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Journal of Mathematical Biology

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https://www.readbyqxmd.com/read/28434024/chaotic-dynamics-in-the-seasonally-forced-sir-epidemic-model
#1
Pablo G Barrientos, J Ángel Rodríguez, Alfonso Ruiz-Herrera
We prove analytically the existence of chaotic dynamics in the forced SIR model. Although numerical experiments have already suggested that this model can exhibit chaotic dynamics, a rigorous proof (without computer-aided) was not given before. Under seasonality in the transmission rate, the coexistence of low birth and mortality rates with high recovery and transmission rates produces infinitely many periodic and aperiodic patterns together with sensitive dependence on the initial conditions.
April 22, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28434023/developing-a-statistically-powerful-measure-for-quartet-tree-inference-using-phylogenetic-identities-and-markov-invariants
#2
Jeremy G Sumner, Amelia Taylor, Barbara R Holland, Peter D Jarvis
Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site patterns that, in expectation value, either vanish for particular evolutionary trees (in the case of phylogenetic invariants) or have well understood transformation properties (in the case of Markov invariants). While both approaches have been valued for their intrinsic mathematical interest, it is not clear how they relate to each other, and to what extent they can be used as practical tools for inference of phylogenetic trees...
April 22, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28417166/vaccine-impact-in-homogeneous-and-age-structured-models
#3
F M G Magpantay
A general model of an imperfect vaccine for a childhood disease is presented and the effects of different types of vaccine failure on transmission were investigated using models that consider both homogeneous and age-specific mixing. The models are extensions of the standard SEIR equations with an additional vaccinated component that allows for five different vaccine parameters: three types of vaccine failure in decreasing susceptibility to infection via failure in degree ("leakiness"), take ("all-or-nothingness") and duration (waning of vaccine-derived immunity); one parameter reflecting the relative reduction in infectiousness of vaccinated individuals who get infected; and one parameter that reflects the relative reduction in reporting probability of vaccinated individuals due to a possible reduction in severity of symptoms...
April 17, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28409223/the-relationships-between-message-passing-pairwise-kermack-mckendrick-and-stochastic-sir-epidemic-models
#4
Robert R Wilkinson, Frank G Ball, Kieran J Sharkey
We consider a very general stochastic model for an SIR epidemic on a network which allows an individual's infectious period, and the time it takes to contact each of its neighbours after becoming infected, to be correlated. We write down the message passing system of equations for this model and prove, for the first time, that it has a unique feasible solution. We also generalise an earlier result by proving that this solution provides a rigorous upper bound for the expected epidemic size (cumulative number of infection events) at any fixed time [Formula: see text]...
April 13, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28405746/structured-models-of-cell-migration-incorporating-molecular-binding-processes
#5
Pia Domschke, Dumitru Trucu, Alf Gerisch, Mark A J Chaplain
The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological scenarios such as wound healing and cancer. Information about the various structures embedded within these processes allows a detailed exploration of the binding of molecular species to cell-surface receptors within the evolving cell population. In this paper we establish a general spatio-temporal-structural framework that enables the description of molecular binding to cell membranes coupled with the cell population dynamics...
April 12, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28401266/dynamic-flux-balance-analysis-with-nonlinear-objective-function
#6
Xiao Zhao, Stephan Noack, Wolfgang Wiechert, Eric von Lieres
Dynamic flux balance analysis (DFBA) extends flux balance analysis and enables the combined simulation of both intracellular and extracellular environments of microbial cultivation processes. A DFBA model contains two coupled parts, a dynamic part at the upper level (extracellular environment) and an optimization part at the lower level (intracellular environment). Both parts are coupled through substrate uptake and product secretion rates. This work proposes a Karush-Kuhn-Tucker condition based solution approach for DFBA models, which have a nonlinear objective function in the lower-level part...
April 11, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28396937/bifurcation-analysis-and-global-dynamics-of-a-mathematical-model-of-antibiotic-resistance-in-hospitals
#7
Xiuli Cen, Zhilan Feng, Yiqiang Zheng, Yulin Zhao
Antibiotic-resistant bacteria have posed a grave threat to public health by causing a number of nosocomial infections in hospitals. Mathematical models have been used to study transmission dynamics of antibiotic-resistant bacteria within a hospital and the measures to control antibiotic resistance in nosocomial pathogens. Studies presented in Lipstich et al. (Proc Natl Acad Sci 97(4):1938-1943, 2000) and Lipstich and Bergstrom (Infection control in the ICU environment. Kluwer, Boston, 2002) have provided valuable insights in understanding the transmission of antibiotic-resistant bacteria in a hospital...
April 10, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28391511/normal-and-pathological-dynamics-of-platelets-in-humans
#8
Gabriel P Langlois, Morgan Craig, Antony R Humphries, Michael C Mackey, Joseph M Mahaffy, Jacques Bélair, Thibault Moulin, Sean R Sinclair, Liangliang Wang
We develop a mathematical model of platelet, megakaryocyte, and thrombopoietin dynamics in humans. We show that there is a single stationary solution that can undergo a Hopf bifurcation, and use this information to investigate both normal and pathological platelet production, specifically cyclic thrombocytopenia. Carefully estimating model parameters from laboratory and clinical data, we then argue that a subset of parameters are involved in the genesis of cyclic thrombocytopenia based on clinical information...
April 8, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28378145/spatial-spreading-model-and-dynamics-of-west-nile-virus-in-birds-and-mosquitoes-with-free-boundary
#9
Zhigui Lin, Huaiping Zhu
In this paper, a reaction-diffusion system is proposed to model the spatial spreading of West Nile virus in vector mosquitoes and host birds in North America. Transmission dynamics are based on a simplified model involving mosquitoes and birds, and the free boundary is introduced to model and explore the expanding front of the infected region. The spatial-temporal risk index [Formula: see text], which involves regional characteristic and time, is defined for the simplified reaction-diffusion model with the free boundary to compare with other related threshold values, including the usual basic reproduction number [Formula: see text]...
April 4, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28374100/how-old-is-this-bird-the-age-distribution-under-some-phase-sampling-schemes
#10
Sophie Hautphenne, Melanie Massaro, Peter Taylor
In this paper, we use a finite-state continuous-time Markov chain with one absorbing state to model an individual's lifetime. Under this model, the time of death follows a phase-type distribution, and the transient states of the Markov chain are known as phases. We then attempt to provide an answer to the simple question "What is the conditional age distribution of the individual, given its current phase"? We show that the answer depends on how we interpret the question, and in particular, on the phase observation scheme under consideration...
April 3, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28361242/optimal-resource-allocation-enables-mathematical-exploration-of-microbial-metabolic-configurations
#11
Laurent Tournier, Anne Goelzer, Vincent Fromion
Central to the functioning of any living cell, the metabolic network is a complex network of biochemical reactions. It may also be viewed as an elaborate production system, integrating a diversity of internal and external signals in order to efficiently produce the energy and the biochemical precursors to ensure all cellular functions. Even in simple organisms like bacteria, it shows a striking level of coordination, adapting to very different growth media. Constraint-based models constitute an efficient mathematical framework to compute optimal metabolic configurations, at the scale of a whole genome...
March 30, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28352964/the-limits-of-weak-selection-and-large-population-size-in-evolutionary-game-theory
#12
Christine Sample, Benjamin Allen
Evolutionary game theory is a mathematical approach to studying how social behaviors evolve. In many recent works, evolutionary competition between strategies is modeled as a stochastic process in a finite population. In this context, two limits are both mathematically convenient and biologically relevant: weak selection and large population size. These limits can be combined in different ways, leading to potentially different results. We consider two orderings: the [Formula: see text] limit, in which weak selection is applied before the large population limit, and the [Formula: see text] limit, in which the order is reversed...
March 28, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28289838/a-stochastic-analysis-of-autoregulation-of-gene-expression
#13
Renaud Dessalles, Vincent Fromion, Philippe Robert
This paper analyzes, in the context of a prokaryotic cell, the stochastic variability of the number of proteins when there is a control of gene expression by an autoregulation scheme. The goal of this work is to estimate the efficiency of the regulation to limit the fluctuations of the number of copies of a given protein. The autoregulation considered in this paper relies mainly on a negative feedback: the proteins are repressors of their own gene expression. The efficiency of a production process without feedback control is compared to a production process with an autoregulation of the gene expression assuming that both of them produce the same average number of proteins...
March 13, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28283740/two-parameter-bifurcations-in-lpa-model
#14
Veronika Hajnová, Lenka Přibylová
The structured population LPA model is studied. The model describes flour beetle (Tribolium) population dynamics of four stage populations: eggs, larvae, pupae and adults with cannibalism between these stages. We concentrate on the case of non-zero cannibalistic rates of adults on eggs and adults on pupae and no cannibalism of larvae on eggs, but the results can be numerically continued to non-zero cannibalism of larvae on eggs. In this article two-parameter bifurcations in LPA model are analysed. Various stable and unstable invariant sets are found, different types of hysteresis are presented and abrupt changes in dynamics are simulated to explain the complicated way the system behaves near two-parameter bifurcation manifolds...
March 10, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28280922/reaction-diffusion-and-non-local-interaction
#15
Hirokazu Ninomiya, Yoshitaro Tanaka, Hiroko Yamamoto
Recent years have seen the introduction of non-local interactions in various fields. A typical example of a non-local interaction is where the convolution kernel incorporates short-range activation and long-range inhibition. This paper presents the relationship between non-local interactions and reaction-diffusion systems in the following sense: (a) the relationship between the instability induced by non-local interaction and diffusion-driven instability; (b) the realization of non-local interactions by reaction-diffusion systems...
March 9, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28275824/from-homogeneous-eigenvalue-problems-to-two-sex-population-dynamics
#16
Horst R Thieme
Enclosure theorems are derived for homogeneous bounded order-preserving operators and illustrated for operators involving pair-formation functions introduced by Karl-Peter Hadeler in the late 1980s. They are applied to a basic discrete-time two-sex population model and to the relation between the basic turnover number and the basic reproduction number.
March 8, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28271271/a-kinetic-model-to-study-the-regulation-of-formula-see-text-catenin-apc-and-axin-in-the-human-colonic-crypt
#17
Brooks Emerick, Gilberto Schleiniger, Bruce M Boman
The Wnt/[Formula: see text]-catenin pathway plays a crucial role in stem cell renewal and differentiation in the normal human colonic crypt. The balance between [Formula: see text]-catenin and APC along the crypt axis determines its normal functionality. The mechanism that deregulates this balance may give insight into the initiation of colorectal cancer. This is significant because the spatial dysregulation of [Formula: see text]-catenin by the mutated tumor suppressor gene/protein APC in human colonic crypts is responsible for the initiation and growth of colorectal cancer...
March 7, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28255663/towards-quantitative-root-hydraulic-phenotyping-novel-mathematical-functions-to-calculate-plant-scale-hydraulic-parameters-from-root-system-functional-and-structural-traits
#18
F Meunier, V Couvreur, X Draye, J Vanderborght, M Javaux
Predicting root water uptake and plant transpiration is crucial for managing plant irrigation and developing drought-tolerant root system ideotypes (i.e. ideal root systems). Today, three-dimensional structural functional models exist, which allows solving the water flow equation in the soil and in the root systems under transient conditions and in heterogeneous soils. Yet, these models rely on the full representation of the three-dimensional distribution of the root hydraulic properties, which is not always easy to access...
March 2, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28243721/mathematical-modeling-and-its-analysis-for-instability-of-the-immune-system-induced-by-chemotaxis
#19
Seongwon Lee, Se-Woong Kim, Youngmin Oh, Hyung Ju Hwang
In this paper, we study how chemotaxis affects the immune system by proposing a minimal mathematical model, a reaction-diffusion-advection system, describing a cross-talk between antigens and immune cells via chemokines. We analyze the stability and instability arising in our chemotaxis model and find their conditions for different chemotactic strengths by using energy estimates, spectral analysis, and bootstrap argument. Numerical simulations are also performed to the model, by using the finite volume method in order to deal with the chemotaxis term, and the fractional step methods are used to solve the whole system...
February 27, 2017: Journal of Mathematical Biology
https://www.readbyqxmd.com/read/28243720/extracting-cellular-automaton-rules-from-physical-langevin-equation-models-for-single-and-collective-cell-migration
#20
J M Nava-Sedeño, H Hatzikirou, F Peruani, A Deutsch
Cellular automata (CA) are discrete time, space, and state models which are extensively used for modeling biological phenomena. CA are "on-lattice" models with low computational demands. In particular, lattice-gas cellular automata (LGCA) have been introduced as models of single and collective cell migration. The interaction rule dictates the behavior of a cellular automaton model and is critical to the model's biological relevance. The LGCA model's interaction rule has been typically chosen phenomenologically...
February 27, 2017: Journal of Mathematical Biology
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