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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/28739172/emergence-and-maintenance-of-menopause-in-humans-a-game-theory-model
#1
Valentin Thouzeau, Michel Raymond
Menopause, the permanent cessation of ovulation, occurs in women well before the end of their expected life span. Several adaptive hypotheses have been proposed to solve this evolutionary puzzle, each based on a possible fitness benefit derived from an early reproductive senescence, but no consensus has emerged. The construction of a game theory model allowed us to jointly study the main adaptive hypotheses in emergence and maintenance of menopause. Four classical hypotheses on the benefits of menopause were considered (decreased maternal mortality, increased grandmothering, decreased conflict over reproductive resources between older and younger females, and changes in their relatedness) plus a fifth one derived from a possible pleiotropic trade-off...
July 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28735858/asymmetric-disease-dynamics-in-multihost-interconnected-networks
#2
Shai Pilosof, Gili Greenbaum, Boris R Krasnov, Yuval R Zelnik
Epidemic spread in single-host systems strongly depends on the population's transmission network. However, little is known regarding the spread of epidemics across networks representing populations of multiple hosts. We explored cross-species transmission in a multilayer network where layers represent populations of two distinct hosts, and disease can spread across intralayer (within-host) and interlayer (between-host) edges. We developed an analytic framework for the SIR epidemic model to examine the effect of (i) source of infection and (ii) between-host asymmetry in infection probabilities, on disease risk...
July 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28735076/quantifying-the-influence-of-oscillatory-flow-disturbances-on-blood-flow
#3
Sargon A Gabriel, Yan Ding, Yuqing Feng
Pulsatile blood flow is renowned for inducing localised flow disturbances that are characterised by significant oscillations. These flow disturbances are recognised to have a physiologic significance within the cardiovascular system, particularly with respect to their proatherogenic expression on endothelial cells. Flow disturbances also impart significant influence on the mechanics of cardiovascular flow and are formally shown in the present study to be coupled to the period-average behaviour of a pulsatile flow field, causing it to be misrepresented by its steady-equivalent; which is often used in models of atherogenesis and hence limits their reliability...
July 19, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28735075/an-entropic-model-of-gaia
#4
R Arthur, A Nicholson
We modify the Tangled Nature Model of Christensen et. al. so that the agents affect the carrying capacity. This leads to a model of species-environment co-evolution where the system tends to have a larger carrying capacity with life than without. We discuss the model as an example of an entropic hierarchy and some implications for Gaia theory.
July 19, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28733187/a-confidence-building-exercise-in-data-and-identifiability-modeling-cancer-chemotherapy-as-a-case-study
#5
Marisa C Eisenberg, Harsh V Jain
Mathematical modeling has a long history in the field of cancer therapeutics, and there is increasing recognition that it can help uncover the mechanisms that underlie tumor response to treatment. However, making quantitative predictions with such models often requires parameter estimation from data, raising questions of parameter identifiability and estimability. Even in the case of structural (theoretical) identifiability, imperfect data and the resulting practical unidentifiability of model parameters can make it difficult to infer the desired information, and in some cases, to yield biologically correct inferences and predictions...
July 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28728995/a-mechanistic-model-quantifies-artemisinin-induced-parasite-growth-retardation-in-blood-stage-plasmodium-falciparum-infection
#6
Pengxing Cao, Nectarios Klonis, Sophie Zaloumis, David S Khoury, Deborah Cromer, Miles P Davenport, Leann Tilley, Julie A Simpson, James M McCaw
Falciparum malaria is a major parasitic disease causing widespread morbidity and mortality globally. Artemisinin derivatives-the most effective and widely-used antimalarials that have helped reduce the burden of malaria by 60% in some areas over the past decade-have recently been found to induce growth retardation of blood-stage Plasmodium falciparum when applied at clinically relevant concentrations. To date, no model has been designed to quantify the growth retardation effect and to predict the influence of this property on in vivo parasite killing...
July 18, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28728997/sepsis-reconsidered-identifying-novel-metrics-for-behavioral-landscape-characterization-with-a-high-performance-computing-implementation-of-an-agent-based-model
#7
Chase Cockrell, Gary An
OBJECTIVES: Sepsis affects nearly 1 million people in the United States per year, has a mortality rate of 28-50% and requires more than $20 billion a year in hospital costs. Over a quarter century of research has not yielded a single reliable diagnostic test or a directed therapeutic agent for sepsis. Central to this insufficiency is the fact that sepsis remains a clinical/physiological diagnosis representing a multitude of molecularly heterogeneous pathological trajectories. Advances in computational capabilities offered by High Performance Computing (HPC) platforms call for an evolution in the investigation of sepsis to attempt to define the boundaries of traditional research (bench, clinical and computational) through the use of computational proxy models...
July 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28728996/conditions-for-success-of-engineered-underdominance-gene-drive-systems
#8
Matthew P Edgington, Luke S Alphey
Engineered underdominance is one of a number of different gene drive strategies that have been proposed for the genetic control of insect vectors of disease. Here we model a two-locus engineered underdominance based gene drive system that is based on the concept of mutually suppressing lethals. In such a system two genetic constructs are introduced, each possessing a lethal element and a suppressor of the lethal at the other locus. Specifically, we formulate and analyse a population genetics model of this system to assess when different combinations of release strategies (i...
July 17, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28720411/modeling-mechanical-control-of-spindle-orientation-of-intestinal-crypt-stem-cells
#9
Zsolt Bertalan, Stefano Zapperi, Caterina A M La Porta
Tissue development requires a control over the sequence of symmetric and asymmetric stem cell divisions to obtain the specific numbers of differentiated cells populating the tissue and stem cells residing in the niche. A good experimental model to study this process is the mouse intestinal crypt development, where it has been shown that stem cells follow an optimal strategy in which asymmetric division occurs only after all symmetric divisions have taken place to reach a fixed number of cells in the niche in the shortest time...
July 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28716385/protein-lipograms
#10
Jason Laurie, Amit K Chattopadhyay, Darren R Flower
Linguistic analysis of protein sequences is an underexploited technique. Here, we capitalize on the concept of the lipogram to characterize sequences at the proteome levels. A lipogram is a literary composition which omits one or more letters. A protein lipogram likewise omits one or more types of amino acid. In this article, we establish a usable terminology for the decomposition of a sequence collection in terms of the lipogram. Next, we characterize Uniref50 using a lipogram decomposition. At the global level, protein lipograms exhibit power-law properties...
July 15, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28716386/comparing-the-rankings-obtained-from-two-biodiversity-indices-the-fair-proportion-index-and-the-shapley-value
#11
Kristina Wicke, Mareike Fischer
The Shapley Value and the Fair Proportion Index of phylogenetic trees have been frequently discussed as prioritization tools in conservation biology. Both indices rank species according to their contribution to total phylogenetic diversity, allowing for a simple conservation criterion. While both indices have their specific advantages and drawbacks, it has recently been shown that both values are closely related. However, as different authors use different definitions of the Shapley Value, the specific degree of relatedness depends on the specific version of the Shapley Value - it ranges from a high correlation index to equality of the indices...
July 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28709942/generation-time-and-fitness-tradeoffs-during-the-evolution-of-multicellularity
#12
Martin P Leslie, Deborah E Shelton, Richard E Michod
The evolution of multicellular organisms from their unicellular ancestors is an example of an evolutionary transition in individuality (ETI), i.e. a change in the units of selection and adaptation. The theory of ETIs poses particular challenges because, by definition, key theoretical constructs such as fitness are shifting during an ETI. Past work emphasized the importance of life history tradeoffs during ETIs in which lower level units form groups and become individuals at a higher level. In particular, it has been hypothesized that the convexity of the lower-level tradeoff between viability and fecundity changes with group size and determines the optimality of lower-level specialization in the fitness components of the group...
July 12, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28709943/propagation-and-control-of-gene-expression-noise-with-non-linear-translation-kinetics
#13
J David Van Dyken
Gene expression is a stochastic process involving small numbers of molecules. As a consequence, cells in a clonal population vary randomly and sometimes substantially from one another in the concentration of mRNA and protein species, a phenomenon known as gene expression noise. Previous theoretical models of gene expression noise assumed that translation is first-order (linear) in mRNA concentration, leading to unfiltered propagation of mRNA noise to the protein level. Here I consider the biological ramifications of relaxing this assumption...
July 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28709941/evolvability-and-robustness-a-paradox-restored
#14
Christine Mayer, Thomas F Hansen
Evolvability and robustness are crucial for the origin and maintenance of complex organisms, but may not be simultaneously achievable as robust traits are also hard to change. Andreas Wagner has proposed a solution to this paradox by arguing that the many-to-few aspect of genotype-phenotype maps creates neutral networks of genotypes coding for the same phenotype. Phenotypes with large networks are genetically robust, but they may also have more neighboring phenotypes and thus higher evolvability. In this paper, we explore the generality of this idea by sampling large numbers of random genotype-phenotype maps for Boolean genotypes and phenotypes...
July 11, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28689889/independent-channels-for-mirna-biosynthesis-ensure-efficient-static-and-dynamic-control-in-the-regulation-of-the-early-stages-of-myogenesis
#15
Jonathan Fiorentino, Andrea De Martino
Motivated by recent experimental work, we define and study a deterministic model of the complex miRNA-based regulatory circuit that putatively controls the early stage of myogenesis in human. We aim in particular at a quantitative understanding of (i) the roles played by the separate and independent miRNA biosynthesis channels (one involving a miRNA-decoy system regulated by an exogenous controller, the other given by transcription from a distinct genomic locus) that appear to be crucial for the differentiation program, and of (ii) how competition to bind miRNAs can efficiently control molecular levels in such an interconnected architecture...
July 8, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28689891/collective-strategies-and-cyclic-dominance-in-asymmetric-predator-prey-spatial-games
#16
Annette Cazaubiel, Alessandra F Lütz, Jeferson J Arenzon
Predators may attack isolated or grouped prey in a cooperative, collective way. Whether a gregarious behavior is advantageous to each species depends on several conditions and game theory is a useful tool to deal with such a problem. We here extend the Lett et al. (2004) to spatially distributed populations and compare the resulting behavior with their mean-field predictions for the coevolving densities of predator and prey strategies. Besides its richer behavior in the presence of spatial organization, we also show that the coexistence phase in which collective and individual strategies for each group are present is stable because of an effective, cyclic dominance mechanism similar to a well-studied generalization of the Rock-Paper-Scissors game with four species, a further example of how ubiquitous this coexistence mechanism is...
July 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28689890/the-dose-dense-principle-in-chemotherapy
#17
Álvaro G López, Kelly C Iarosz, Antonio M Batista, Jesús M Seoane, Ricardo L Viana, Miguel A F Sanjuán
Chemotherapy is a cancer treatment modality that uses drugs to kill tumor cells. A typical chemotherapeutic protocol consists of several drugs delivered in cycles of three weeks. We present mathematical analyses demonstrating the existence of a maximum time between cycles of chemotherapy for a protocol to be effective. A mathematical equation is derived, which relates such a maximum time with the variables that govern the kinetics of the tumor and those characterizing the chemotherapeutic treatment. Our results suggest that there are compelling arguments supporting the use of dose-dense protocols...
July 6, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28687224/numerical-simulation-of-colloidal-self-assembly-of-super-hydrophobic-arachnid-cerotegument-structures
#18
Alexander É Filippov, Jonas O Wolff, Michael Seiter, Stanislav N Gorb
Certain arachnids exhibit complex coatings of their exoskeleton, consisting of globular structures with complex surface features. This, so-called, cerotegument is formed by a multi-component colloidal secretion that self-assembles and cures on the body surface, and leads to high water repellency. Previous ultrastructural studies revealed the involvement of different glandular cells that contribute different components to the secretion mixture, but the overall process of self-assembly into the complex regular structures observed remained highly unclear...
July 4, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28684294/survival-phenotype-selfish-individual-versus-darwinian-phenotype
#19
József Garay, Villő Csiszár, Tamás F Móri
Consider and infinitely large asexual population without mutations and direct interactions. The activities of an individual determine the fecundity and the survival probability of individuals, moreover each activity takes time. We view this population model as a simple combination of life history and optimal foraging models. The phenotypes are given by probability distributions on these activities. We concentrate on the following phenotypes defined by optimization of different objective functions: selfish individual (maximizes the average offspring number during life span), survival phenotype (maximizes the probability of non-extinction of descendants) and Darwinian phenotype (maximizes the phenotypic growth rate)...
July 4, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/28684295/on-the-origin-of-mitosing-cells-a-historical-appraisal-of-lynn-margulis-endosymbiotic-theory
#20
Antonio Lazcano, Juli Peretó
Although for a long-time symbiosis was considered to be quite rare and with no role in evolutionary processes, Lynn Margulis demonstrated that endosymbiotic events played a key role in the origin and evolution of eukaryotic cells. Starting with her seminal assay in the Journal of Theoretical Biology in 1967 (authored as Lynn Sagan), her lifelong work on eukaryogenesis and the role of symbiosis in evolution stands as a valid and authoritative contribution to science. As was quick to acknowledge, she was not the first to discuss the significance of symbiosis to explain the origin of mitochondria and chloroplasts, but no one else had done it to her extent and depth, nor had anyone provided a variety of testable hypotheses...
July 3, 2017: Journal of Theoretical Biology
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