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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/28442239/roadmap-to-control-hbv-and-hdv-epidemics-in-china
#1
Ashish Goyal, John M Murray
PURPOSE: Hepatitis B virus (HBV) is endemic in China. Almost 10% of HBV infected individuals are also infected with hepatitis D virus (HDV) which has a 5-10 times higher mortality rate than HBV mono-infection. The aim of this manuscript is to devise strategies that can not only control HBV infections but also HDV infections in China under the current health care budget in an optimal manner. METHODS: Using a mathematical model, an annual budget of $10 billion was optimally allocated among five interventions namely, testing and HBV adult vaccination, treatment for mono-infected and dually-infected individuals, second line treatment for HBV mono-infections, and awareness programs...
April 22, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28435014/maximum-likelihood-estimates-of-pairwise-rearrangement-distances
#2
Stuart Serdoz, Attila Egri-Nagy, Jeremy Sumner, Barbara R Holland, Peter D Jarvis, Mark M Tanaka, Andrew R Francis
Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. Distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. Corresponding corrections for genome rearrangement distances fall into 3 categories: Empirical computational studies, Bayesian/MCMC approaches, and combinatorial approaches. Here, we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using a group-theoretic approach to modelling inversions introduced recently...
April 20, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28433392/quantifying-rates-of-cell-migration-and-cell-proliferation-in-co-culture-barrier-assays-reveals-how-skin-and-melanoma-cells-interact-during-melanoma-spreading-and-invasion
#3
Parvathi Haridas, Catherine J Penington, Jacqui A McGovern, D L Sean McElwain, Matthew J Simpson
Malignant spreading involves the migration of cancer cells amongst other native cell types. For example, in vivo melanoma invasion involves individual melanoma cells migrating through native skin, which is composed of several distinct subpopulations of cells. Here, we aim to quantify how interactions between melanoma and fibroblast cells affect the collective spreading of a heterogeneous population of these cells in vitro. We perform a suite of circular barrier assays that includes: (i) monoculture assays with fibroblast cells; (ii) monoculture assays with SK-MEL-28 melanoma cells; and (iii) a series of co-culture assays initiated with three different ratios of SK-MEL-28 melanoma cells and fibroblast cells...
April 19, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28427819/size-dependent-axial-instability-of-microtubules-surrounded-by-cytoplasm-of-a-living-cell-based-on-nonlocal-strain-gradient-elasticity-theory
#4
S Sahmani, M M Aghdam
Microtubules including tubulin heterodimers arranging in a parallel shape of cylindrical hollow plays an important role in the mechanical stiffness of a living cell. In the present study, the nonlocal strain gradient theory of elasticity including simultaneously the both nonlocality and strain gradient size dependency is put to use within the framework of a refined orthotropic shell theory with hyperbolic distribution of shear deformation to analyze the size-dependent buckling and postbuckling characteristics of microtubules embedded in cytoplasm under axial compressive load...
April 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28427818/a-necessary-condition-for-dispersal-driven-growth-of-populations-with-discrete-patch-dynamics
#5
Chris Guiver, David Packman, Stuart Townley
We revisit the question of when can dispersal-induced coupling between discrete sink populations cause overall population growth? Such a phenomenon is called dispersal driven growth and provides a simple explanation of how dispersal can allow populations to persist across discrete, spatially heterogeneous, environments even when individual patches are adverse or unfavourable. For two classes of mathematical models, one linear and one non-linear, we provide necessary conditions for dispersal driven growth in terms of the existence of a common linear Lyapunov function, which we describe...
April 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28427817/reducing-discrepancies-between-3d-and-2d-simulations-due-to-cell-packing-density
#6
LETTER
Robert J Clegg, Jan-Ulrich Kreft
Modelling all three spatial dimensions is often much more computationally expensive than modelling a two-dimensional simplification of the same system. Researchers comparing these approaches in individual-based models of microbial biofilms report quantitative, but not qualitative, differences between 2D and 3D simulations. We show that a large part of the discrepancy is due to the different space packing densities of circles versus spheres, and demonstrate methods to compensate for this: the internal density of individuals or the distances between them can be scaled...
April 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28419864/how-to-be-a-good-neighbour-facilitation-and-competition-between-two-co-flowering-species
#7
Mohsen B Mesgaran, Juliette Bouhours, Mark A Lewis, Roger D Cousens
Empirical evidence suggests that co-flowering species can facilitate each other through shared pollinators. However, the extent to which one co-flowering species can relieve pollination limitation of another while simultaneously competing for abiotic resource has rarely been examined. Using a deterministic model we explored the demographic outcome for one ("focal") species of its co-occurrence with a species that shares pollinators and competes for both pollinator visitation and abiotic resources. In this paper we showed how the overall impact can be positive or negative, depending on the balance between enhanced fertilization versus increased competition...
April 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28414087/quantifying-the-potential-and-flux-landscapes-of-multi-locus-evolution
#8
Li Xu, Jin Wang
Exploration of multi-locus evolution is critically important for understanding evolutionary dynamics. Recombination and epistasis lead to complex evolutionary dynamics. Quantifying the stability and function of such multi-locus evolutionary systems globally is a long-standing challenge for evolutionary biologists. The conventional Wright, Fisher and quasi-linkage equilibrium (QLE) theories can only be applied to highly restricted, simplified and special evolutionary scenarios. In this study, we developed a non-equilibrium potential and flux landscape theory to explore the multi-locus evolution beyond Wright, Fisher and the QLE...
April 13, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28414086/deadbeats-or-losers-discretionary-male-parental-investment-can-make-females-less-choosy
#9
Frazer Meacham, Thomas Getty
Two of the most important reproductive decisions that animals face are how to choose mates and how to invest in offspring. In species where both males and females provide offspring care, these selection pressures will often be reciprocally intertwined: mate preferences may depend on parental investment patterns while parental investment patterns may depend on mate preferences. We describe and analyze a mathematical model of this interaction, in which females can choose amongst males who have high attractiveness or low attractiveness, while males can decide whether to provide offspring care...
April 13, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28414085/lost-in-space-generalising-subtree-prune-and-regraft-to-spaces-of-phylogenetic-networks
#10
Magnus Bordewich, Simone Linz, Charles Semple
Over the last fifteen years, phylogenetic networks have become a popular tool to analyse relationships between species whose past includes reticulation events such as hybridisation or horizontal gene transfer. However, the space of phylogenetic networks is significantly larger than that of phylogenetic trees, and how to analyse and search this enlarged space remains a poorly understood problem. Inspired by the widely-used rooted subtree prune and regraft (rSPR) operation on rooted phylogenetic trees, we propose a new operation-called subnet prune and regraft (SNPR)-that induces a metric on the space of all rooted phylogenetic networks on a fixed set of leaves...
April 13, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28411111/s-sulfpred-a-sensitive-predictor-to-capture-s-sulfenylation-sites-based-on-a-resampling-one-sided-selection-undersampling-synthetic-minority-oversampling-technique
#11
Cangzhi Jia, Yun Zuo
Protein S-sulfenylation is a reversible post-translational modification involving covalent attachment of hydroxide to the thiol group of cysteine residues, which is involved in various biological processes including cell signaling, response to stress and protein functions. Herein we present S-SulfPred, a support vector machine based model to capture potential S-sulfenylation sites and improve the efficiency and relevance of experimental identification of protein S-sulfenylation sites. One-sided selection (OSS) undersampling and synthetic minority oversampling technique (SMOTE) oversampling were combined to establish balanced training datasets...
April 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28408315/the-corr-hypothesis-for-genes-in-organelles
#12
John F Allen
Chloroplasts and mitochondria perform energy transduction in photosynthesis and respiration. These processes can be described in physico-chemical terms with no obvious requirement for co-located genetic systems, separat from those of the rest of the cell. Accordingly, biochemists once tended to regard endosymbiosis as untestable evolutionary speculation. Lynn Sagan's seminal 1967 paper "On the Origin of Mitosing Cells" outlined the evolution of eukaryotic cells by endosymbiosis of prokaryotes. The endosymbiont hypothesis is consistent with presence of DNA in chloroplasts and mitochondria, but does not assign it a function...
April 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28400108/continuum-approximations-for-lattice-free-multi-species-models-of-collective-cell-migration
#13
Oleksii M Matsiaka, Catherine J Penington, Ruth E Baker, Matthew J Simpson
Cell migration within tissues involves the interaction of many cells from distinct subpopulations. In this work, we present a discrete model of collective cell migration where the motion of individual cells is driven by random forces, short range repulsion forces to mimic crowding, and longer range attraction forces to mimic adhesion. This discrete model can be used to simulate a population of cells that is composed of K ≥ 1 distinct subpopulations. To analyse the discrete model we formulate a hierarchy of moment equations that describe the spatial evolution of the density of agents, pairs of agents, triplets of agents, and so forth...
April 8, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28400107/optimal-and-stable-random-pattern-formations
#14
Vladimir Mityushev
We develop a graph model to describe the vast range of patterns observed in biological structures. For any given number of spotty patterns, a finite number of structures (optimal graphs) is precisely described. The construction of the optimal graphs is based on the minimization of the diffusion dissipation energy. The notion of geometrical stability of structures is introduced. It is demonstrated that the hexagonal array is stable and the square array is not. This explains the reason why the hexagonal array appears more frequently in practice than the square one...
April 8, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28396125/modeling-and-analysis-of-modular-structure-in-diverse-biological-networks
#15
Al-Anzi Bader, Gerges Sherif, Olsman Noah, Ormerod Christopher, Piliouras Georgios, Ormerod John, Zinn Kai
Biological networks, like most engineered networks, are not the product of a singular design but rather are the result of a long process of refinement and optimization. Many large real-world networks are comprised of well-defined and meaningful smaller modules. While engineered networks are designed and refined by humans with particular goals in mind, biological networks are created by the selective pressures of evolution. In this paper, we seek to define aspects of network architecture that are shared among different types of evolved biological networks...
April 8, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28392184/on-the-origin-of-non-membrane-bound-organelles-and-their-physiological-function
#16
Wylie Stroberg, Santiago Schnell
The origin of cellular compartmentalization has long been viewed as paralleling the origin of life. Historically, membrane-bound organelles have been presented as the canonical examples of compartmentalization. However, recent interest in cellular compartments that lack encompassing membranes has forced biologists to reexamine the form and function of cellular organization. The intracellular environment is now known to be full of transient macromolecular structures that are essential to cellular function, especially in relation to RNA regulation...
April 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28392183/evaluating-the-influence-of-mechanical-stress-on-anticancer-treatments-through-a-multiphase-porous-media-model
#17
Pietro Mascheroni, Daniela Boso, Luigi Preziosi, Bernhard A Schrefler
Drug resistance is one of the leading causes of poor therapy outcomes in cancer. As several chemotherapeutics are designed to target rapidly dividing cells, the presence of a low-proliferating cell population contributes significantly to treatment resistance. Interestingly, recent studies have shown that compressive stresses acting on tumor spheroids are able to hinder cell proliferation, through a mechanism of growth inhibition. However, studies analyzing the influence of mechanical compression on therapeutic treatment efficacy have still to be performed...
April 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28390842/third-party-punishment-as-a-costly-signal-of-high-continuation-probabilities-in-repeated-games
#18
Jillian J Jordan, David G Rand
Why do individuals pay costs to punish selfish behavior, even as third-party observers? A large body of research suggests that reputation plays an important role in motivating such third-party punishment (TPP). Here we focus on a recently proposed reputation-based account (Jordan et al., 2016) that invokes costly signaling. This account proposed that "trustworthy type" individuals (who are incentivized to cooperate with others) typically experience lower costs of TPP, and thus that TPP can function as a costly signal of trustworthiness...
April 5, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28385668/cooperation-induces-other-cooperation-fruiting-bodies-promote-the-evolution-of-macrocysts-in-dictyostelium-discoideum
#19
Shota Shibasaki, Yuka Shirokawa, Masakazu Shimada
Biological studies of the evolution of cooperation are challenging because this process is vulnerable to cheating. Many mechanisms, including kin discrimination, spatial structure, or by-products of self-interested behaviors, can explain this evolution. Here we propose that the evolution of cooperation can be induced by other cooperation. To test this idea, we used a model organism Dictyostelium discoideum because it exhibits two cooperative dormant phases, the fruiting body and the macrocyst. In both phases, the same chemoattractant, cyclic AMP (cAMP), is used to collect cells...
April 4, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28385667/a-genetic-approach-to-the-rock-paper-scissors-game
#20
Wendell P Barreto, Flavia M D Marquitti, Marcus A M de Aguiar
Polymorphisms are usually associated with defenses and mating strategies, affecting the individual's fitness. Coexistence of different morphs is, therefore, not expected, since the fittest morph should outcompete the others. Nevertheless, coexistence is observed in many natural systems. For instance, males of the side-blotched lizards (Uta stansburiana) present three morphs with throat colors orange, yellow and blue, which are associated with mating strategies and territorial behavior. The three male morphs compete for females in a system that is well described by the rock-paper-scissors dynamics of game theory...
April 4, 2017: Journal of Theoretical Biology
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