BMGTools : a community tool to handle model grid and bathymetry

A software called BathyMeshGridTools is proposed to facilitate the construction of gridded bathymetry data for hydrodynamic ocean models from global to coastal scales. These tools consist of a graphical interface written in Java and a computational core written in FORTRAN, which are freely distributed under LGPL and GPL licenses (http://www.ifremer.fr/bmgtools). The process of gridded bathymetry creation relies on three successive tasks : (1) creation of structured grid using graphic user interface for positioning, resizing and creating a hierarchy of nested model grids on map ; (2) data interpolation using a grid-to-grid interpolation algorithm for interpolation of Digital Terrain Model and kriging algorithm for bathymetric sounding data interpolation ; (3) visual inspection and manual editing of the interpolated bathymetry field. These three steps can be used in the same process of construction of bathymetry gridded data and can also be used independently (e.g. one can use only the visualization tool for checking and modifying manually a bathymetry field previously created with an other tool)

Diagnostic Accuracy of a Noninvasive Test for Detection of Helicobacter pylori and Resistance to Clarithromycin in Stool by the Amplidiag H. pylori+ClariR Real-Time PCR Assay

International audienceThe noninvasive detection of Helicobacter pylori and its resistance to clarithromycin could revolutionize the management of H. pylori-infected patients by tailoring eradication treatment without any need for endoscopy when histology is not necessary. Several real-time PCR tests performed on stools have been proposed, but their performances were either poor or they were tested on too few patients to be properly evaluated. We conducted a prospective, multicenter study including 1,200 adult patients who were addressed for gastroduodenal endoscopy with gastric biopsies and who were naive for eradication treatment in order to evaluate the performance of the Amplidiag H. pyloriϩClariR assay recently developed by Mobidiag (Espoo, Finland). The results of the Amplidiag H. pyloriϩClariR assay performed on DNA from stools (automatic extraction with the EasyMag system [bioMérieux]) were compared with those of culture/Etest and quadruplex real-time PCRs performed on two gastric biopsy samples (from the antrum and corpus) to detect the H. pylori glmM gene and mutations in the 23S rRNA genes conferring clarithromycin resistance. The sensitivity and specificity of the detection of H. pylori were 96.3% (95% confidence interval [CI], 92 to 98%) and 98.7% (95% CI, 97 to 99%), respectively. The positive and negative predictive values were evaluated to be 92.2% (95% CI, 92 to 98%) and 99.3% (95% CI, 98 to 99%), respectively. In this cohort, 160 patients (14.7%) were found to be infected (positive by culture and/or PCR). The sensitivity and specificity for detecting resistance to clarithromycin were 100% (95% CI, 88 to 100%) and 98.4% (95% CI, 94 to 99%), respectively

Membres du comité d’organisation scientifique et logistique

SPEEAGESTADAGROSUPMembres du comité d’organisation scientifique et logistique. 23. Conférence du COLUMA - Journées Internationales sur la Lutte contre les Mauvaises Herbe

Social foraging European shags: GPS tracking reveals birds from neighbouring colonies have shared foraging grounds

Developments in tracking technologies have enhanced our understanding of the behaviours of many seabird species. However few studies have examined the social aspects of seabird foraging behaviour, despite the effect this might have on the distribution of foraging areas and the differences that might arise between colonies. Here we use bird-borne GPS and behavioural observation to study the social foraging behaviour and habitat use of breeding shags from three breeding colonies in the Isles of Scilly, UK. Thirteen breeding shags from three colonies (six at two colonies and a single bird from another) were tracked between 2010 and 2012 and related to observations of conspecific foraging aggregations (2013-2014). Tracked shags had short foraging ranges (1.74 ± 1.6 km) mostly travelling to shallow waters between the islands and observations revealed that many shags foraged in large social groups that were consistent in time and space. There were also no clear differences in foraging distributions among colonies—birds shared similar foraging grounds. Our finding provides important insight into the use of social information among foraging seabirds and how this may lead to shared foraging areas, as well as space partitioning