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A novel multi-scale immuno-epidemiological model of visceral leishmaniasis in dogs 一种新的犬内脏利什曼病多尺度免疫流行病学模型
Q2 Agricultural and Biological Sciences Pub Date : 2019-01-23 DOI: 10.11145/J.BIOMATH.2019.01.026
J. Welker, M. Martcheva
Leishmaniasis is a neglected and emerging disease prevalent in Mediterranean and tropical climates. As such, the study and development of new models are of increasing importance. We introduce a new immuno-epidemiological model of visceral leishmaniasis in dogs. The within-host system is based on previously  collected  and published data, showing the movement and proliferation of the parasite in the skin and the bone-marrow, as well as the IgG response. The between-host system structures the infected individuals in  time-since-infection and is of vector-host type. The within-host system has a parasite-free equilibrium and at least one endemic equilibrium, consistent with the fact that infected dogs do not recover without treatment. We compute the basic reproduction number R0 of the immuno-epidemiological model  and provide the existence and stability results of the population-level  disease-free equilibrium. Additionally, we prove existence of an unique  endemic equilibrium when R0 > 1, and evidence of backward bifurcation and existence of multiple endemic equilibria when R0 < 1.
利什曼病是地中海和热带气候中流行的一种被忽视的新发疾病。因此,研究和开发新模型变得越来越重要。我们介绍了一种新的免疫流行病学模型内脏利什曼病的狗。宿主内系统是基于先前收集和发表的数据,显示寄生虫在皮肤和骨髓中的运动和增殖,以及IgG反应。宿主间系统是一种媒介宿主系统,以感染后的时间为单位对感染个体进行结构分析。宿主内系统具有无寄生虫平衡和至少一种地方性平衡,这与受感染犬不经治疗就无法康复的事实相一致。我们计算了免疫流行病学模型的基本繁殖数R0,并给出了种群水平无病平衡的存在性和稳定性结果。此外,我们还证明了当R0 < 1时存在一个唯一的地方性平衡,并证明了当R0 < 1时存在向后分叉和多个地方性平衡。
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引用次数: 3
Bi-stable dynamics of a host-pathogen model 宿主-病原体模型的双稳态动力学
Q2 Agricultural and Biological Sciences Pub Date : 2019-01-23 DOI: 10.11145/J.BIOMATH.2019.01.029
R. Anguelov, R. Bekker, Y. Dumont
Crop host-pathogen interaction have been a main issue for decades, in particular for food security. In this paper, we focus on the modeling and long term behavior of soil-borne pathogens. We first develop a new compartmental temporal model, which exhibits bi-stable asymptotical dynamics. To investigate the long term behavior, we use LaSalle Invariance Principle to derive sufficient conditions for global asymptotic stability of the pathogen free equilibrium and monotone dynamical systems theory to provide sufficient conditions for permanence of the system. Finally, we develop a partially degenerate reaction diffusion system, providing a numerical exploration based on the results obtained for the temporal system. We show that a traveling wave solution may exist where the speed of the wave follows a power law.
几十年来,作物-宿主-病原体的相互作用一直是一个主要问题,特别是在粮食安全方面。在本文中,我们重点研究了土壤传播病原体的建模和长期行为。我们首先开发了一个新的房室时间模型,该模型表现出双稳态渐近动力学。为了研究系统的长期行为,我们利用拉萨尔不变原理导出了无病原体平衡全局渐近稳定的充分条件,并利用单调动力系统理论给出了系统持久性的充分条件。最后,我们发展了一个部分简并的反应扩散系统,在时间系统的结果的基础上进行了数值探索。我们证明,当波的速度遵循幂律时,可能存在行波解。
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引用次数: 3
Modeling outbreak data: Analysis of a 2012 Ebola virus disease epidemic in DRC. 疫情数据建模:2012 年刚果(金)埃博拉病毒疾病疫情分析。
Q2 Agricultural and Biological Sciences Pub Date : 2019-01-01 Epub Date: 2019-10-15 DOI: 10.11145/j.biomath.2019.10.037
Boseung Choi, Sydney Busch, Dieudonné Kazadi, Benoit Ilunga, Emile Okitolonda, Yi Dai, Robert Lumpkin, Omar Saucedo, Wasiur R KhudaBukhsh, Joseph Tien, Marcel Yotebieng, Eben Kenah, Grzegorz A Rempala

We describe two approaches to modeling data from a small to moderate-sized epidemic outbreak. The first approach is based on a branching process approximation and direct analysis of the transmission network, whereas the second one is based on a survival model derived from the classical SIR equations with no explicit transmission information. We compare these approaches using data from a 2012 outbreak of Ebola virus disease caused by Bundibugyo ebolavirus in city of Isiro, Democratic Republic of the Congo. The branching process model allows for a direct comparison of disease transmission across different environments, such as the general community or the Ebola treatment unit. However, the survival model appears to yield parameter estimates with more accuracy and better precision in some circumstances.

我们介绍了对中小规模疫情数据建模的两种方法。第一种方法基于分支过程近似和对传播网络的直接分析,而第二种方法则基于由经典 SIR 方程推导出的生存模型,没有明确的传播信息。我们利用 2012 年在刚果民主共和国伊西罗市爆发的由本迪布吉埃博拉病毒引起的埃博拉病毒病的数据对这两种方法进行了比较。分支过程模型可直接比较疾病在不同环境中的传播情况,如普通社区或埃博拉治疗单位。不过,在某些情况下,生存模型似乎能得出更准确、更精确的参数估计。
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引用次数: 0
A tribute to the use of minimalistic spatially-implicit models of savanna vegetation dynamics to address broad spatial scales in spite of scarce data 赞扬在数据稀少的情况下,使用草原植被动力学的极简空间隐式模型来处理广泛的空间尺度
Q2 Agricultural and Biological Sciences Pub Date : 2018-12-20 DOI: 10.11145/J.BIOMATH.2018.12.167
V. Yatat, Alexis Tamen Tchuinte, Y. Dumont, P. Couteron
The savanna biome encompasses a variety of vegetation physiognomies that traduce complex dynamical responses of plants to the rainfall gradients leading from tropical forests to hot deserts. Such responses are shaped by interactions between woody and grassy plants that can be either direct, disturbance-mediated or both. There has been increasing evidence that several vegetation physiognomies, sometimes highly contrasted, may durably coexist under similar rainfall conditions suggesting multi-stability or at least not abrupt transitions. These fascinating questions have triggered burgeoning modelling efforts which have, however, not yet delivered an integrated picture liable to furnish sensible predictions of potential vegetation at broad scales. In this paper, we will recall the key ecological processes and resulting vegetation dynamics that models should take into account. We will also present the main modelling options present in the literature and advocate the use of minimalistic models, capturing only the essential processes while retaining sufficient mathematical tractability and restricting themselves to a minimal set of parameters assessable from the overall literature.
稀树草原生物群落包括各种植被地貌,这些地貌使植物对从热带森林到炎热沙漠的降雨梯度产生复杂的动力反应。这种反应是由木本植物和草本植物之间的相互作用形成的,这种相互作用可以是直接的,也可以是干扰介导的,或者两者兼而有之。越来越多的证据表明,几种植被地貌(有时是高度对比的)可能在类似的降雨条件下持久共存,这表明存在多重稳定性或至少不会发生突变。这些迷人的问题引发了蓬勃发展的建模工作,然而,这些工作还没有提供一个能够在大范围内对潜在植被进行合理预测的综合图像。在本文中,我们将回顾模型应该考虑的关键生态过程和由此产生的植被动力学。我们还将介绍文献中的主要建模选项,并提倡使用极简主义模型,只捕捉基本过程,同时保持足够的数学可处理性,并将其限制在可从整体文献中评估的最小参数集内。
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引用次数: 15
Inverse problem of the Holling-Tanner model and its solution Holling-Tanner模型的逆问题及其求解
Q2 Agricultural and Biological Sciences Pub Date : 2018-12-19 DOI: 10.11145/J.BIOMATH.2018.12.057
A. Adeniji, I. Fedotov, M. Shatalov
In this paper we undertake to consider the inverse problem of parameter identification of nonlinear system of ordinary differential equations for a specific case of complete information about solution of the Holling-Tanner model for finite number of points for the finite time interval. In this model the equations are nonlinearly dependent on the unknown parameters. By means of the proposed transformation the obtained equations become linearly dependent on new parameters functionally dependent on the original ones. This simplification is achieved by the fact that the new set of parameters becomes dependent and the corresponding constraint between the parameters is nonlinear. If the conventional approach based on introduction of the Lagrange multiplier is used this circumstance will result in a nonlinear system of equations. A novel algorithm of the problem solution is proposed in which only one nonlinear equation instead of the system of six nonlinear equations has to be solved. Differentiation and integration methods of the problem solution are implemented and it is shown that the integration method produces more accurate results and uses less number of points on the given time interval.
在本文中,我们致力于考虑非线性常微分方程组参数辨识的反问题,对于有限时间间隔内有限点的Holling-Tanner模型解的完全信息的特定情况。在该模型中,方程非线性地依赖于未知参数。通过所提出的变换,所获得的方程在函数上与新参数线性相关。这种简化是通过以下事实实现的:新的参数集变得依赖,并且参数之间的相应约束是非线性的。如果使用基于拉格朗日乘子引入的传统方法,这种情况将导致非线性方程组。提出了一种新的问题求解算法,该算法只需求解一个非线性方程,而不必求解六个非线性方程组。实现了问题求解的微分和积分方法,结果表明,积分方法在给定的时间间隔内产生了更准确的结果,并且使用了更少的点数。
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引用次数: 2
Simulation of a time dependent advection-reaction-diffusion problem using operator splitting and discontinuous Galerkin methods with application to plant root growth 用算子分裂和不连续伽辽金方法模拟随时间变化的平流-反应-扩散问题,并应用于植物根系生长
Q2 Agricultural and Biological Sciences Pub Date : 2018-12-18 DOI: 10.11145/J.BIOMATH.2018.12.037
E. Peynaud
The time dependant advection-reaction-diffusion equation is used in the C-Root model to simulate root growth. This equation can also be applied in many others applications in life sciences. In this context the unknown is related to densities and one of the important property of the problem is that the solution is non-negative for positive initial conditions. One of the difficulty at the discrete level is to preserve the positivity of the approximated solution during the simulations. In this work we solved the model using Discontinuous Galerkin elements combined with an operator splitting technique. The DG method is briefly presented then we motivated the use of the operator splitting technique by doing some numerical experiments. Those experiments showed that the same time approximation scheme may not be suitable for all the operators of the model. We validated our implementation of the splitting technique in a simple test case. Then we performed a simulation of a plagiotropic root of Eucalyptus.
C-Root模型采用随时间变化的平流-反应-扩散方程来模拟根系生长。这个方程也可以应用于生命科学中的许多其他应用。在这种情况下,未知与密度有关,问题的一个重要性质是,对于正初始条件,解是非负的。离散级别的困难之一是在模拟过程中保持近似解的正性。在这项工作中,我们使用不连续伽辽金单元结合算子分裂技术来求解模型。简要介绍了DG方法,然后通过一些数值实验,推动了算子分裂技术的应用。这些实验表明,相同的时间近似方案可能不适用于模型的所有算子。我们在一个简单的测试用例中验证了拆分技术的实现。然后,我们对桉树的一个斜生根进行了模拟。
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引用次数: 0
Mechanotransduction caused by a point force in the extracellular space 由细胞外空间的点力引起的机械转导
Q2 Agricultural and Biological Sciences Pub Date : 2018-10-27 DOI: 10.11145/J.BIOMATH.2018.10.197
B. Roth
The mechanical bidomain model is a mathematical description of biological tissue that focuses on mechanotransduction. The model’s fundamental hypothesis is that differences in the intracellular and extracellular displacements activate integrins, causing a cascade of biological effects. This paper presents analytical solutions of the bidomain equations for an extracellular point force. The intra- and extracellular spaces are incompressible, isotropic, and coupled. The expressions for the intra- and extracellular displacements each contain three terms: a monodomain term that is identical in the two spaces, and two bidomain terms, one of which decays exponentially. Near the origin the intracellular displacement remains finite and the extracellular displacement diverges. Far from the origin the monodomain displacement decays in inverse proportion to the distance, the strain decays as the distance squared, and the difference between the intra- and extracellular displacements decays as the distance cubed. These predictions could be tested by applying a force to a magnetic nanoparticle embedded in the extracellular matrix and recording the mechanotransduction response.
力学双域模型是对生物组织的一种数学描述,其重点是力学转导。该模型的基本假设是,细胞内和细胞外位移的差异激活整合素,导致一系列生物效应。本文给出了胞外点力的双域方程的解析解。细胞内和细胞外的空间是不可压缩的、各向同性的、耦合的。细胞内和细胞外位移的表达式分别包含三个项:一个在两个空间中相同的单域项和两个双域项,其中一个呈指数衰减。在原点附近,胞内位移保持有限,胞外位移发散。远离原点时,单畴位移与距离成反比衰减,应变随距离的平方衰减,胞内和胞外位移之差随距离的立方衰减。这些预测可以通过对嵌入细胞外基质中的磁性纳米颗粒施加力并记录机械转导反应来测试。
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引用次数: 1
Modelling cell-cell collision and adhesion with the filament based lamellipodium model 用基于细丝的lamellipound模型模拟细胞间碰撞和粘附
Q2 Agricultural and Biological Sciences Pub Date : 2018-09-20 DOI: 10.11145/J.BIOMATH.2018.11.097
Nikolaos Sfakianakis, D. Peurichard, Aaron Brunk, C. Schmeiser
We extend the live-cell motility Filament Based Lamellipodium Model (FBLM) to incorporate the forces exerted on the lamellipodium of the cells due to cell-cell collision and cadherin induced cell-cell adhesion. We take into account the nature of these forces via physical and biological constraints and modelling assumptions. We investigate the effect these new components have in the migration and morphology of the cells through particular experiments. We exhibit moreover the similarities between our simulated cells and HeLa cancer cells.
我们扩展了活细胞运动的基于纤维的板层平台模型(FBLM),以纳入由于细胞间碰撞和钙粘蛋白诱导的细胞间粘附而施加在细胞板层平台上的力。我们通过物理和生物限制以及建模假设来考虑这些力的性质。我们通过特定的实验研究了这些新成分对细胞迁移和形态的影响。此外,我们还展示了模拟细胞与HeLa癌细胞之间的相似性。
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引用次数: 6
Some properties of the Blumberg's hyper-log-logistic curve Blumberg超对数逻辑曲线的一些性质
Q2 Agricultural and Biological Sciences Pub Date : 2018-08-14 DOI: 10.11145/J.BIOMATH.2018.07.317
R. Anguelov, N. Kyurkchiev, S. Markov
The paper considers the sigmoid function definedthrough the hyper-log-logistic model introduced by Blumberg. We study the Hausdorff distance of this sigmoid to the Heaviside function, which characterises the shape of switching from 0 to 1. Estimates of the Hausdorff distance in terms of the intrinsic growth rate are derived. We construct a family of recurrence generated sigmoidal functions based on the hyper-log-logistic function. Numerical illustrations are provided.
本文考虑了由Blumberg引入的超对数逻辑模型定义的s型函数。我们研究了这个s型曲线到Heaviside函数的Hausdorff距离,它具有从0切换到1的形状。用固有增长率来估计豪斯多夫距离。在超对数逻辑函数的基础上构造了一类递归生成的s型函数。给出了数值说明。
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引用次数: 27
Modelling and analysis of a within-host model of hepatitis B and D co-infections 乙型肝炎和丁型肝炎合并感染宿主内模型的建模和分析
Q2 Agricultural and Biological Sciences Pub Date : 2018-08-07 DOI: 10.11145/J.BIOMATH.2018.07.219
P. T. Mouofo, J. Tewa, S. Bowong
The Hepatitis delta virus (HDV) is a defect RNA virus that requires the presence of the hepatitis B virus (HBV) for cellular infection. A co-infection may result in a more severe acute disease and a higher risk  of developing acute liver failure compared with those infected with HBV alone. At the present time, there has been very little to the modeling of  HDV. The derivation and analysis of such a mathematical model poses difficulty as it requires the inclusion of (HBV).  In this paper, a within-host model for the co-interaction of HDV and HBV   is presented and rigorously analyzed. We calculate the basic reproduction number (Ro), the disease-free equilibrium, boundary equilibrium, which we define as the existence of one disease along with the complete eradication of the other disease, and the co-infection equilibrium. We determine stability criteria for the disease-free and boundary equilibrium. We also use the optimal control theory to assess the disease control. Numerical simulations have been presented to illustrate analytical results.
德尔塔型肝炎病毒(HDV)是一种缺陷RNA病毒,需要存在乙型肝炎病毒(HBV)才能进行细胞感染。与单独感染HBV的患者相比,合并感染可能导致更严重的急性疾病和更高的急性肝衰竭风险。目前,对HDV的建模很少。这种数学模型的推导和分析带来了困难,因为它需要包含(HBV)。本文提出了HDV和HBV相互作用的宿主内模型,并对其进行了严格的分析。我们计算了基本繁殖数(Ro)、无病平衡、边界平衡,我们将其定义为一种疾病的存在以及另一种疾病完全根除,以及共同感染平衡。我们确定了无病和边界平衡的稳定性标准。我们还使用最优控制理论来评估疾病控制。已经给出了数值模拟来说明分析结果。
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引用次数: 0
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Biomath
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