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Journal of Theoretical Biology

Matan Danino, Nadav M Shnerb
A fundamental problem in the fields of population genetics, evolution, and community ecology, is the fate of a single mutant, or invader, introduced in a finite population of wild types. For a fixed-size community of N individuals, with Markovian, zero-sum dynamics driven by stochastic birth-death events, the mutant population eventually reaches either fixation or extinction. The classical analysis, provided by Kimura and his coworkers, is focused on the neutral case, [where the dynamics is only due to demographic stochasticity (drift)], and on time-independent selective forces (deleterious/beneficial mutation)...
January 9, 2018: Journal of Theoretical Biology
L Dinh, G Chowell, R Rothenberg
The early dynamics of an infectious disease outbreak can be affected by various factors including the transmission mode of the disease and host-specific factors. While recent works have highlighted the presence of sub-exponential growth patterns during the early phase of epidemics, empirical studies examining the contribution of different factors to early epidemic growth dynamics are lacking. Here we aim to characterize and explain the early incidence growth patterns of local HIV/AIDS epidemics in Brazil as a function of socio-demographic factors...
January 9, 2018: Journal of Theoretical Biology
Uduak Z George, Sharon R Lubkin
Lung branching morphogenesis proceeds in three stereotyped modes (domain, planar, and orthogonal branching). Much is known about the molecular players, including growth factors such as fibroblast growth factor 10 but it is unknown how these signals could actuate the different branching patterns. With the aim of identifying mechanisms that may determine the different branching modes, we developed a computational model of the epithelial lung bud and its surrounding mesenchyme. We studied transport of morphogens and localization of morphogen flux at lobe surfaces and lobe edges...
January 9, 2018: Journal of Theoretical Biology
Mainak Patel, Badal Joshi
Reciprocal inhibition is a common motif exploited by neuronal networks; an intuitive and tractable way to examine the behaviors produced by reciprocal inhibition is to consider a pair of neurons that synaptically inhibit each other and receive constant or noisy excitatory driving currents. In this work, we examine reciprocal inhibition using two models (a voltage-based and a current-based integrate-and-fire model with instantaneous or temporally structured input), and we use analytic and computational tools to examine the bifurcations that occur and study the various possible monostable, bistable, and tristable regimes that can exist; we find that, depending on system parameters (and on choice of neuron model), there can exist up to 3 distinct monostable regimes (denoted M0, M1, M2), 3 distinct bistable regimes (denoted B, B1, B2), and a single tristable regime (denoted T)...
January 9, 2018: Journal of Theoretical Biology
Sumit Tarafder, Md Toukir Ahmed, Sumaiya Iqbal, Md Tamjidul Hoque, M Sohel Rahman
Accessible Surface Area (ASA) of a protein residue is an effective feature for protein structure prediction, binding region identification, fold recognition problems etc. Improving the prediction of ASA by the application of effective feature variables is a challenging but explorable task to consider, specially in the field of machine learning. Among the existing predictors of ASA, REGAd3p is a highly accurate ASA predictor which is based on regularized exact regression with polynomial kernel of degree 3. In this work, we present a new predictor RBSURFpred, which extends REGAd3p on several dimensions by incorporating 58 physicochemical, evolutionary and structural properties into 9-tuple peptides via Chou's general PseAAC, which allowed us to obtain higher accuracies in predicting both real-valued and binary ASA...
January 2, 2018: Journal of Theoretical Biology
Martina Devi, Esther Chingbiaknem, R H Duncan Lyngdoh
The GA codon box incorporates the two-fold degeneracy of aspartic acid and of glutamic acid. Using the molecular mechanics approach of the AMBER suite, the four codons of the GA box are paired via H-bonding with two aspartic acid anticodons and two glutamic acid anticodons to yield 8 cognate and 11 non-cognate codon-anticodon duplexes. In addition four select non-cognate duplexes between the GA box codons and three alanine anticodons are also studied. These 23 duplexes display a variety of base-pairing possibilities at the wobble position...
January 2, 2018: Journal of Theoretical Biology
Peng-Bi Cui, Lei Gao, Wei Wang
Drug resistance and strong contacts actually play crucial roles in epidemic spread in complex systems. Nevertheless, neither theoretical model or methodology is proposed to address this. We thus consider an edge-based epidemic spread model considering the two key ingredients, in which the contacts are grouped into two classes: strong contacts and normal ones. Next, we present a unified edge-based compartmental approach to the spread dynamics on Erdös-Rényi (ER) networks and validate its results by extensive numerical simulations...
January 2, 2018: Journal of Theoretical Biology
Lichao Zhang, Liang Kong
Gene recombination is a key process to produce hereditary differences. Recombination spot identification plays an important role in revealing genome evolution and promoting DNA function study. However, traditional experiments are not good at identifying recombination spot with huge amounts of DNA sequences springed up by sequencing. At present, some machine learning methods have been proposed to speed up this identification process. However, the correlations between nucleotides pairs at different positions along DNA sequence is often ignored, which reflects the important sequence order information...
January 2, 2018: Journal of Theoretical Biology
Alfonso Jiménez-Sánchez
No abstract text is available yet for this article.
January 2, 2018: Journal of Theoretical Biology
Mayuko Iwamoto, Daishin Ueyama
One of the fundamental problems in biology concerns the method by which a cluster of organisms can regulate the proportion of individuals that perform various roles or modes as if each individual is aware of the overall situation without a leader. In various species, a specific ratio exists at multiple levels, from the process of cell differentiation in multicellular organisms to the situation of social dilemma in a group of human beings. This study determines a common basis for regulating collective behavior that is realized by a series of local contacts between individuals...
December 28, 2017: Journal of Theoretical Biology
Madhurima Nath, Yihui Ren, Yasamin Khorramzadeh, Stephen Eubank
We demonstrate a general method to analyze the sensitivity of attack rate in a network model of infectious disease epidemiology to the structure of the network. We use Moore and Shannon's "network reliability" statistic to measure the epidemic potential of a network. A number of networks are generated using exponential random graph models based on the properties of the contact network structure of one of the Add Health surveys. The expected number of infections on the original Add Health network is significantly different from that on any of the models derived from it...
December 29, 2017: Journal of Theoretical Biology
Atsushi Yamauchi, Minus van Baalen, Maurice Sabelis
In kin selection theory in the evolution of social behaviours, the relatedness between interacting individuals is influenced by the spatial structure of the population. It is generally considered that in the 'viscous' population competition among individuals tends to suppress the evolution of altruism. We consider that more complex interactions produce specific spatial patterns in the presence of competitive interaction, which could alter the process of kin selection in a given space. Here, we theoretically studied the joint evolution of altruism and resource exploitation in a spatially structured population...
December 28, 2017: Journal of Theoretical Biology
Di Hu, Cai-Hua Xiong, Ming-Jin Liu
Human exhibits the most dexterous manual manipulation among the anthropoids. The sophisticated dexterity of human hand has been linked to its distinctive morphology compared to the nonhuman anthropoids. The human hand is derived from the ancestral hands after longtime evolution. However, there are more possible morphologies that the hands could take during the evolutionary process. It remains unknown whether better hands for manipulation than the human hand exist among these possible hands. To answer the question, the relationship between the manipulative capability and hand morphology need to be investigated in the region of more possible hands...
December 26, 2017: Journal of Theoretical Biology
M S Ghuchani
No abstract text is available yet for this article.
December 26, 2017: Journal of Theoretical Biology
Yanir Damti, Ilan Gronau, Shlomo Moran, Irad Yavneh
Distance-based methods for phylogenetic reconstruction are based on a two-step approach: first, pairwise distances are computed from DNA sequences associated with a given set of taxa, and then these distances are used to reconstruct the phylogenetic relationships between taxa. Because the estimated distances are based on finite sequences, they are inherently noisy, and this noise may result in reconstruction errors. Previous attempts to improve reconstruction accuracy focused either on improving the robustness of reconstruction algorithms to this stochastic noise, or on improving the accuracy of the distance estimates...
December 22, 2017: Journal of Theoretical Biology
Adrien Fauré, Shizuo Kaji
Many discrete models of biological networks rely exclusively on Boolean variables and many tools and theorems are available for analysis of strictly Boolean models. However, multilevel variables are often required to account for threshold effects, in which knowledge of the Boolean case does not generalise straightforwardly. This motivated the development of conversion methods for multilevel to Boolean models. In particular, Van Ham's method has been shown to yield a one-to-one, neighbour and regulation preserving dynamics, making it the de facto standard approach to the problem...
December 22, 2017: Journal of Theoretical Biology
L A Crompton, L L McKnight, C K Reynolds, J A N Mills, J L Ellis, M D Hanigan, J Dijkstra, B J Bequette, A Bannink, J France
An isotope dilution model to describe the partitioning of phenylalanine (PHE) and tyrosine (TYR) in the bovine liver was developed. The model comprises four intracellular and six extracellular pools and various flows connecting these pools and external blood. Conservation of mass principles were applied to generate the fundamental equations describing the behaviour of the system in the steady state. The model was applied to datasets from multi-catheterised dairy cattle during a constant infusion of [1-13C] phenylalanine and [2,3,5,6-2H] tyrosine tracers...
December 22, 2017: Journal of Theoretical Biology
Aiko Kawasumi-Kita, Daisuke Ohtsuka, Yoshihiro Morishita
An objective, continuous, and robust method for staging developing embryos or organs is essential for providing a common measure of time when studying quantitative/systems developmental biology. However, classical methods based on factors such as somite number or qualitative visual attributes are discrete and/or ambiguous due to observers' subjectivity. Thus, an alternative staging method based on an explicit and continuous description of developmental states over time, such as anatomy/morphology, is needed...
December 22, 2017: Journal of Theoretical Biology
Luděk Berec, Veronika Bernhauerová, Barbara Boldin
The search for mates is often accompanied with conspicuous behaviour or morphology that can be exploited by predators. Here we explore the evolutionary consequences of a trade-off that arises naturally between mate acquisition and risk of predation and study evolution of the rate at which male prey search for mates in a population subject to a mate-finding Allee effect and exposed to either generalist or specialist predators. Since we show that the mate search rate determines the strength of the mate-finding Allee effect, we can alternatively view this as evolution of the mate-finding Allee effect in prey...
December 22, 2017: Journal of Theoretical Biology
Andrés J Cortés
The prevalence of the HIV-1 infection has decayed in the last decades in western heterosexual populations. However, among men who have sex with men (MSM) the prevalence is still high, despite intensive campaigns and treatment programs that keep infected men as undetectable (Beyrer et al. 2012). Promiscuity and condom fatigue (Adam et al. 2005), which are not unique to the MSM community, are making unprotected anal intercourse (UAI) more common and sexually transmitted infections (STIs) presumably harder to track...
December 19, 2017: Journal of Theoretical Biology
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