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Bulletin of Mathematical Biology

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https://read.qxmd.com/read/30847643/number-of-source-patches-required-for-population-persistence-in-a-source-sink-metapopulation-with-explicit-movement
#1
Julien Arino, Nicolas Bajeux, Steve Kirkland
We consider a simple metapopulation model with explicit movement of individuals between patches, in which each patch is either a source or a sink. We prove that similarly to the case of patch occupancy metapopulations with implicit movement, there exists a threshold number of source patches such that the population potentially becomes extinct below the threshold and established above the threshold. In the case where the matrix describing the movement of populations between spatial locations is irreducible, the result is global; further, assuming a complete mobility graph with equal movement rates, we use the principle of equitable partitions to obtain an explicit expression for the threshold...
March 7, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30843137/an-improved-version-of-the-classical-banister-model-to-predict-changes-in-physical-condition
#2
Marcos Matabuena, Rosana Rodríguez-López
In this paper, we formulate and provide the solutions to two new models to predict changes in physical condition by using the information of the training load of an individual. The first model is based on a functional differential equation, and the second one on an integral differential equation. Both models are an extension to the classical Banister model and allow to overcome its main drawback: the variations in physical condition are influenced by the training loads of the previous days and not only of the same day...
March 6, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30843136/modeling-pancreatic-cancer-dynamics-with-immunotherapy
#3
Xiaochuan Hu, Guoyi Ke, Sophia R-J Jang
We develop a mathematical model of pancreatic cancer that includes pancreatic cancer cells, pancreatic stellate cells, effector cells and tumor-promoting and tumor-suppressing cytokines to investigate the effects of immunotherapies on patient survival. The model is first validated using the survival data of two clinical trials. Local sensitivity analysis of the parameters indicates there exists a critical activation rate of pro-tumor cytokines beyond which the cancer can be eradicated if four adoptive transfers of immune cells are applied...
March 6, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30834485/emergence-of-oscillations-in-a-mixed-mechanism-phosphorylation-system
#4
Carsten Conradi, Maya Mincheva, Anne Shiu
This work investigates the emergence of oscillations in one of the simplest cellular signaling networks exhibiting oscillations, namely the dual-site phosphorylation and dephosphorylation network (futile cycle), in which the mechanism for phosphorylation is processive, while the one for dephosphorylation is distributive (or vice versa). The fact that this network yields oscillations was shown recently by Suwanmajo and Krishnan. Our results, which significantly extend their analyses, are as follows. First, in the three-dimensional space of total amounts, the border between systems with a stable versus unstable steady state is a surface defined by the vanishing of a single Hurwitz determinant...
March 4, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30830675/data-driven-model-validation-across-dimensions
#5
Marissa Renardy, Timothy Wessler, Silvia Blemker, Jennifer Linderman, Shayn Peirce, Denise Kirschner
Data-driven model validation across dimensions in mathematical and computational biology assumptions are often made (e.g., symmetry) to reduce the problem from three spatial dimensions (3D) to two (2D). However, some experimental datasets, such as cell counts obtained via flow cytometry, represent the entire 3D biological object. For purpose of model calibration and validation, it is sometimes necessary to compare these biological datasets with model outputs. We propose a methodology for scaling 2D model outputs to compare with 3D experimental datasets, and we discuss the application of this methodology to two examples: agent-based models of granuloma formation and skeletal muscle tissue...
March 4, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30820832/global-sensitivity-analysis-of-high-dimensional-neuroscience-models-an-example-of-neurovascular-coupling
#6
J L Hart, P A Gremaud, T David
The complexity and size of state-of-the-art cell models have significantly increased in part due to the requirement that these models possess complex cellular functions which are thought-but not necessarily proven-to be important. Modern cell models often involve hundreds of parameters; the values of these parameters come, more often than not, from animal experiments whose relationship to the human physiology is weak with very little information on the errors in these measurements. The concomitant uncertainties in parameter values result in uncertainties in the model outputs or quantities of interest (QoIs)...
February 28, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30815837/using-experimental-data-and-information-criteria-to-guide-model-selection-for-reaction-diffusion-problems-in-mathematical-biology
#7
David J Warne, Ruth E Baker, Matthew J Simpson
Reaction-diffusion models describing the movement, reproduction and death of individuals within a population are key mathematical modelling tools with widespread applications in mathematical biology. A diverse range of such continuum models have been applied in various biological contexts by choosing different flux and source terms in the reaction-diffusion framework. For example, to describe the collective spreading of cell populations, the flux term may be chosen to reflect various movement mechanisms, such as random motion (diffusion), adhesion, haptotaxis, chemokinesis and chemotaxis...
February 27, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30809774/resource-allocation-for-epidemic-control-across-multiple-sub-populations
#8
Ciara E Dangerfield, Martin Vyska, Christopher A Gilligan
The number of pathogenic threats to plant, animal and human health is increasing. Controlling the spread of such threats is costly and often resources are limited. A key challenge facing decision makers is how to allocate resources to control the different threats in order to achieve the least amount of damage from the collective impact. In this paper we consider the allocation of limited resources across n independent target populations to treat pathogens whose spread is modelled using the susceptible-infected-susceptible model...
February 26, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30809773/a-mathematical-model-for-amyloid-formula-see-text-aggregation-in-the-presence-of-metal-ions-a-timescale-analysis-for-the-progress-of-alzheimer-disease
#9
Eda Asili, Shantia Yarahmadian, Hadi Khani, Meisam Sharify
The aggregation of amyloid-[Formula: see text] (A[Formula: see text]) proteins through their self-assembly into oligomers, fibrils, or senile plaques is advocated as a key process of Alzheimer's disease. Recent studies have revealed that metal ions play an essential role in modulating the aggregation rate of amyloid-[Formula: see text] (A[Formula: see text]) into senile plaques because of high binding affinity between A[Formula: see text] proteins and metal ions. In this paper, we proposed a mathematical model as a set of coupled kinetic equations that models the self-assembly of amyloid-[Formula: see text] (A[Formula: see text]) proteins in the presence of metal ions...
February 26, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30805856/asymptotic-state-of-a-two-patch-system-with-infinite-diffusion
#10
Yuanshi Wang
Mathematical theory has predicted that populations diffusing in heterogeneous environments can reach larger total size than when not diffusing. This prediction was tested in a recent experiment, which leads to extension of the previous theory to consumer-resource systems with external resource input. This paper studies a two-patch model with diffusion that characterizes the experiment. Solutions of the model are shown to be nonnegative and bounded, and global dynamics of the subsystems are completely exhibited...
February 25, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30805855/modeling-the-spatial-spread-of-chagas-disease
#11
Vanessa Steindorf, Norberto Aníbal Maidana
The aim of this work is to understand the spatial spread of Chagas disease, which is primarily transmitted by triatomines. We propose a mathematical model using a system of partial differential reaction-diffusion equations to study and describe the spread of this disease in the human population. We consider the respective subclasses of infected and uninfected individuals within the human and triatomine populations. The dynamics of the infected human subpopulation considers two disease phases: acute and chronic...
February 25, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30796683/lesion-dynamics-under-varying-paracrine-pdgf-signaling-in-brain-tissue
#12
Susan Christine Massey, Andrea Hawkins-Daarud, Jill Gallaher, Alexander R A Anderson, Peter Canoll, Kristin R Swanson
Paracrine PDGF signaling is involved in many processes in the body, both normal and pathological, including embryonic development, angiogenesis, and wound healing as well as liver fibrosis, atherosclerosis, and cancers. We explored this seemingly dual (normal and pathological) role of PDGF mathematically by modeling the release of PDGF in brain tissue and then varying the dynamics of this release. Resulting simulations show that by varying the dynamics of a PDGF source, our model predicts three possible outcomes for PDGF-driven cellular recruitment and lesion growth: (1) localized, short duration of growth, (2) localized, chronic growth, and (3) widespread chronic growth...
February 22, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30790189/computing-weakly-reversible-deficiency-zero-network-translations-using-elementary-flux-modes
#13
Matthew D Johnston, Evan Burton
We present a computational method for performing structural translation, which has been studied recently in the context of analyzing the steady states and dynamical behavior of mass-action systems derived from biochemical reaction networks. Our procedure involves solving a binary linear programming problem where the decision variables correspond to interactions between the reactions of the original network. We call the resulting network a reaction-to-reaction graph and formalize how such a construction relates to the original reaction network and the structural translation...
February 21, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30788691/multistationarity-in-structured-reaction-networks
#14
Alicia Dickenstein, Mercedes Pérez Millán, Anne Shiu, Xiaoxian Tang
Many dynamical systems arising in biology and other areas exhibit multistationarity (two or more positive steady states with the same conserved quantities). Although deciding multistationarity for a polynomial dynamical system is an effective question in real algebraic geometry, it is in general difficult to determine whether a given network can give rise to a multistationary system, and if so, to identify witnesses to multistationarity, that is, specific parameter values for which the system exhibits multiple steady states...
February 20, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30788690/interplay-between-the-persistent-random-walk-and-the-contact-inhibition-of-locomotion-leads-to-collective-cell-behaviors
#15
Abdel-Rahman Hassan, Thomas Biel, David M Umulis, Taeyoon Kim
Cell migration plays an important role in physiology and pathophysiology. It was observed in the experiments that cells, such as fibroblast, leukocytes, and cancer cells, exhibit a wide variety of migratory behaviors, such as persistent random walk, contact inhibition of locomotion, and ordered behaviors. To identify biophysical mechanisms for these cellular behaviors, we developed a rigorous computational model of cell migration on a two-dimensional non-deformable substrate. Cells in the model undergo motion driven by mechanical interactions between cellular protrusions and the substrate via the balance of tensile forces...
February 20, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30788689/analysis-of-an-epidemic-system-with-two-response-delays-in-media-impact-function
#16
Pengfei Song, Yanni Xiao
A functional differential model of SEIS-M type with two time delays, representing the response time for mass media to cover the current infection and for individuals' behavior changes to media coverage, was proposed to examine the delayed media impact on the transmission dynamics of emergent infectious diseases. The threshold dynamics were established in terms of the basic reproduction number [Formula: see text]. When there are no time delays, we showed that if the media impact is low, the endemic equilibrium is globally asymptotically stable for [Formula: see text], while the endemic equilibrium may become unstable and Hopf bifurcation occurs for some appropriate conditions by taking the level of media impact as bifurcation parameter...
February 20, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30778833/a-diffuse-interface-framework-for-modeling-the-evolution-of-multi-cell-aggregates-as-a-soft-packing-problem-driven-by-the-growth-and-division-of-cells
#17
J Jiang, K Garikipati, S Rudraraju
We present a model for cell growth, division and packing under soft constraints that arise from the deformability of the cells as well as of a membrane that encloses them. Our treatment falls within the framework of diffuse interface methods, under which each cell is represented by a scalar phase field and the zero level set of the phase field represents the cell membrane. One crucial element in the treatment is the definition of a free energy density function that penalizes cell overlap, thus giving rise to a simple model of cell-cell contact...
February 18, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30761456/exact-variance-reduced-simulation-of-lattice-continuous-time-markov-chains-with-applications-in-reaction-networks
#18
P A Maginnis, M West, G E Dullerud
We propose an algorithm to reduce the variance of Monte Carlo simulation for the class of countable-state, continuous-time Markov chains, or lattice CTMCs. This broad class of systems includes all processes that can be represented using a random-time-change representation, in particular reaction networks. Numerical studies demonstrate order-of-magnitude reduction in MSE for Monte Carlo mean estimates using our approach for both linear and nonlinear systems. The algorithm works by simulating pairs of negatively correlated, identically distributed sample trajectories of the stochastic process and using them to produce variance-reduced, unbiased Monte Carlo estimates, effectively generalizing the method of antithetic variates into the domain of stochastic processes...
February 13, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30756234/quasi-steady-state-approximations-derived-from-the-stochastic-model-of-enzyme-kinetics
#19
Hye-Won Kang, Wasiur R KhudaBukhsh, Heinz Koeppl, Grzegorz A Rempała
The paper outlines a general approach to deriving quasi-steady-state approximations (QSSAs) of the stochastic reaction networks describing the Michaelis-Menten enzyme kinetics. In particular, it explains how different sets of assumptions about chemical species abundance and reaction rates lead to the standard QSSA, the total QSSA, and the reverse QSSA. These three QSSAs have been widely studied in the literature in deterministic ordinary differential equation settings, and several sets of conditions for their validity have been proposed...
February 12, 2019: Bulletin of Mathematical Biology
https://read.qxmd.com/read/30756233/comparison-of-deterministic-and-stochastic-regime-in-a-model-for-cdc42-oscillations-in-fission-yeast
#20
Bin Xu, Hye-Won Kang, Alexandra Jilkine
Oscillations occur in a wide variety of essential cellular processes, such as cell cycle progression, circadian clocks and calcium signaling in response to stimuli. It remains unclear how intrinsic stochasticity can influence these oscillatory systems. Here, we focus on oscillations of Cdc42 GTPase in fission yeast. We extend our previous deterministic model by Xu and Jilkine to construct a stochastic model, focusing on the fast diffusion case. We use SSA (Gillespie's algorithm) to numerically explore the low copy number regime in this model, and use analytical techniques to study the long-time behavior of the stochastic model and compare it to the equilibria of its deterministic counterpart...
February 12, 2019: Bulletin of Mathematical Biology
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