Éditeur(s) : Oxford university press
Résumé : The eastern Baltic cod stock collapsed as a consequence of climate-driven adverse hydrographic conditions and over fishing and has remained at historically low levels. Spatio-temporal fishing closures [Marine Protected Areas (MPAs)] have been implemented since 1995, to protect and restore the spawning stock. However, no signs of recovery have been observed yet, either suggesting that MPAs are an inappropriate management measure or pointing towards suboptimal closure design. We used the spatially explicit fishery simulation model ISIS-Fish to evaluate proposed and implemented fishery closures, combining an age-structured population module with a multifleet exploitation module and a management module in a single model environment. The model is parameterized based on (i) the large amount of biological knowledge available for cod and (ii) an analysis of existing spatially disaggregated fishery data. As the population dynamics of eastern Baltic cod depend strongly on the climate-driven hydrographic regime, we considered two production regimes of the stock. MPAs were only effective for stock recovery when they reduced overall fishing effort. The performance of MPAs needs to be evaluated relative to environmental regimes, especially for stocks facing strong environmental variability.
ICES Journal of Marine Science (1054-3139) (Oxford university press), 2009 , Vol. 66 , N. 1 , P. 109-121

Droits : 2008 ICES/CIEM
http://archimer.ifremer.fr/doc/2009/publication-6094.pdf
DOI:10.1093/icesjms/fsn166
http://archimer.ifremer.fr/doc/00000/6094/

Éditeur(s) : HAL CCSD Geological Society of America
Résumé : International audience
We present the first recorded global positioning system (GPS) data from Myanmar measured at the northern tip of the Sagaing fault. This area is in a very complex geodynamic context, where rigid and semirigid plates interact. The 12 GPS sites measured in 2005 and 2008 in northern Myanmar show that the slip rate is 18 mm/yr and is localized along a single active narrow fault trace (<20 km wide). The same rate was previously demonstrated and remeasured, 500 km southward, in central Myanmar. Despite the geodynamic regional complexity induced by interaction between the Sunda and India plates, the Burma microplate, and the highly deformable eastern Himalayan syntaxis, the slip rate remains surprisingly constant along this fault. However, the modeled locking depth varies from 20 km in central Myanmar to 5 km in the north.
ISSN: 0091-7613

hal-00673712
https://hal.archives-ouvertes.fr/hal-00673712
DOI : 10.1130/G30872.1

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The kinetics of hydrogenation of dry iron-bearing olivine single crystals was determined by performing hydration experiments under hydrothermal conditions at high pressure. The experiments were performed in a multi-anvil press at 3 GPa, for a temperature range between 900 and 1200 °C and for various durations. The oxygen fugacity was buffered along Ni-NiO joint. Polarized Fourier transform infrared spectroscopy and recent empirical calibration were used to quantify the hydroxyl distributions in the samples along crystallographic axes after the experiments. The chemical diffusion coefficients are similar (barely slower) than in olivine hydrated at lower pressure (0.2 and 0.3 GPa) for the same diffusion mechanism. Under the given experimental conditions, the anisotropy of diffusion is the same as for proton-vacancy mechanism, with diffusion along the [0 0 1] axis faster than along the [1 0 0]. However, the anisotropy at 3 GPa is weaker compared to measurements at lower pressures and the analysis of concentration profiles using 3D models shows that an isotropic solution could also be relevant. Fits of the diffusion data to an Arrhenius law yield activation energies for the slightly faster [0 0 1] axis of the crystallographic axes around 198 ± 5 kJ mol−1, a value only slightly lower than the results from previous experimental studies for natural iron-bearing olivine hydrogenated at lower confining pressure. At 3 GPa, hydrogenation can be well approximated by a single mechanism controlled by coupled diffusion of protons and octahedral vacancies (di- and tri-valent ions). The diffusion rates are fast enough to alter hydrogen concentration within olivine in xenoliths ascending from the mantle or experiencing hydrogen-rich metasomatism events, but too slow to permit complete homogenization of hydrogen in olivine-rich rocks at kilometer scale in less than one My.
ISSN: 0031-9201

hal-01412663
https://hal.archives-ouvertes.fr/hal-01412663
DOI : 10.1016/j.pepi.2016.08.005

Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Although heterokaryons have been reported in nature, multicellular organisms are generally assumed genetically homogeneous. Here, we investigate the case of arbuscular mycorrhizal fungi (AMF) that form symbiosis with plant roots. The growth advantages they confer to their hosts are of great potential benefit to sustainable agricultural practices. However, measuring genetic diversity for these coenocytes is a major challenge: Within the same cytoplasm, AMF contain thousands of nuclei and show extremely high levels of genetic variation for some loci. The extent and physical location of polymorphism within and between AMF genomes is unclear. We used two complementary strategies to estimate genetic diversity in AMF, investigating polymorphism both on a genome scale and in putative single copy loci. First, we used data from whole-genome pyrosequencing of four AMF isolates to describe genetic diversity, based on a conservative network-based clustering approach. AMF isolates showed marked differences in genome-wide diversity patterns in comparison to a panel of control fungal genomes. This clustering approach further allowed us to provide conservative estimates of Rhizophagus spp. genomes sizes. Second, we designed new putative single copy genomic markers, which we investigated by massive parallel amplicon sequencing for two Rhizophagus irregularis and one Rhizophagus sp. isolates. Most loci showed high polymorphism, with up to 103 alleles per marker. This polymorphism could be distributed within or between nuclei. However, we argue that the Rhizophagus isolates under study might be heterokaryotic, at least for the putative single copy markers we studied. Considering that genetic information is the main resource for identification of AMF, we suggest that special attention is warranted for the study of these ecologically important organisms.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01224215
http://hal.upmc.fr/hal-01224215
http://hal.upmc.fr/hal-01224215/document
http://hal.upmc.fr/hal-01224215/file/Genome%20Biol%20Evol-2015-Boon-505-21.pdf
DOI : 10.1093/gbe/evv002

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The purpose of this investigation was to characterize the management and prognosis of severe Pneumocystis jirovecii pneumonia (PJP) in human immunodeficiency virus (HIV)-negative patients. An observational cohort study of HIV-negative adults with PJP documented by bronchoalveolar lavage (BAL) through Gomori-Grocott staining or immunofluorescence, admitted to one intensive care unit (ICU) for acute respiratory failure, was undertaken. From 1990 to 2010, 70 patients (24 females, 46 males) were included, with a mean age of 58.6 ± 18.3 years. The mean Simplified Acute Physiology Score (SAPS)-II was 36.9 ± 20.4. Underlying conditions included hematologic malignancies (n = 21), vasculitis (n = 13), and solid tumors (n = 13). Most patients were receiving systemic corticosteroids (n = 63) and cytotoxic drugs (n = 51). Not a single patient received trimethoprim-sulfamethoxazole as PJP prophylaxis. Endotracheal intubation (ETI) was required in 42 patients (60.0 %), including 38 with acute respiratory distress syndrome (ARDS). In-ICU mortality was 52.9 % overall, reaching 80.9 % and 86.8 %, respectively, for patients who required ETI and for patients with ARDS. In the univariate analysis, in-ICU mortality was associated with SAPS-II (p = 0.0131), ARDS (p < 0.0001), shock (p < 0.0001), and herpes simplex virus (HSV) or cytomegalovirus (CMV) on BAL (p = 0.0031). In the multivariate analysis, only ARDS was associated with in-ICU mortality (odds ratio [OR] 23.4 [4.5-121.9], p < 0.0001). PJP in non-HIV patients remains a serious disease with high in-hospital mortality. Pulmonary co-infection with HSV or CMV may contribute to fatal outcome.
ISSN: 0934-9723

inserm-00872789
http://www.hal.inserm.fr/inserm-00872789
DOI : 10.1007/s10096-012-1730-7
PUBMED : 22930407

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
Progress in seismic methodology and ambitious large-scale seismic projects are enabling high-resolution imaging of the continental crust. The ability to constrain interpretations of crustal seismic data is based on laboratory measurements on rock samples and calculations of seismic properties. Seismic velocity calculations and their directional dependence are based on the rock microfabric, which consists of mineral aggregate properties including crystallographic preferred orientation (CPO), grain shape and distribution, grain boundary distribution, and misorientation within grains. Single-mineral elastic constants and density are crucial for predicting seismic velocities, preferably at conditions that span the crust. However, high-temperature and high-pressure elastic constant data are not as common as those determined at standard temperature and pressure (STP; atmospheric conditions). Continental crust has a very diverse mineral composition; however, a select number of minerals appear to dominate seismic properties because of their high-volume fraction contribution. Calculations of microfabric-based seismic properties and anisotropy are performed with averaging methods that in their simplest form takes into account the CPO and modal mineral composition, and corresponding single crystal elastic constants. More complex methods can take into account other microstructural characteristics, including the grain shape and distribution of mineral grains and cracks and pores. Dynamic or active wave propagation schemes have recently been developed, which offer a complementary method to existing static averaging methods generally based on the use of the Christoffel equation. A challenge for the geophysics and rock physics communities is the separation of intrinsic factors affecting seismic anisotropy, due to properties of crystals within a rock and apparent sources due to extrinsic factors like cracks, fractures, and alteration. This is of particular importance when trying to deduce crustal composition and the state of deformation from seismic parameters.
ISSN: 8755-1209

Droits : info:eu-repo/semantics/OpenAccess
hal-01685568
https://hal.archives-ouvertes.fr/hal-01685568
https://hal.archives-ouvertes.fr/hal-01685568/document
https://hal.archives-ouvertes.fr/hal-01685568/file/Almqvist_et_al-2017-Reviewssur Geophysics.pdf
DOI : 10.1002/2016RG000552

Éditeur(s) : HAL CCSD
Résumé : International audience
This paper presents the background for the calculation of anisotropic piezoelectric properties of single crystals and the graphical display of the results in two or three dimensions, and the calculation of the aggregate properties from constituent crystals and the texture of the aggregate in a coherent manner. The texture data can be obtained from a wide range of sources, including pole figure diffraction and single orientation measurements (electron backscattered diffraction, electron channelling pattern, Laue Pattern, optical microscope universal-stage). We consider the elastic wave propagation in piezoelectric crystals as an example of the interaction of electrical (2nd rank tensor), piezoelectric (3rd rank tensor) and elastic properties (4th rank tensor). In particular, we give explicit formulae for the calculation of the Voigt averaged tensor from individual orientations or from an orientation distribution function. For the latter we consider numerical integration and an approach based on the expansion into spherical harmonics. We illustrate the methods using single crystals, polycrystalline quartz measured using electron channelling patterns and ideal Curie limiting groups applied to quartz aggregates. This paper also serves as a reference paper for the mathematical tensor capabilities of the texture analysis software MTEX
Geological Society Special Publication, 409

hal-01277789
https://hal.archives-ouvertes.fr/hal-01277789
DOI : 10.1144/SP409.2

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Cigarette smoke condensate (CSC) has previously been shown to impair activity and expression of hepatic drug transporters. In the present study, we provided evidence that CSC also hinders activity of organic anion transporters (OATs), notably expressed at the kidney level. CSC thus cis-inhibited OAT substrate uptake in OAT1- and OAT3-transfected HEK293 cells, in a concentration-dependent manner (IC50=72.1μg/mL for OAT1 inhibition and IC50=27.3μg/mL for OAT3 inhibition). By contrast, OAT4 as well as the renal organic cation transporter (OCT) 2 were less sensitive to the inhibitory effect of CSC (IC50=351.5μg/mL and IC50=226.2μg/mL, for inhibition of OAT4 and OCT2, respectively). OAT3 activity was further demonstrated to be blocked by some single chemicals present in cigarette smoke such as the heterocyclic amines AαC (IC50=11.3μM) and PhIP (IC50=1.9μM), whereas other major cigarette smoke components used at 100μM, like nicotine, the nitrosamine NNK and the polycyclic aromatic hydrocarbons benzo(a)pyrene and phenanthrene, were without effect. AαC and PhIP however failed to trans-stimulate activity of OAT3, suggesting that they were not substrates for this transporter. Taken together, these data establish OAT1 and OAT3 transporters as targets of cigarette smoke chemicals, which may contribute to smoking-associated pharmacokinetics alterations.
ISSN: 0887-2333

hal-01579604
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01579604
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01579604/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01579604/file/Sayyed%20et%20al.%20-%20Inhibition%20of%20organic%20anion%20transporter%20%28OAT%29%20acti.pdf
DOI : 10.1016/j.tiv.2017.06.014

Éditeur(s) : HAL CCSD MDPI
Résumé : International audience
The Taylor power law (or temporal fluctuation scaling), is a scaling relationship of the form σ ~ (P)λ where !! is the standard deviation and hPi the mean value of a sample of a time series has been observed for power output data sampled at 5 min and 1 s and from five wind farms and a single wind turbine, located at different places. Furthermore, an analogy with the turbulence field is performed, consequently allowing the establishment of a scaling relationship between the turbulent production IP and the mean value (P)
ISSN: 2079-9276

hal-01528077
https://hal.archives-ouvertes.fr/hal-01528077
https://hal.archives-ouvertes.fr/hal-01528077/document
https://hal.archives-ouvertes.fr/hal-01528077/file/resources-04-00787.pdf
DOI : 10.3390/resources4040787

Éditeur(s) : Pêche thonière et dispositifs de concentration de poissons, Caribbean-Martinique, 15-19 Oct 1999
Résumé : French Polynesia started it's Fish Aggregating Device programme in June 1981 with the positioning of the first buoy offshore of the main island of Tahiti. Since then, 251 structures have been installed throughout the 5 archipelagoes of this French overseas territory. The shape and size of the devices have evolved 8 times over this period, however, a single model has not yet been adopted. Trials are currently underway using lighter structures similar to those found in the Indian Ocean. The anchoring lines have progressively been modified through better knowledge of material and product availability, as well as better understanding of environmental constraints. The programme is entirely financed by the territorial government and managed by the public sector. This ongoing technical assistance, aimed towards the local small-scale coastal fishery, is considered an important factor to maintaining this activity alive. Up until 1997, this economical support policy of outer island populations far from the metropolis central town, along with incidental fishing methods around FADs, have given mitigated results without nevertheless putting into cause this programme. The use of 'drifting handlines' retained at the surface by small indicator floats are one of the contributing factors to the degradation of the anchor lines. It is now commonly accepted that a new fishing strategy must be adopted so that professional coastal fishermen become more aware with regards to an expensive work tool due to local bathymetric conditions, so that fishing effort is increased through the development of better adapted fishing techniques, and finally so that community spirit rules over individualism.Original Abstract: Le programme d'ancrage de DCP en Polynesie francaise a vu le jour en juin 1981 avec l'implantation d'un premier dispositif au large des cotes de Tahiti. Depuis cette date, ce sont 251 structures qui ont ete installees dans les cinq archipels de ce pays d'outre-mer. La forme et la taille des bouees ont evolue huit fois sans etre definitivement arretees a un seul modele et des essais sur des structures legeres de type " Ocean Indien " sont en cours. Les lignes d'ancrage ont fait l'objet de modifications progressives en raison de meilleures connaissances des produits ainsi que des contraintes du milieu environnant. Ce programme est finance en totalite par le territoire de la Polynesie francaise et gere par le secteur public. Il s'adresse a la pecherie artisanale et cotiere qui considere depuis de nombreuses annees cette assistance technique comme un atout indispensable au maintien de son activite. La politique d'engagement de ce soutien economique jusqu'en 1997 aupres des populations d'iles et atolls tres eloignes de la capitale ainsi que l'incidence de la technique de peche la plus repandue autour des DCP ont abouti a des resultats mitiges sans pour autant remettre en cause ce programme. En effet, les lignes a main derivantes et retenues en surface par une petite bouee temoin sont un des principaux facteurs de degradation des lignes d'ancrage. Il est desormais reconnu par tous les intervenants qu'une nouvelle strategie doit etre deployee afin que les pecheurs cotiers professionnels soient mieux responsabilises face a un outil de travail onereux en raison de la bathymetrie environnante, pour que l'effort de peche soit accru par l'utilisation de techniques de peche mieux adaptees, et enfin que l'esprit communautaire prime sur l'individualisme.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/00042/15292/12649.pdf
http://archimer.ifremer.fr/doc/00042/15292/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The identification of a large OIB-type volcanic sequence on top of an obducted nappe in the Lesser Caucaus of Armenia helps us explain the obduction processes in the Caucasus region that are related to dramatic change in the global tectonics of the Tethyan region in the late Lower Cretaceous. The ophiolitic nappe preserves three distinct magmatic series, obducted in a single tectonic slice over the South Armenian Block during the Coniacian-Santonian (88-83 Ma), the same time as the Oman ophiolite. Similar geological, petrological, geochemical and age features for various Armenian ophiolitic massifs (Sevan, Stepanavan, and Vedi) argue for the presence of a single large obducted ophiolite unit. The ophiolite, shows evidence for a slow-spreading oceanic environment in Lower to Middle Jurassic. Serpentinites, gabbros and plagiogranites were exhumed by normal faults, and covered by radiolarites. Few pillow-lava flows have infilled the rift grabens. The ophiolite lavas have hybrid geochemical composition intermediate between Arc and MORB signatures: (La/Yb)(N) = 0.6-0.9: (Nb/Th)(N) = 0.17-0.57; (Nd-143/Nd-144)(i) = 0.51273-0.51291; (Sr-87/Sr-86)(i) = 0.70370-0.70565; (Pb-207/Pb-204)(i) = 15.4587-15.5411; (Pb-208/Pb-204)(i) = 37.4053-38.2336; (Pb-206/Pb-204)(i) = 17.9195-18.4594. These compositions suggest they were probably formed in a back-arc basin by melting of a shallow asthenosphere source contaminated by a deeper mantle source modified by subducted slab-derived products. Sr-87/Sr-86 ratios and petrological evidence show that these lavas have been intensely altered by mid-oceanic hydrothermalism as well as by serpentinites, which are interpreted as exhumed mantle peridotites. The gabbros have almost the same geochemical composition as related pillow-lavas: (La/Yb)(N) = 0.2-2.3; (Nb/Th)(N) = 0.1-2.8; (Nd-143/Nd-144)(i) = 0.51264-0.51276: (Sr-87/Sr-86)(i) = 0.70386-0.70557; (Pb-207/Pb-204)(i) = 15.4888-15.5391; (Pb-208/Pb-204)(i) = 37.2729-37.8713; (Pb-206/Pb-204)(i) = 17.6296-17.9683. Plagiogranites show major and trace element features similar to other Neo-Tethyan plagiogranites (La/Yb)(N) = 1.10-7.92; (Nb/Th)(N) = 0.10-0.94; but display a less radiogenic Nd isotopic composition than basalts [(Nd-143/Nd-144)(i) = 0.51263] and more radiogenic (Sr-87/Sr-86)(i) ratios. This oceanic crust sequence is covered by variable thicknesses of unaltered pillowed OIB alkaline lavas emplaced in marine conditions. Ar-40/Ar-39 dating of a single-grain amphibole phenocryst provides a Lower Cretaceous age of 117.3 +/- 0.9 Ma, which confirms a distinct formation age of the OIB lavas. The geochemical composition of these alkaline lavas is similar to plateau-lavas [(La/Yb)(N) = 6-14; (Nb/Th)(N) = 0.23-0.76; (Nd-143/Nd-144)(i) = 0.51262-0.51271; (Sr-87/Sr-86)(i) = 0.70338-0.70551; (Pb-207/Pb-204)(i) = 15.5439-15.6158; (Pb-208/Pb-204)(i) = 38.3724-39.3623; (Pb-206/Pb-204)(i) = 18.4024-19.6744].;They have significantly more radiogenic lead isotopic compositions than phiolitic rocks, and fit the geochemical compositions of hot-spot derived lavas mixed with various proportions of oceanic mantle. In addition, this oceanic + plateau sequence is covered by Upper Cretaceous calc-alkaline lavas: (La/Yb)(N) = 2.07-2.31; (Nb/Th)(N) = 0.08-0.15; (Nd-144/Nd-143)(i) = 0.51271-0.51282; (Sr-117/Sr-116)(i) = 0.70452-0.70478), which were likely formed in a supra-subduction zone environment. During the late Lower to early Upper Cretaceous period, hot-spot related magmatism related to plateau events may have led to significant crustal thickening in various zones of the Middle-eastern Neotethys. These processes have likely hindered subduction of some of the hot and thickened oceanic crust segments, and allowed them to be obducted over small continental blocks such as the South Armenian Block.
ISSN: 0024-4937

hal-00443855
https://hal.archives-ouvertes.fr/hal-00443855
DOI : 10.1016/j.lithos.2009.02.006

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
We report trace element concentrations of silicate phases in chondrules from LL3 ordinary chondrites Bishunpur and Semarkona. Results are similar to previously reported data for carbonaceous chondrites, with rare earth element (REE) concentrations increasing in the sequence olivine < pyroxene < mesostasis, and heavy REE (HREE) being enriched by 1–2 orders of magnitude (CI-normalized) relative to light REE (LREE) in ferromagnesian silicates, although no single olivine with very large LREE/HREE fractionation has been found. On average, olivine in type II chondrules is poorer in refractory lithophile incompatible elements (such as REE) than its type I counterpart by a factor of ∼2. This suggests that olivine in type I and II chondrules formed by batch and fractional crystallization, respectively, implying that type II chondrules formed under faster cooling rates (>∼10 K/h) than type I chondrules. Appreciable Na concentrations (3–221 ppm) are measured in olivine from both chondrule types; type II chondrules seem to have behaved as closed systems, which may require chondrule formation in the vicinity of protoplanets or planetesimals. At any rate, higher solid concentrations in type II chondrule forming regions may explain the higher oxygen fugacities they record compared to type I chondrules. Type I and type II chondrules formed in different environments and the correlation between high solid concentrations and/or oxygen fugacities with rapid cooling rates is a key constraint that chondrule formation models must account for.
ISSN: 0016-7037

hal-01174084
https://hal.archives-ouvertes.fr/hal-01174084
DOI : 10.1016/j.gca.2015.02.005

Éditeur(s) : ISTPM
Résumé : The first part describes the evolution of the world sea fisheries from 1950 to 1977 and their present state : a decline of the growing rate of the catches, their biological structure and their distribution in the oceans according to the depth, the distance from the continent and the latitude. Then the biogeographical fishery complexes are defined, being characterized by assemblages of commercially valuable and actually caught species. These complexes are arranged according to the latitude with sometimes longitudinal subdivisions. At last with technical and economical criteria, such as the yield of the fisheries, the finality of the catches and the conditions of the exploitation which add themselves to the biogeographical complexes, the authors attempt to single out geographical fishing provinces.
La première partie analyse l'évolution de la pêche mondiale de 1950 à 1977 et sa situation présente : ralentissement du rythme de la croissance des captures, composition faunistique et répartition des pêches dans l'océan selon la profondeur, la distance à la côte et la latitude. Ensuite sont définis les complexes biogéographiques de pêche, caractérisés par des assemblages d'espèces commercialement intéressantes et effectivement utilisées. Ces complexes s'ordonnent selon la latitude avec parfois des subdivisions méridiennes. Enfin, à l'aide de critères techniques et économiques, tels que le rendement des pêches, la finalité des captures et les modalités de l'exploitation qui viennent se superposer aux complexes biogéographiques, les auteurs tentent d'individualiser des provinces géographiques de pêche.
Revue des Travaux de l'Institut des Pêches Maritimes (0035-2276) (ISTPM), 1980-06 , Vol. 44 , N. 2 , P. 89-117

Droits : Ifremer
http://archimer.ifremer.fr/doc/1980/publication-1947.pdf
http://archimer.ifremer.fr/doc/00000/1947/

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
Anti-Aspergillus IgG antibodies are important biomarkers for the diagnosis of chronic pulmonary aspergillosis (CPA) and allergic bronchopulmonary aspergillosis (ABPA). We compared the performance of a new commercial EIA (Bordier Affinity Products) with those of the Bio-Rad and VirionSerion EIAs. This assay is novel in the association of two recombinant antigens with somatic and metabolic antigens of A. fumigatus. In a prospective multicentre study, 436 serum samples from 147 patients diagnosed with CPA (136 sera/104 patients) or ABPA (94 sera/43 patients) and from 205 controls (206 sera) were tested. We obtained sensitivities of 97%, 91.7%, and 86.1%, and specificities of 90.3%, 91.3%, and 81.5% for the Bordier, Bio-Rad and VirionSerion tests, respectively. The Bordier kit was more sensitive than the Bio-Rad kit (p < 0.01), which was itself more sensitive than the VirionSerion kit (p=0.04). The Bordier and Bio-Rad kits had similar specificities (p=0.8), both higher than that of the VirionSerion kit (p=0.02). The areas under the ROC curves confirmed the superiority of the Bordier kit over the Bio-Rad and the VirionSerion kits (0.977, 0.951 and 0.897, respectively; p < 0.01 for each comparison). In a subset analysis of 279 sera tested with the Bordier and Bio-Rad kits and an in-house immunoprecipitin assay (IPD), the Bordier kit had the highest sensitivity (97.7%), but the IPD tended to be more specific (71.2 and 84.7%, respectively; p=0.10).The use of recombinant, somatic and metabolic antigens in a single EIA improved the balance between sensitivity and specificity, resulting in an assay highly suitable for use in the diagnosis of chronic and allergic aspergillosis.
ISSN: 0095-1137

hal-01282328
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01282328
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01282328/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01282328/file/Prospective%20evaluation%20of%20a%20new%20Aspergillus.pdf
DOI : 10.1128/JCM.03261-15

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Purpose: Active surveillance is a treatment option for favorable risk prostate cancer. However, data are missing on populations of African descent. We evaluated the safety and benefit of active surveillance in an African Caribbean cohort with favorable risk prostate cancer. Materials and Methods: Between 2005 and 2016, a single center, prospective cohort study was performed in Guadeloupe, French West Indies, including patients on active surveillance who had low risk prostate cancer (prostate specific antigen 10 ng/ml or less and Gleason score 6 or less) or favorable intermediate risk prostate cancer (prostate specific antigen 10 to 20 ng/ml, Gleason score 3 + 4 or less and life expectancy less than 10 years). Treatment was recommended in case of grade progression, increased tumor volume, prostate cancer doubling time less than 36 months or patient wish. Overall survival, disease specific survival and duration of active surveillance were calculated with the KaplanMeier method. Multivariate analysis was performed using the Cox proportional hazards model to identify predictors of active surveillance termination. Results: A total of 234 patients with a median age of 64 years were enrolled in study. Median followup was 4 years (IQR 2.3-5.5). Overall survival at 30 months, 5 years and 10 years was 99.5%, 98.5% and 90.7%, respectively. Disease specific survival at 30 months, and 5 and 10 years was 100%. At 30 months, 5 years and 10 years 72.7%, 52.6% and 40.4% of patients, respectively, remained untreated and on active surveillance. Age (HR 0.96 per additional year, 95% CI 0.93-0.99) and prostate specific antigen density (HR 1.52 per additional 0.1 ng/ml, 95% CI 1.20-1.89) were found to be independent predictors of active surveillance termination. Conclusions: Active surveillance is safe and beneficial for highly selected African Caribbean patients. It seems to be feasible for patients at low risk and intermediate favorable risk. Prostate specific antigen density could help better select these patients.
ISSN: 0022-5347

hal-01519251
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01519251
DOI : 10.1016/j.juro.2016.12.047
PUBMED : 27993665

Éditeur(s) : HAL CCSD Taylor & Francis
Résumé : Modern geochronology has moved beyond the acquisition of dates: the goal is to understand the significance of these numbers for the geodynamic evolution of Earth at all scales. The coupling of the laser-ablation microprobe (LAM) to inductively coupled plasma mass spectrometers (ICPMS, multicollector (MC)-ICPMS) has revolutionised geochronology and geochemistry over the last 10 years. These systems enable the rapid and precise in situ analysis of trace-element patterns and isotopic systems, while adding information related to microstructural context and major-element composition. The integration of these multiple sources of data is crucial in constraining the origin of the sample and the processes leading to its formation, so that we can understand the meaning of a date in terms of geological events. LAM-ICPMS measurement of U-Pb ages and trace-element patterns in zircon, coupled with LAM-MC-ICPMS analysis of Hf isotopes in the same grains, gives new insights into the processes of magma genesis. Applied to detrital zircons from modern drainages or sedimentary rocks (the TerraneChron approach), it becomes a powerful tool to investigate problems of crustal evolution on scales ranging from single terranes to continents. The in situ analysis (LAM-MC-ICPMS) of Re-Os systematics in single grains of sulfides in mantle-derived peridotites has demonstrated that most mantle rocks contain several generations of Os-bearing sulfides; whole-rock analyses are mixtures reflecting multiple melting and metasomatic events in the lithospheric mantle. These deep-seated events are commonly mirrored in the crust; Os model-age spectra from xenolith suites show age 'peaks' that correspond to the ages of thermal/tectonic events in the overlying crust, suggesting strong linkages between crust and mantle. Integrated studies of the timing and nature of crustal and mantle events, using these techniques, will be important for understanding the large-scale dynamics of the Earth.
ISSN: 0812-0099

hal-00411328
https://hal.archives-ouvertes.fr/hal-00411328
DOI : 10.1080/08120090802097450

Éditeur(s) : HAL CCSD
Résumé : International audience
A prospective study on randomized patients was conducted to determine how morphokinetic parameters are altered in embryos grown in sequential versus global culture media. Eleven morphokinetic parameters of 160 single embryos transferred were analyzed by time lapse imaging involving two University-affiliated in vitro fertilization (IVF) centers. We found that the fading of the two pronuclei occurred earlier in global (22.56±2.15 hpi) versus sequential media (23.63±2.71 hpi; p=0.0297). Likewise, the first cleavage started earlier at 24.52±2.33 hpi vs 25.76±2.95 hpi (p=0.0158). Also, the first cytokinesis was shorter in global medium, lasting 18±10.2 minutes in global versus 36±37.8 minutes in sequential culture medium (p <0.0001). We also observed a significant shortening in the duration of the 2-cell stage in sequential medium: 10.64 h±2.75 versus 11.66 h±1.11 in global medium (p=0.0225) which suggested a faster progression of the embryos through their first mitotic cell cycle. In conclusion, morphokinetic analysis of human embryos by Time lapse imaging reveals significant differences in five kinetic variables according to culture medium. Our study highlights the need to adapt morphokinetic analysis accordingly to the type of media used to best support human early embryo development.
Annales de Biologie Clinique

hal-01579406
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01579406
DOI : 10.1684/abc.2017.1259
PUBMED : 28751285

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Advances in groundwater storage monitoring are crucial for water resource management and hydrological processes understanding. The evaluation of water storage changes (WSC) often involve point measurements (observation wells, moisture probes, etc.), which may be inappropriate in heterogeneous media. Over the past few years, there has been an increasing interest in the use of gravimetry for hydrological studies. In the framework of the GHYRAF (Gravity and Hydrology inAfrica) project, 3 yr of repeated absolute gravity measurements using a FG5-type gravimeter have been undertaken at Nalohou, a Sudanian site in northern Benin. Hydrological data are collected within the long-term observing system AMMA-Catch. Once corrected for solid earth tides, ocean loading, air pressure effects, polar motion contribution and non-local hydrology, seasonal gravity variations reach up to 11 μGal, equivalent to a WSC of 260-mm thick infinite layer of water. Absolute temporal gravity data are compared to WSC deduced from neutron probe and water-table variations through a direct modelling approach. First, we use neutronic measurements available for the whole vertical profile where WSC occur (the vadose zone and a shallow unconfined aquifer). The RMSD between observed and modelled gravity variations is 1.61 μGal, which falls within the error bars of the absolute gravity data. Second, to acknowledge for the spatial variability of aquifer properties, we use a 2-D model for specific yield (Sy) derived from resistivity mapping and Magnetic Resonance Soundings (MRS). The latter provides a water content (θMRS) known to be higher than the specific yield. Hence, we scaled the 2-D model of θMRS with a single factor (α). WSC are calculated from water-table monitoring in the aquifer layer and neutronic measurements in the vadose layer. The value of α is obtained with aMonte-Carlo sampling approach, minimizing the RMSD between modelled and observed gravity variations. This leads to α = Sy/θMRS = 0.63 ± 0.15, close to what is found in the literature on the basis of pumping tests experiments, with a RMSD value of 0.94 μGal. This hydrogeophysical experiment is a first step towards the use of time-lapse gravity data as an integrative tool to monitor interannual WSC even in complicated subsurface distribution.
ISSN: 0956-540X

hal-00821181
https://hal.archives-ouvertes.fr/hal-00821181
DOI : 10.1093/gji/ggt146

Éditeur(s) : HAL CCSD Wiley/Blackwell
Résumé : International audience
Microsatellites are widely used in population genetics to uncover recent evolutionary events. They are typically genotyped using capillary sequencer, which capacity is usually limited to 9, at most 12 loci for each run, and which analysis is a tedious task that is performed by hand. With the rise of next-generation sequencing (NGS), a much larger number of loci and individuals are available from sequencing: for example, on a single run of a GS Junior, 28 loci from 96 individuals are sequenced with a 30X cover. We have developed an algorithm to automatically and efficiently genotype microsatellites from a collection of reads sorted by individual (e.g. specific PCR amplifications of a locus or a collection of reads that encompass a locus of interest). As the sequencing and the PCR amplification introduce artefactual insertions or deletions, the set of reads from a single microsatellite allele shows several length variants. The algorithm infers, without alignment, the true unknown allele(s) of each individual from the observed distributions of microsatellites length of all individuals. MicNeSs, a python implementation of the algorithm, can be used to genotype any microsatellite locus from any organism and has been tested on 454 pyrosequencing data of several loci from fruit flies (a model species) and red deers (a nonmodel species). Without any parallelization, it automatically genotypes 22 loci from 441 individuals in 11 hours on a standard computer. The comparison of MicNeSs inferences to the standard method shows an excellent agreement, with some differences illustrating the pros and cons of both methods.
ISSN: 1755-098X

hal-01544754
https://hal.archives-ouvertes.fr/hal-01544754
DOI : 10.1111/1755-0998.12467

Éditeur(s) : HAL CCSD
Résumé : International audience
High Pressure - Low Temperature (HP-LT) rocks testify for burying and exhumation of crustal material in subduction zones. The question of their exhumation is nevertheless still unclear. The Aegean domain offers several HP-LT belts. Especially, the Attic-Cycladic Blueschist unit (ACBU) is an example of a HP-LT unit exhumed in a convergent and then in a divergent context. It actually appears in metamorphic core complexes (MCCs) formed in the back-arc of the subduction. The syn-convergence "message" is however difficult to read because of the post-convergence structural and thermal overprint that accompanied the formation of the MCCs. Particularly, the geometry, the timing and the amount of the syn-orogenic exhumation remain unclear. We investigate theses questions with metamorphic petrology (Andros and Ios islands) and phengite population, single grain and in situ 40Ar-39Ar geochronology (Andros, Tinos, Syros and Ios islands). Based on these new constraints and a synthesis of published data, we are able to refine the geometry, the timing and the modes of the exhumation of the ACBU. Data from the whole Cyclades exhibit little differences in the age and P-T conditions at the successive stages of syn-orogenic exhumation. The peak of pressure (500±50 °C-18±1 kbar) has been reached at 50-55 Ma. The onset of the exhumation occurred at 40-45 Ma in blueschist facies conditions, between a basal thrust and a summital detachment. The following decompression was accompanied by cooling until 30-35 Ma (400±50 °C-8±1 kbar). At that time, the boundary conditions switched to extension. The change in boundary conditions is recorded by slowing of the exhumation and isobare heating. The conditions of post-orogenic exhumation differ from an island to another. The onset of post-orogenic exhumation is dated around 30 Ma in the northern Cyclades and 25 Ma in the southern Cyclades. It is related to top-to-the-North deformation in all the studied domain. The end of ductile deformation below the detachments is also diachronous (21 Ma in the North and 18 Ma in the South). Finally, we propose a model for the final steps of the exhumation related to the intrusion of granitic bodies around 14 Ma.
American Geophysical Union, Fall Meeting
San Francisco, United States

insu-00860510
https://hal-insu.archives-ouvertes.fr/insu-00860510
BIBCODE : 2010AGUFM.T23C2301L