Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
We report the development of the ReproGenomics Viewer (RGV), a multi-and cross-species working environment for the visualization, mining and comparison of published omics data sets for the reproductive science community. The system currently embeds 15 published data sets related to gametogenesis from nine model organisms. Data sets have been curated and conveniently organized into broad categories including biological topics, technologies, species and publications. RGV's modular design for both organisms and genomic tools enables users to upload and compare their data with that from the data sets embedded in the system in a cross-species manner. The RGV is freely available at http://rgv.genouest.org.
ISSN: 0305-1048

hal-01146120
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146120
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146120/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146120/file/nar.gkv345.full.pdf
PUBMED : 25883147

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Mantle-derived xenoliths hosted by melilitite lavas from In Teria (Ahaggar, SE Algeria) include garnet and spinel peridotites, pyroxenite and phlogopite megacrysts. The spinel and garnet peridotites record an early deformation event, which formed porphyroclastic microstructures and olivine crystal preferred orientations, followed by static infiltration of hydrous alkaline melts. This metasomatic stage (stage 1) is characterized by the crystallization of phlogopite in the garnet and spinel peridotites, amphibole in the spinel peridotites and clinopyroxene in the garnet peridotite, which record chemical equilibration with an alkaline silicate melt. These early events were largely overprinted by carbonatitic metasomatism (stage 2), which is observed only in the spinel peridotites. Spinel peridotite major and trace element compositions, as well as the compositions of newly formed minerals, are characteristic of interaction with carbonate melt, associated with strong enrichment in incompatible trace elements in clinopyroxene. This second stage was followed by crystallization of pyroxenites (stage 3) in vein conduits, probably segregated from alkaline melts. We propose a scenario in which the different metasomatic imprints record successive stages of interaction between lithospheric mantle and sublithospheric melts throughout the Cenozoic. In Sr–Nd isotope space, the host melilitites and several xenoliths are clustered and plot close to the HIMU mantle end-member. However, some peridotite xenoliths are shifted towards more radiogenic 87Sr/86Sr values. In 207Pb/204Pb–206Pb/204Pb and 208Pb/204Pb–06Pb/204Pb space the In Teria samples define a relatively large domain characterized by high 206Pb/204Pb and 208Pb/204Pb, consistent with a contribution of an HIMU component, considered to represent a sublithospheric signature. The highest 87Sr/86Sr values are comparable with those ascribed to the EM1 mantle end-member, representing the signature of the lower continental lithosphere, and are probably inherited from the pre-metasomatic lithospheric mantle beneath In Teria. Numerical modelling of porous percolation of melt of sublithospheric origin through an EM1-like lithospheric mantle protolith reproduces the In Teria peridotite compositions, using moderately sub-chondritic Sr/Nd values for the peridotite (e.g. In Teria garnet peridotite) and moderately super-chondritic Sr/Nd values in the melt (approximately ocean island basalt values). A few spinel peridotites require a component characterized by a 143Nd/144Nd signature higher than both the EM1 end-member and the local Ahaggar basalts; the 208Pb/204Pb compositions of several samples point to a component with a depleted mid-ocean ridge basalt (MORB) mantle (DMM) signature. Thus the lithospheric mantle beneath In Teria probably did not have a uniform EM1 signature before the onset of metasomatism; it included a DMM peridotite component as well as some peridotites with elevated 143Nd/144Nd values recording long-term LREE depletion.
ISSN: 0022-3530

hal-01356781
https://hal.archives-ouvertes.fr/hal-01356781
DOI : 10.1093/petrology/egw009

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
ISSN: 0305-7453

hal-01470808
https://hal.archives-ouvertes.fr/hal-01470808
DOI : 10.1093/jac/dkw352
PUBMED : 27609051

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
To improve earthquake location, we create a 3-D a priori P-wave velocity model (3-DVM) that approximates the large velocity variations of the Ecuadorian subduction system. The 3-DVM is constructed from the integration of geophysical and geological data that depend on the structural geometry and velocity properties of the crust and the upper mantle. In addition, specific station selection is carried out to compensate for the high station density on the Andean Chain. 3-D synthetic experiments are then designed to evaluate the network capacity to recover the event position using only P arrivals and the MAXI technique. Three synthetic earthquake location experiments are proposed: (1) noise-free and (2) noisy arrivals used in the 3-DVM, and (3) noise-free arrivals used in a 1-DVM. Synthetic results indicate that, under the best conditions (exact arrival data set and 3-DVM), the spatiotemporal configuration of the Ecuadorian network can accurately locate 70 per cent of events in the frontal part of the subduction zone (average azimuthal gap is 289° ± 44°). Noisy P arrivals (up to ± 0.3 s) can accurately located 50 per cent of earthquakes. Processing earthquake location within a 1-DVM almost never allows accurate hypocentre position for offshore earthquakes (15 per cent), which highlights the role of using a 3-DVM in subduction zone. For the application to real data, the seismicity distribution from the 3-D-MAXI catalogue is also compared to the determinations obtained in a 1-D-layered VM. In addition to good-quality location uncertainties, the clustering and the depth distribution confirm the 3-D-MAXI catalogue reliability. The pattern of the seismicity distribution (a 13 yr record during the inter-seismic period of the seismic cycle) is compared to the pattern of rupture zone and asperity of the Mw = 7.9 1942 and the Mw = 7.7 1958 events (the Mw = 8.8 1906 asperity patch is not defined). We observe that the nucleation of 1942, 1958 and 1906 events coincides with areas of positive Simple Bouguer anomalies and areas where marine terraces are still preserved on the coastal morphology. From north to south: (1) the 1958 rupture zone is almost aseismic and is attributed to a zone of high coupling; (2) south of the Galera alignment (perpendicular to the trench), the 1942 rupture zone presents moderate seismicity, deeper on the seismogenic interplate zone, and abutting on the Jama cluster (to the south). This cluster is facing the Cabo Pasado cap and positive Bouguer anomalies on the overriding margin. We suspect that this cluster reflects a zone of local asperity (partial coupling). South of the Jama cluster, the spherical aseismic zone in the Bahia area is interpreted as having a low seismic coupling (steady creep motion or slow slip events). We suspect that the site that generated the three M > 7 events (1896, 1956 and 1998) correspond to a small patch of strong coupling. To the south, in the Manta-Puerto Lopez zone, the seismicity is mainly organized in earthquake swarms (1998, 2002, 2005). Although slow slip events have been observed in the area (Vallée et al. submitted), we infer from the coastline shape, the marine terraces and the high positive Bouguer anomalies that the seismicity here might reveal a significant amount of seismic coupling.
ISSN: 0956-540X

hal-00873478
https://hal.archives-ouvertes.fr/hal-00873478
DOI : 10.1093/gji/ggs083

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The mantle above a subducting slab is the site of complex interactions between deformation, partial melting, fluid migration and magma transport. To constrain these interactions and their effects on olivine deformation, we analyze microstructures, crystal preferred orientations, and water contents of peridotite xenoliths entrained by andesites of the Avacha volcano, southern Kamchatka arc. These xenoliths are refractory spinel harzburgites that have coarse-grained microstructures with widely spaced subgrain boundaries and sinuous grain boundaries in olivine, consistent with deformation by dislocation creep under low deviatoric stress (< 13 MPa) and with a significant contribution from diffusional processes. Analysis of crystal preferred orientations (CPO) indicates dominant activation of high-temperature, low-stress {0kl}[100] slip systems in olivine and of(100)[001] in orthopyroxene. In most samples, coarse opx crystals, elongated parallel to the lineation, enclose small olivine grains in crystallographic continuity with neighbouring crystals, indicating crystallization of orthopyroxene at the expense of olivine as a result of reactive percolation of Si-rich fluids coeval with the high-temperature deformation. Secondary crystallization of interstitial orthopyroxene led locally to development of opx-rich lenses parallel to the foliation, characterized by a decrease in olivine grain size and dispersion of the olivine CPO without changing the dominant slip systems. Half of the samples also show acicular orthopyroxene aggregates with which is associated a fine-grained matrix composed of rounded strain-free olivine, orthopyroxene, spinel, and rare amphibole crystals. This matrix occurs pervasively along grain boundaries or forms millimeter-scale irregular lenses and anastomosing veinlets that crosscut the coarse crystals and their ductile deformation structures. Both acicular orthopyroxene and the fine-grained matrix are interpreted as resulting from reactive transport of H2O-rich fluids under static conditions, probably in the lithospheric mantle. Infrared analyses show that olivine contains 1-8 center dot 6 ppm by weight of water. These low water contents are similar to those observed in spinel peridotites from other subduction zones and probably record both the low solubility of water in olivine at low pressure and dehydration during exhumation of the xenoliths. Water contents in orthopyroxene are highly variable (25-506 ppm H2O), probably recording spatially heterogeneous interaction with fluids or melts and compositional disequilibrium in the studied samples. Change in the dominant percolation mechanism from porous flow to fracturing suggests cooling, consistent with the low temperatures estimated from pyroxene thermometry (< 800-900 degrees C). The Avacha xenoliths therefore record pervasive deformation of a region of the mantle under asthenospheric conditions, followed by its accretion to the base of the lithosphere, probably as a result of cooling of the mantle wedge. Percolation of Si-rich fluids or hydrous melts is recorded at all stages; this probably enhanced diffusion and lowered deviatoric stresses during ductile deformation, but did not change the dominant slip direction in olivine from [100] to [001].
ISSN: 0022-3530

hal-00456053
https://hal.archives-ouvertes.fr/hal-00456053
DOI : 10.1093/petrology/egp085

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Defining homologous genes is important in many evolutionary studies but raises obvious issues. Some of these issues are conceptual and stem from our assumptions of how a gene evolves, others are practical, and depend on the algorithmic decisions implemented in existing software. Therefore, to make progress in the study of homology, both ontological and epistemological questions must be considered. In particular, defining homologous genes cannot be solely addressed under the classic assumptions of strong tree thinking, according to which genes evolve in a strictly tree-like fashion of vertical descent and divergence and the problems of homology detection are primarily methodological. Gene homology could also be considered under a different perspective where genes evolve as ``public goods,'' subjected to various introgressive processes. In this latter case, defining homologous genes becomes a matter of designing models suited to the actual complexity of the data and how such complexity arises, rather than trying to fit genetic data to some a priori tree-like evolutionary model, a practice that inevitably results in the loss of much information. Here we show how important aspects of the problems raised by homology detection methods can be overcome when even more fundamental roots of these problems are addressed by analyzing public goods thinking evolutionary processes through which genes have frequently originated. This kind of thinking acknowledges distinct types of homologs, characterized by distinct patterns, in phylogenetic and nonphylogenetic unrooted or multirooted networks. In addition, we define `` family resemblances'' to include genes that are related through intermediate relatives, thereby placing notions of homology in the broader context of evolutionary relationships. We conclude by presenting some payoffs of adopting such a pluralistic account of homology and family relationship, which expands the scope of evolutionary analyses beyond the traditional, yet relatively narrow focus allowed by a strong tree-thinking view on gene evolution.
ISSN: 0737-4038

hal-01544794
https://hal.archives-ouvertes.fr/hal-01544794
DOI : 10.1093/molbev/mst228

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Island arc picrites and boninites are magnesian magmatic rocks believed to be generated by high degrees of melting of depleted mantle sources fluxed by subduction-derived, volatile-rich components. These magmas can be probes of both the mantle wedge protoliths and subduction components, but are rare among other, usually more evolved, types of arc lavas. Furthermore, many arc picrites and boninites show evidence for late-stage differentiation prior to or during eruption, masking their primary, mantle-derived geochemical signatures. We report textural and chemical data on spinel-hosted melt inclusions of mantle origin in amphibole-bearing websterite veins cross-cutting spinel harzburgite xenoliths from the active andesitic Avacha volcano (south Kamchatka, Russia). The data are used to constrain the composition and origin of melts that formed the websterite veins in the sub-arc lithospheric mantle. The melt inclusions typically contain euhedral orthopyroxene and clinopyroxene and occasionally minor amphibole in silicate glass. The melt inclusions were homogenized using heating stages and gas-mixing furnaces. The homogenized glasses range from subalkaline primitive silica-rich picrite and high-Ca boninite (>15 wt % MgO, 48–54 wt % SiO2) to rhyolite. High-Ca boninite glasses have moderate volatile and low heavy rare earth element contents and elevated Cs, Rb, Ba, U, Sr, and Li abundances, with extremely high U/Th. In turn, the glasses display no negative spikes in the high field strength elements Nb, Ta, Zr, Hf, and Ti. We show that the silica-rich picrite and high-Ca boninite liquids in this study formed by high degrees of melting (>25%), at volatile under-saturation, of hybrid melt-depleted but silica-rich mantle sources at ≥1·5 GPa. The hybrid sources formed in two stages: first, by extraction of ∼15% melt from the convecting mantle to form a refractory protolith, which was subsequently enriched in silica via interaction with subduction-derived components prior to or during remelting in the mantle wedge. The subduction-derived components were enriched in fluid-mobile elements and probably oxidized. Overall, our results suggest that silica-rich picrites and high-Ca boninites can be primary melts in mature subduction zones and differentiate within the mantle wedge and the deep arc crust to form more evolved andesite magmas.
ISSN: 0022-3530

hal-01553676
https://hal.archives-ouvertes.fr/hal-01553676
DOI : 10.1093/petrology/egw066

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Three kilns and a collection of baked bricks from Italian archaeological sites have been studied for archaeointensity determination using the Thellier method as modified by Coe. All sites are dated based on archaeological information and their ages range from 500 to 800 AD and 1500 to 1700 AD. Rock magnetic studies identify magnetite, Ti- magnetite and hematite as the main magnetic minerals, and magnetic susceptibility versus temperature shows a good thermal stability of the samples. The intensity results have been corrected for anisotropy of the thermoremanent magnetization and cooling rate effects. The new data together with 136 previously published results are used to estimate the variation of the Earth's magnetic field over the past three millennia. The time distribution of the Italian absolute intensity data is irregular with the majority of determinations concentrated during the last four centuries, while older periods are very poorly covered. Most of the data come from volcanic rocks and show significant discrepancies. All data have been compared with archaeointensity results from Europe and regional and global models predictions. This work indicates the need to obtain more high quality archaeointensity results, in particular for the periods older than 200 BC and between 200 and 1000 AD, in order to determine a robust Italian intensity secular variation curve that, in combination with directional data, could be used for archaeomagnetic dating.
ISSN: 0956-540X

hal-00452451
https://hal.archives-ouvertes.fr/hal-00452451
DOI : 10.1111/j.1365-246X.2009.04455.x

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : We present whole-rock major- and trace-element and Nd–Sr–Pb radiogenic isotope data for Cretaceous igneous suites from eastern Cuba. These rocks are related to the Greater Antilles paleo-island arc magmatism and have three different igneous styles. Group 1 consists of tholeiitic basalts and rare basaltic andesites that have normal mid-ocean ridge basalt (N-MORB)-like compositions similar to those found in back-arc basin basalts (TiO2 = 1·2–2·9 wt%; La/Yb(N) = 0·7–0·9, Th/Nb = 0·06–0·08, and initial 208Pb/ 204Pb = 37·65–37·74). Group 2 comprises basaltic and rare basaltic andesitic subvolcanic dykes with major- and trace-element and isotopic compositions similar to those of island arc tholeiites (TiO2 = 0·7–1·4 wt%; La/Yb(N) = 0·6–0·9, Th/Nb = 0·06–0·68, and initial 208Pb/ 204Pb = 37·74–38·25). Group 3 is composed of low-Ti (TiO2 = 0·3–0·9 wt%) calcalkaline igneous rocks that have an unambiguous subduction-related character (La/Yb(N) = 1·1–5·0, Th/Nb = 0·35–1·55, and initial 208Pb/ 204Pb = 37·94–38·39). The parental magmas of the three groups formed by variable melting degrees (< 5–25%) of spinel lherzolite, with more depleted mantle sources for Groups 2 and 3 than Group 1. The trace-element and radiogenic isotope compositions of primitive Group 3 samples are strongly bimodal. One subgroup of samples is characterized by low Ta/Yb (0·02–0·03) and Th/La (0·10–0·13), slightly subchondritic Nb/Ta (13·3–17·3), and relatively high initial 206Pb/204Pb (18·57–18·62) and {varepsilon}Nd (7·6–9·4). The remaining primitive Group 3 samples have higher Ta/Yb (0·06–0·11) and Th/La (0·24–0·32), and highly subchondritic Nb/Ta (7·6–9·1), coupled with lower initial 206Pb/204Pb (18·24–18·29) and {varepsilon}Nd (3·4–5·5). These signatures were induced by two distinct slab components that mainly reflect the contributions of Cretaceous Atlantic marine and North American continental sediments, respectively. Nb/Ta in the first subgroup was influenced by melting of rutile-bearing subducted crust, whereas in the second it was inherited from recycled continental sediments. The involvement of Atlantic and North American sediments in Cuban Cretaceous magmatism indicates that the Proto-Caribbean (North American-Proto Atlantic) lithosphere subducted beneath the Greater Antilles arc during the Late Cretaceous (pre-Campanian), consistent with geotectonic models involving onset of SW-dipping subduction beneath the Greater Antilles paleo-arc during the Aptian. The variable mantle source depletion and magnitude of the subduction component probably reflect different settings across the arc, from the arc front to a back-arc spreading ridge.
ISSN: 0022-3530

hal-00406373
https://hal.archives-ouvertes.fr/hal-00406373
DOI : 10.1093/petrology/egm040

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Some epidemiological investigations have revealed that frequent consumption of well-done cooked meats and tobacco smoking are risk factors for breast cancer in women. 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) is a heterocyclic aromatic amine that is formed in well-done cooked meat, and 4-aminobiphenyl (4-ABP) is an aromatic amine that arises in tobacco smoke and occurs as a contaminant in the atmosphere. Both compounds are rodent mammary carcinogens, and putative DNA adducts of PhIP and 4-ABP have been frequently detected, by immunohistochemistry (IHC) or (32)P-post-labeling methods, in mammary tissue of USA women. Because of these findings, PhIP and 4-ABP have been implicated as causal agents of human breast cancer. However, the biomarker data are controversial: both IHC and (32)P-post-labeling are non-selective screening methods and fail to provide confirmatory spectral data. Consequently, the identities of the lesions are equivocal. We employed a specific and sensitive liquid chromatography/mass spectrometry (MS) method, to screen tumor-adjacent normal mammary tissue for DNA adducts of PhIP and 4-ABP. Only 1 of 70 biopsy samples obtained from Minneapolis, Minnesota breast cancer patients contained a PhIP-DNA adduct. The level was three adducts per 10(9) nucleotides, a level that is 100-fold lower than the mean level of PhIP adducts reported by IHC or (32)P-post-labeling methods. The occurrence of 4-ABP-DNA adducts was nil in those same breast tissues. Our findings, derived from a specific mass spectrometry method, signify that PhIP and 4-ABP are not major DNA-damaging agents in mammary tissue of USA women and raise questions about the roles of these chemicals in breast cancer.
ISSN: 0143-3334

hal-00682453
https://hal.archives-ouvertes.fr/hal-00682453
DOI : 10.1093/carcin/bgr252
PUBMED : 22072616

Éditeur(s) : HAL CCSD Oxford University Press (OUP): Policy F
Résumé : JEL classification: C40, C60, L60, R12
We propose new methods for evaluating the spatial distribution of firms. To assess whether firms are concentrated or dispersed, economists have tradi-tionally used indices that analyse the heterogeneity of a spatial structure at a single geographic level. We introduce distance-based methods, Besag's L function (derived from Ripley's K function) and Diggle and Chetwynd's D function to describe simultaneously spatial distribution at different geographical scales. Our empirical applications consider the distribution of French manufacturing firms in the Paris area and in France generally. For some geographic levels, results show significant concentration or dispersion of firms according to their sector of activity.
ISSN: 1468-2702

halshs-00372646
https://halshs.archives-ouvertes.fr/halshs-00372646

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
We investigate the deformation induced by water pressure variations in hydrologically active natural fractures, and recorded by tiltmeters and strainmeters. The deformation associated with a single fracture is derived using finite-element modelling (FEM). A range in fracture geometries is explored, first to highlight the sensitivity of each geometrical parameter to the deformation, and secondly to allow transfer to observation sites. Water level variations in the fracture are then derived from a hydrological model, driven by observed rainfall, and calibrated on fracture water flow measurements. The modelling results are explicitly applied to constrain the local hydrological contribution to observations with the 100-m-long hydrostatic tiltmeter installed at Sainte-Croix-aux-Mines (France). Our study shows that well-founded physical modelling of local hydrological effect allows a substantial correction of records in observatories.
ISSN: 0956-540X

hal-00708093
https://hal.archives-ouvertes.fr/hal-00708093
https://hal.archives-ouvertes.fr/hal-00708093/document
https://hal.archives-ouvertes.fr/hal-00708093/file/fracture_v72.pdf
BIBCODE : 2009GeoJI.178..667L

Éditeur(s) : HAL CCSD Oxford University Press (OUP): Policy F
Résumé : International audience
We discuss a property of distance-based measures that has not been addressed with regard to evaluating the geographic concentration of economic activities. The article focuses on the choice between a probability density function of point-pair distances or a cumulative function. We begin by introducing a new cumulative function, M, for evaluating the relative geographic concentration and the co-location of industries in a non-homogeneous spatial framework. Secondly, some rigorous comparisons are made with the leading probability density function of Duranton and Overman (2005), Kd. The merits of the simultaneous use of Kd and M is proved, underlining the complementary nature of the results they provide.
Journal of Economic Geography

hal-01094082
https://hal-agroparistech.archives-ouvertes.fr/hal-01094082
DOI : 10.1093/jeg/lbp056

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
ISSN: 0022-0957

hal-01080844
https://hal-agroparistech.archives-ouvertes.fr/hal-01080844
DOI : 10.1093/jxb/erm268

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Ocean loading effects cause 3-D displacements large enough to affect space geodesy measurements either at the subdiurnal periods or at longer time scales by the means of spurious signals. GPS measurements, in turn, could provide local improvements of the models in coastal areas if their ability to precisely monitor such rapid displacements is assessed. In this paper, we use 105 days of continuous GPS measurements collected in 2004 in the French Brittany and Cotentin region to investigate: (1) the precision achieved by the GPS analysis on measuring 3-D subdiurnal displacements and amplitude and phase of the tidal constituents, (2) the quality of the most recent ocean tide model FES2004 in such a complex coastal context. Indeed, in this area, tide amplitudes are among the largest in the world (up to 16 cm of loading displacements on the vertical component) and are believed to show strong shallow-water tides. From a state of the art GPS analysis using the scientific GAMIT software over 2-h sessions, we test two independent strategies for the realization of the reference frame. The position time series are then compared with the displacements predicted by the FES2004 model applied on an elastic Earth model. The two sets of results are consistent with each other at the same level of agreement than with the predicted displacements, namely 3–5 mm on the horizontal components, 10 mm on the vertical. This assesses the capability of this technique for measuring 3-D ocean tide loading deformation. We validate the FES2004 model in the Brittany area, even though it slightly (2–7 mm) underestimates the three components amplitudes. With a harmonic analysis of the observed position time series, we obtain nevertheless an agreement at a submillimetre level for the M2, N2, O1, Q1 tidal constituents and at a millimetre level for the K1 and S2 tidal constituents. Moreover, we can extract a significant M4 load signal at the 95 per cent confidence level from the GPS time series at the stations located in the Mont St Michel area. The detection of other shallow-water constituents would be helpful to understand the amplitude deficit between the FES2004 predicted and GPS observed displacements.
ISSN: 0956-540X

insu-00335909
https://hal-insu.archives-ouvertes.fr/insu-00335909
https://hal-insu.archives-ouvertes.fr/insu-00335909/document
https://hal-insu.archives-ouvertes.fr/insu-00335909/file/Vergnolle_GJI_08_revised.pdf
DOI : 10.1111/j.1365-246X.2008.03734.x

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
DNA sequencing technology is becoming more accessible to a variety of researchers as costs continue to decline. As researchers begin to sequence novel transcriptomes, most of these data sets lack a reference genome and will have to rely on de novo assemblers. Making comparisons across assemblies can be difficult: each program has its strengths and weaknesses, and no tool exists to comparatively evaluate these data sets. We developed software in R, called Sequence Comparative Analysis using Networks (SCAN), to perform statistical comparisons between distinct assemblies. SCAN uses a reference data set to identify the most accurate de novo assembly and the ``good'' transcripts in the user's data. We tested SCAN on three publicly available transcriptomes, each assembled using three assembly programs. Moreover, we sequenced the transcriptome of the oomycete Achlya hypogyna and compared de novo assemblies from Velvet, ABySS, and the CLC Genomics Workbench assembly algorithms. One thousand one hundred twenty-eight of the CLC transcripts were statistically similar to the reference, compared with 49 of the Velvet transcripts and 937 of the ABySS transcripts. SCAN's strength is providing statistical support for transcript assemblies in a biological context. However, SCAN is designed to compare distinct node sets in networks, therefore it can also easily be extended to perform statistical comparisons on any network graph regardless of what the nodes represent.
ISSN: 0737-4038

hal-01544800
https://hal.archives-ouvertes.fr/hal-01544800
DOI : 10.1093/molbev/mst087

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
OBJECTIVES: Invasive fungal disease (IFD) remains a major concern in patients with haematological conditions. We describe diagnoses, therapeutic management and outcomes in unselected consecutive patients from haematological facilities treated for suspected or documented IFD. METHODS: In this observational prospective study, children/adults with haematological conditions or haematopoietic stem cell transplantation (HSCT) were recruited upon start of non-prophylactic systemic antifungal treatment in 37 French haematological facilities (December 2007 to December 2008). IFD episodes were classified according to the 2008 EORTC/MSG criteria. RESULTS: The cohort included 419 patients (298 adults and 121 children): 88% haematological malignancies, 28% HSCT recipients and 68% neutropenic. Patients had 423 IFD episodes: 21% mycologically documented (59% probable/proven aspergillosis, 32% proven candidiasis and 9% probable/proven other IFD) and 20% classified as possible IFD. The remaining cases were assigned to two groups: febrile neutropenia (34%) and unclassified (25%), 9% of which were classified as possible/probable/proven IFD by day 7. Treatment was thus initiated early in 59% of patients; liposomal amphotericin B and caspofungin were the most common single-agent therapies. The 12 week mortality was 18% for probable/proven aspergillosis, 15% for proven candidiasis, 10% for probable/proven other IFD, 9% for possible IFD, 3% for febrile neutropenia and 12% for unclassified episodes (log rank P = 0.016); it was dependent on age, complete remission of underlying haematological disease and mechanical ventilation. CONCLUSIONS: In this comprehensive sample of haematological patients receiving antifungal treatment, we observe a widespread resort to early therapy and a low mortality rate, including in patients with probable or proven IFD.
ISSN: 0305-7453

hal-00874741
https://hal.archives-ouvertes.fr/hal-00874741
DOI : 10.1093/jac/dks266
PUBMED : 22850692

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
ISSN: 0035-9203

hal-00715418
https://hal.univ-antilles.fr/hal-00715418
PUBMED : 153022

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The interpretation of coseismic surface deformation measurements through inversion techniques is of major importance to understand the mechanical behaviour of a seismic fault. Dense geodetic data sets in the vicinity of the ruptured fault provide unique constraints on detailed fault geometry and slip distribution at depth, making them complementary to seismological data. Bam earthquake (Mw 6.6, 2003 December 26) induced surface deformation has been precisely mapped by Envisat ASAR interferometry and by subpixel correlation techniques applied to Spot-5 and ASAR amplitude images. These oblique and horizontal estimations of deformation have been completed with one levelling profile along the main road crossing the rupture from west to east. We process these data (separately and jointly) in a two-step inversion technique, within the elastic half-space theory framework. Our objective is to determine the dislocation model at depth that satisfies simultaneously all the geodetic constraints. Also, we estimate the relative contribution of each geodetic data set to this inversion process.We first use a stochastic direct approach called neighbourhood algorithm in order to estimate the average characteristics of the rupture, and their relative uncertainty. Constraining in this way the geometry of the ruptured fault, we then linearize the inverse problem and compute the slip distribution on the fault using a standard weighted least-square technique, assuming the solution is smooth to some degree. At each step, we discuss the optimal models, their stability as well as the relative influence of each data set on the derived models parameters. Our preferred model reveals a shallow dislocation on a quasi-vertical fault, slightly dipping towards east. The slip vector has a strike-slip component as high as 2 m, while the dip-slip component seems negligible.However, the estimation of the resolution matrices emphasizes the fact that the details of deep fault slip distribution remain out of the scope of this ill-conditioned inverse problem. Yet, our preferred model suggests a main dislocation limited at depth between 1 and 6 km. By contrast, the aftershocks observed in the months following the earthquake are located just beneath the estimated main shock.
ISSN: 0956-540X

hal-00314173
https://hal.archives-ouvertes.fr/hal-00314173
https://hal.archives-ouvertes.fr/hal-00314173/document
https://hal.archives-ouvertes.fr/hal-00314173/file/GJI-2007-169-849-briole.pdf
DOI : 10.1111/j.1365-246X.2007.03358.x

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The nature of factors governing the tempo and mode of protein evolution is a fundamental issue in evolutionary biology. Specifically, whether or not interactions between different sites, or epistasis, are important in directing the course of evolution became one of the central questions. Several recent reports have scrutinized patterns of long-term protein evolution claiming them to be compatible only with an epistatic fitness landscape. However, these claims have not yet been substantiated with a formal model of protein evolution. Here, we formulate a simple covarion-like model of protein evolution focusing on the rate at which the fitness impact of amino acids at a site changes with time. We then apply the model to the data on convergent and divergent protein evolution to test whether or not the incorporation of epistatic interactions is necessary to explain the data. We find that convergent evolution cannot be explained without the incorporation of epistasis and the rate at which an amino acid state switches from being acceptable at a site to being deleterious is faster than the rate of amino acid substitution. Specifically, for proteins that have persisted in modern prokaryotic organisms since the last universal common ancestor for one amino acid substitution approximately ten amino acid states switch from being accessible to being deleterious, or vice versa. Thus, molecular evolution can only be perceived in the context of rapid turnover of which amino acids are available for evolution.
ISSN: 0737-4038

hal-01544755
https://hal.archives-ouvertes.fr/hal-01544755
DOI : 10.1093/molbev/msu318