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
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
We present a new interpretation of anisotropy of magnetic susceptibility (AMS) fabrics in basaltic lava flows based on the detailed study of magnetic mineralogy and silicate crystallographic fabric of a Quaternary lava flow from the French Massif Central (La Palisse). We consider the model of AMS fabric imbrication between magnetic foliation and flow surface, as initially proposed for dykes. At the two sampling sites, the concordance between the flow direction deduced from the AMS foliation and that deduced from field observations indicates that the imbrication model could apply to the lava flows. However, the flow senses inferred fromAMSare systematically opposed between the two sampling sites suggesting permutations between K1 and K3 AMS axes, a configuration referred to as inverse fabric. Electron backscatter diffraction (EBSD) measurements show strong lattice-preferred orientations (LPO) for plagioclase, especially the (010) plagioclase plane, which tends to be parallel to the flow. Clinopyroxene LPO remains less marked than plagioclase LPO, whereas titanomagnetite does not display a significant LPO. Comparison between magnetic and crystallographic fabrics suggests that the AMS fabric of the lava flow results from the distribution of titanomagnetite grains, which is in turn controlled by the fabric of the silicate framework. Magnetic hysteresis parameters and anisotropy of remanent magnetization (ARM) measurements exclude a significant contribution from single-domain grains, often called upon to explain inverse magnetic fabrics. The origin of the observed inverse magnetic fabric may relate to the dip of the palaeosurface, which is the only remarkable difference between the two sampling sites. AMS appears as a good tool to determine the direction of basaltic lava flows and coupling with local crystallographic fabric data provides a valuable control of relationships between magnetic fabrics and flow and thus contributes to better constrain the AMS signature of lava flows.
ISSN: 0956-540X

hal-00903561
https://hal.archives-ouvertes.fr/hal-00903561
https://hal.archives-ouvertes.fr/hal-00903561/document
https://hal.archives-ouvertes.fr/hal-00903561/file/TB-GJI-193-2-Orig.pdf
DOI : 10.1093/gji/ggs115

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The nature and extent of the regional lithosphere-asthenosphere interaction beneath Ireland and Britain remains unclear. Although it has been established that ancient Caledonian signatures pervade the lithosphere, tertiary structure related to the Iceland plume has been inferred to dominate the asthenosphere. To address this apparent contradiction in the literature, we image the 3-D lithospheric and deeper upper-mantle structure beneath Ireland via non-linear, iterative joint teleseismic-gravity inversion using data from the ISLE (Irish Seismic Lithospheric Experiment), ISUME (Irish Seismic Upper Mantle Experiment) and GRACE (Gravity Recovery and Climate Experiment) experiments. The inversion combines teleseismic relative arrival time residuals with the GRACE long wavelength satellite derived gravity anomaly by assuming a depth-dependent quasilinear velocity-density relationship. We argue that anomalies imaged at lithospheric depths probably reflect compositional contrasts, either due to terrane accretion associated with Iapetus Ocean closure, frozen decompressional melt that was generated by plate stretching during the opening of the north Atlantic Ocean, frozen Iceland plume related magmatic intrusions, or a combination thereof. The continuation of the anomalous structure across the lithosphere-asthenosphere boundary is interpreted as possibly reflecting sub-lithospheric small-scale convection initiated by the lithospheric compositional contrasts. Our hypothesis thus reconciles the disparity which exists between lithospheric and asthenospheric structure beneath this region of the north Atlantic rifted margin.
ISSN: 0956-540X

hal-00617815
https://hal.archives-ouvertes.fr/hal-00617815
DOI : 10.1111/j.1365-246X.2011.04921.x

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 : The Fars arc accommodates the oblique convergence between the Arabic plate and the Iran block. Many geological observations suggest block rotations from regional to local scales. We present palaeomagnetic investigations in the Fars arc and its eastern termination, the Zagros-Makran syntaxis. Sixty-four sites have been sampled covering the Palaeocene Pabdeh Fm. to Mio-Pliocene Agha-Jhari Fm., the latest being the most sampled formation. We document pre-tilting components in all formations. However, coarse fractions of Agha-Jhari clastics formation retain a post-tilting remagnetization. As a whole, block rotations rarely exceed 20 degrees. In the western Fars arc, clockwise and counter-clockwise rotations of small amplitudes are consistent with the torsions observed near the strike slip Kazerun and Mangarak faults. In the Zagros Makran syntaxis, counter-clockwise and clockwise rotations are observed, respectively, in the western and eastern part. This pattern is consistent with an amplification of the shape of the syntaxis. Between Zagros and Makran, palaeomagnetic data support that the present-day arcuate shape of the arc is secondary. We assume that most of the block rotations took place during the Plio-Pleistocene, during a blocking stage of the Zagros-Makran syntaxis. We emphasize the role of Oman Peninsula which plays as an indenter for the propagation of the Fars thrust belt.
ISSN: 0956-540X

hal-00411142
https://hal.archives-ouvertes.fr/hal-00411142
DOI : 10.1111/j.1365-246X.2008.03732.x

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Detailed structural and petrological mapping in the Beni Bousera peridotite (Rif Belt, northern Morocco) shows that this orogenic peridotite massif is composed of four tectono-metamorphic domains with consistent kinematics, marked by a pervasive, shallowly dipping foliation with a NW-SE stretching lineation that progressively rotates towards a NNE-SSW orientation in the lowermost part of the massif. From top to bottom, these domains are garnet-spinel mylonites, Ariègite subfacies fine-grained porphyroclastic spinel peridotites, Ariègite-Seiland subfacies porphyroclastic, and Seiland subfacies coarse-porphyroclastic to coarse-granular spinel peridotites. Microstructures and crystal preferred orientations point to deformation dominantly by dislocation creep in all domains, but the continuous increase in average olivine grain size indicates decreasing plastic work rates from top to bottom. This evolution in deformation conditions is consistent with the change in synkinematic pressure and temperature conditions, from 900°C at 2*0 GPa in garnet-spinel mylonites to 1150°C at 1*8 GPa in the Seiland domain. A pervasive diffuse dunitic-websteritic layering subparallel to the foliation suggests deformation in the presence of melt in the Seiland domain. Gravitational instabilities owing to local melt accumulation may account for <200 m wide areas exhibiting a vertical lineation in this domain. To account for the consistent kinematics and the tectono-metamorphic evolution, which implies a temperature gradient of c. 125°C km−1 preserved across the Beni Bousera massif, we propose that the entire massif records the functioning of a low-angle shear zone, a few kilometres wide, which accommodated exhumation of the base of the lithosphere from ∼90 to ∼60 km depth. Partial melting in the Seiland domain may be explained by fast decompression of the footwall, without the need for exotic heat sources. Moreover, if the present-day orientation of the shear zone is similar to that when it was active in the mantle, the stretching lineations at high angle to the metamorphic gradient imply that shearing parallel to the trend of the belt accompanied thinning; that is, a transtensional deformation of the margin.
ISSN: 0022-3530

hal-00950056
https://hal.archives-ouvertes.fr/hal-00950056
DOI : 10.1093/petrology/egt067

Éditeur(s) : HAL CCSD Oxford University Press
Résumé : International audience
Chronic rhinosinusitis (CRS) rank second at chronic inflammatory diseases in industrialized countries and are an important public health concern. Diagnosis relies on a set of arguments including clinical signs, imaging, histopathologic and mycological analyses of sinus specimens, collected during nasal endoscopy. The sensitivity of fungal cultures is reported to be poor, even when direct examination is positive, thus the epidemiology of fungal chronic sinusitis is ill-known. This study evaluated the sensitivity of molecular diagnosis in 70 consecutive samples (61 patients with CRS) analysed at the University Hospital of Rennes during a 3-year period. DNA detection was performed using a conventional PCR method targeting the ITS1/ITS2 sequence and the resulting amplification products were sequenced. Fungal CRS was proven in 42 patients (69%), of which only 20 (48%) had a positive culture. 37/42 (88%) patients were diagnosed with a fungus ball, 3 with allergic fungal CRS and 2 with undetermined fungal CRS. PCR was positive in all 42 cases and direct sequencing allowed to identify fungi in all cases but one, and detected multiple infection in 3. Aspergillus fumigatus was present in 69% of patients; Cladosporium cladosporoides in 9.5%, Scedosporium sp., A. nidulans and A. flavus in 7% each. In 2/19 patients with negative direct examination, sequencing analysis revealed the presence of Capnobotryella sp. and C. cladosporoides, in clinical settings compatible with fungal sinusitis. In conclusion, ITS1/ITS2 PCR had a twice better sensitivity than culture, and combined sequencing provides accurate epidemiological data on fungal CRS.
ISSN: 1369-3786

hal-01383632
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01383632
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01383632/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01383632/file/Contribution%20of%20molecular%20tools%20for%20the%20diagnosis.pdf
DOI : 10.1093/mmy/myw041

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)
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)
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
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
OBJECTIVES: Tracheobronchial stenosis (TBS) is noted in 12-23% of patients with granulomatosis with polyangiitis (GPA), and includes subglottic stenosis and bronchial stenosis. We aimed to analyse the endoscopic management of TBS in GPA and to identify factors associated with the efficacy of endoscopic interventions. METHODS: We conducted a French nationwide retrospective study that included 47 patients with GPA-related TBS. RESULTS: Compared with patients without TBS, those with TBS were younger, more frequently female and had less frequent kidney, ocular and gastrointestinal involvement and mononeuritis multiplex. Endoscopic procedures included 137 tracheal and 50 bronchial interventions, mainly endoscopic dilatation, local steroid injection and conservative laser surgery, and less frequently stenting. After the first endoscopic procedure, the cumulative incidence of endoscopic treatment failure was 49% at 1 year, 70% at 2 years and 80% at 5 years. Factors significantly associated with a higher cumulative incidence of treatment failure were a shorter time from GPA diagnosis to endoscopic procedure [hazard ratio (HR) 1.08 (95% CI 1.01, 1.14); P = 0.01] and a bronchial stenosis [HR 1.96 (95% CI 1.28, 3.00); P = 0.002]. A prednisone dose ≥30 mg/day at the time of the procedure was associated with a lower cumulative incidence of treatment failure [HR 0.53 (95% CI 0.31, 0.89); P = 0.02]. CONCLUSION: TBS represents severe and refractory manifestations with a high rate of restenosis. High-dose systemic CSs at the time of the procedure and increased time from GPA diagnosis to bronchoscopic intervention are associated with a better event-free survival. In contrast, bronchial stenoses are associated with a higher rate of restenosis than subglottic stenosis.
ISSN: 1462-0324

hal-01155105
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01155105
DOI : 10.1093/rheumatology/kev129
PUBMED : 26001634

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

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The Ryukyu subduction is known to generate very few earthquakes in its central segment contrarily to its two extremities. We focus in this study on the southernmost part of the Ryukyu subduction zone offshore east Taiwan. Our first task was to build a homogeneous earthquake catalogue for the period 1900–2007. The new catalogue provides homogenized M′W magnitudes and shows that several M′W≥ 7.0 earthquakes occurred offshore Hualien and Suao cities. We then focused on the 1920 June 5 earthquake (reported surface wave magnitude 8.1) previously located beneath the accretionary prism. The revised moment magnitude has been estimated in our catalogue at 7.7 ± 0.2. It is the biggest earthquake ever recorded in the Taiwan area but the fault that has produced this earthquake has not yet been identified with confidence. We relocated this event using regional phases (seismological bulletins archived at the Central Weather Bureau of Taiwan) about 50 km NNE and shallower of its former location, that is, within the Ryukyu Arc basement. According to earthquake bulletin information, revised magnitude, new hypocentral determination and known regional faults, we propose four potential active faults as candidates for the slip associated to this event: (1) the interplate seismogenic zone (ISZ), (2) an out-of-sequence thrust cutting through the forearc and branching on the ISZ, (3) a NS strike-slip fault cutting through the Ryukyu arc and (4) a N–S, westward dipping thrust fault, affecting the Philippine Sea Plate east of the Luzon Arc. The best compromise is to consider a rupture along the ISZ with a shallow nucleation possibly along a splay-fault followed by a downward and lateral propagation of the rupture that would explain the lack of significant seafloor motion and subsequent tsunami. We also estimate the maximum seismic coupling of the ISZ in the region east of Taiwan to about 0.4. In parallel, the evidences of aseismic slip occurring along the ISZ allow us to conclude that this region should only be affected by M < 8 earthquakes.
ISSN: 0956-540X

hal-00545459
https://hal.archives-ouvertes.fr/hal-00545459
https://hal.archives-ouvertes.fr/hal-00545459/document
https://hal.archives-ouvertes.fr/hal-00545459/file/theunisseGJI2010.pdf
DOI : 10.1111/j.1365-246X.2010.04813.x

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Serpentinization of olivine-rich troctolite from core 227, Integrated Ocean Drilling Program (IODP) Hole U1309D ranges from 10 to 90. Two episodes of serpentinization are recognized. The first, dominant in weakly serpentinized samples, is an approximately isochemical (except for water) replacement of olivine (Fo(8485)) by a mixture of serpentine (antigorite, Mg-number 92) and brucite (amakinite-rich; Mg-number 65). The compositions of the minerals in type 1 veins are a reflection of FeMg exchange between olivine and the brucite serpentine formed during early serpentinization. The early serpentinite veins (type 1) are thin ( 005 mm), irregular, and exploit pre-existing cracks in olivine. The presence of antigorite suggests that early serpentinization occurred at T 300C. Type 1 veins reflect rock-dominated serpentinization, became isolated early in their history, and persist as relicts in all but the most altered samples. The main episode of serpentinization is manifested by through-going lizardite (average Mg-number 96)magnetite veins (type 2). Type 2 veins define an anastomosing foliation, may be several millimeters in width and appear to exploit pre-existing, favorably oriented type 1 veins. Type 2 veins reflect open-system serpentinization. Magnetite in these veins formed by oxidation of the Fe in brucite and serpentine, whereas addition of silica to the system converted the Mg-component of the brucite to serpentine. Magnetite forms one or more distinct bands in the interior of the vein and is never in direct contact with relict olivine. A bruciteserpentine mixture, similar to that found in type 1 veins, but with lizardite instead of antigorite, is commonly present at the margins of type 2 veins (i.e. where they are in reaction contact with relict olivine). We interpret type 2 veins as a steady-state system where brucite continually forms at the olivinevein contact and then reacts out in the interior of the vein. This continual formation and destruction of brucite imposes an exceptionally low a(SiO2) on the system. Magnetite and olivine are never in contact in type 2 veins (or anywhere else) because the olivine-out reaction yields ferroan brucite and not magnetite. The desilication of serpentine in the type 2 veins is a reflection of the inherent instability of Fe-rich serpentine with respect to magnetite at low silica activity. Thus, the composition of serpentine in equilibrium with magnetite in serpentinites is a function of serpentinemagnetite and not serpentineolivine equilbria.
ISSN: 0022-3530

hal-00420931
https://hal.archives-ouvertes.fr/hal-00420931
DOI : 10.1093/petrology/egp004

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Deciphering the evolutionary processes driving nucleotide variation in multiallelic genes is limited by the number of genetic systems in which such genes occur. The complementary sex determiner (csd) gene in the honey bee Apis mellifera is an informative example for studying allelic diversity and the underlying evolutionary forces in a well-described model of balancing selection. Acting as the primary signal of sex determination, diploid individuals heterozygous for csd develop into females, whereas csd homozygotes are diploid males that have zero fitness. Examining 77 of the functional heterozygous csd allele pairs, we established a combinatorical criteria that provide insights into the minimum number of amino acid differences among those pairs. Given a data set of 244 csd sequences, we show that the total number of csd alleles found in A. mellifera ranges from 53 (locally) to 87 (worldwide), which is much higher than was previously reported (20). Using a coupon-collector model, we extrapolate the presence of in total 116-145 csd alleles worldwide. The hypervariable region (HVR) is of particular importance in determining csd allele specificity, and we provide for this region evidence of high evolutionary rate for length differences exceeding those of microsatellites. The proportion of amino acids driven by positive selection and the rate of nonsynonymous substitutions in the HVR-flanking regions reach values close to 1 but differ with respect to the HVR length. Using a model of csd coalescence, we identified the high originating rate of csd specificities as a major evolutionary force, leading to an origin of a novel csd allele every 400,000 years. The csd polymorphism frequencies in natural populations indicate an excess of new mutations, whereas signs of ancestral transspecies polymorphism can still be detected. This study provides a comprehensive view of the enormous diversity and the evolutionary forces shaping a multiallelic gene.
ISSN: 0737-4038

hal-01544758
https://hal.archives-ouvertes.fr/hal-01544758
DOI : 10.1093/molbev/mst207

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
The Eastern Rift System (ERS) of northern Tanzania and southern Kenya, where a cratonic lithosphere is in the early stages of rifting, offers an ideal venue for investigating the roles of magma and other fluids in such an environment. To illuminate these roles, we jointly invert arrival times of locally recorded P and S body waves, phase delays of ambient noise generated Rayleigh waves and Bouguer anomalies from gravity observations to generate a 3-D image of P and S wave speeds in the upper 25 km of the crust. While joint inversion of gravity and arrival times requires a relationship between density and wave speeds, the improvement in resolution obtained by the combination of these disparate data sets serves to further constrain models, and reduce uncertainties. The most significant features in the 3-D model are (1) P and S wave speeds that are 10–15 per cent lower beneath the rift zone than in the surrounding regions, (2) a relatively high wave speed tabular feature located along the western edge of the Natron and Manyara rifts, and (3) low (∼1.71) values of Vp/Vs throughout the upper crust, with the lowest ratios along the boundaries of the rift zones. The low P and S wave speeds at mid-crustal levels beneath the rift valley are an expected consequence of active volcanism, and the tabular, high-wave speed feature is interpreted to be an uplifted footwall at the western edge of the rift. Given the high levels of CO2 outgassing observed at the surface along border fault zones, and the sensitivity of Vp/Vs to pore-fluid compressibility, we infer that the low Vp/Vs values in and around the rift zone are caused by the volcanic plumbing in the upper crust being suffused by a gaseous CO2 froth on top of a deeper, crystalline mush. The repository for molten rock is likely located in the lower crust and upper mantle, where the Vp/Vs ratios are significantly higher.
ISSN: 0956-540X

hal-01622055
https://hal.archives-ouvertes.fr/hal-01622055
https://hal.archives-ouvertes.fr/hal-01622055/document
https://hal.archives-ouvertes.fr/hal-01622055/file/roeckerGJI2017.pdf
DOI : 10.1093/gji/ggx220