13,813 results match your criteria Journal of theoretical biology[Journal]


Maximization of fertility transfers from rangeland to cropland: the contribution of control theory.

J Theor Biol 2019 Feb 15. Epub 2019 Feb 15.

UMR Eco&Sols, Univ Montpellier, IRD, INRA, Montpellier Supagro, CIRAD, Montpellier, France.

In traditional mixed farming systems, soil fertility in cropland relies on the transfer of fertility from rangeland through the transfer of manure produced by livestock that grazes in rangeland. In this work, we introduce a simple meta-ecosystem model in which the mixed farming system is represented by a cropland sub-system connected to a rangeland sub-system by nutrient fluxes. The livestock plays the role of nutrient-pump from the rangeland sub-system to the cropland sub-system. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.039DOI Listing
February 2019

Methods for approximating stochastic evolutionary dynamics on graphs.

J Theor Biol 2019 Feb 14. Epub 2019 Feb 14.

Department of Mathematical Sciences, University of Liverpool, Mathematical Sciences Building, Liverpool L69 7ZL, UK.

Population structure can have a significant effect on evolution. For some systems with sufficient symmetry, analytic results can be derived within the mathematical framework of evolutionary graph theory which relate to the outcome of the evolutionary process. However, for more complicated heterogeneous structures, computationally intensive methods are required such as individual-based stochastic simulations. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.02.009DOI Listing
February 2019

SPrenylC-PseAAC: A sequence-based model developed via Chou's 5-steps rule and general PseAAC for identifying S-prenylation sites in proteins.

J Theor Biol 2019 Feb 12;468:1-11. Epub 2019 Feb 12.

Gordon Life Science Institute, Boston, MA 02478, USA.

The protein prenylation (or S-prenylation) is one of the most essential modifications, required for the association of membrane of a plethora of signalling proteins with the key biological process such as protein trafficking, cell growth, proliferation and differentiation. Due to the ubiquitous nature of S-prenylation and its role in cellular functions, any defect in the biosynthesis or regulation of the isoprenoid leads to the occurrence of a variety of diseases including neurodegenerative disorders, metabolic issues, cardiovascular diseases and one of the most fatal diseases, cancer. This depicts the strong biological significance of S-prenylation, thus, the timely and accurate identification of S-prenylation sites is crucial and may provide with possible ways to understand the mechanism of this modification in proteins. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.02.007DOI Listing
February 2019

An efficient genomic signature ranking method for genomic island prediction from a single genome.

J Theor Biol 2019 Feb 12;467:142-149. Epub 2019 Feb 12.

College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, People's Republic of China; Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, TX 75080, USA. Electronic address:

Genomic islands that are associated with microbial adaptations and carry genomic signatures different from that of the host, and thus many methods have been proposed to select the informative genomic signatures from a range of organisms and discriminate genomic islands from the rest of the genome in terms of these signature biases. However, they are of limited use when closely related genomes are unavailable. In the present work, we proposed a kurtosis-based ranking method to select the informative genomic signatures from a single genome. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.02.008DOI Listing
February 2019

Spatial-Stochastic modelling of synthetic gene regulatory networks.

J Theor Biol 2019 Feb 10;468:27-44. Epub 2019 Feb 10.

School of Mathematics and Statistics, Mathematical Institute, University of St Andrews, United Kingdom, KY16 9SS. Electronic address:

Transcription factors are important molecules which control the levels of mRNA and proteins within cells by modulating the process of transcription (the mechanism by which mRNA is produced within cells) and hence translation (the mechanism by which proteins are produced within cells). Transcription factors are part of a wider family of molecular interaction networks known as gene regulatory networks (GRNs) which play an important role in key cellular processes such as cell division and apoptosis (e.g. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.02.003DOI Listing
February 2019
1 Read

Memory in plants: Boolean modeling of the learning and store/recall memory functions in response to environmental stimuli.

J Theor Biol 2019 Feb 10;467:123-133. Epub 2019 Feb 10.

University of Rouen, 67 rue de Lévis, 75017 Paris, France.

This paper presents a new model of memory functions in plants, which improves the previous approaches done by René Thomas and colleagues. We have decomposed the plant memory processing into three main functions: learning, storing and recalling. We propose as main mechanism for these three functions the occurrence of a calcium wave consecutive to an environmental stimulus, followed by the activation of specific genes and proteins changing their phosphorylated state. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.019DOI Listing
February 2019

Managing yield and resilience in a harvested tritrophic food chain model.

J Theor Biol 2019 Feb 8. Epub 2019 Feb 8.

Department of Mathematics, National Institute of Technology Meghalaya, Bijni Complex, Shillong 793003, Meghalaya, India. Electronic address:

In this article, we compare the two ecological services known as yield and resilience, for a tritrophic food chain model consisting of a prey, an intermediate predator and a top predator. For this comparison process, we use both analytical and numerical techniques. It is shown that a variety of patterns are possible based on the intensity of efforts distributed among different trophic levels. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.02.006DOI Listing
February 2019

Equilibrium properties of the spatial SIS model as a point pattern dynamics - How is infection distributed over space?

J Theor Biol 2019 Feb 7;468:12-26. Epub 2019 Feb 7.

Department of Environmental Science, Nara Women's University, Kita-Uoya Nishimachi, Nara 630-8506, Japan. Electronic address:

We revisit the classical epidemiological SIS model as a stochastic point pattern dynamics with special focus on its spatial distribution at equilibrium. In this model, each point on a continuous space is either susceptible S or infectious I, and infection occurs with an infection kernel as a function of distance from I to S. This stochastic process has been mathematically described by the hierarchical dynamics of the probabilities that a point, a pair made by two points, and a triplet made by three points, etc. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.02.005DOI Listing
February 2019

Dynamics in schizo-obsessive spectrum disorders: a computational approach.

J Theor Biol 2019 Feb 6. Epub 2019 Feb 6.

Department of Mathematical Analysis, Budapest University of Technology and Economics, Budapest, Hungary.

The co-morbidity of obsessive-compulsive disorder (OCD) and schizophrenia is higher than what would be expected by chance and the common underlying neuropathophysiology is not well understood. Repetitive stereotypes and routines can be caused by perseverative thoughts and motor sequences in both of these disorders. We extended a previously published computational model to investigate cortico-striatal network dynamics. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.038DOI Listing
February 2019
2 Reads

Can evolution paths be explained by chance alone?

J Theor Biol 2019 Feb 6;467:63-65. Epub 2019 Feb 6.

Department of Mathematics, University of Colorado at Colorado Springs, United States. Electronic address:

We propose a purely probabilistic model to explain the evolution path of a population maximum fitness. We show that after n births in the population there are about ln n upwards jumps. This is true for any mutation probability and any fitness distribution and therefore suggests a general law for the number of upwards jumps. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.02.004DOI Listing
February 2019

Formalizing and enriching phenotype signatures using Boolean networks.

J Theor Biol 2019 Feb 6;467:66-79. Epub 2019 Feb 6.

University of Rennes, Inria, CNRS, IRISA, Rennes, F-35000, France. Electronic address:

In order to predict the behavior of a biological system, one common approach is to perform a simulation on a dynamic model. Boolean networks allow to analyze the qualitative aspects of the model by identifying its steady states and attractors. Each of them, when possible, is associated with a phenotype which conveys a biological interpretation. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.015DOI Listing
February 2019

Effects of gene duplication, epistasis, recombination and gene conversion on the fixation time of compensatory mutations.

J Theor Biol 2019 Feb 6;467:134-141. Epub 2019 Feb 6.

Professor Emeritus, Kyushu Dental University, Kitakyushu, Japan.

Gene duplication is one of the major mechanisms of molecular evolution. Gene duplication enables copies of a gene to accumulate mutations through functional redundancy. If a gene encodes a specific protein that interacts with other proteins, RNA, or DNA, the relaxation of selective constraints caused by gene duplication might contribute to the fixation of compensatory mutations that occur at the interacting sites. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.02.001DOI Listing
February 2019
1 Read

Assessing the effects of modeling the spectrum of clinical symptoms on the dynamics and control of Ebola.

J Theor Biol 2019 Feb 6;467:111-122. Epub 2019 Feb 6.

Department of Mathematics, Purdue University, West Lafayette, IN 47907, USA. Electronic address:

Mathematical modelers have attempted to capture the dynamics of Ebola transmission and to evaluate the effectiveness of control measures, as well as to make predictions about ongoing outbreaks. Many of their models consider only infections with typical symptoms, but Ebola presents clinically in a more complicated way. Even the most common symptom, fever, is not experienced by 13% of patients. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.013DOI Listing
February 2019

Risk management, signal processing and econometrics: A new tool for forecasting the risk of disease outbreaks.

J Theor Biol 2019 Feb 6;467:57-62. Epub 2019 Feb 6.

Qazvin University of Medical Sciences, Qazvin, Iran. Electronic address:

This paper takes a novel approach for forecasting the risk of disease emergence by combining risk management, signal processing and econometrics to develop a new forecasting approach. We propose quantifying risk using the Value at Risk criterion and then propose a two staged model based on Multivariate Singular Spectrum Analysis and Quantile Regression (MSSA-QR model). The proposed risk measure (PLVaR) and forecasting model (MSSA-QR) is used to forecast the worst cases of waterborne disease outbreaks in 22 European and North American countries based on socio-economic and environmental indicators. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.032DOI Listing
February 2019
2.116 Impact Factor

Foraging decisions as multi-armed bandit problems: Applying reinforcement learning algorithms to foraging data.

Authors:
Juliano Morimoto

J Theor Biol 2019 Feb 6;467:48-56. Epub 2019 Feb 6.

Department of Biological Sciences, Macquarie University, North Ryde, NSW 2109, Australia; Programa de Pós-Graduação em Ecologia e Conservação, Federal University of Paraná, Curitiba, Brazil, 19031, CEP, 81531-990. Electronic address:

Finding resources is crucial for animals to survive and reproduce, but the understanding of the decision-making underlying foraging decisions to explore new resources and exploit old resources remains lacking. Theory predicts an 'exploration-exploitation trade-off' where animals must balance their effort into either stay and exploit a seemingly good resource or move and explore the environment. To date, however, it has been challenging to generate flexible yet tractable statistical models that can capture this trade-off, and our understanding of foraging decisions is limited. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.02.002DOI Listing
February 2019

The heart function as a motor-brake system.

J Theor Biol 2019 Feb 1;467:23-30. Epub 2019 Feb 1.

Dept. of Mathematics & Physics, Università Roma Tre, Italy. Electronic address:

The controversy between passive and active ventricular filling has been debated for decades and the question about the existence of an active diastole remains open. In this work, we advocate the model of active diastole by considering the heart as a suction pump and we add some more clues to support this point of view by the analysis of the pressure-volume (PV) loops of the left heart, comprising of the left ventricle (LV) and atrium (LA). Our working hypothesis is based on the dichotomy motor-brake: the cardiac muscle can act as a motor, when shortening against a load, or as a brake, when lengthening to a load. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.034DOI Listing
February 2019

Sub- or supercritical transmissibilities in a finite disease outbreak: Symmetry in outbreak properties of a disease conditioned on extinction.

J Theor Biol 2019 Jan 31;467:80-86. Epub 2019 Jan 31.

School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK. Electronic address:

This work is concerned with the transmissibility of a disease, on observation of an outbreak of limited size. When such an outbreak occurs, an accurate estimate of the transmissibility of the responsible pathogen is essential for an appropriate response to future outbreaks. Transmissibility is usually characterised in terms of the reproduction number, R, which is the mean number of new cases of infection produced by a single infectious individual. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.033DOI Listing
January 2019

A neutral evolution test derived from a theoretical amino acid substitution model.

J Theor Biol 2019 Jan 31;467:31-38. Epub 2019 Jan 31.

Theoretical Biology Group, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, CDMX, C.P, Ciudad de México 04510, Mexico. Electronic address:

A neutral evolution model that explicitly considers codons, amino acids, and the degeneracy of the genetic code is developed. The model is built from nucleotides up to amino acids, and it represents a refinement of the neutral theory of molecular evolution. The model is based on a stochastic process that leads to a stationary probability distribution of amino acids. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.027DOI Listing
January 2019

Population dynamics of chemotrophs in anaerobic conditions where the metabolic energy acquisition per redox reaction is limited.

J Theor Biol 2019 Jan 31. Epub 2019 Jan 31.

Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Gakuen 2-1, Sanda-shi, Hyogo 669-1337, Japan.

We present a new model of microbial population growth that focuses on the acquisition of metabolic energy through chemosynthesis and how this depends on the concentration of resources and byproducts. Due to entropy effects, organisms extract the greater energy (i.e. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.037DOI Listing
January 2019

Ensembles, dynamics, and cell types: Revisiting the statistical mechanics perspective on cellular regulation.

J Theor Biol 2019 Jan 31;467:15-22. Epub 2019 Jan 31.

Institute for Systems Biology, Seattle, WA 98109, USA.

Genetic regulatory networks control ontogeny. For fifty years Boolean networks have served as models of such systems, ranging from ensembles of random Boolean networks as models for generic properties of gene regulation to working dynamical models of a growing number of sub-networks of real cells. At the same time, their statistical mechanics has been thoroughly studied. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.036DOI Listing
January 2019
1 Read

Identifying N-methyladenosine sites using extreme gradient boosting system optimized by particle swarm optimizer.

J Theor Biol 2019 Jan 31;467:39-47. Epub 2019 Jan 31.

Key Laboratory of Intelligent Information Processing of Jilin Universities, Northeast Normal University, Changchun 130117, China. Electronic address:

N-methyladenosine (mA) is the one of the most important RNA modifications, playing the role of splicing events, mRNA exporting and stability to cell differentiation. Because of wide distribution of mA in genes, identification of mA sites in RNA sequences has significant importance for basic biomedical research and drug development. High-throughput laboratory methods are time consuming and costly. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00225193193005
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http://dx.doi.org/10.1016/j.jtbi.2019.01.035DOI Listing
January 2019
3 Reads

Comment on the paper "Peristaltic transport of multilayered power-law fluids with distinct viscosities: A mathematical model for intestinal flows, S.K. Pandey, M.K. Chaube, Dharmendra Tripathi, Journal of Theoretical Biology 278 (2011) 11-19".

J Theor Biol 2019 Jan 30. Epub 2019 Jan 30.

School of Engineering, Democritus University of Thrace, 67100 Xanthi, Greece. Electronic address:

The present comment concerns some doubtful results included in the above paper. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.026DOI Listing
January 2019

Potential relations between post-spliced introns and mature mRNAs in the Caenorhabditis elegans genome.

J Theor Biol 2019 Jan 30;467:7-14. Epub 2019 Jan 30.

School of Life Science, Inner Mongolia University, Hohhot 010021, China; Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Huhhot 010031 China.

There are potential interactions between introns and their corresponding coding sequences (CDSs) in ribosomal protein genes that have been proposed by our group and the interactions are achieved by sequence matches between the two kinds of sequences. Here, the optimal matching relations between mature mRNAs and their corresponding introns in Caenorhabditis elegans (C.elegans) were investigated by improved Smith-Waterman local alignment software. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.031DOI Listing
January 2019

Neural crest migration with continuous cell states.

J Theor Biol 2019 Jan 29. Epub 2019 Jan 29.

MCR Centre for Regenerative Medicine, University of Edinburgh United Kingdom. Electronic address:

Models of cranial neural crest cell migration in cell-induced (or self-generated) gradients have included a division of labour into leader and follower migratory states, which undergo chemotaxis and contact guidance, respectively. Despite validated utility of these models through experimental perturbation of migration in the chick embryo and gene expression analysis showing relevant heterogeneity at the single cell level, an often raised question has been whether the discrete cell states are necessary, or if a continuum of cell behaviours offers a functionally equivalent description. Here we argue that this picture is supported by recent single-cell transcriptome data. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.029DOI Listing
January 2019

A modified association test for rare and common variants based on affected sib-pair design.

J Theor Biol 2019 Jan 29;467:1-6. Epub 2019 Jan 29.

Department of Statistics, School of Mathematical Sciences, Heilongjiang University and Heilongjiang Provincial Key Laboratory of the Theory and Computation of Complex Systems, Harbin 150080, China. Electronic address:

Current genome-wide association analysis has identified a great number of rare and common variants associated with common complex traits, however, more effective approaches for detecting associations between rare and common variants with common diseases are still demanded. Approaches for detecting rare variant association analysis will compromise the power when detecting the effects of rare and common variants simultaneously. In this paper, we extend an existing method of testing for rare variant association based on affected sib pairs (TOW-sib) and propose a variable weight test for rare and common variants association based on affected sib pairs (abbreviated as VW-TOWsib). Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.014DOI Listing
January 2019
1 Read

Role of resource allocation and transport in emergence of cross-feeding in microbial consortia.

J Theor Biol 2019 Jan 29;467:150-163. Epub 2019 Jan 29.

Montana State University, Bozeman, MT 59717, USA.

Microbial communities that implement mutual cross-feeding are commonly observed in nature and with synthetic constructs in laboratory experiments. A mathematical model of competition in a chemostat is developed to investigate the role that resource allocation and transport of metabolites play in cooperation. The model contains four cell types that differ by whether they produce two, one, or none of two essential metabolites. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.030DOI Listing
January 2019

Stochastic cellular automata model of tumorous neurosphere growth: Roles of developmental maturity and cell death.

J Theor Biol 2019 Jan 29;467:100-110. Epub 2019 Jan 29.

Complex Dynamic Systems and Control Laboratory, Department of Mechanical and Industrial Engineering, Northeastern University, Boston, MA, USA.

The neurosphere assay is a powerful in vitro system for studying stem/progenitor-cell-driven tissue growth. By employing a stochastic cellular automata model, we simulated the development of tumorous neurospheres in response to transformation of a randomly selected progenitor cell into a brain tumor stem cell. Simulated tumorous neurospheres were distinguished from normal neurospheres by their size, which exceeded that of normal neurospheres typically manifold. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.028DOI Listing
January 2019

Broad cross-reactivity of the T-cell repertoire achieves specific and sufficiently rapid target searching.

Authors:
Jin Xu Junghyo Jo

J Theor Biol 2019 Apr 27;466:119-127. Epub 2019 Jan 27.

Asia Pacific Center for Theoretical Physics (APCTP), 67 Cheongam-ro, Pohang, 37673, South Korea; Department of Physics, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Pohang, 37673, South Korea; School of Computational Sciences, Korea Institute for Advanced Study (KIAS), 85 Hoegiro, Seoul, 02455, South Korea; Department of Statistics, Keimyung University, 1095 Dalgubeol-daero, Daegu, 42601, South Korea. Electronic address:

The molecular recognition of T-cell receptors is the hallmark of the adaptive immunity. Given the finiteness of the T-cell repertoire, individual T-cell receptors are necessary to be cross-reactive to multiple antigenic peptides. In this study, we quantify the variability of the cross-reactivity by using a string model that estimates the binding affinity between two sequences of amino acids. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00225193193003
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http://dx.doi.org/10.1016/j.jtbi.2019.01.025DOI Listing
April 2019
4 Reads

On the interplay of harvesting and various diffusion strategies for spatially heterogeneous populations.

J Theor Biol 2019 Apr 25;466:106-118. Epub 2019 Jan 25.

Department of Math. and Stats., University of Calgary, 2500 University Drive N.W., Calgary, AB T2N 1N4, Canada; Department of Computer Science, City University of New York-College of Staten Island, The Graduate Center of City University of New York, 365 Fifth Avenue, New York 10314, United States.

The paper explores the influence of harvesting (or culling) on the outcome of the competition of two species in a spatially heterogeneous environment. The harvesting effort is assumed to be proportional to the space-dependent intrinsic growth rate. The differences between the two populations are the diffusion strategy and the harvesting intensity. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.024DOI Listing

The impact of truncation selection and diffusion on cooperation in spatial games.

J Theor Biol 2019 Apr 24;466:64-83. Epub 2019 Jan 24.

Department of Applied Mathematics, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.

Natural Selection is frequently modelled via proportional selection where survival is proportional to the average payoff differential. There has been little attention devoted to modelling truncation selection where replicators below a threshold are culled and survivors reproduce. Here, we systematically explore truncation selection for two strategy games in a spatial setting. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.023DOI Listing

A mathematical model of the use of supplemental oxygen to combat surgical site infection.

J Theor Biol 2019 Apr 16;466:11-23. Epub 2019 Jan 16.

School of Mathematics and Statistics, University of Melbourne, Australia. Electronic address:

Infections are a common complication of any surgery, often requiring a recovery period in hospital. Supplemental oxygen therapy administered during and immediately after surgery is thought to enhance the immune response to bacterial contamination. However, aerobic bacteria thrive in oxygen-rich environments, and so it is unclear whether oxygen has a net positive effect on recovery. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.021DOI Listing
April 2019
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On logical bifurcation diagrams.

J Theor Biol 2019 Apr 15;466:39-63. Epub 2019 Jan 15.

INESC-ID / Instituto Superior Técnico - Universidade de Lisboa, Lisboa, Portugal.

Bifurcation theory provides a powerful framework to analyze the dynamics of differential systems as a function of specific parameters. Abou-Jaoudé et al. (2009) introduced the concept of logical bifurcation diagrams, an analog of bifurcation diagrams for the logical modeling framework. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.008DOI Listing
April 2019
2 Reads

Evolution of the genetic code based on conservative changes of codons, amino acids, and aminoacyl tRNA synthetases.

Authors:
Scott O Rogers

J Theor Biol 2019 Apr 15;466:1-10. Epub 2019 Jan 15.

Department of Biological Sciences, Bowling Green State University, Bowling Green, OH, United States. Electronic address:

The genetic code, as arranged in the standard tabular form, displays a non-random structure relating to the characteristics of the amino acids. An alternative arrangement can be made by organizing the code according to aminoacyl-tRNA synthetases (aaRSs), codons, and reverse complement codons, which illuminates a coevolutionary process that led to the contemporary genetic code. As amino acids were added to the genetic code, they were recognized by aaRSs that interact with stereochemically similar amino acids. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.022DOI Listing
April 2019
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Molecular docking of anti-inflammatory drug diclofenac with metabolic targets: Potential applications in cancer therapeutics.

J Theor Biol 2019 Mar 14;465:117-125. Epub 2019 Jan 14.

School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India. Electronic address:

Diclofenac is a potent NSAID of clinical choice, which is widely used for containing inflammation. Moreover, recent experimental evidences overwhelmingly substantiate its antineoplastic potential. However, the precise molecular mechanisms of diclofenac's anticancer activity remain poorly understood. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.020DOI Listing
March 2019
2 Reads

Presenting a Neuroid model of wind-up based on dynamic synapse.

J Theor Biol 2019 Mar 11;465:45-50. Epub 2019 Jan 11.

Institute for Cognitive & Brain Sciences (ICBS), Department of Cognitive Modeling and Cognitive Rehabilitation, Shahid Beheshti University, Basir Eye Health Research Center, Tehran, Iran. Electronic address:

The treatment of chronic pain depends mainly on our understanding of the mechanisms such as central sensitization which is involved in it. Wind-up of spinal cord is one of the most important phenomena in the study of central sensitization which has received considerable attention in recent years. Wind-up is a form of short-term synaptic plasticity (STP) that can lead to central sensitivity. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.018DOI Listing

Superinfection and cell regeneration can lead to chronic viral coinfections.

J Theor Biol 2019 Apr 11;466:24-38. Epub 2019 Jan 11.

Department of Physics and Astronomy, Texas Christian University, Fort Worth, TX, United States.

Molecular diagnostic techniques have revealed that approximately 43% of the patients hospitalized with influenza-like illness are infected by more than one viral pathogen, sometimes leading to long-lasting infections. It is not clear how the heterologous viruses interact within the respiratory tract of the infected host to lengthen the duration of what are usually short, self-limiting infections. We develop a mathematical model which allows for single cells to be infected simultaneously with two different respiratory viruses (superinfection) to investigate the possibility of chronic coinfections. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.011DOI Listing
April 2019
1 Read

Dose finding for new vaccines: The role for immunostimulation/immunodynamic modelling.

J Theor Biol 2019 Mar 10;465:51-55. Epub 2019 Jan 10.

Vaccitech, Oxford, UK.

Current methods to optimize vaccine dose are purely empirically based, whereas in the drug development field, dosing determinations use far more advanced quantitative methodology to accelerate decision-making. Applying these established methods in the field of vaccine development may reduce the currently large clinical trial sample sizes, long time frames, high costs, and ultimately have a better potential to save lives. We propose the field of immunostimulation/immunodynamic (IS/ID) modelling, which aims to translate mathematical frameworks used for drug dosing towards optimizing vaccine dose decision-making. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00225193193001
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http://dx.doi.org/10.1016/j.jtbi.2019.01.017DOI Listing
March 2019
5 Reads

Microbial cross-feeding promotes multiple stable states and species coexistence, but also susceptibility to cheaters.

J Theor Biol 2019 Mar 9;465:63-77. Epub 2019 Jan 9.

W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, MI 49060, USA; Department of Plant Biology, Department of Integrative Biology, and Program in Ecology, Evolutionary Biology and Behavior, Michigan State University, East Lansing, MI 48824, USA.

Mutualism, interspecific cooperation that yields reciprocal benefits, can promote species coexistence, enhancing biodiversity. As a specific form of mutualism, cross-feeding, where each of two mutualists produces a resource the other one needs, has been broadly studied. However, few theoretical studies have examined competition between cross-feeding mutualists and cheaters, who do not synthesize resources themselves. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00225193193001
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http://dx.doi.org/10.1016/j.jtbi.2019.01.009DOI Listing
March 2019
4 Reads

Computational analysis in designing T cell epitopes enriched peptides of Ebola glycoprotein exhibiting strong binding interaction with HLA molecules.

J Theor Biol 2019 Mar 10;465:34-44. Epub 2019 Jan 10.

Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, 147004 Punjab, India. Electronic address:

Computational approach has shown remarkable progress in epitope mapping, paving the way to finding vaccine candidates against different viruses. In the current study, prediction algorithms and molecular docking were applied to select peptides containing multiple Ebola glycoprotein epitopes showing interaction with different HLA molecules. Six peptides containing overlapping multiple HLA I (CD8) and II (CD4) restricted T cell epitopes were generated via consensus approach applying six different prediction tools. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.016DOI Listing
March 2019
2.116 Impact Factor

Mathematical model and computer simulations of telomere loss.

J Theor Biol 2019 Mar 8;465:78-89. Epub 2019 Jan 8.

Department of Mathematics, Faculty of Science, University of Zagreb, Bijeniçka 30, Zagreb 10000, Croatia. Electronic address:

The molecular mechanisms that control the limited number of human cell divisions has occupied researchers ever since its first description in 1961. There is evidence that this limited growth capacity, referred to as cellular or replicative senescence, is the basis for organismal ageing. Numerous studies point to the molecular mechanisms of telomere involvement in this phenomenon. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00225193193000
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http://dx.doi.org/10.1016/j.jtbi.2019.01.007DOI Listing
March 2019
4 Reads

Data-driven selection and parameter estimation for DNA methylation mathematical models.

J Theor Biol 2019 Jan 10;467:87-99. Epub 2019 Jan 10.

Division of Applied Mathematics, Brown University, Providence, Rhode Island 02912, USA. Electronic address:

Epigenetics is coming to the fore as a key process which underpins health. In particular emerging experimental evidence has associated alterations to DNA methylation status with healthspan and aging. Mammalian DNA methylation status is maintained by an intricate array of biochemical and molecular processes. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.012DOI Listing
January 2019
1 Read

On the multistationarity of chemical reaction networks.

J Theor Biol 2019 Mar 8;465:126-133. Epub 2019 Jan 8.

CNRS et IHES, Le Bois-Marie, 35 route de Chartres, Bures-sur-Yvette 91440, France. Electronic address:

We present a new conjecture about a necessary condition that a (bio)chemical network has to satisfy for it to exhibit multistationarity. According to a Theorem of Feliu and Wiuf (Wiuf and Feliu, 2013; Feliu and Wiuf, 2015), the conjecture is known for strictly monotonic kinetics. We give several examples illustrating our conjecture. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.010DOI Listing
March 2019
1 Read

Diverse stochasticity leads a colony of ants to optimal foraging.

J Theor Biol 2019 Mar 7;465:7-16. Epub 2019 Jan 7.

Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-hiroshima 739-8526, Japan. Electronic address:

A mathematical model of garden ants (Lasius japonicus) is introduced herein to investigate the relationship between the distribution of the degree of stochasticity in following pheromone trails and the group foraging efficiency. Numerical simulations of the model indicate that depending on the systematic change of the feeding environment, the optimal distribution of stochasticity shifts from a mixture of almost deterministic and mildly stochastic ants to a contrasted mixture of almost deterministic ants and highly stochastic ants. In addition, the interaction between the stochasticity and the pheromone path regulates the dynamics of the foraging efficiency optimization. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.002DOI Listing

Evolutionary game dynamics of the Wright-Fisher process with different selection intensities.

J Theor Biol 2019 Mar 8;465:17-26. Epub 2019 Jan 8.

School of Management, Wuhan University of Technology, Wuhan 430072, China.

Evolutionary game dynamics in finite populations can be described by a frequency-dependent, stochastic Wright-Fisher process. The fitness of individuals in a population is not only linked to environmental conditions but also tightly coupled to the types and frequencies of competitors, leading to different types of individuals with different selection intensities. We studied a 2 × 2 symmetric game in a finite population and established a dynamic model of the Wright-Fisher process by introducing different selection intensities for different strategies. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.006DOI Listing

Bridging blood cancers and inflammation: The reduced Cancitis model.

J Theor Biol 2019 Mar 4;465:90-108. Epub 2019 Jan 4.

Department of Science and Environment, Roskilde University, Denmark.

A novel mechanism-based model - the Cancitis model - describing the interaction of blood cancer and the inflammatory system is proposed, analyzed and validated. The immune response is divided into two components, one where the elimination rate of malignant stem cells is independent of the level of the blood cancer and one where the elimination rate depends on the level of the blood cancer. A dimensional analysis shows that the full 6-dimensional system of nonlinear ordinary differential equations may be reduced to a 2-dimensional system - the reduced Cancitis model - using Fenichel theory. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00225193193000
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http://dx.doi.org/10.1016/j.jtbi.2019.01.001DOI Listing
March 2019
7 Reads

Optimal control of HCV transmission under liquoring.

J Theor Biol 2019 Mar 5;465:27-33. Epub 2019 Jan 5.

Department of Mathematics, Gujarat University, Ahmedabad 38009, Gujarat, India.

Chronic hepatitis C virus (HCV) and alcohol are common causes of chronic liver diseases and both are recognized as major causes of liver disease worldwide. Each poses a major public and economic burden to society, and when the two co-exist they appear to have a synergistic effect in the progression of chronic liver disease. In this research, we developed a SIRS model of transmission of the hepatitis C virus (HCV) under effect of liquoring in six compartments: Susceptible, Low liquoring, High liquoring, Acute, Chronic and Recovered Individuals. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.004DOI Listing
March 2019
1 Read

Characteristic, completion or matching timescales? An analysis of temporary boundaries in enzyme kinetics.

J Theor Biol 2019 Jan 5. Epub 2019 Jan 5.

Department of Molecular & Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA. Electronic address:

Scaling analysis exploiting timescale separation has been one of the most important techniques in the quantitative analysis of nonlinear dynamical systems in mathematical and theoretical biology. In the case of enzyme catalyzed reactions, it is often overlooked that the characteristic timescales used for the scaling the rate equations are not ideal for determining when concentrations and reaction rates reach their maximum values. In this work, we first illustrate this point by considering the classic example of the single-enzyme, single-substrate Michaelis-Menten reaction mechanism. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.005DOI Listing
January 2019

Quantifying heterogeneity of stochastic gene expression.

J Theor Biol 2019 Mar 4;465:56-62. Epub 2019 Jan 4.

Graduate School of Medicine, Tohoku University, Sendai 980-8575, Japan. Electronic address:

The heterogeneity of stochastic gene expression, which refers to the temporal fluctuation in a gene product and its cell-to-cell variation, has attracted considerable interest from biologists, physicists, and mathematicians. The dynamics of protein production and degradation have been modeled as random processes with transition probabilities. However, there is a gap between theory and phenomena, particularly in terms of analytical formulation and parameter estimation. Read More

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http://dx.doi.org/10.1016/j.jtbi.2019.01.003DOI Listing
March 2019
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Corrigendum to "A confidence building exercise in data and identifiability: Modeling cancer chemotherapy as a case study" [Journal of Theoretical Biology 431 (2017) 63-78].

J Theor Biol 2019 Mar 8;464:179. Epub 2019 Jan 8.

Mathematics, Florida State University, United States. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2018.12.042DOI Listing

On a three-stage structured model for the dynamics of malaria transmission with human treatment, adult vector demographics and one aquatic stage.

J Theor Biol 2019 Jan 2. Epub 2019 Jan 2.

Department of Mathematics and Applied Mathematics, University of Pretoria, South Africa; Institute of Mathematics, Lodz University of Technology, Lodz, Poland.

A modelling framework that describes the dynamics of populations of the female Anopheles sp mosquitoes is used to develop and analyse a deterministic ordinary differential equation model for dynamics and transmission of malaria amongst humans and varying mosquito populations. The framework includes a characterization of the gonotrophic cycle of the female mosquito. The epidemiological model also captures a novel feature whereby treated human's blood can become mosquitocidal to the questing mosquitoes upon the successful ingestion of the treated human's blood. Read More

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http://dx.doi.org/10.1016/j.jtbi.2018.12.043DOI Listing
January 2019
2.116 Impact Factor