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Immune responses may make HIV-1 therapeutic interfering particles less effective 免疫反应可能使HIV-1治疗干扰颗粒效果降低。
IF 2 4区 数学 Q2 BIOLOGY Pub Date : 2026-02-21 Epub Date: 2025-11-29 DOI: 10.1016/j.jtbi.2025.112317
Griffin Kutler Dodd, Rob J. de Boer
The current standard treatment for HIV-1 infection is antiretroviral therapy, which effectively suppresses viral replication but requires a lifelong drug regimen. An alternative treatment approach is a single injection of a modified version of the HIV-1 virus, termed a therapeutic interfering particle (TIP), that lacks replication machinery and suppresses the wild-type virus by competing for viral proteins. Here, we derive a novel ordinary differential equation model of TIP dynamics. We confirm results from previous models that TIPs can reduce viral load when doubly infected cells produce at least as many virus particles as singly infected cells. By deriving the basic reproduction number R0T of a TIP, we predict that concurrent antiretroviral therapy should make it more difficult for a TIP to persist in a host. Adding an immune response to our model reveals that even a moderate immune response against virally infected cells drastically decreases the range of parameter values for which therapy is effective. Together, these results show that the success of TIPs depend on the properties of the wild-type virus and even more strongly on the immune response, which makes it hard to predict therapeutic success.
目前治疗HIV-1感染的标准疗法是抗逆转录病毒疗法,这种疗法能有效抑制病毒复制,但需要终生服药。另一种治疗方法是单次注射HIV-1病毒的修饰版本,称为治疗干扰粒子(TIP),它缺乏复制机制,通过竞争病毒蛋白来抑制野生型病毒。本文推导了一种新型的TIP动力学常微分方程模型。我们证实了先前模型的结果,即当双重感染的细胞产生至少与单一感染的细胞一样多的病毒颗粒时,TIPs可以减少病毒载量。通过推导TIP的基本繁殖数R0T,我们预测同时进行抗逆转录病毒治疗会使TIP更难以在宿主中持续存在。在我们的模型中加入免疫反应表明,即使是针对病毒感染细胞的适度免疫反应也会大大降低治疗有效的参数值范围。总之,这些结果表明,TIPs的成功取决于野生型病毒的特性,甚至更强烈地取决于免疫反应,这使得很难预测治疗成功。
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引用次数: 0
Emergence of longitudinal queue behavior based on topological interaction and asynchronous dynamics 基于拓扑交互和异步动态的纵向队列行为的出现。
IF 2 4区 数学 Q2 BIOLOGY Pub Date : 2026-02-07 Epub Date: 2025-11-12 DOI: 10.1016/j.jtbi.2025.112318
Decheng Kong, Kai Xue, Ping Wang, Zeyu Xu, Zhiqin Huang
Coordinated longitudinal queue behavior in biological groups, such as migratory bird flocks, remains underexplored in classical collective motion models that focus on metric-based interactions and synchronous dynamics. This study utilizes a modified self-propelled particle model incorporating topological interactions, gliding asynchrony, and limited view angle to investigate the mechanisms driving longitudinal queue formation. Simulations reveal that interacting with only two topological neighbors is critical for stable queue emergence, with an optimal view angle range of [200°, 270°] balancing frontward tracking and lateral collision avoidance. Gliding asynchrony enhances queue formation efficiency by reducing neighbor interaction frequency, leading to higher success rates and lower interaction complexity compared to synchronous or random update mechanisms. Topological interaction networks exhibit high connectivity and stability, fundamentally supporting queue maintenance, while metric-based or Voronoi interactions fail to produce linear order. The study highlights the interplay of limited sensory perception, low neighbor connectivity, and asynchronous dynamics in self-organized migration queues, providing a theoretical guidance for understanding animal collective behavior and guiding robotic swarm design.
生物群体(如候鸟群)的协调纵向队列行为,在经典的基于度量的相互作用和同步动力学的集体运动模型中仍未得到充分研究。本研究利用一个改进的自推进粒子模型,结合拓扑相互作用、滑行异步和有限视角来研究驱动纵向队列形成的机制。仿真结果表明,仅与两个拓扑邻居相互作用对于稳定的队列涌现至关重要,最佳视角范围为[200°,270°],以平衡前向跟踪和侧避碰撞。与同步或随机更新机制相比,滑动异步通过降低邻居交互频率来提高队列形成效率,从而获得更高的成功率和更低的交互复杂性。拓扑交互网络表现出高度的连通性和稳定性,从根本上支持队列维护,而基于度量或Voronoi的交互不能产生线性秩序。该研究突出了自组织迁移队列中有限感官知觉、低邻居连通性和异步动力学的相互作用,为理解动物集体行为和指导机器人群体设计提供了理论指导。
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引用次数: 0
Direct reciprocity in multi-action repeated games 多动作重复游戏中的直接互惠性。
IF 2 4区 数学 Q2 BIOLOGY Pub Date : 2026-02-07 Epub Date: 2025-11-07 DOI: 10.1016/j.jtbi.2025.112312
Feipeng Zhang , Lei Zhou , Guofeng Zhang , Long Wang
Direct reciprocity is a fundamental mechanism for sustaining cooperation in repeated interactions, where individuals adjust their behavior based on past experiences. Most previous models have focused on the prisoner’s dilemma, in which individuals face a strict choice between full cooperation and complete defection. However, this dichotomy oversimplifies the complexity of real-world reciprocal interactions. To address this, we introduce additional actions between these extremes, thereby increasing action diversity. Our analysis demonstrates that a broader range of available actions fosters cooperation more effectively than a binary choice. Through evolutionary analysis, we identify which types of intermediate actions promote cooperation. Moreover, equilibrium analysis establishes the theoretical conditions underlying this effect. While the increased computational complexity makes it infeasible to simulate scenarios with an arbitrarily large number of actions, our theoretical analysis remains applicable to settings with more actions, offering broader insights into the role of action diversity in promoting cooperation. These findings deepen our understanding of direct reciprocity and highlight the importance of action diversity in shaping cooperative behavior.
直接互惠是在重复互动中维持合作的基本机制,个体根据过去的经验调整自己的行为。大多数先前的模型关注的是囚犯困境,在这种困境中,个体面临着完全合作和完全背叛之间的严格选择。然而,这种二分法过分简化了现实世界中相互作用的复杂性。为了解决这个问题,我们在这两个极端之间引入了额外的行动,从而增加了行动的多样性。我们的分析表明,与二元选择相比,更广泛的行动范围能更有效地促进合作。通过演化分析,我们确定了哪种类型的中间行为促进了合作。此外,平衡分析建立了这种效应的理论条件。虽然计算复杂性的增加使得模拟具有任意大量动作的场景变得不可行,但我们的理论分析仍然适用于具有更多动作的设置,为行动多样性在促进合作中的作用提供了更广泛的见解。这些发现加深了我们对直接互惠的理解,并强调了行动多样性在塑造合作行为中的重要性。
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引用次数: 0
Mathematical modelling of tumor-immune interactions in breast cancer 乳腺癌中肿瘤-免疫相互作用的数学模型。
IF 2 4区 数学 Q2 BIOLOGY Pub Date : 2026-02-07 Epub Date: 2025-11-08 DOI: 10.1016/j.jtbi.2025.112310
Haifeng Zhang , Chenghang Li
The dynamic interplay between tumors and immune system is pivotal to the progression of breast cancer. To systematically investigate how interactions between tumor cells and immune cells shape breast cancer evolution, we developed a mathematical model that incorporates tumor cells, dendritic cells (DCs), natural killer (NK) cells, regulatory T cells (Tregs) and CD8+ T cells. We first established analytical conditions for the local stability of the tumor-free equilibrium, identifying key constraints on tumor growth imposed by immune activity. The existence of a positive equilibrium solution further suggests the potential coexistence of tumor and immune cells. Numerical simulations demonstrate that effective tumor control is achieved under a high baseline level of CD8+ T cell precursors coupled with a low level of regulatory T cell precursors. These results highlight the important role of balancing immunostimulatory and immunosuppressive forces within the tumor microenvironment. Through bifurcation analysis, we identified regimes of bistability in which both high-tumor and low-tumor equilibria coexist with dynamic features that may underlie divergent clinical outcomes and present a critical challenge for clinical therapeutic intervention. Moreover, simulations of tumor-immune dynamics in virtual cohorts reveal that tumor control hinges on CD8+ T cell infiltration, whereas regulatory T cell abundance is a potent predictor of immune escape. Finally, we formulated an optimal control framework to design adaptive CD8+ T cell injection protocols. Numerical solutions demonstrate that such optimized strategies achieve superior tumor reduction compared with constant dosing, despite using the same total injection dose of CD8+ T cells and identical treatment intervals. Collectively, our findings provide a mechanistic understanding of breast cancer progression and establish a theoretical foundation for developing personalized therapeutic strategies to optimize clinical outcomes.
肿瘤与免疫系统之间的动态相互作用对乳腺癌的发展至关重要。为了系统地研究肿瘤细胞和免疫细胞之间的相互作用如何影响乳腺癌的进化,我们开发了一个包含肿瘤细胞、树突状细胞(dc)、自然杀伤细胞(NK)、调节性T细胞(Tregs)和CD8+ T细胞的数学模型。我们首先建立了无肿瘤平衡局部稳定性的分析条件,确定了免疫活性对肿瘤生长的关键限制。正平衡溶液的存在进一步表明肿瘤细胞和免疫细胞可能共存。数值模拟表明,在高基线水平的CD8+ T细胞前体加上低水平的调节性T细胞前体的情况下,可以实现有效的肿瘤控制。这些结果强调了在肿瘤微环境中平衡免疫刺激和免疫抑制力量的重要作用。通过分岔分析,我们确定了双稳定性机制,其中高肿瘤和低肿瘤平衡共存,动态特征可能是不同临床结果的基础,并为临床治疗干预提出了关键挑战。此外,虚拟队列中的肿瘤免疫动力学模拟显示,肿瘤控制取决于CD8+ T细胞浸润,而调节性T细胞丰度是免疫逃逸的有效预测因子。最后,我们制定了一个最优控制框架来设计自适应CD8+ T细胞注射方案。数值解表明,尽管使用相同的CD8+ T细胞总注射剂量和相同的治疗间隔,与恒定剂量相比,这种优化策略取得了更好的肿瘤减少效果。总的来说,我们的研究结果提供了对乳腺癌进展的机制理解,并为制定个性化治疗策略以优化临床结果奠定了理论基础。
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引用次数: 0
Mechanisms of reentry arrhythmia termination with ephaptic coupling and gap junctional coupling 再入性心律失常终止与心动偶联和间隙连接偶联的机制。
IF 2 4区 数学 Q2 BIOLOGY Pub Date : 2026-02-07 Epub Date: 2025-11-18 DOI: 10.1016/j.jtbi.2025.112308
Ning Wei , Joyce Lin
Cardiac cells communicate electrically to coordinate heart contractions and pump blood. Gap junctions in the intercalated discs (ID) between myocytes form low-resistance pathways that facilitate electrical propagation. Traditionally, gap junctional coupling is considered the primary mechanism for cell communication, but experimental studies show that conduction can persist even with impaired gap junctions. For example, in gap junction-deficient rats, the heart still shows slow, discontinuous signal propagation, suggesting the existence of other communication mechanisms. One such mechanism is ephaptic coupling (EpC), an electrical field effect in the ID that maintains conduction even in the absence of gap junctions. EpC has been explored experimentally and numerically, especially in altered ID under normal and diseased conditions. However, a lack of direct evidence emphasizes the need to study its physiological role in the heart. Some research indicates that EpC can increase conduction velocity (CV) and reduce conduction failure, but its effects on cardiac arrhythmias are not well understood. Our study focuses on reentry arrhythmia, where rapid, irregular heartbeats can lead to cardiac arrest. Previous modeling work suggests that strong EpC can terminate reentry in ischemic hearts, though the mechanism remains unclear. We aim to investigate the mechanisms underlying reentry termination across different levels of EpC and gap junctional coupling using a two-dimensional discrete bidomain model with EpC. Our results identify two mechanisms: (1) Strong EpC terminates reentry through self-attenuation, driven by inactivation of fast sodium currents and (2) moderate EpC terminates reentry through self-collision, influenced by increased CV and anisotropy. A boundary where termination does not occur is also observed.
心脏细胞通过电通信来协调心脏收缩和泵血。肌细胞间的间隙连接形成低阻通路,促进电传播。传统上,缝隙连接耦合被认为是细胞通讯的主要机制,但实验研究表明,即使缝隙连接受损,传导也可以持续。例如,在间隙连接缺陷大鼠中,心脏仍然表现出缓慢、不连续的信号传播,这表明存在其他通信机制。其中一种机制是触觉耦合(ephaptic coupling, EpC),这是一种电场效应,即使在没有间隙连接的情况下,也能保持传导。EpC已经在实验和数值上进行了探索,特别是在正常和病变条件下改变的ID。然而,缺乏直接证据强调了研究其在心脏中的生理作用的必要性。一些研究表明,EpC可以提高传导速度(CV),减少传导衰竭,但其对心律失常的影响尚不清楚。我们的研究重点是再入性心律失常,其中快速,不规则的心跳可导致心脏骤停。先前的建模工作表明,强EpC可以终止缺血心脏的再入,尽管机制尚不清楚。我们的目的是利用二维离散双域模型研究不同EpC水平和间隙连接耦合的再入终止机制。我们的研究结果确定了两种机制:(1)强EpC通过自衰减终止再入,由快速钠电流失活驱动;(2)中等EpC通过自碰撞终止再入,受CV和各向异性增加的影响。还观察到不发生终止的边界。
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引用次数: 0
Integrating community level transmission geographical networks into a dynamical system for better epidemic control 将社区层面的传播地理网络整合为动态系统,以更好地控制疫情。
IF 2 4区 数学 Q2 BIOLOGY Pub Date : 2026-02-07 Epub Date: 2025-11-15 DOI: 10.1016/j.jtbi.2025.112319
Arni S.R. Srinivasa Rao , Steven G. Krantz , John P. Barile
Despite the widespread use of deterministic models in understanding and controlling epidemics, they are often criticized for their inability to provide timely practical solutions during rapid spread. Similarly, conventional stochastic and statistical models also have limitations in providing time-sensitive solutions. These models are useful for implementing policy measures when there is enough time to make changes. In this article, we propose a novel approach to address these limitations by introducing a graphical network model with time-sensitive data blending to enhance deterministic epidemic models like the SIR model. This innovative approach could be valuable for rapidly spreading epidemics, providing timely model-based solutions to control their spread. For the first time, this article introduces higher-dimensional transmission rate functions in the literature and methods to obtain such functions.
AMS MSC 2020 classifications: 92D30; 62P10; 65T60.
尽管确定性模型被广泛用于了解和控制流行病,但它们经常因无法在快速传播期间提供及时的实际解决方案而受到批评。同样,传统的随机和统计模型在提供时间敏感的解决方案方面也有局限性。当有足够的时间进行更改时,这些模型对于实施政策措施非常有用。在本文中,我们提出了一种新的方法来解决这些限制,通过引入具有时间敏感数据混合的图形网络模型来增强确定性流行病模型,如SIR模型。这种创新的方法对于迅速传播的流行病可能很有价值,可以提供及时的基于模型的解决方案来控制其传播。本文首次介绍了文献中已有的高维传输速率函数,以及高维传输速率函数的获取方法。AMS MSC 2020分类:92D30;62 p10;65诸如 T60。
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引用次数: 0
Treatment of methanol toxicity through ethanol and folinic acid: A mathematical study 乙醇和亚叶酸处理甲醇毒性的数学研究。
IF 2 4区 数学 Q2 BIOLOGY Pub Date : 2026-02-07 Epub Date: 2025-11-10 DOI: 10.1016/j.jtbi.2025.112304
Sanju Sardar , Priti Kumar Roy , Sk Mosaraf Ahammed , Tushar Ghosh , David Greenhalgh
Methanol poisoning is an infrequent but immensely dangerous intoxication, causing severe metabolic disturbances, neurological dysfunction, and even death, if not treated timely and properly. In this article, we formulate a mathematical model based on the chemical kinetics reaction, to analyse the effect of co-administration of the antidote ethanol and folinic acid for the treatment of methanol toxicity. The maximum concentration level of formic acid has been identified, and through a one-dimensional impulsive system, we determined the maximum dosing interval of folinic acid. Under appropriate assumptions we have demonstrated the existence and stability of the equilibrium-like periodic orbit of our system with impulsive administration of folinic acid and ethanol. The dynamical changes of toxic metabolites are illustrated numerically for different doses and dosing intervals. We performed a sensitivity analysis to identify the key parameters affecting formic acid concentration during treatment. Model results were validated by comparing them with clinical and experimental data on methanol half-life during ethanol therapy and formic acid clearance under folinic acid treatment. Based on our detailed analytical and numerical analysis, we recommend an effective dosing regimen of folinic acid and ethanol to detoxify the human body and clearly identify the conditions beyond which hemodialysis becomes essential. We verified all of our analytical outcomes through numerical simulation.
甲醇中毒是一种不常见但非常危险的中毒,如果治疗不及时和适当,会引起严重的代谢紊乱、神经功能障碍,甚至死亡。本文建立了基于化学动力学反应的数学模型,分析了解毒剂乙醇与亚叶酸共给药治疗甲醇中毒的效果。确定了甲酸的最大浓度水平,并通过一维脉冲系统确定了亚叶酸的最大给药间隔。在适当的假设下,我们证明了该系统的类平衡周期轨道的存在性和稳定性。数值说明了不同剂量和给药间隔下毒性代谢物的动态变化。我们进行了敏感性分析,以确定治疗期间影响甲酸浓度的关键参数。通过将模型结果与乙醇治疗时甲醇半衰期和亚叶酸治疗时甲酸清除率的临床和实验数据进行比较,验证了模型结果。基于我们详细的分析和数值分析,我们推荐了一种有效的叶酸和乙醇的剂量方案来解毒人体,并清楚地确定了超过血液透析必须的条件。我们通过数值模拟验证了所有的分析结果。
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引用次数: 0
Fast approximate Bayesian inference of HIV indicators using PCA adaptive Gauss-Hermite quadrature 基于PCA自适应高斯-埃尔米特正交的HIV指标快速近似贝叶斯推断。
IF 2 4区 数学 Q2 BIOLOGY Pub Date : 2026-02-07 Epub Date: 2025-11-11 DOI: 10.1016/j.jtbi.2025.112290
Adam Howes , Alex Stringer , Seth R. Flaxman , Jeffrey W. Imai–Eaton
Naomi is a spatial evidence synthesis model used to produce district-level HIV epidemic indicators in sub-Saharan Africa. Multiple outcomes of policy interest, including HIV prevalence, HIV incidence, and antiretroviral therapy treatment coverage are jointly modelled using both household survey data and routinely reported health system data. The model is provided as a tool for countries to input their data to and generate estimates with during a yearly process supported by UNAIDS. Previously, inference has been conducted using empirical Bayes and a Gaussian approximation, implemented via the TMB R package. We propose a new inference method based on an extension of adaptive Gauss-Hermite quadrature to deal with more than 20 hyperparameters. Using data from Malawi, our method improves the accuracy of inferences for model parameters, while being substantially faster to run than Hamiltonian Monte Carlo with the No-U-Turn sampler. Our implementation leverages the existing TMB C++ template for the model’s log-posterior, and is compatible with any model with such a template.
Naomi是一个空间证据综合模型,用于编制撒哈拉以南非洲地区一级的艾滋病毒流行指标。使用住户调查数据和常规报告的卫生系统数据,对包括艾滋病毒流行率、艾滋病毒发病率和抗逆转录病毒治疗覆盖在内的多种政策结果进行了联合建模。该模型是作为一种工具提供的,供各国在艾滋病规划署支助的年度进程中输入其数据并产生估计数。以前,推理是使用经验贝叶斯和高斯近似进行的,通过TMBR包实现。提出了一种基于自适应高斯-埃尔米特正交扩展的超参数推理方法。使用来自马拉维的数据,我们的方法提高了模型参数推断的准确性,同时比使用无u型转弯采样器的哈密顿蒙特卡罗运行速度快得多。我们的实现利用现有的TMBC++模板进行模型的对数后验,并且与具有这种模板的任何模型兼容。
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引用次数: 0
Stability and threshold analysis of a class of epidemic models in a multi-patch environment 多斑块环境下一类流行病模型的稳定性和阈值分析。
IF 2 4区 数学 Q2 BIOLOGY Pub Date : 2026-02-07 Epub Date: 2025-11-07 DOI: 10.1016/j.jtbi.2025.112285
Linhe Zhu , Le He , Haoyan Sha , Shuling Shen
Spatial heterogeneity and population migration may affect transmission threshold and the asymptotic behavior of epidemic transmission near the steady state. To investigate this issue, an epidemic transmission model with nonlinear natural growth mechanism and linear migration mechanism based on multi-patch structure is established. First, we study the findings related to the equilibrium state of the system and the transmission threshold, proving the uniqueness and the existence of epidemic-free equilibrium points, the existence of positive equilibrium points under certain conditions and the non-existence of mixed equilibrium points. Meanwhile, we discuss the asymptotic behavior of various types of equilibrium points and define the global basic reproduction number and the local basic reproduction number, demonstrating some of their unequal relationships. Further, we also consider the impact of the blocking mechanism on the patch model, illustrating that the epidemic disappears or persists in single patch under certain conditions. Finally, we carry out the numerical simulation analysis of our system. The results suggest that the epidemic may form a certain oscillatory pattern in space and there are multiple positive equilibrium points for the system. At the same time, the blocking mechanism may lead to different types of equilibrium states in different patches, but it is not effective in reducing the total number of infected individuals and the convergence time of the system.
空间异质性和人口迁移可能影响传播阈值和接近稳态的流行病传播渐近行为。为了研究这一问题,建立了基于多斑块结构的具有非线性自然生长机制和线性迁移机制的流行病传播模型。首先,我们研究了系统平衡状态和传播阈值的相关发现,证明了无流行病平衡点的唯一性和存在性,在一定条件下正平衡点的存在性和混合平衡点的不存在性。同时,我们讨论了各种类型平衡点的渐近性,定义了全局基本再生数和局部基本再生数,并证明了它们之间的一些不相等关系。此外,我们还考虑了阻断机制对斑块模型的影响,说明在一定条件下,流行病在单个斑块中消失或持续存在。最后,对系统进行了数值仿真分析。结果表明,疫情在空间上可能形成一定的振荡模式,系统存在多个正平衡点。同时,阻断机制可能在不同的斑块中导致不同类型的平衡状态,但在减少感染个体总数和系统收敛时间方面并不有效。
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引用次数: 0
Rapid cell turnover to model adipocyte size distribution 快速细胞更新以模拟脂肪细胞大小分布。
IF 2 4区 数学 Q2 BIOLOGY Pub Date : 2026-02-07 Epub Date: 2025-11-10 DOI: 10.1016/j.jtbi.2025.112311
Louis Fostier , Aloïs Dauger , Romain Yvinec , Magali Ribot , Chloe Audebert , Hedi Soula
White adipose tissue, composed of adipocyte cells, primarily stores energy as lipid droplets. The size of adipocytes varies significantly within the tissue according to the amount of stored lipids. A striking observation is that the adipocyte size distribution is bimodal, and thus, this tissue is lacking a characteristic size.
We propose a novel dynamical model, based on a partial differential equation, to represent the adipocyte size distribution. The model assumes continuous adipocyte growth, with a velocity dependent on cell radius and extracellular lipid availability, together with constant rates of cell recruitment and death.
We prove the existence and local stability of a unique stationary solution for a broad range of growth velocity functions. Choosing a parcimonious formulation, we show that only three parameters are enough to describe adipocyte size distributions measurements in rats. These parameters are robustly estimated through approximate Bayesian computation, and the model demonstrates excellent agreement with experimental data. This mechanistic, three-parameter framework offers a new and interpretable approach to characterizing adipocyte size distributions.
白色脂肪组织由脂肪细胞组成,主要以脂滴的形式储存能量。脂肪细胞的大小在组织内根据储存的脂质量有显著变化。一个引人注目的观察是,脂肪细胞的大小分布是双峰的,因此,该组织缺乏特征大小。我们提出了一个新的动态模型,基于偏微分方程,以表示脂肪细胞的大小分布。该模型假设脂肪细胞持续生长,其速度取决于细胞半径和细胞外脂质可用性,同时细胞招募和死亡的速率恒定。证明了一类大范围生长速度函数的唯一平稳解的存在性和局部稳定性。选择一个和谐的公式,我们表明只有三个参数足以描述脂肪细胞的大小分布测量在大鼠。通过近似贝叶斯计算对这些参数进行了稳健估计,模型与实验数据吻合良好。这种机制,三参数框架提供了一个新的和可解释的方法来表征脂肪细胞的大小分布。
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引用次数: 0
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Journal of Theoretical Biology
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