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Journal of Theoretical Biology

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https://www.readbyqxmd.com/read/30012517/free-energy-minimization-in-joint-agent-environment-systems-a-niche-construction-perspective
#1
Jelle Bruineberg, Erik Rietveld, Thomas Parr, Leendert van Maanen, Karl J Friston
The free-energy principle is an attempt to explain the structure of the agent and its brain, starting from the fact that an agent exists (Friston and Stephan, 2007; Friston et al., 2010). More specifically, it can be regarded as a systematic attempt to understand the 'fit' between an embodied agent and its niche, where the quantity of free-energy is a measure for the 'misfit' or disattunement (Bruineberg and Rietveld, 2014) between agent and environment. This paper offers a proof-of-principle simulation of niche construction under the free-energy principle...
July 13, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30012516/an-important-role-of-the-biarticular-hamstrings-is-to-exert-internal-external-rotation-moments-on-the-tibia-during-vertical-jumping
#2
Daniel J Cleather
Most research considering biarticular muscle function has tended to focus on the sagittal plane. Instead, the purpose of this study was to evaluate the internal/external rotation moment arms of the biarticular muscles of the knee, and then to explore their function. The FreeBody musculoskeletal model of the lower limb was used to calculate the moment arms and moments that each of the muscles of the knee exerted on the proximal tibia of 12 athletic males during vertical jumping. Biceps femoris and tensor fascia latae were external rotators of the tibia, whereas semimembranosus, semitendinosus, sartorius, gracilis, popliteus and the patellar tendon were internal rotators...
July 13, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30009794/inferring-parameters-of-prey-switching-in-a-1-predator-2-prey-plankton-system-with-a-linear-preference-tradeoff
#3
Sofia H Piltz, Lauri Harhanen, Mason A Porter, Philip K Maini
We construct two ordinary-differential-equation models of a predator feeding adaptively on two prey types, and we evaluate the models' ability to fit data on freshwater plankton. We model the predator's switch from one prey to the other in two different ways: (i) smooth switching using a hyperbolic tangent function; and (ii) by incorporating a parameter that changes abruptly across the switching boundary as a system variable that is coupled to the population dynamics. We conduct linear stability analyses, use approximate Bayesian computation (ABC) combined with a population Monte Carlo (PMC) method to fit model parameters, and compare model results quantitatively to data for ciliate predators and their two algal prey groups collected from Lake Constance on the German-Swiss-Austrian border...
July 13, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30009793/why-does-hyperglycinemia-exhibit-so-grave-brain-anomalies-and-so-severe-neurological-symptoms
#4
Kohji Sato
Nonketotic-hyperglycinemia (NKH) is an autosomal recessive disorder associated with grave brain malformations and severe neurological symptoms, and also characterized by accumulation of a large amount of glycine in body fluids. NKH is caused by an inherited deficiency of the glycine cleavage system (GCS), which is the main system to degrade glycine in mammalians. These severe symptoms and grave bran malformations are not normally observed in the other amino acid metabolic disorders, suggesting that GCS should have unknown pivotal roles in brain development and function...
July 12, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30017945/examining-the-effect-of-reoccurring-disturbances-on-population-persistence-with-application-to-marine-mammals
#5
Amy Veprauskas, Azmy S Ackleh, Tingting Tang
We develop a two-state Markov chain to describe the effect of reoccurring disturbances on a population that is modeled by discrete-time matrix model. The environment is described by three parameters that define the magnitude of impact of a disturbance, the average duration of impact of a disturbance, and the average time between disturbances. We derive an approximation for the stochastic growth rate in order to examine how these three parameters affect population growth. From this approximation, we calculate the sensitivity and elasticity of the growth rate with respect to the environmental parameters...
July 11, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30017944/the-role-of-stochastic-sequestration-dynamics-for-intrinsic-noise-filtering-in-signaling-network-motifs
#6
Debdas Paul, Nicole Radde
The relation between design principles of signaling network motifs and their robustness against intrinsic noise still remains illusive. In this work we investigate the role of cascading for coping with intrinsic noise due to stochasticity in molecular reactions. We use stochastic approaches to quantify fluctuations in the terminal kinase of phosphorylation-dephosphorylation cascade motifs and demonstrate that cascading highly affects these fluctuations. We show that this purely stochastic effect can be explained by time-varying sequestration of upstream kinase molecules...
July 11, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30017943/vaccination-threshold-size-and-backward-bifurcation-of-sir-model-with-state-dependent-pulse-control
#7
Qianqian Zhang, Biao Tang, Sanyi Tang
Depending on the potential susceptible human size, we consider the state-dependent integrated infectious disease control strategies including vaccination, isolation and treatment. Correspondingly, we propose a state-dependent pulse SIR model, in which whether the control measures implemented or not depends on the threshold size of susceptible population. By defining the Poincaré map, we first investigate the existence and global stability of the semi-trivial (or disease free) periodic solution, and the threshold condition is proposed...
July 11, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30006002/mathematical-analysis-to-prioritise-strategies-for-malaria-elimination
#8
Nakul Chitnis, Allan Schapira, Christian Schindler, Melissa Penny, Thomas Smith
Malaria and some other tropical diseases are currently targeted for elimination and eventually eradication. Since resources are limited, prioritisation of countries or areas for elimination is often necessary. However, this prioritisation is frequently conducted in an ad hoc manner. Lower transmission areas are usually targeted for elimination first, but for some areas this necessitates long and potentially expensive surveillance programs while transmission is eliminated from neighbouring higher transmission areas...
July 10, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30018001/dynamics-of-hiv-1-coinfection-in-different-susceptible-target-cell-populations-during-cell-free-infection
#9
Yusuke Ito, Alexandra Tauzin, Azaria Remion, Keisuke Ejima, Fabrizio Mammano, Shingo Iwami
HIV-1 mutations rapidly accumulate through genetic recombination events, which require the infection of a single cell by two virions (coinfection). Accumulation of mutations in the viral population may lead to immune escape and high-level drug resistance. The existence of cell subpopulations characterized by different susceptibility to HIV-1 infection has been proposed as an important parameter driving coinfection (Dang et al., 2004). While the mechanism and the quantification of HIV-1 coinfection have been recently investigated by mathematical models, the detailed dynamics of this process during cell-free infection remains elusive...
July 7, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29990466/beyond-replicator-dynamics-from-frequency-to-density-dependent-models-of-evolutionary-games
#10
Vlastimil Křivan, Theodore E Galanthay, Ross Cressman
Game theoretic models of evolution such as the Hawk-Dove game assume that individuals gain fitness (which is a proxy of the per capita growth rate) in pair-wise contests only. These models assume that the equilibrium distribution of phenotypes involved (e.g., Hawks and Doves) in the population is given by the Hardy-Weinberg law, which is based on instantaneous, random pair formation. On the other hand, models of population dynamics do not consider pairs, newborns are produced by singles, and interactions between phenotypes or species are described by the mass action principle...
July 7, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29981757/an-agent-based-model-of-nest-site-selection-in-a-mass-recruiting-ant
#11
Adam L Cronin
Complex systems are modular entities which can collectively generate sophisticated emergent solutions through interactions based on simple, local rules. In this study, I use an agent-based model to elucidate how numerous individual-level components contribute to the collective decision process during house-hunting in a mass-recruiting ant species. Myrmecina nipponica combines the use of pheromone trails with a quorum decision rule in collective decisions among nest sites when searching for a new home. The model employed only individual-level rules but accurately emulated group-level properties observed in empirical studies...
July 5, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29981756/impacts-of-infection-avoidance-for-populations-affected-by-sexually-transmitted-infections
#12
Michal Theuer, Luděk Berec
Sexually transmitted infections are ubiquitous in nature and affect many populations. The key process for their transmission is mating, usually preceded by mate choice. Susceptible individuals may avoid mating with infected individuals to prevent infection provided it is recognizable. We show that accounting for infection avoidance significantly alters host population dynamics. We observe bistability between the disease-free and endemic or disease-induced extinction equilibria, significant abrupt reduction in the host population size and disease-induced host extinction...
July 5, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29981338/the-influence-of-social-behavior-on-competition-between-virulent-pathogen-strains
#13
Joe Pharaon, Chris T Bauch
Infectious disease interventions like contact precautions and vaccination have proven effective in disease control and elimination. The priority given to interventions can depend strongly on how virulent the pathogen is, and interventions may also depend partly for their success on social processes that respond adaptively to disease dynamics. However, mathematical models of competition between pathogen strains with differing natural history profiles typically assume that human behaviour is fixed. Here, our objective is to model the influence of social behaviour on the competition between pathogen strains with differing virulence...
July 4, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29981337/a-network-hierarchy-based-method-for-functional-module-detection-in-protein-protein-interaction-networks
#14
Wei Liu, Liangyu Ma, Byeungwoo Jeon, Ling Chen, Bolun Chen
In the post-genomic era, one of the important tasks is to identify protein complexes and functional modules from high-throughput protein-protein interaction data, so that we can systematically analyze and understand the molecular functions and biological processes of cells. Although a lot of functional module detection studies have been proposed, how to design correctly and efficiently functional modules detection algorithms is still a challenging and important scientific problem in computational biology. In this paper, we present a novel Network Hierarchy-Based method to detect functional modules in PPI networks (named NHB-FMD)...
July 4, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29981336/use-of-image-texture-analysis-to-find-dna-sequence-similarities
#15
Weiyang Chen, Bo Liao, Weiwei Li
Sequence similarity analysis is a basic method in computational biological studies. Determining the similarity of biological sequences is a vital step in much research, such as exploring the evolutionary relationship among species, gene function analysis, protein structure prediction, and sequence retrieving. This paper introduces a method that uses the theory of the gray-level co-occurrence matrix, which is important in image texture analysis, to define and calculate the features of a DNA sequence. The proposed method can make a quantitative analysis and compute the defined texture features of a DNA sequence...
July 4, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29997059/a-solution-for-private-assessment-in-indirect-reciprocity-using-solitary-observation
#16
Isamu Okada, Tatsuya Sasaki, Yutaka Nakai
Although indirect reciprocity is a fundamental mechanism in the evolution of human cooperation, most studies assume public assessment in which individuals are not permitted to obtain private assessments of others. Existing studies on private assessment have used individual-based simulations because of the analytical difficulty involved. Here, we develop an analytical method using solitary observation to solve private assessment in indirect reciprocity problem without any approximation. In this study, we formulate a model of solitary observation and calculate the replicator dynamics systems of five leading norms of indirect reciprocity...
July 3, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/30008397/models-for-the-bystander-effect-in-gradient-radiation-fields-range-and-signalling-type
#17
Valery Peng, Natalka Suchowerska, Ana Dos Santos Esteves, Linda Rogers, Elizabeth Claridge Mackonis, Joanne Toohey, David R McKenzie
Bystander responses to radiation are responsible for a significant fraction of cell death, but are not included in the conventional linear-quadratic (LQ) radiobiological model. Strong dose gradients in radiation fields affect the distribution of bystander signals and can be used to decrease the survival of cancer cells. Predictive models incorporating bystander effects are needed to design the dose gradients in modulated fields to improve cancer treatments. Fundamental questions concern the nature and range of bystander signalling...
July 2, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29969599/propagation-of-regulatory-fluctuations-induces-coordinated-switching-of-flagellar-motors-in-chemotaxis-signaling-pathway-of-single-bacteria
#18
Toshinori Namba, Tatsuo Shibata
The random motion of E. coli is driven by multiple flagella motors. When all motors rotate in the counter clockwise direction, the bacteria swims smoothly. A recent experimental report by Terasawa et al. [Biophys J,100,2193,(2011)] demonstrated that a coordination of the motors can occur through signaling pathways, and perturbation of a regulatory molecule disrupted the coordination. Here, we develop a mathematical model to show that a large temporal fluctuation in the regulator concentration can induce a correlated switching of the multiple motors...
June 30, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29969598/the-dynamics-of-integration-viral-suppression-and-cell-cell-transmission-in-the-development-of-occult-hepatitis-b-virus-infection
#19
Ashish Goyal, Ranjit Chauhan
BACKGROUND: Out of several phases of HBV infection, the least understood phase is occult hepatitis virus infection. The paucity of data due to non-availability of biological tissues and the prerequisite of ultra-sensitive assays for the detection of occult hepatitis virus infection prompted us to utilize mathematical modeling in determining mechanisms that lead to occult hepatitis virus infection and characteristics of HBV infection during occult hepatitis virus infection. METHODS: We proposed two mathematical models (M1 and M2), considering two different phenomenon for episomal maintenance and accumulation of covalently closed circular DNA (cccDNA) in infected hepatocytes: (i) M1 - recirculation of the relaxed circular DNA/double-stranded linear DNA from cytoplasm to the nucleus, and (ii) M2 - reinfection of infected hepatocytes with virions...
June 30, 2018: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29964065/information-sharing-for-a-coordination-game-in-fluctuating-environments
#20
Keith Paarporn, Ceyhun Eksin, Joshua S Weitz
Collective action dilemmas pervade the social and biological sciences - from human decision-making to bacterial quorum sensing. In these scenarios, individuals sense cues from the environment to adopt a suitable phenotype or change in behavior. However, when cues include signals from other individuals, then the appropriate behavior of each individual is linked. Here, we develop a framework to quantify the influence of information sharing on individual behavior in the context of two player coordination games...
June 28, 2018: Journal of Theoretical Biology
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