Showing papers in "Journal of Theoretical Biology in 2008"

TL;DR: This work develops methods for applying existing analytical tools to perform analyses on a variety of mathematical and computer models and provides a complete methodology for performing these analyses, in both deterministic and stochastic settings, and proposes novel techniques to handle problems encountered during these types of analyses.

TL;DR: In this article, the authors investigate a neutral model for speciation and extinction, the constant rate birth-death process, conditioned to have n extant species today, and look at the tree distribution of the reconstructed trees, i.e., the trees without the extinct species.

TL;DR: This is the first paper in a two-part series in which a diffuse interface continuum model of multispecies tumor growth and tumor-induced angiogenesis in two and three dimensions is developed, analyzed, and simulated.

TL;DR: It is shown that along with the usual single population epidemic threshold the metapopulation network exhibits a global threshold for the subpopulation invasion, and an explicit analytic expression for the invasion threshold is found that determines the minimum number of individuals traveling among subpopulations in order to have the infection of a macroscopic number of subpopulation.

TL;DR: A minimal ventricular (MV) human model is presented that is designed to reproduce important tissue-level characteristics of epicardial, endocardial and midmyocardial cells, including action potential amplitudes and morphologies, upstroke velocities, steady-state action potential duration (APD) and conduction velocity (CV) restitution curves, minimum APD, and minimum diastolic interval.

TL;DR: A novel continuum model of cancer cell invasion of tissue which explicitly incorporates the important biological processes of cell-cell and cell-matrix adhesion is formulated and can form the basis for future models incorporating more details of the invasion process.

TL;DR: A hierarchical agent-based model simulating a suggested feedback loop that links VEGF-A tip cell induction with delta-like 4 (Dll4)/notch-mediated lateral inhibition is introduced and the role of cell morphology in tip/stalk patterning is investigated, highlighting filopodia as lateral inhibition amplifiers.

TL;DR: A method that combines increment of diversity with modified Mahalanobis Discriminant, called IDQD, is presented to predict 208 OMPs, 206 transmembrane helical proteins (TMHPs) and 673 globular proteins (GPs) by using Chou's pseudo amino acid compositions as parameters, suggesting that the pseudo aminoacid composition can better reflect the core feature of membrane proteins than the classical amino acid composition.

TL;DR: Numerical simulations of compromised healing situations showed that the establishment of a vascular network in response to angiogenic growth factors is a key factor in the healing process and a correct description of cell migration is shown to be essential to the prediction of realistic spatiotemporal tissue distribution patterns in the fracture callus.

TL;DR: The model provides a framework for analyzing the dynamics of the segmentation clock in terms of a network of oscillating modules involving the Wnt, Notch and FGF signaling pathways.

TL;DR: Mathematical results suggest that vaccination is helpful for disease control by decreasing the basic reproduction number, which is a necessary condition for successful elimination of disease.

TL;DR: It is concluded that muscle fibre length and tendon compliance combinations may be tuned to maximise efficiency under a given gait condition.

TL;DR: Diverse experimental evidence showing that, often, those biochemical pathways are operative that allow fast but low-yield synthesis of important products, such as fermentation in Saccharomyces cerevisiae and several other yeast species, leads to the conclusion that maximization of molar yield is by no means a universal principle.

TL;DR: This work describes an application of proper orthogonal decomposition (POD) for assigning importances to kinematic variables, using dimensional complexity as a metric, and uncovers three groups of joints that move together during flight by using POD to quantify correlations of motion.

TL;DR: The results thus obtained in predicting protein structural classification are quite encouraging, indicating that the current approach may also be used to improve the prediction quality of other protein attributes, or at least can play a complimentary role to the existing methods in the relevant areas.

TL;DR: This work theoretically investigates the influence of individuals' mobility on the spatial structures emerging in rock-paper-scissors games, and devise a quantitative approach to analyze the spatial patterns self-forming in the course of the stochastic time evolution.

TL;DR: The model was established by showing that it can correctly predict several aspects of bone healing, including cell and tissue distributions during normal fracture healing, and was able to predict experimentally established alterations due to excessive mechanical stimulation, periosteal stripping and impaired effects of cartilage remodeling.

TL;DR: Whenever the active dynamics of links is sufficiently fast, population structure leads to a simple transformation of the payoff matrix, effectively changing the game under consideration, and hence paving the way for reciprocators to dominate defectors.

TL;DR: To understand the fine details of the molecular interactions between these proteinase inhibitors and the SARS virus via complexation, molecular dynamics simulations were carried out and showed that flap closing was clearly observed when the inhibitors bind to the active site of SARS-CoV 3CLpro.

TL;DR: This work uses numerical simulations to explore conditions for which the model predicts successful therapy and tumor eradication, and exhibits damped, as well as stable oscillations in a range of parameter values.

TL;DR: The results suggest that it is the combined effect of the oxygen concentration and matrix density that creates an environment where the glycolytic phenotype has a growth advantage and consequently is most likely to appear.

TL;DR: Compartmental models for influenza that include control by vaccination and antiviral treatment are formulated and predictions of the deterministic compartmental models are in general agreement with those of the stochastic simulation models.

TL;DR: Optimal biphasic models based on the distinction between pre- and post-maturation growth and an explicit description of energy allocation within a growing season have advantages over the vB model, both in quality of fit, and in the information contained in the fitted parameters.

TL;DR: An individual based model is developed to examine how different behaviors involved in microcolony formation on a surface determine patterns of group sizes and link patterns to bacterial fitness.

TL;DR: An engineering approach for the systematic design of targeted drug delivery into the human brain based on first principles transport and chemical kinetics models as well as accurate reconstruction of the brain geometry from patient-specific diffusion tensor magnetic resonance imaging is proposed.

TL;DR: A model describing the stomatal density response to changes in C(a) is introduced, based on the diffusion of water vapour and CO(2), photosynthesis and an optimisation principle concerning gas exchange and water availability.

TL;DR: The first quantitative assessment of the way cooperators arrange in space during invasion is provided and it is found that the macroscopic properties and the emerging spatial patterns reveal information about the characteristics of the underlying microscopic interactions.

TL;DR: It is found that influenza A/Albany/1/98 (H3N2) virions under normal experimental conditions at 37 degrees C rapidly lose infectivity with a half-life of approximately 6.6+/-0.2 h, and that the lifespan of productively infected MDCK cells is approximately 13 h.

TL;DR: A geometrical interpretation of the ESS condition on graphs is provided and theoretical predictions are compared with computer simulations for random regular graphs and for lattices.

TL;DR: Fitness of the different pathogens varied according to the seasonal pattern of immature tick activity, which was different under the temperature conditions projected for the 2020s, 2050s and 2080s, where pathogens that were long-lived, highly transmissible and had little impact on rodent mortality rates were the fittest.