url":null,"abstract":"<div><p>Of Chargaff’s four rules on DNA base quantity, his second parity rule (PR-2) is the most contentious. Various biometricians (e.g., Sueoka, Lobry) regarded PR-2 compliance as a non-adaptive feature of modern genomes that could be modeled through interrelations among mutation rates. However, PR-2 compliance with stem-loop potential was considered adaptively relevant by biochemists familiar with analyses of nucleic acid structure (e.g., of Crick) and of meiotic recombination (e.g., of Kleckner). Meanwhile, other biometricians had shown that PR-2 complementarity extended beyond individual bases (1-mers) to oligonucleotides (k-mers), possibly reflecting “advantageous DNA structure” (Nussinov). An “introns early” hypothesis (Reanney, Forsdyke) had suggested a primordial nucleic acid world with recombination-mediated error-correction requiring genome-wide stem-loop potential to have evolved prior to localized intrusions of protein-encoding potential (exons). Thus, a primordial genome was equivalent to one long intron. Indeed, when assessed as the base order-dependent component (correcting for local influences of GC%), modern genes, especially when evolving rapidly under positive Darwinian selection, display high intronic stem-loop potential. This suggests forced migration from neighboring exons by competing protein-encoding potential. PR-2 compliance may have first arisen non-adaptively. Primary prototypic structures were later strengthened by their adaptive contribution to recombination. Thus, contentious views may actually be in harmony.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111943"},"PeriodicalIF":1.9,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S0022519324002285/pdfft?md5=519c85205d674dc45843d7e184f3269f&pid=1-s2.0-S0022519324002285-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142233037","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

Solving the prisoner’s dilemma trap in Hamilton’s model of temporarily formed random groups 在汉密尔顿的临时随机群体模型中破解囚徒困境陷阱

IF 1.9 4区数学

Journal of Theoretical Biology Pub Date : 2024-09-11 DOI: 10.1016/j.jtbi.2024.111946

José F. Fontanari , Mauro Santos

{"title":"Solving the prisoner’s dilemma trap in Hamilton’s model of temporarily formed random groups","authors":"José F. Fontanari , Mauro Santos","doi":"10.1016/j.jtbi.2024.111946","DOIUrl":"10.1016/j.jtbi.2024.111946","url":null,"abstract":"<div><p>Explaining the evolution of cooperation in the strong altruism scenario, where a cooperator does not benefit from her contribution to the public goods, is a challenging problem that requires positive assortment among cooperators (i.e., cooperators must tend to associate with other cooperators) or punishment of defectors. The need for these drastic measures stems from the analysis of a group selection model of temporarily formed random groups introduced by Hamilton nearly fifty years ago to describe the fate of altruistic behavior in a population. Challenging conventional wisdom, we show analytically here that strong altruism evolves in Hamilton’s original model in the case of biparental sexual reproduction. Moreover, when the cost of cooperation is small and the amplified contribution shared by group members is large, cooperation is the only stable strategy in equilibrium. Thus, our results provide a solution to the ‘problem of origination’ of strong altruism, i.e. how cooperation can take off from an initial low frequency of cooperators. We discuss a possible reassessment of cooperation in cases of viral co-infection, as cooperation may even be favored in situations where the prisoner’s dilemma applies.</p></div>","PeriodicalId":54763,"journal":{"name":"Journal of Theoretical Biology","volume":"595 ","pages":"Article 111946"},"PeriodicalIF":1.9,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142227992","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