On the design of high order residual-based dissipation for unsteady compressible flows

none3The numerical dissipation operator of Residual-Based Compact (RBC) schemes of high accuracy is identified and analysed for hyperbolic systems of conservation laws. A necessary and sufficient condition (-criterion) is found that ensures dissipation in 2-D and 3-Dfor any order of the RBC scheme. Numerical applications of RBC schemes of order 3, 5 and 7 to a diagonal wave advection and to a converging cylindrical shock problem confirm the theoretical results.A. Lerat; K. Grimich; P. CinnellaA., Lerat; K., Grimich; Cinnella, Paol

Isolated hypoglossal palsy due to cervical osteophyte

SummaryIntroductionIsolated hypoglossal nerve palsy is rare, and etiological diagnosis is difficult. We report a case of isolated hypoglossal compression by a cervical osteophyte in the hypoglossal canal exit.Case studyAn 86-year-old woman with history of cervical spondylotic myelopathy consulted for a lesion of the free edge of the tongue with impaired elocution. Clinical examination found a bite lesion on the right free edge of the tongue with right lingual amyotrophy and associated left deviation on retraction. Isolated right hypoglossal palsy was diagnosed. Skull base CT found a cervical osteophyte compressing the hypoglossal nerve at the exit from the right hypoglossal canal. Surgery was contra-indicated by the patient's general health status. No motor recovery was observed at 6 months’ follow-up, but the elocution disorders regressed under speech therapy.ConclusionHypoglossal palsy is infrequent, but generally a sign of skull base pathology. History-taking and careful examination guide rational selection of the radiological examinations required for etiological diagnosis

Comment passer d'un modèle hydrologique à un système de prévision des crues? Ecueils liés à la structure des modèles et aux échelles d'espace et de temps

Les modèles hydrologiques Pluie Débit sont des outils très utiles pour la prévision des crues. À l'heure actuelle, il n'est pas possible d'utiliser directement les modèles de simulation pour effectuer une bonne prévision. Nous explorons ici les différences entre modèles de simulation et modèles de prévision. Puis nous examinons l'importance relative des informations apportées au modèle : dans le passé, les forçages climatiques et les dernières observations de débit ; dans le futur, les prévisions de précipitations. La question des échelles spatiales est ensuite abordée et les limites d'une approche globale sont discutées dans une perspective opérationnelle. / Rainfall Runoff models are very useful tools for flood forecasting. As of today, the direct use of simulation models is not possible to get accurate predictions especially when it concerns short-term forecasting. In this paper, we explore the main differences between simulation and forecasting models. Then we assess the relative importance of every information provided to the model: the past climatic forcing and the last observed discharges; the future precipitation scenarios. Spatial scales are also examined and the limits of a global forecasting approach for operational purposes are discussed

Recent Progress in High-Order Residual-Based Compact Schemes for Compressible Flow Simulations: Toward Scale-Resolving Simulations and Complex Geometries

Recent developments about the extension of high-order Residual-Based Compact schemes to unsteady flows and complex configurations are discussed, with application to scale-resolving simulations and complex turbomachinery flows

What traits are carried on mobile genetic elements, and why?

Although similar to any other organism, prokaryotes can transfer genes vertically from mother cell to daughter cell, they can also exchange certain genes horizontally. Genes can move within and between genomes at fast rates because of mobile genetic elements (MGEs). Although mobile elements are fundamentally self-interested entities, and thus replicate for their own gain, they frequently carry genes beneficial for their hosts and/or the neighbours of their hosts. Many genes that are carried by mobile elements code for traits that are expressed outside of the cell. Such traits are involved in bacterial sociality, such as the production of public goods, which benefit a cell's neighbours, or the production of bacteriocins, which harm a cell's neighbours. In this study we review the patterns that are emerging in the types of genes carried by mobile elements, and discuss the evolutionary and ecological conditions under which mobile elements evolve to carry their peculiar mix of parasitic, beneficial and cooperative genes

Predicting Prokaryotic Ecological Niches Using Genome Sequence Analysis

Automated DNA sequencing technology is so rapid that analysis has become the rate-limiting step. Hundreds of prokaryotic genome sequences are publicly available, with new genomes uploaded at the rate of approximately 20 per month. As a result, this growing body of genome sequences will include microorganisms not previously identified, isolated, or observed. We hypothesize that evolutionary pressure exerted by an ecological niche selects for a similar genetic repertoire in those prokaryotes that occupy the same niche, and that this is due to both vertical and horizontal transmission. To test this, we have developed a novel method to classify prokaryotes, by calculating their Pfam protein domain distributions and clustering them with all other sequenced prokaryotic species. Clusters of organisms are visualized in two dimensions as ‘mountains’ on a topological map. When compared to a phylogenetic map constructed using 16S rRNA, this map more accurately clusters prokaryotes according to functional and environmental attributes. We demonstrate the ability of this map, which we term a “niche map”, to cluster according to ecological niche both quantitatively and qualitatively, and propose that this method be used to associate uncharacterized prokaryotes with their ecological niche as a means of predicting their functional role directly from their genome sequence

Repetitive Elements May Comprise Over Two-Thirds of the Human Genome

Transposable elements (TEs) are conventionally identified in eukaryotic genomes by alignment to consensus element sequences. Using this approach, about half of the human genome has been previously identified as TEs and low-complexity repeats. We recently developed a highly sensitive alternative de novo strategy, P-clouds, that instead searches for clusters of high-abundance oligonucleotides that are related in sequence space (oligo “clouds”). We show here that P-clouds predicts >840 Mbp of additional repetitive sequences in the human genome, thus suggesting that 66%–69% of the human genome is repetitive or repeat-derived. To investigate this remarkable difference, we conducted detailed analyses of the ability of both P-clouds and a commonly used conventional approach, RepeatMasker (RM), to detect different sized fragments of the highly abundant human Alu and MIR SINEs. RM can have surprisingly low sensitivity for even moderately long fragments, in contrast to P-clouds, which has good sensitivity down to small fragment sizes (∼25 bp). Although short fragments have a high intrinsic probability of being false positives, we performed a probabilistic annotation that reflects this fact. We further developed “element-specific” P-clouds (ESPs) to identify novel Alu and MIR SINE elements, and using it we identified ∼100 Mb of previously unannotated human elements. ESP estimates of new MIR sequences are in good agreement with RM-based predictions of the amount that RM missed. These results highlight the need for combined, probabilistic genome annotation approaches and suggest that the human genome consists of substantially more repetitive sequence than previously believed

Origin and Examination of a Leafhopper Facultative Endosymbiont

Eukaryotes engage in intimate interactions with microbes that range in age and type of association. Although many conspicuous examples of ancient insect associates are studied (e.g., Buchneraaphidicola), fewer examples of younger associations are known. Here, we further characterize a recently evolved bacterial endosymbiont of the leafhopper Euscelidius variegatus (Hemiptera, Cicadellidae), called BEV. We found that BEV, continuously maintained in E. variegatus hosts at UC Berkeley since 1984, is vertically transmitted with high fidelity. Unlike many vertically transmitted, ancient endosymbioses, the BEV–E. variegatus association is not obligate for either partner, and BEV can be cultivated axenically. Sufficient BEV colonies were grown and harvested to estimate its genome size and provide a partial survey of the genome sequence. The BEV chromosome is about 3.8 Mbp, and there is evidence for an extrachromosomal element roughly 53 kb in size (e.g., prophage or plasmid). We sequenced 438 kb of unique short-insert clones, representing about 12% of the BEV genome. Nearly half of the gene fragments were similar to mobile DNA, including 15 distinct types of insertion sequences (IS). Analyses revealed that BEV not only shares virulence genes with plant pathogens, but also is closely related to the plant pathogenic genera Dickeya, Pectobacterium, and Brenneria. However, the slightly reduced genome size, abundance of mobile DNA, fastidious growth in culture, and efficient vertical transmission suggest that symbiosis with E. variegatus has had a significant impact on genome evolution in BEV

The endogenous retrovirus ENS-1 provides active binding sites for transcription factors in embryonic stem cells that specify extra embryonic tissue

<p>Abstract</p> <p>Background</p> <p>Long terminal repeats (LTR) from endogenous retroviruses (ERV) are source of binding sites for transcription factors which affect the host regulatory networks in different cell types, including pluripotent cells. The embryonic epiblast is made of pluripotent cells that are subjected to opposite transcriptional regulatory networks to give rise to distinct embryonic and extraembryonic lineages. To assess the transcriptional contribution of ERV to early developmental processes, we have characterized <it>in vitro </it>and <it>in vivo </it>the regulation of ENS-1, a host adopted and developmentally regulated ERV that is expressed in chick embryonic stem cells.</p> <p>Results</p> <p>We show that <it>Ens-1 </it>LTR activity is controlled by two transcriptional pathways that drive pluripotent cells to alternative developmental fates. Indeed, both Nanog that maintains pluripotency and Gata4 that induces differentiation toward extraembryonic endoderm independently activate the LTR. Ets coactivators are required to support Gata factors' activity thus preventing inappropriate activation before epigenetic silencing occurs during differentiation. Consistent with their expression patterns during chick embryonic development, Gata4, Nanog and Ets1 are recruited on the LTR in embryonic stem cells; in the epiblast the complementary expression of Nanog and Gata/Ets correlates with the <it>Ens-1 </it>gene expression pattern; and Ens-1 transcripts are also detected in the hypoblast, an extraembryonic tissue expressing Gata4 and Ets2, but not Nanog. Accordingly, over expression of Gata4 in embryos induces an ectopic expression of <it>Ens-1</it>.</p> <p>Conclusion</p> <p>Our results show that <it>Ens-1 </it>LTR have co-opted conditions required for the emergence of extraembryonic tissues from pluripotent epiblasts cells. By providing pluripotent cells with intact binding sites for Gata, Nanog, or both, <it>Ens-1 </it>LTR may promote distinct transcriptional networks in embryonic stem cells subpopulations and prime the separation between embryonic and extraembryonic fates.</p