Cosmological Simulations on a Grid of Computers

The work presented in this paper aims at restricting the input parameter values of the semi-analytical model used in GALICS and MOMAF, so as to derive which parameters influence the most the results, e.g., star formation, feedback and halo recycling efficiencies, etc. Our approach is to proceed empirically: we run lots of simulations and derive the correct ranges of values. The computation time needed is so large, that we need to run on a grid of computers. Hence, we model GALICS and MOMAF execution time and output files size, and run the simulation using a grid middleware: DIET. All the complexity of accessing resources, scheduling simulations and managing data is harnessed by DIET and hidden behind a web portal accessible to the users.Comment: Accepted and Published in AIP Conference Proceedings 1241, 2010, pages 816-82

Seismic vulnerability reduction: numerical modeling of FRP reinforcement using multifiber beams elements

This paper presents a simplified modeling strategy for reproducing the behavior of beam-column structures reinforced with Polymer Reinforced Fibers (FRP). A 1D concrete constitutive model has been recently proposed, suitable for both monotonic and cycling loadings. The model is inspired on two well-known concrete laws, one based on damage mechanics theory (La Borderie concrete damage model) and one based on experimental studies (Eid & Paultre's confined concrete model). Spatial discretization is done using multifiber Timoshenko beam elements. Validation of the strategy is provided using two case studies: a retrofitted bridge pier and a vulnerability analysis on an existing building

Cell shape characteristics of human skeletal muscle cells as a predictor of myogenic competency: A new paradigm towards precision cell therapy

Skeletal muscle-derived cells (SMDC) hold tremendous potential for replenishing dysfunctional muscle lost due to disease or trauma. Current therapeutic usage of SMDC relies on harvesting autologous cells from muscle biopsies that are subsequently expanded in vitro before re-implantation into the patient. Heterogeneity can arise from multiple factors including quality of the starting biopsy, age and comorbidity affecting the processed SMDC. Quality attributes intended for clinical use often focus on minimum levels of myogenic cell marker expression. Such approaches do not evaluate the likelihood of SMDC to differentiate and form myofibres when implanted in vivo, which ultimately determines the likelihood of muscle regeneration. Predicting the therapeutic potency of SMDC in vitro prior to implantation is key to developing successful therapeutics in regenerative medicine and reducing implementation costs. Here, we report on the development of a novel SMDC profiling tool to examine populations of cells in vitro derived from different donors. We developed an image-based pipeline to quantify morphological features and extracted cell shape descriptors. We investigated whether these could predict heterogeneity in the formation of myotubes and correlate with the myogenic fusion index. Several of the early cell shape characteristics were found to negatively correlate with the fusion index. These included total area occupied by cells, area shape, bounding box area, compactness, equivalent diameter, minimum ferret diameter, minor axis length and perimeter of SMDC at 24 h after initiating culture. The information extracted with our approach indicates live cell imaging can detect a range of cell phenotypes based on cell-shape alone and preserving cell integrity could be used to predict propensity to form myotubes in vitro and functional tissue in vivo

Retrofitting reinforced concrete structures with FRP: Numerical simulations using multifiber beam elements

In structural engineering, seismic vulnerability reduction of existing structures is a crucial issue. External reinforcement by Polymer Reinforced Fibers (FRP) is an interesting tool in order to fulfill this aim. However, the use of FRP reinforcement as a retrofitting method is limited, one of the reasons being the lack of predicting numerical tools for cyclic loading. This paper presents a method to predict the behavior of beam-column structures considering the FRP reinforcement effect. It describes the construction of a 1D concrete constitutive model suitable for monotonic and cycling loadings. The model is inspired on two well-known concrete models, the first one based on the damage mechanics theory (La Borderie concrete damage model), and the second one based on experimental studies (Eid & Paultre's confined concrete model). Validation of the approach is done using experimental results on reinforced concrete beam and columns submitted to axial and flexural cyclic loading. The proposed method deals also with steel bar rupture considering low cycle fatigue effects. All the simulations are done using multifiber Timoshenko beam elements

Stacks and D-Brane Bundles

In this paper we describe explicitly how the twisted ``bundles'' on a D-brane worldvolume in the presence of a nontrivial B field, can be understood in terms of sheaves on stacks. We also take this opportunity to provide the physics community with a readable introduction to stacks and generalized spaces.Comment: 24 pages, LaTeX; v2: references adde

THESEUS1 and RALF34 monitor cell wall integrity

The cell wall is a rigid network being the first barrier between a plant cell and its environment, but at the same time has to be a dynamic network whose cell growth and shape is given by deposition and remodeling of the cell wall. Maintaining cell wall integrity (CWI) is essential for correct plant development and stress response. Members of the family of Catharanthus roseus receptor-like kinase 1-like (CrRLK1L) proteins have been shown to play a role in cell wall homeostasis, mechanoperception, CWI maintenance and growth control. One of the 17 members in Arabidopsis, THESEUS1 (THE1), was identified in a suppressor screen of a cellulose deficient mutant, revealing that the reduction in growth is part of a THE1-mediated compensatory response to cell wall perturbation (Hématy et al., 2007). Interestingly, several CrRLK1L members have been shown to be receptors for Rapid Alkalinisation Factor (RALF) peptides. RALFs are on average 50 amino acids highly basic, cysteine-rich peptides, most of which are predicted to be cleaved from a highly acidic prodomain by a subtilisin protease. Recently, THE1 has been identified as a receptor for RALF34 (Gonneau et al., 2018). However, this peptide might not be the only THE1 ligand, since ralf34 loss-of-function mutants do not phenocopy all aspects of the1 mutants. RALF24 and RALF31 clustered together with RALF34, based on expression values across different tissues. We generated CRISPR/Cas9 mutants on RALF24, RALF31 and RALF34 with the aim to study which THE1 responses depend on these peptides. Our data suggest that RALF34 could not be the ligand for CWI response of THE1. The presence of RALF34 is acting negatively through THE1, inhibiting its response to cell wall damage.Universidad de Málaga. Campus de Excelencia Internacional Andalucía Tech

Investigations on path indexing for graph databases

Graph databases have become an increasingly popular choice for the management of the massive network data sets arising in many contemporary applications. We investigate the effectiveness of path indexing for accelerating query processing in graph database systems, using as an exemplar the widely used open-source Neo4j graph database. We present a novel path index design which supports efficient ordered access to paths in a graph dataset. Our index is fully persistent and designed for external memory storage and retrieval. We also describe a compression scheme that exploits the limited differences between consecutive keys in the index, as well as a workload-driven approach to indexing. We demonstrate empirically the speed-ups achieved by our implementation, showing that the path index yields query run-times from 2x up to 8000x faster than Neo4j. Empirical evaluation also shows that our scheme leads to smaller indexes than using general-purpose LZ4 compression. The complete stand-alone implementation of our index, as well as supporting tooling such as a bulk-loader, are provided as open source for further research and development