Cell-based computational modeling of vascular morphogenesis using Tissue Simulation Toolkit.

Computational modeling has become a widely used tool for unraveling the mechanisms of higher level cooperative cell behavior during vascular morphogenesis. However, experimenting with published simulation models or adding new assumptions to those models can be daunting for novice and even for experienced computational scientists. Here, we present a step-by-step, practical tutorial for building cell-based simulations of vascular morphogenesis using the Tissue Simulation Toolkit (TST). The TST is a freely available, open-source C++ library for developing simulations with the two-dimensional cellular Potts model, a stochastic, agent-based framework to simulate collective cell behavior. We will show the basic use of the TST to simulate and experiment with published simulations of vascular network formation. Then, we will present step-by-step instructions and explanations for building a recent simulation model of tumor angiogenesis. Demonstrated mechanisms include cell-cell adhesion, chemotaxis, cell elongation, haptotaxis, and haptokinesis.

A mixed finite element method for nonlinear diffusion equations

We propose a mixed finite element method for a class of nonlinear diffusion equations, which is based on their interpretation as gradient flows in optimal transportation metrics. We introduce an appropriate linearization of the optimal transport problem, which leads to a mixed symmetric formulation. This formulation preserves the maximum principle in case of the semi-discrete scheme as well as the fully discrete scheme for a certain class of problems. In addition solutions of the mixed formulation maintain exponential convergence in the relative entropy towards the steady state in case of a nonlinear Fokker-Planck equation with uniformly convex potential. We demonstrate the behavior of the proposed scheme with 2D simulations of the porous medium equations and blow-up questions in the Patlak-Keller-Segel model.

Elemente

(Résumé de l'ouvrage) Die RGG4 bietet in 15 665 Artikeln und Teilartikeln einen fundierten Überblick über Religion und Religionen, wie sie gelebt und gedacht wurden und werden. Sie bietet den neuesten Forschungsstand, dargestellt von 3 972 ausgewiesenen Kennern der jeweiligen Materie aus 74 Ländern.

Simulation-based systematic review of imatinib population pharmacokinetics and PK-PD relationships in chronic myeloid leukemia (CML) patients

Objectives: Several population pharmacokinetic (PPK) and pharmacokinetic-pharmacodynamic (PK-PD) analyses have been performed with the anticancer drug imatinib. Inspired by the approach of meta-analysis, we aimed to compare and combine results from published studies in a useful way - in particular for improving the clinical interpretation of imatinib concentration measurements in the scope of therapeutic drug monitoring (TDM). Methods: Original PPK analyses and PK-PD studies (PK surrogate: trough concentration Cmin; PD outcomes: optimal early response and specific adverse events) were searched systematically on MEDLINE. From each identified PPK model, a predicted concentration distribution under standard dosage was derived through 1000 simulations (NONMEM), after standardizing model parameters to common covariates. A "reference range" was calculated from pooled simulated concentrations in a semi-quantitative approach (without specific weighting) over the whole dosing interval. Meta-regression summarized relationships between Cmin and optimal/suboptimal early treatment response. Results: 9 PPK models and 6 relevant PK-PD reports in CML patients were identified. Model-based predicted median Cmin ranged from 555 to 1388 ng/ml (grand median: 870 ng/ml and inter-quartile range: 520-1390 ng/ml). The probability to achieve optimal early response was predicted to increase from 60 to 85% from 520 to 1390 ng/ml across PK-PD studies (odds ratio for doubling Cmin: 2.7). Reporting of specific adverse events was too heterogeneous to perform a regression analysis. The general frequency of anemia, rash and fluid retention increased however consistently with Cmin, but less than response probability. Conclusions: Predicted drug exposure may differ substantially between various PPK analyses. In this review, heterogeneity was mainly attributed to 2 "outlying" models. The established reference range seems to cover the range where both good efficacy and acceptable tolerance are expected for most patients. TDM guided dose adjustment appears therefore justified for imatinib in CML patients. Its usefulness remains now to be prospectively validated in a randomized trial.

Nash equilibrium strategies in discrete-time finite-horizon dynamic games with risk-and effort-averse players

The objective of this paper is to re-examine the risk-and effort attitude in the context of strategic dynamic interactions stated as a discrete-time finite-horizon Nash game. The analysis is based on the assumption that players are endogenously risk-and effort-averse. Each player is characterized by distinct risk-and effort-aversion types that are unknown to his opponent. The goal of the game is the optimal risk-and effort-sharing between the players. It generally depends on the individual strategies adopted and, implicitly, on the the players' types or characteristics.

On estimation and identifiability issues of sex-linked inheritance with a case study of pigmentation in Swiss barn owl (Tyto alba)

Genetic evaluation using animal models or pedigree-based models generally assume only autosomal inheritance. Bayesian animal models provide a flexible framework for genetic evaluation, and we show how the model readily can accommodate situations where the trait of interest is influenced by both autosomal and sex-linked inheritance. This allows for simultaneous calculation of autosomal and sex-chromosomal additive genetic effects. Inferences were performed using integrated nested Laplace approximations (INLA), a nonsampling-based Bayesian inference methodology. We provide a detailed description of how to calculate the inverse of the X- or Z-chromosomal additive genetic relationship matrix, needed for inference. The case study of eumelanic spot diameter in a Swiss barn owl (Tyto alba) population shows that this trait is substantially influenced by variation in genes on the Z-chromosome (sigma(2)(z) = 0.2719 and sigma(2)(a) = 0.4405). Further, a simulation study for this study system shows that the animal model accounting for both autosomal and sex-chromosome-linked inheritance is identifiable, that is, the two effects can be distinguished, and provides accurate inference on the variance components.

Analysis of a finite volume element method for the Stokes problem

In this paper we propose a stabilized conforming finite volume element method for the Stokes equations. On stating the convergence of the method, optimal a priori error estimates in different norms are obtained by establishing the adequate connection between the finite volume and stabilized finite element formulations. A superconvergence result is also derived by using a postprocessing projection method. In particular, the stabilization of the continuous lowest equal order pair finite volume element discretization is achieved by enriching the velocity space with local functions that do not necessarily vanish on the element boundaries. Finally, some numerical experiments that confirm the predicted behavior of the method are provided.

Agent based simulation to optimise emergency departments

Nowadays, many of the health care systems are large and complex environments and quite dynamic, specifically Emergency Departments, EDs. It is opened and working 24 hours per day throughout the year with limited resources, whereas it is overcrowded. Thus, is mandatory to simulate EDs to improve qualitatively and quantitatively their performance. This improvement can be achieved modelling and simulating EDs using Agent-Based Model, ABM and optimising many different staff scenarios. This work optimises the staff configuration of an ED. In order to do optimisation, objective functions to minimise or maximise have to be set. One of those objective functions is to find the best or optimum staff configuration that minimise patient waiting time. The staff configuration comprises: doctors, triage nurses, and admissions, the amount and sort of them. Staff configuration is a combinatorial problem, that can take a lot of time to be solved. HPC is used to run the experiments, and encouraging results were obtained. However, even with the basic ED used in this work the search space is very large, thus, when the problem size increases, it is going to need more resources of processing in order to obtain results in an acceptable time.

Evolutionary and convergence stability for continuous phenotypes in finite populations derived from two-allele models.

The evolution of a quantitative phenotype is often envisioned as a trait substitution sequence where mutant alleles repeatedly replace resident ones. In infinite populations, the invasion fitness of a mutant in this two-allele representation of the evolutionary process is used to characterize features about long-term phenotypic evolution, such as singular points, convergence stability (established from first-order effects of selection), branching points, and evolutionary stability (established from second-order effects of selection). Here, we try to characterize long-term phenotypic evolution in finite populations from this two-allele representation of the evolutionary process. We construct a stochastic model describing evolutionary dynamics at non-rare mutant allele frequency. We then derive stability conditions based on stationary average mutant frequencies in the presence of vanishing mutation rates. We find that the second-order stability condition obtained from second-order effects of selection is identical to convergence stability. Thus, in two-allele systems in finite populations, convergence stability is enough to characterize long-term evolution under the trait substitution sequence assumption. We perform individual-based simulations to confirm our analytic results.

On finite unions and finite products with the D-property

We show that the product of a subparacompact C-scattered space and a Lindelöf D-space is D. In addition, we show that every regular locally D-space which is the union of a finite collection of subparacompact spaces and metacompact spaces has the D-property. Also, we extend this result from the class of locally D-spaces to the wider class of D-scattered spaces. All the results are shown in a direct way.

Artificial Snow Optimization in Winter Sport Destinations Using a Multi-agent Simulation

This paper presents the Juste-Neige system for predicting the snow height on the ski runs of a resort using a multi-agent simulation software. Its aim is to facilitate snow cover management in order to i) reduce the production cost of artificial snow and to improve the profit margin for the companies managing the ski resorts; and ii) to reduce the water and energy consumption, and thus to reduce the environmental impact, by producing only the snow needed for a good skiing experience. The software provides maps with the predicted snow heights for up to 13 days. On these maps, the areas most exposed to snow erosion are highlighted. The software proceeds in three steps: i) interpolation of snow height measurements with a neural network; ii) local meteorological forecasts for every ski resort; iii) simulation of the impact caused by skiers using a multi-agent system. The software has been evaluated in the Swiss ski resort of Verbier and provides useful predictions.

Simulation des caractéristiques ECG du syndrome de Brugada à l'aide d'un programme de modélisation 3D

Introduction : Le syndrome de Brugada, décrit en 1992 par Pedro et Josep Brugada, est un syndrome cardiaque caractérisé par un sus-décalage particulier du segment ST associé à un bloc de branche droit atypique au niveau des dérivations ECG V1 à V3. Les altérations ECG du syndrome de Brugada sont classifiées en 3 types dont seul le type 1 est diagnostique. Les mécanismes physiopathologiques exacts de ce syndrome sont pour le moment encore controversés. Plusieurs hypothèses sont proposées dans la littérature dont deux principales retiennent l'attention : 1) le modèle du trouble de repolarisation stipule des potentiels d'action réduits en durée et en amplitude liés à un changement de répartition de canaux potassiques 2) le modèle du trouble de dépolarisation spécifie un retard de conduction se traduisant par une dépolarisation retardée. Dans le STEMI, un sus-décalage ST ressemblant à celui du syndrome de Brugada est expliqué par deux théories : 1) le courant de lésion diastolique suggère une élévation du potentiel diastolique transformé artificiellement en sus-décalage ST par les filtres utilisés dans tous les appareils ECG.¦Objectif : Recréer les manifestations ECG du syndrome de Brugada en appliquant les modifications du potentiel d'action des cardiomyocytes rapportées dans la littérature.¦Méthode : Pour ce travail, nous avons utilisé "ECGsim", un simulateur informatique réaliste d'ECG disponible gratuitement sur www.ecgsim.org. Ce programme est basé sur une reconstruction de l'ECG de surface à l'aide de 1500 noeuds représentant chacun les potentiels d'action des ventricules droit et gauche, épicardiques et endocardiques. L'ECG simulé peut être donc vu comme l'intégration de l'ensemble de ces potentiels d'action en tenant compte des propriétés de conductivité des tissus s'interposant entre les électrodes de surface et le coeur. Dans ce programme, nous avons définit trois zones, de taille différente, comprenant la chambre de chasse du ventricule droit. Pour chaque zone, nous avons reproduit les modifications des potentiels d'action citées dans les modèles du trouble de repolarisation et de dépolarisation et des théories de courant de lésion systolique et diastolique. Nous avons utilisé, en plus des douze dérivations habituelles, une électrode positionnée en V2IC3 (i.e. 3ème espace intercostal) sur le thorax virtuel du programme ECGsim.¦Résultats : Pour des raisons techniques, le modèle du trouble de repolarisation n'a pas pu être entièrement réalisée dans ce travail. Le modèle du trouble de dépolarisation ne reproduit pas d'altération de type Brugada mais un bloc de branche droit plus ou moins complet. Le courant de lésion diastolique permet d'obtenir un sus-décalage ST en augmentant le potentiel diastolique épicardique des cardiomyocytes de la chambre de chasse du ventricule droit. Une inversion de l'onde T apparaît lorsque la durée du potentiel d'action est prolongée. L'amplitude du sus-décalage ST dépend de la valeur du potentiel diastolique, de la taille de la lésion et de sa localisation épicardique ou transmurale. Le courant de lésion systolique n'entraîne pas de sus-décalage ST mais accentue l'amplitude de l'onde T.¦Discussion et conclusion : Dans ce travail, l'élévation du potentiel diastolique avec un prolongement de la durée du potentiel d'action est la combinaison qui reproduit le mieux les altérations ECG du Brugada. Une persistance de cellules de type nodal au niveau de la chambre de chasse du ventricule droit pourrait être une explication à ces modifications particulières du potentiel d'action. Le risque d'arythmie dans la Brugada pourrait également être expliqué par une automaticité anormale des cellules de type nodal. Ainsi, des altérations des mécanismes cellulaires impliqués dans le maintien du potentiel diastolique pourraient être présentes dans le syndrome de Brugada, ce qui, à notre connaissance, n'a jamais été rapporté dans la littérature.

Dynamic simulation of regulatory networks using SQUAD.

BACKGROUND: The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of these networks, it becomes possible to study their dynamical behavior as a whole and discover what is the specific role of each of their components. Since the behavior of a network is by no means intuitive, it becomes necessary to use computational models to understand its behavior and to be able to make predictions about it. Unfortunately, most current computational models describe small networks due to the scarcity of kinetic data available. To overcome this problem, we previously published a methodology to convert a signaling network into a dynamical system, even in the total absence of kinetic information. In this paper we present a software implementation of such methodology. RESULTS: We developed SQUAD, a software for the dynamic simulation of signaling networks using the standardized qualitative dynamical systems approach. SQUAD converts the network into a discrete dynamical system, and it uses a binary decision diagram algorithm to identify all the steady states of the system. Then, the software creates a continuous dynamical system and localizes its steady states which are located near the steady states of the discrete system. The software permits to make simulations on the continuous system, allowing for the modification of several parameters. Importantly, SQUAD includes a framework for perturbing networks in a manner similar to what is performed in experimental laboratory protocols, for example by activating receptors or knocking out molecular components. Using this software we have been able to successfully reproduce the behavior of the regulatory network implicated in T-helper cell differentiation. CONCLUSION: The simulation of regulatory networks aims at predicting the behavior of a whole system when subject to stimuli, such as drugs, or determine the role of specific components within the network. The predictions can then be used to interpret and/or drive laboratory experiments. SQUAD provides a user-friendly graphical interface, accessible to both computational and experimental biologists for the fast qualitative simulation of large regulatory networks for which kinetic data is not necessarily available.