Éditeur(s) : HAL CCSD
Résumé : International audience
In vitro susceptibility of 933 Candida isolates, from 16 French hospitals, to micafungin was determined using the Etest in each center. All isolates were then sent to a single center for determination of MICs by the EUCAST reference method. Overall essential agreement between the two tests was 98.5% at ±2 log2 dilutions and 90.2% at ±1 log2 dilutions. Categorical agreement was 98.2%. The Etest is a valuable alternative to EUCAST for the routine determination of micafungin MICs in medical mycology laboratories. Copyright © 2016, American Society for Microbiology. All Rights Reserved.
Antimicrobial Agents and Chemotherapy

hal-01367142
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367142
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367142/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01367142/file/Multicenter%20comparison%20of%20the%20Etest.pdf
DOI : 10.1128/AAC.00630-16

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The Iranian plateau is a flat ~ 1.5–2 km high plateau thought to result from the collision between the Arabian and Eurasian plates since ~ 30 ± 5 Ma, and may represent a young analogue to the so far better studied Tibetan plateau. In order to constrain the exhumation history of the internal Zagros and of the Iranian plateau, we herein present apatite (U-Th)/He (AHe) and apatite (AFT) and zircon fission-track (ZFT) data on plutonic rocks from the Sanandaj–Sirjan Zone (SSZ), Urumieh–Dokhtar magmatic arc (UDMA), Central Iran and Kopet Dagh. Thermochronologic data show that the SSZ was exhumed early in the collision process (essentially before 25–20 Ma), with a likely acceleration of cooling during the late Eocene, from 0.04 to 0.3 mm/year. Results suggest that cooling of the internal Zagros migrated from the SSZ to the UDMA during a more mature stage of the continental collision, after ~ 17 Ma (i.e., coeval with the outward propagation of deformation and topography fronts in the external Zagros). Constant exhumation rates in the UDMA (~ 0.3 mm/year) suggest that no significant variation of erosion rates occurred since the onset of continental collision. In Central Iran, the overlap of ZFT, AFT and AHe ages from gneissic samples points to rapid cooling during the late Eocene (~ 42 °C/Myr), which is consistent with previous reports on the formation of Eocene metamorphic core-complexes.
ISSN: 0024-4937

hal-01115691
https://hal.archives-ouvertes.fr/hal-01115691
DOI : 10.1016/j.lithos.2014.07.021

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Subduction infancy corresponds to the first few million years following subduction initiation, when slabs start their descent into the mantle. It coincides with the transient (yet systematic) transfer of material from the top of the slab to the upper plate, as witnessed by metamorphic soles welded beneath obducted ophiolites. Combining structure–lithology–pressure–temperature–time data from metamorphic soles with flow laws derived from experimental rock mechanics, this study highlights two main successive rheological switches across the subduction interface (mantle wedge vs. basalts, then mantle wedge vs. sediments; at ∼800 °C and ∼600 °C, respectively), during which interplate mechanical coupling is maximized by the existence of transiently similar rheologies across the plate contact. We propose that these rheological switches hinder slab penetration and are responsible for slicing the top of the slab and welding crustal pieces (high- then low-temperature metamorphic soles) to the base of the mantle wedge during subduction infancy. This mechanism has implications for the rheological properties of the crust and mantle (and for transient episodes of accretion/exhumation of HP-LT rocks in mature subduction systems) and highlights the role of fluids in enabling subduction to overcome the early resistance to slab penetration.
ISSN: 0012-821X

hal-01383368
http://hal.upmc.fr/hal-01383368
http://hal.upmc.fr/hal-01383368/document
http://hal.upmc.fr/hal-01383368/file/Agard_2016_Plate_interface.pdf
DOI : 10.1016/j.epsl.2016.06.054

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Preface
ISSN: 0024-4937

hal-00903596
https://hal.archives-ouvertes.fr/hal-00903596
DOI : 10.1016/j.lithos.2013.06.006

Éditeur(s) : HAL CCSD
Résumé : International audience
Idiopathic pulmonary fibrosis (IPF) is the most frequent chronic idiopathic interstitial pneumonia in adults. The management of rare diseases in France has been organised by a national plan for rare diseases, which endorsed a network of expert centres for rare diseases throughout France. This article is an overview of the executive summary of the French guidelines for the management of IPF, an initiative that emanated from the French National Reference Centre and the Network of Regional Competence Centres for Rare Lung Diseases. This review aims at providing pulmonologists with a document that: 1) combines the current available evidence; 2) reviews practical modalities of diagnosis and management of IPF; and 3) is adapted to everyday medical practice. The French practical guidelines result from the combined efforts of a coordination committee, a writing committee and a multidisciplinary review panel, following recommendations from the Haute Autorité de Santé. All recommendations included in this article received at least 90% agreement by the reviewing panel. Herein, we summarise the main conclusions and practical recommendations of the French guidelines.
Eur Respir Rev

hal-01063982
https://hal.archives-ouvertes.fr/hal-01063982
DOI : 10.1183/09059180.00001814
PUBMED : 24881074

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
Toxoplasmosis is a life-threatening infection in immunocompromised patients (ICPs). The definite diagnosis relies on parasite DNA detection, but the incidence and burden of disease are ill-known in HIV-negative patients. A three-year retrospective study was conducted in 15 reference laboratories from the network of the French National Reference Center for Toxoplasmosis, to record the frequency of Toxoplasma DNA detection in ICPs, to review the molecular methods used for diagnosis and the prevention measures implemented in transplant patients. During the study period, out of 31,640 PCR performed in ICPs, 610 were positive (323 patients). Blood (n=337), cerebrospinal fluid (n=101) and aqueous humor (n=100) samples were more frequently positive. Chemoprophylaxis schemes in transplant patients differed between centers. PCR follow-up of allogeneic hematopoietic stem-cell transplant (allo-HSCT) patients was implemented in 8/15 centers. Data from 180 patients (13 centers) were further analyzed regarding clinical setting and outcome. Only 68/180 (38%) patients were HIV+; the remaining 62% consisted in 72 HSCT, 14 solid-organ transplants, and 26 miscellaneous immunodeficiencies. Cerebral toxoplasmosis and disseminated toxoplasmosis were most frequently observed in HIV and transplant patients, respectively. Of 72 allo-HSCT patients with a positive PCR, 23 were asymptomatic; all were diagnosed in centers performing systematic blood PCR follow-up, and received specific treatment. Overall survival of allo-HSCT patients at two months was better in centers with PCR follow-up than in other centers (p<0.01). This study provides updated data on the frequency of toxoplasmosis in HIV-negative ICPs and suggests that regular PCR follow-up of allo-HSCT patients could guide pre-emptive treatment and improve outcome.
ISSN: 0095-1137

hal-01134189
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01134189
DOI : 10.1128/JCM.03282-14
PUBMED : 25762774

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Serpentinites are one of the major components of the oceanic lithosphere and are stable in the slab and the mantle wedge up to 100-150 km depth in subduction zones. During oceanic mantle hydration and alteration, they trap trace and fluid mobile (FME: B, Li, As, Sb, Rb, Ba, Cs, Sr, U and Pb) elements that participate to elemental transfer occurring between the dehydrating slab and the mantle wedge in subduction context. The Lanzo massif is an eclogitized oceanic lithosphere that preserved its oceanic structure and recorded different steps of serpentinization/de-serpentinization from oceanic lizardite to prograde antigorite in subduction context, up to its dehydration and secondary olivine crystallization, and finally retrograde antigorite during massif exhumation. It constitutes a suitable place to study trace element behavior during serpentinization/de-serpentinization processes and associated chemical transfers between the different envelopes of the oceanic lithosphere and the mantle wedge. Geochemical analyses of serpentine and associated minerals show that the serpentinization/de-serpentinization of the Lanzo massif took place in a relatively closed system without significant trace element transfer between the different parts of the oceanic lithosphere. In the deeper part of the lithosphere, from the slightly serpentinized mantle peridotites (SSP, < 20% serpentinization) to the paleo-Moho, composed of massive serpentinites (MS, 80% serpentinization), the trace elements mobility is reduced. The chemical composition of lizardite and antigorite is homogenized with the local degree of serpentinization: in SSP, serpentine veins composition is inherited from the host mineral while, in MS, their composition is homogenous between destabilized phases at the scale of the outcrop (~ 5 m). In the shallowest part of the oceanic lithosphere, from the paleo-Moho to the oceanic paleo-seafloor, the serpentinites are foliated (FS, > 90% serpentinization). In that zone, the alpine deformation enhances the mobility of trace elements and permits their redistribution and the homogenization of antigorite composition at massif scale. Locally, in the SSP and MS, the crystallization of metamorphic veins of ~ 1-2 m corresponds to channelized fluid flows that allowed fluid transfers - and thereby trace elements - to longer distance. The successive crystallizations of antigorite and then olivine are accompanied by a diminution of some FME (B, Li, As, Sb, Ba, Rb) and Eu contents attesting that these elements are removed from slab to mantle wedge during subduction.
ISSN: 0009-2541

hal-00937661
https://hal.archives-ouvertes.fr/hal-00937661
DOI : 10.1016/j.chemgeo.2013.08.025

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
Estimations of zenith total delays (ZTD) were obtained during postprocessing of a high-resolution (2.4 km) nonhydrostatic atmospheric model (Méso-NH). These estimations were used to determine their sensitivity with respect to formulations of atmospheric refractivity, the approximation of zenith hydrostatic delays (ZHD) deduced from ground pressure, and the contributions of hydrometeors. The factor k for the conversion of zenith wet delay (ZWD) to integrated water vapor (IWV) was examined. Méso-NH is applied here to the extreme flash flood event of 8–9 September 2002 in southeastern France. The use of the hydrostatic formulation (to infer ZHD) leads to an overestimation of up to 18 mm with respect to the vertical integration of refractivity. Delay contributions of hydrometeors simulated by the high-resolution model reached more than 70 mm (%11 kg/m 2 IWV) in the heart of the convective cells in the case of the extreme flood event. The mean variations of IWV due to the use of different conversion factors (k used to transform ZWD to IWV) are evaluated to be less than 0.3 kg/m 2. This is less than the mean underestimation of IWV by 0.6 kg/m 2 relative to the GPS-like evaluation of IWV using the hydrostatic formulation and the ground temperature. In this study we also use GPS ZTD observations to validate three different numerical simulations of this extreme flood event. The simulation with the best fit to the GPS observations is also in best agreement with the surface rainfall measurements.
ISSN: 2169-897X

hal-01417608
https://hal.archives-ouvertes.fr/hal-01417608
https://hal.archives-ouvertes.fr/hal-01417608/document
https://hal.archives-ouvertes.fr/hal-01417608/file/Brenot_JGR_2006.pdf
DOI : 10.1029/2004JD005726

Éditeur(s) : HAL CCSD Institute of Electrical and Electronics Engineers
Résumé : International audience
ISSN: 0018-9499

hal-01632372
https://hal.archives-ouvertes.fr/hal-01632372
DOI : 10.1109/TNS.2010.2089063

Éditeur(s) : HAL CCSD Pergamon
Résumé : This paper presents an experimental study of the deformation of Beaucaire marl subjected to drained triaxial tests under a wide range of confining pressure. Several methods of observation have been used: X-ray computed tomography, scanning electronic microscopy, quantitative image analysis of thin sections and mercury porosimetry. The analysis at the grain scale shows the existence of various deformation modes depending on the mean stress level. These modes are classified with reference to the brittle and ductile regimes. In specimens deformed under low confining pressure, macro-cracks are localised in a band more contracting than the rest of the specimen. In specimens deformed under moderate confining pressure, a series of micro-scale shear bands characterised by a grain re-orientation towards the direction of macro-shear is detected in the zones of localised deformation. The material in between the micro-scale shear bands is contracting more than the rest of the specimen in some cases; in other cases, a schistosity is detected also in the rest of the specimen outside the localisation zones. In the specimen deformed under high confining pressure, no localisation occurs, and a schistosity is observable throughout the specimen.
ISSN: 1365-1609

hal-00411208
https://hal.archives-ouvertes.fr/hal-00411208
DOI : 10.1016/j.ijrmms.2007.08.007

Éditeur(s) : HAL CCSD
Résumé : International audience
At the time of the collision with India (55Ma), the southern margin of Asia was a composite continental domainresulting from an already long history of successive accretions of different terranes having different rheologies.Knowledge about the structure, composition and thermal state of the Tibetan lithosphere through time is thusfundamental to understand the respective contributions of pre-Cenozoïc and Cenozoïc tectonics in the building ofthe Plateau to its present-day elevations.We focused on the boundary between the Qiangtang terrane to the south, and the Songpan-Ganze terrane to thenorth.We jointly studied deep crustal xenoliths and associated (ultra-)potassic magmatism from the Eocene basinsof Nangqian and Xialaxiu (Qinghai Province, China), north of the Qiangtang terrane. The aims were to retrievethe composition and the thermal state of the lower crust during Eocene times, to study the behavior of the lowercrust and lithospheric mantle of the Eastern Qiangtang terrane and the adjacent Songpan-Ganze terrane at the timeof the collision, and the link with the magmatic activity.Crustal xenoliths are of two types: biotite-rich, amphibole bearing metasediments; and garnet-bearing quartzofeldspathicgneisses. Such assemblages are typical of very high-grade amphibolite and granulite faciesmetamorphism; further study should allow us to quantify the pressures and temperatures those rocks experienceduntil the time they were sampled by their host lavas.Major element geochemistry places the c.a. 51-49 Ma (Spurlin et al., 2005) Xialaxiu volcanic field in a fairlydifferentiated (SiO265-70 wt%) high-K field of the calc-alcaline series. Trace element analysis suggests a strongcrustal contamination of the primary mantellic melts. C.a. 38-37 Ma (Spurlin et al., 2005) Nangqian magmaticbodies span across the alkaline series, with high to extreme (K2O6wt%) values. Complex major and traceelement patterns, coupled with high-resolution microprobe data on pyroxene xenocrysts, suggest that enrichmentoccurred at the source by metasomatism of the lithospheric mantle.Further work will precise which mechanisms could have accounted for such a metasomatism of the mantle beneaththe Northern Qiangtang terrane during Eocene, and whether the lower crust had an autochtonous or allochtonousnature.
Geophysical Research Abstracts
Vienne, Austria

insu-01308919
https://hal-insu.archives-ouvertes.fr/insu-01308919

Éditeur(s) : HAL CCSD Georg Thieme Verlag
Résumé : International audience
Oil from the nuts of Calophyllum inophyllum, locally called "Tamanu oil" in French Polynesia, was traditionally used for wound healing and to cure various skin problems and ailments. The skin-active effect of "Tamanu oil emulsion" was investigated on human skin cells (keratinocytes and dermal fibroblasts) and showed cell proliferation, glycosaminoglycan and collagen production, and wound healing activity. Transcriptomic analysis of the treated cells revealed gene expression modulation including genes involved in the metabolic process implied in O-glycan biosynthesis, cell adhesion, and cell proliferation. The presence of neoflavonoids as bioactive constituents in Tamanu oil emulsion may contribute to these biological activities. Altogether, consistent data related to targeted histological and cellular functions brought new highlights on the mechanisms involved in these biological processes induced by Tamanu oil effects in skin cells.
ISSN: 0032-0943

hal-01592246
https://hal.archives-ouvertes.fr/hal-01592246
DOI : 10.1055/s-0042-108205

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : Characterizing the trophic relationships between large herbivores and the outstanding plant diversity in rainforest is a major challenge because of their elusiveness. This is crucial to understand the role of these herbivores in the functioning of the rainforest ecosystems. We tested a non-invasive approach based on the high-throughput sequencing of environmental samples using small plant plastid sequences (the trnL P6 loop) and ribosomal ITS1 primers, referred to as DNA metabarcoding, to investigate the diet of the largest neotropical herbivore, the lowland tapir. Sequencing was performed on plant DNA extracted from tapir faeces collected at the Nouragues station, a protected area of French Guiana. In spite of a limited sampling, our approach reliably provided information about the lowland tapir's diet at this site. Indeed, 95.1% and 74.4% of the plant families and genera identified thanks to the trnL P6 loop, respectively, matched with taxa already known to be consumed by tapirs. With this approach we were able to show that two families and eight new genera are also consumed by the lowland tapir. The taxonomic resolution of this method is limited to the plant family and genera. Complementary barcodes, such as a small portion of ITS1, can be used to efficiently narrow identifications down to the species in some problematic families. We will discuss the remaining limitations of this approach and how useful it is at this stage to unravel the diet of elusive rainforest herbivores and better understand their role as engineers of the ecosystem.
ISSN: 1932-6203

hal-01190578
https://hal.archives-ouvertes.fr/hal-01190578
PRODINRA : 209109
PUBMED : 23560107
DOI : 10.1371/journal.pone.0060799

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Adverse pregnancy outcomes entail a large health burden for the mother and offspring; a part of it might be avoided by better understanding the role of environmental factors in their etiology. Our aims were to review the assessment tools to characterize fecundity troubles and pregnancy-related outcomes in human populations and their sensitivity to environmental factors. For each outcome, we reviewed the possible study designs, main sources of bias, and their suggested cures. In terms of study design, for most pregnancy outcomes, cohorts with recruitment early during or even before pregnancy allow efficient characterization of pregnancy-related events, time-varying confounders, and in utero exposures that may impact birth outcomes and child health. Studies on congenital anomalies require specific designs, assessment of anomalies in medical pregnancy terminations, and, for congenital anomalies diagnosed postnatally, follow-up during several months after birth. Statistical analyses should take into account environmental exposures during the relevant time windows; survival models are an appropriate approach for fecundity, fetal loss, and gestational duration/preterm delivery. Analysis of gestational duration could distinguish pregnancies according to delivery induction (and possibly pregnancy-related conditions). In conclusion, careful design and analysis are required to better characterize environmental effects on human reproduction.
ISSN: 0193-936X

hal-01002724
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01002724
DOI : 10.1093/epirev/mxt011
PUBMED : 24363355

Éditeur(s) : HAL CCSD
Résumé : International audience
The Chromosome-Centric Human Proteome Project (C-HPP) aims to identify "missing" proteins in the neXtProt knowledgebase. We present an in-depth proteomics analysis of the human sperm proteome to identify testis-enriched missing proteins. Using protein extraction procedures and LC-MS/MS analysis, we detected 235 proteins (PE2-PE4) for which no previous evidence of protein expression was annotated. Through LC-MS/MS and LC-PRM analysis, data mining, and immunohistochemistry, we confirmed the expression of 206 missing proteins (PE2-PE4) in line with current HPP guidelines (version 2.0). Parallel reaction monitoring acquisition and sythetic heavy labeled peptides targeted 36 ≪one-hit wonder≫ candidates selected based on prior peptide spectrum match assessment. 24 were validated with additional predicted and specifically targeted peptides. Evidence was found for 16 more missing proteins using immunohistochemistry on human testis sections. The expression pattern for some of these proteins was specific to the testis, and they could possibly be valuable markers with fertility assessment applications. Strong evidence was also found of four "uncertain" proteins (PE5); their status should be re-examined. We show how using a range of sample preparation techniques combined with MS-based analysis, expert knowledge, and complementary antibody-based techniques can produce data of interest to the community. All MS/MS data are available via ProteomeXchange under identifier PXD003947. In addition to contributing to the C-HPP, we hope these data will stimulate continued exploration of the sperm proteome. © 2016 American Chemical Society.
Journal of Proteome Research

hal-01406074
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01406074
DOI : 10.1021/acs.jproteome.6b00400
PUBMED : 27444420