Numerical approximation of the shallow water equations with coriolis source term

We investigate in this work a class of numerical schemes dedicated to the non-linear Shallow Water equations with topography and Coriolis force. The proposed algorithms rely on Finite Volume approximations formulated on collocated and staggered meshes, involving appropriate diffusion terms in the numerical fluxes, expressed as discrete versions of the linear geostrophic balance. It follows that, contrary to standard Finite-Volume approaches, the linear versions of the proposed schemes provide a relevant approximation of the geostrophic equilibrium. We also show that the resulting methods ensure semi-discrete energy estimates. Numerical experiments exhibit the efficiency of the approach in the presence of Coriolis force close to the geostrophic balance, especially at low Froude number regimes

PPARα transcriptionally induces AhR expression in Caco-2, but represses AhR pro-inflammatory effects

International audienceIn this work we demonstrate that Caco-2 cell treatment with WY-14643 (a potent PPARa agonist) causes an increase in AhR expression. Luciferase assays and directed mutagenesis experiments showed that induction mainly occurred at transcriptional level and involved a PPRE site located within the AhR promoter. These results were further confirmed by the use of PPARa knockout mice in which AhR induction by WY14643 was abrogated. In addition to CYP1 regulation, AhR has been described as being involved in inflammation , so we also studied the effect of AhR regulation by PPARa on the expression of some inflammation target genes. 3-Methylcho-lanthrene (a potent AhR agonist) increased the expression (mRNA) of the major inflammatory targets IL-1b and MMP9. WY-14643 co-treatment abrogated the 3-methylcholanthrene pro-inflammatory effect. Hence the anti-inflammatory effect of PPARa overrides the pro-inflammatory effect of AhR

Ultra-fast sequence clustering from similarity networks with SiLiX

<p>Abstract</p> <p>Background</p> <p>The number of gene sequences that are available for comparative genomics approaches is increasing extremely quickly. A current challenge is to be able to handle this huge amount of sequences in order to build families of homologous sequences in a reasonable time.</p> <p>Results</p> <p>We present the software package <monospace>SiLiX</monospace> that implements a novel method which reconsiders single linkage clustering with a graph theoretical approach. A parallel version of the algorithms is also presented. As a demonstration of the ability of our software, we clustered more than 3 millions sequences from about 2 billion BLAST hits in 7 minutes, with a high clustering quality, both in terms of sensitivity and specificity.</p> <p>Conclusions</p> <p>Comparing state-of-the-art software, <monospace>SiLiX</monospace> presents the best up-to-date capabilities to face the problem of clustering large collections of sequences. <monospace>SiLiX</monospace> is freely available at <url>http://lbbe.univ-lyon1.fr/SiLiX</url>.</p

Neo/adjuvant chemotherapy does not improve outcome in resected primary synovial sarcoma: a study of the French Sarcoma Group

Background: There are only scarce data about the benefit of adjunctive chemotherapy in patients with localized synovial sarcoma (SS). Patients and methods: Data from 237 SS patients recorded in the database of the French Sarcoma Group were retrospectively analyzed. The respective impact of radiotherapy, neo-adjuvant chemotherapy and adjuvant chemotherapy on overall survival (OS), local recurrence-free survival (LRFS) and distant recurrence-free survival (DRFS) were assessed after adjustment to prognostic factors. Results: The median follow-up was 58 months (range 1-321). Adjuvant, neo-adjuvant chemotherapy and postoperative radiotherapy were administered in 112, 45 and 181 cases, respectively. In all, 59% of patients treated with chemotherapy received an ifosfamide-containing regimen. The 5-year OS, LRFS and DRFS rates were 64.0%, 70% and 57%, respectively. On multivariate analysis, age >35 years old, grade 3 and not-R0 margins were highly significant independent predictors of worse OS. After adjustment to prognostic factors, radiotherapy significantly improved LRFS but not DRFS or OS. Neither neo-adjuvant nor adjuvant chemotherapy had significant impact on OS, LRFS or DRFS. Conclusion: As for other high-grade soft-tissue sarcomas, well-planned wide surgical excision with adjuvant radiotherapy remains the cornerstone of treatment for SS. Neo-adjuvant or adjuvant chemotherapy should not be delivered outside a clinical trial settin

Performance status is the most powerful risk factor for early death among patients with advanced soft tissue sarcoma The European Organisation for Research and Treatment of Cancer – Soft Tissue and Bone Sarcoma Group (STBSG) and French Sarcoma Group (FSG) study

BACKGROUND: We investigated prognostic factors (PFs) for 90-day mortality in a large cohort of advanced/metastatic soft tissue sarcoma (STS) patients treated with first-line chemotherapy. METHODS: The PFs were identified by both logistic regression analysis and probability tree analysis in patients captured in the Soft Tissue and Bone Sarcoma Group (STBSG) database (3002 patients). Scores derived from the logistic regression analysis and algorithms derived from probability tree analysis were subsequently validated in an independent study cohort from the French Sarcoma Group (FSG) database (404 patients). RESULTS: The 90-day mortality rate was 8.6 and 4.5% in both cohorts. The logistic regression analysis retained performance status (PS; odds ratio (OR) = 3.83 if PS = 1, OR = 12.00 if PS >= 2), presence of liver metastasis (OR = 2.37) and rare site metastasis (OR = 2.00) as PFs for early death. The CHAID analysis retained PS as a major discriminator followed by histological grade (only for patients with PS >= 2). In both models, PS was the most powerful PF for 90-day mortality. CONCLUSION: Performance status has to be taken into account in the design of further clinical trials and is one of the most important parameters to guide patient management. For those patients with poor PS, expected benefits from therapy should be weighed up carefully against the anticipated toxicities. British Journal of Cancer (2011) 104, 1544-1550. doi: 10.1038/bjc.2011.136 www.bjcancer.com Published online 19 April 2011 (C) 2011 Cancer Research U

ESMO Clinical Research Observatory (ECRO): improving the efficiency of clinical research through rationalisation of bureaucracy

During the last years, there has been a dramatic increase in the administrative and bureaucratic burden associated with cli

A filled duration illusion in music: Effects of metrical subdivision on the perception and production of beat tempo.

This study replicates and extends previous findings suggesting that metrical subdivision slows the perceived beat tempo (Repp, 2008). Here, musically trained participants produced the subdivisions themselves and were found to speed up, thus compensating for the perceived slowing. This was shown in a synchronization-continuation paradigm (Experiment 1) and in a reproduction task (Experiment 2a). Participants also judged the tempo of a subdivided sequence as being slower than that of a preceding simple beat sequence (Experiment 2b). Experiment 2 also included nonmusician participants, with similar results. Tempo measurements of famous pianists’ recordings of two variation movements from Beethoven sonatas revealed a strong tendency to play the first variation (subdivided beats) faster than the theme (mostly simple beats). A similar tendency was found in musicians’ laboratory performances of a simple theme and variations, despite instruc-tions to keep the tempo constant (Experiment 3a). When playing melodic sequences in which only one of three beats per measure was subdivided, musicians tended to play these beats faster and to perceive them as longer than adjacent beats, and they played the whole sequence faster than a sequence without any subdivisions (Experiments 3b and 3c). The results amply demonstrate a filled duration illusion in rhythm perception and music performance: Intervals containing events seem longer than empty intervals and thus must be shortened to be perceived as equal in duration