Into the Intracellular Logistics of Cross-Presentation

The induction of cytotoxic CD8+ T cell responses requires the presentation of antigenic peptides by MHC class I molecules (MHC I). MHC I usually present peptides derived from endogenous proteins. However, some subtypes of dendritic cells have developed the ability to efficiently present peptides derived from exogenous antigens on MHC I via a process called cross-presentation. Cross-presentation is intimately linked to the induction of anti-viral, -bacterial, and -tumor cytotoxic T cell (CTL) responses, as well as a wide variety of CTL-mediated diseases and transplant rejections. The molecular and cellular mechanisms underlying cross-presentation have been studied intensively since its original description, yet understanding of this process is incomplete and on the forefront of immunological research. Numerous pathways and models, some of them conflicting, have been described so far. Here, we review the various pathways reported as involved in cross-presentation, highlighting the complexity of this process. We also discuss in detail the different intracellular steps required, from antigen capture and routing, to processing, and finally peptide loading, emphasizing the need for a better understanding of the cell biology of this phenomenon

FullSWOF_Paral: Comparison of two parallelization strategies (MPI and SKELGIS) on a software designed for hydrology applications

In this paper, we perform a comparison of two approaches for the parallelization of an existing, free software, FullSWOF 2D (http://www. univ-orleans.fr/mapmo/soft/FullSWOF/ that solves shallow water equations for applications in hydrology) based on a domain decomposition strategy. The first approach is based on the classical MPI library while the second approach uses Parallel Algorithmic Skeletons and more precisely a library named SkelGIS (Skeletons for Geographical Information Systems). The first results presented in this article show that the two approaches are similar in terms of performance and scalability. The two implementation strategies are however very different and we discuss the advantages of each one.Comment: 27 page

A finite-element toolbox for the simulation of solid-liquid phase-change systems with natural convection

International audienceWe present and distribute a new numerical system using classical finite elements with mesh adaptivity for computing two-dimensional liquid-solid phase-change systems involving natural convection. The programs are written as a toolbox for FreeFem++ (www.freefem.org), a free finite-element software available for all existing operating systems. The code implements a single domain approach. The same set of equations is solved in both liquid and solid phases: the incompressible Navier-Stokes equations with Boussinesq approximation for thermal effects. This model describes naturally the evolution of the liquid flow which is dominated by convection effects. To make it valid also in the solid phase, a Carman-Kozeny-type penalty term is added to the momentum equations. The penalty term brings progressively (through an artificial mushy region) the velocity to zero into the solid. The energy equation is also modified to be valid in both phases using an enthalpy (temperature-transform) model introducing a regularized latent-heat term. Model equations are discretized using Galerkin triangular finite elements. Piecewise quadratic (P2) finite-elements are used for the velocity and piecewise linear (P1) for the pressure. For the temperature both P2 or P1 discretizations are possible. The coupled system of equations is integrated in time using a second-order Gear scheme. Non-linearities are treated implicitly and the resulting discrete equations are solved using a Newton algorithm. An efficient mesh adaptivity algorithm using metrics control is used to adapt the mesh every time step. This allows us to accurately capture multiple solid-liquid interfaces present in the domain, the boundary-layer structure at the walls and the unsteady convection cells in the liquid. We present several validations of the toolbox, by simulating benchmark cases of increasing difficulty: natural convection of air, natural convection of water, melting of a phase-change material, a melting-solidification cycle, and, finally, a water freezing case. Other similar cases could be easily simulated with this toolbox, since the code structure is extremely versatile and the syntax very close to the mathematical formulation of the model