Lagrangian and ALE Formulations For Soil Structure Coupling with Explosive Detonation

Simulation of Soil-Structure Interaction becomes more and more the focus of computational engineering in civil and mechanical engineering, where FEM (Finite element Methods) for soil and structural mechanics and Finite Volume for CFD (Computational Fluid Dynamics) are dominant. New advanced formulations have been developed for FSI (Fluid Structure Interaction) applications using ALE (Arbitrary Lagrangian Eulerian), mesh free and SPH (Smooth Particle Hydrodynamic) methods. In defence industry, engineers have been developing protection systems for many years to reduce the vulnerability of light armoured vehicles (LAV) against mine blast using classical Lagrangian FEM methods. To improve simulations and assist in the development of these protections, experimental tests and new numerical techniques are performed. Initial conditions such as the loading prescribed by a mine on a structure should be simulated adequately in order to conduct these numerical calculations. The effects of blast on structures often depend on how the initial conditions are estimated and applied. This article uses two methods to simulate a mine blast, namely the classical Lagrangian as well as the ALE formulations. The comparison was carried out for a simple and also a more complex target. Particle methods as SPH method can also be used for soil structure interaction

BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments

We present Babelomics, a complete suite of web tools for the functional analysis of groups of genes in high-throughput experiments, which includes the use of information on Gene Ontology terms, interpro motifs, KEGG pathways, Swiss-Prot keywords, analysis of predicted transcription factor binding sites, chromosomal positions and presence in tissues with determined histological characteristics, through five integrated modules: FatiGO (fast assignment and transference of information), FatiWise, transcription factor association test, GenomeGO and tissues mining tool, respectively. Additionally, another module, FatiScan, provides a new procedure that integrates biological information in combination with experimental results in order to find groups of genes with modest but coordinate significant differential behaviour. FatiScan is highly sensitive and is capable of finding significant asymmetries in the distribution of genes of common function across a list of ordered genes even if these asymmetries were not extreme. The strong multiple-testing nature of the contrasts made by the tools is taken into account. All the tools are integrated in the gene expression analysis package GEPAS. Babelomics is the natural evolution of our tool FatiGO (which analysed almost 22 000 experiments during the last year) to include more sources on information and new modes of using it. Babelomics can be found at

Influence of cracks on the soil-atmosphere interaction: numerical coupled model of thermo- atmosphereporous media

Soil shrinks as it desiccates, and the magnitude of shrinkage can be large for clayey soils. The drying of soil leads to cracks formation, causing high suctions to develop within. Cracks expose the deep soil and more evaporation can be expected in dry periods. To illustrate the effect of cracking, a numerical model of soil-atmosphere interaction has been developed taking into account the thermo-fluid coupling of an unsaturated clay soil. The model is used to simulate the evolution of evaporation during the drying process. The main results show a significant influence of the presence of cracks on the evaporation. This study also offers a simple method for taking into account the presence of cracks in the soil-atmosphere exchange

A systematic review and meta-analysis of randomized trials of carotid endarterectomy vs stenting

ObjectiveThe purpose of this systematic review and meta-analysis was to synthesize the available evidence derived from randomized controlled trials (RCTs) regarding the relative efficacy and safety of endarterectomy vs stenting in patients with carotid artery disease.MethodsWe searched MEDLINE, EMBASE, Current Contents, and Cochrane CENTRAL through July 2010 to update previous systematic reviews. Two reviewers determined trial eligibility and extracted descriptive, methodologic, and outcome data (death, nonfatal stroke, and nonfatal myocardial infarction). Random-effects meta-analysis was used to pool relative risks and the I2 statistic was used to assess heterogeneity.ResultsThirteen RCTs proved eligible enrolling 7484 patients, of which 80% had symptomatic disease. Methodological quality was moderate to high, with better quality among RCTs published after 2008. Compared with carotid endarterectomy, stenting was associated with increased risk of any stroke (relative risk [RR], 1.45; 95% confidence interval [CI], 1.06-1.99; I2 = 40%), decreased risk of periprocedural myocardial infarction (MI; RR, 0.43; 95% CI, 0.26- 0.71; I2 = 0%), and nonsignificant increase in mortality (RR, 1.40; 95% CI, 0.85-2.33; I2 = 5%). When analysis was restricted to the two most recent trials with the better methodology and more contemporary technique, we found stenting to be associated with a significant increase in the risk of any stroke (RR, 1.82; 95% CI, 1.35-2.45) and mortality (RR, 2.53; 95% CI, 1.27-5.08) and a nonsignificant reduction of the risk of MI (RR, 0.39; 95% CI, 0.12-1.23). For every 1000 patients opting for stenting rather than endarterectomy, 19 more patients would have strokes and 10 fewer would have MIs. Outcome data in asymptomatic patients were sparse and imprecise; hence, these conclusions apply primarily to symptomatic patients.ConclusionCompared with endarterectomy, carotid artery stenting (CAS) significantly increases the risk of any stroke and decreases the risk of MI

Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies

Genome-wide association studies have become a popular strategy to find associations of genes to traits of interest. Despite the high-resolution available today to carry out genotyping studies, the success of its application in real studies has been limited by the testing strategy used. As an alternative to brute force solutions involving the use of very large cohorts, we propose the use of the Gene Set Analysis (GSA), a different analysis strategy based on testing the association of modules of functionally related genes. We show here how the Gene Set-based Analysis of Polymorphisms (GeSBAP), which is a simple implementation of the GSA strategy for the analysis of genome-wide association studies, provides a significant increase in the power testing for this type of studies. GeSBAP is freely available at http://bioinfo.cipf.es/gesbap

BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments

We present a new version of Babelomics, a complete suite of web tools for functional analysis of genome-scale experiments, with new and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An improved indexing has considerably speeded up several of the modules. An improved version of the FatiScan method for studying the coordinate behaviour of groups of functionally related genes is presented, along with a similar tool, the Gene Set Enrichment Analysis. Babelomics is now more oriented to test systems biology inspired hypotheses. Babelomics can be found at

GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data

The Gene Expression Profile Analysis Suite, GEPAS, has been running for more than three years. With >76 000 experiments analysed during the last year and a daily average of almost 300 analyses, GEPAS can be considered a well-established and widely used platform for gene expression microarray data analysis. GEPAS is oriented to the analysis of whole series of experiments. Its design and development have been driven by the demands of the biomedical community, probably the most active collective in the field of microarray users. Although clustering methods have obviously been implemented in GEPAS, our interest has focused more on methods for finding genes differentially expressed among distinct classes of experiments or correlated to diverse clinical outcomes, as well as on building predictors. There is also a great interest in CGH-arrays which fostered the development of the corresponding tool in GEPAS: InSilicoCGH. Much effort has been invested in GEPAS for developing and implementing efficient methods for functional annotation of experiments in the proper statistical framework. Thus, the popular FatiGO has expanded to a suite of programs for functional annotation of experiments, including information on transcription factor binding sites, chromosomal location and tissues. The web-based pipeline for microarray gene expression data, GEPAS, is available at

GoGene: gene annotation in the fast lane

High-throughput screens such as microarrays and RNAi screens produce huge amounts of data. They typically result in hundreds of genes, which are often further explored and clustered via enriched GeneOntology terms. The strength of such analyses is that they build on high-quality manual annotations provided with the GeneOntology. However, the weakness is that annotations are restricted to process, function and location and that they do not cover all known genes in model organisms. GoGene addresses this weakness by complementing high-quality manual annotation with high-throughput text mining extracting co-occurrences of genes and ontology terms from literature. GoGene contains over 4 000 000 associations between genes and gene-related terms for 10 model organisms extracted from more than 18 000 000 PubMed entries. It does not cover only process, function and location of genes, but also biomedical categories such as diseases, compounds, techniques and mutations. By bringing it all together, GoGene provides the most recent and most complete facts about genes and can rank them according to novelty and importance. GoGene accepts keywords, gene lists, gene sequences and protein sequences as input and supports search for genes in PubMed, EntrezGene and via BLAST. Since all associations of genes to terms are supported by evidence in the literature, the results are transparent and can be verified by the user. GoGene is available at http://gopubmed.org/gogene

Use of GenMAPP and MAPPFinder to analyse pathways involved in chickens infected with the protozoan parasite Eimeria

<p>Abstract</p> <p>Background</p> <p>Microarrays allow genome-wide assays of gene expression. There is a need for user-friendly software to visualise and analyse these data. Analysing microarray data in the context of biological pathways is now common, and several tools exist.</p> <p>Results</p> <p>We describe the use of MAPPFinder, a component of GenMAPP to characterise the biological pathways affected in chickens infected with the protozoan parasite <it>Eimeria. </it>Several pathways were significantly affected based on the unadjusted p-value, including several immune-system pathways.</p> <p>Conclusion</p> <p>GenMAPP/MAPPFinder provides a means to rapidly visualise pathways affected in microarray studies. However, it relies on good genome annotation and having genes reliably linked to pathway objects. We show that GenMAPP/MAPPFinder can produce useful results, and as the annotation of the chicken genome improves, so will the level of information gained.</p