Éditeur(s) : Elsevier
Résumé : A study of organic carbon mineralization from the Congo continental shelf to the abyssal plain through the Congo submarine channel and Angola Margin was undertaken using in situ measurements of sediment oxygen demand as a tracer of benthic carbon recycling. Two measurement techniques were coupled on a single autonomous platform: in situ benthic chambers and microelectrodes, which provided total and diffusive oxygen uptake as well as oxygen microdistributions in porewaters. In addition, sediment trap fluxes, sediment composition (Org-C, Tot-N, CaCO3, porosity) and radionuclide profiles provided measurements of, respectively input fluxes and burial rate of organic and inorganic compounds. The in situ results show that the oxygen consumption on this margin close to the Congo River is high with values of total oxygen uptake (TOU) of 4 +/- 0.6, 3.6 +/- 0.5 mmol m(-2) d(-1) at 1300 and 3100m depth, respectively, and between 1.9 +/- 0.3 and 2.4 +/- 0.2 mmol m(-2) d(-1) at 4000 m depth. Diffusive oxygen uptakes (DOU) were 2.8 +/- 1.1, 2.3 +/- 0.8, 0.8 +/- 0.3 and 1.2 +/- 0.1 mmol m(-2) d(-1), respectively at the same depths. The magnitude of the oxygen demands on the slope is correlated with water depth but is not correlated with the proximity of the submarine channel-levee system, which indicates that cross-slope transport processes are active over the entire margin. Comparison of the vertical flux of organic carbon with its mineralization and burial reveal that this lateral input is very important since the sum of recycling and burial in the sediments is 5-8 times larger than the vertical flux recorded in traps. Transfer of material from the Congo River occurs through turbidity currents channelled in the Congo valley, which are subsequently deposited in the Lobe zone in the Congo fan below 4800 m. Ship board measurements of oxygen profiles indicate large mineralization rates of organic carbon in this zone, which agrees with the high organic carbon content (3%) and the large sedimentation rate (19 mm y(-1)) found on this site. The Lobe region could receive as high as 19 mol C m(-2) y(-1), 1/3 being mineralized and 2/3 being buried and could constitute the largest depocenter of organic carbon in the South Atlantic.
Deep Sea Research Part II: Topical Studies in Oceanography (0967-0645) (Elsevier), 2009-11 , Vol. 56 , N. 23 , P. 2223-2238

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-7316.pdf
DOI:10.1016/j.dsr2.2009.04.005
http://archimer.ifremer.fr/doc/00000/7316/

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
The objective of this study is to assess the association of clinical manifestations of systemic sclerosis (SSc) with the absolute count of circulating blood monocyte subpopulations according to their membrane expression of CD16. Forty-eight consecutive patients fulfilling the 2013 ACR/EULAR classification criteria for SSc were included in this cross-sectional study. CD16+ monocyte absolute count was defined by flow cytometry and confronted to the clinical characteristics of SSc patients. Twenty-three healthy donors (HD) were randomly selected for comparison. SSc patients had an increased number of total circulating blood monocytes compared to HD (p < 0.001). The CD16- subpopulation absolute count was increased in SSc patients compared to HD (p < 0.001) but was similar in limited SSc (lSSc) and diffuse SSc (dSSc). On the contrary, the CD16+ population absolute count was increased in dSSc compared to both HD and lSSc patients (dSSc 0.071 Giga/L (+/- 0.034) vs HD 0.039 Giga/L (+/- 0.030), p < 0.01, and dSSc 0.071 Giga/L (+/- 0.034) vs lSSc 0.048 Giga/L (+/- 0.024), p < 0.05). The CD16+ monocyte subpopulation absolute count was significantly correlated with the severity of skin fibrosis evaluated by the modified Rodnan skin score (p < 0.001). The CD16+ monocyte subpopulation was also associated with pulmonary fibrosis (p < 0.05), with the severity of the restrictive ventilatory defect evaluated by total lung capacity (p < 0.05) and with the pulmonary function impairment reflected by diffusing capacity of the lungs for carbon monoxyde measures (p < 0.01). These results suggest that CD16+ monocytes are associated with the main fibrotic manifestations of SSc and their role in the pathogenesis of fibrosis in this autoimmune disorder should therefore be further considered.
ISSN: 0770-3198

hal-01560150
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01560150
DOI : 10.1007/s10067-017-3597-6
PUBMED : 28293753

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BackgroundFor a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields.ResultsWe compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir’s drift).ConclusionsApart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to complement their studies, trying to identify cross-disciplinary and discipline-specific evolutionary processes. The fact that we found many process-based analogies favoring transfer from biology to linguistics further shows that certain biological methods and models have a broader scope than previously recognized. This opens fruitful paths for collaboration between the two disciplines.
ISSN: 1745-6150

Droits : http://creativecommons.org/licenses/by/
hal-01378396
http://hal.upmc.fr/hal-01378396
http://hal.upmc.fr/hal-01378396/document
http://hal.upmc.fr/hal-01378396/file/unity.pdf
DOI : 10.1186/s13062-016-0145-2

Éditeur(s) : HAL CCSD Wiley
Résumé : International audience
BACKGROUND: An association between education and preterm delivery has been observed in populations across Europe, but differences in methodology limit comparability. We performed a direct cross-cohort comparison of educational disparities in preterm delivery based on individual-level birth cohort data. METHODS: The study included data from 12 European cohorts from Denmark, England, France, Lithuania, the Netherlands, Norway, Italy, Portugal, and Spain. The cohorts included between 2434 and 99 655 pregnancies. The association between maternal education and preterm delivery (22-36 completed weeks of gestation) was reported as risk ratios, risk differences, and slope indexes of inequality with 95% confidence intervals (CIs). RESULTS: Singleton preterm live delivery proportion varied between 3.7% and 7.5%. There were large variations between the cohorts in the distribution of education and maternal characteristics. Nevertheless, there were similar educational differences in risk of preterm delivery in 8 of the 12 cohorts with slope index of inequality varying between 2.2 [95% CI 1.1, 3.3] and 4.0 [95% CI 1.4, 6.6] excess preterm deliveries per 100 singleton deliveries among the educationally most disadvantaged, and risk ratio between the lowest and highest education category varying from 1.4 [95% CI 1.1, 1.8] to 1.9 [95% CI 1.2, 3.1]. No associations were found in the last four cohorts. CONCLUSIONS: Educational disparities in preterm delivery were found all over Europe. Despite differences in the distributions of education and preterm delivery, the results were remarkably similar across the cohorts. For those few cohorts that did not follow the pattern, study and country characteristics did not explain the differences.
ISSN: 0269-5022

hal-01146842
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01146842
DOI : 10.1111/ppe.12185
PUBMED : 25808200

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : Le développement de modèles de dynamique forestière adaptés aux forêts tropicales humides est compliqué par la très grande diversité spécifique caractérisant ces forêts. Les modélisateurs ont souvent eu recours, pour simplifier le problème, à des techniques de regroupement d'espèces. Il existe des méthodes diverses de regroupement, qui relèvent de trois grands types de stratégie : (i) stratégie écologique subjective, (ii) stratégie écologique basée sur l'analyse de données, (iii) stratégie des processus de dynamique populationnelle. Dans le cadre des deux premières stratégies, une espèce est affectée à un groupe et un seul alors que dans le cadre de la troisième, des groupes d'espèces sont définis pour chacun des processus de dynamique (recrutement, croissance, mortalité) pris séparément, et chaque espèce est affectée à trois groupes. Dans la littérature, on trouve peu d'exemples de congruence ou de convergence entre les groupes définis par ces différentes méthodes. Ceci peut être expliqué par l'indépendance existant entre les caractères utilisés pour fabriquer tel ou tel groupe, ou encore par la grande variabilité intra-spécifique de ces caractères. Nous argumentons et concluons sur le fait que le recours à la stratégie des processus de dynamique paraît être la meilleure pour construire des groupes d'espèces adaptés à la prédiction de la dynamique des forêts tropicales.
ISSN: 1286-4560

hal-01032060
https://hal.archives-ouvertes.fr/hal-01032060
DOI : 10.1051/forest:2005084

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
One of the main difficulties encountered when characterizing the hydrodynamic properties of a fractured aquifer is to identify the preferential flow paths within it. Different methods may be applied to determine the variability of the permeability at the borehole scale and to image the structure of the main flow zones between boreholes. In this paper, we compare the information obtained from different measurement techniques performed in a set of three 100 m depth wells (well-to-well spacing: 5­10 m) in a fractured crystalline rock setting. Geophysical logging and borehole-wall imaging are used to identify open and closed fractures intersecting the boreholes and their orientation. The comparison with flowmeter and single packer tests shows that few of the fractures interpreted as open from geophysical logs are significantly transmissive. Cross-borehole connectivity is first investigated from single packer tests with pressure monitoring in adjacent boreholes. To determine fracture zone connectivity, we propose a methodology simply based on the variation with packer depth of the ratio of the drawdown in the observation well and the drawdown in the pumping well. The results are compared to the analysis of cross-borehole flowmeter tests. We show that both methods provide consistent results with a similar level of information on connectivity.
ISSN: 0022-1694

insu-00221380
https://hal-insu.archives-ouvertes.fr/insu-00221380
DOI : 10.1016/j.jhydrol.2007.07.007

Éditeur(s) : HAL CCSD
Résumé : International audience
OBJECTIVE: A better understanding of the perception of the rehabilitative and medical care's by persons with cerebral palsy (CP) and their families may help in providing better adherence to these cares. The main objective of this study was to assess overall satisfaction, self-perception of effectiveness and tolerance of the rehabilitative and medical cares in individuals with CP. MATERIAL AND METHODS: This was a cross-sectional questionnaire-based study. A total of 950 questionnaires were sent to French Britain children and adults with CP. Perceived effectiveness and tolerance were evaluated for each types of care using a Likert scale from 1 to 7 and overall satisfaction by a visual analog scale. Comparison of means and uni-and-multivariate analyzes for correlation analysis were carried out. RESULTS: A total of 512 (53.9%) questionnaires were analyzed; 230 (44.9%) were children and 54% were walkers (GMFCS I, II or III). The overall satisfaction was 6.83/10 (SD 2.21). Orthoptic, orthosis and physical therapy were reported to be the most effective cares (5.34/5.30/5.29) while botulinum toxins, intrathecal baclofen, and speech therapy the least effective (4.42/4.52/5.02). Intrathecal baclofen, orthosis and botulinum toxin were the less well-tolerated therapies (4.75/5.11/5.28). Antiepileptic drugs were reported to be the most effective and best-tolerated drug contrary to analgesics. Overall, satisfaction was inversely correlated to the GMFCS in the multivariate analysis (P=0.013). The perceived effectiveness of occupational therapy, botulinum toxin injections and physiotherapy are inversely related to GMFCS in the univariate analyzes. The tolerance and effectiveness of the orthosis have a positive correlation with the GMFCS in the uni-and-multivariate analyzes. DISCUSSION/CONCLUSION: This study shows a good overall satisfaction on medical and paramedical care but highlights a large discrepancy between user self-perception and evidence base medicine. More communication about the therapies between professionals and individuals with cerebral palsy is needed and comparing opinions of patients and their families to literature can give us the keys to improve communication around these therapies.
Annals of Physical and Rehabilitation Medicine

hal-01477212
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01477212
DOI : 10.1016/j.rehab.2016.07.014
PUBMED : 27676935

Éditeur(s) : HAL CCSD American Geophysical Union
Résumé : International audience
The Iberian Massif is the best exposed segment of the European Variscan Belt. It includes relatively well preserved terranes that were accreted by transpression along time and resulted in a number of geotectonic units that formed part of the Late Paleozoic assembly of the Pangaea Supercontinent. In SW Iberia, these units are the Central Iberian Zone (CIZ), Ossa Morena Zone (OMZ), and the South Portuguese Zone (SPZ). A 210 km long NE-SW magnetotelluric profile was carried out through the CIZ, from the OMZ-CIZ boundary toward the north, reaching the Tagus (Cenozoic) basin. Data dimensionality analysis resulted in a suitable 2-D electrical resistivity structure, allowing a 2-D inversion of the data set. Complementary available geophysical data (deep seismic, gravity and aeromagnetic) and a comparison with a detailed geological cross section led us to constrain the interpretation of the 2-D electrical resistivity structure of the CIZ crust. The results show, for the upper crust, the existence of diverse conductive/resistive bodies that correlate well with known geological features (sedimentary basins, faults, granitic plutons, mineralized systems). A mild but steady conductive band is located along the middle and lower crust that is interpreted as a mafic granulite basement. The upper section of this band connects with several elongated shallow conductors, providing further evidence for the existence, in the Central Iberian Zone, of a complex decollement system where the major faults are rooted. Such a crustal architecture is viewed as the northward continuation of the Variscan large-scale structures previously recognized in the southern sectors (OMZ and SPZ).
ISSN: 0148-0227

hal-00671036
https://hal.archives-ouvertes.fr/hal-00671036
DOI : 10.1029/2010JB007538

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 Springer Verlag
Résumé : International audience
In chemoautotrophic associations, sequence comparison of 16S rRNA has been the method of choice to study bacterial diversity in the context of host/symbiont coevolution. However, the relative low rate of evolution of 16S rRNA has been shown to result in a diminished capacity to discriminate between closely related bacterial strains or species. Within chemoautotrophic associations, as described in several studies, the use of other genetic markers may reveal previously unobserved strain diversity among gill endosymbionts. Herein, we conducted a survey of symbionts harbored by six species within the Lucinidae family using five genetic markers (dnaE, gyrB, aprA, cbbL genes and the 16S-23S internal transcribed spacer). Thus, within the already described SoLuc₁ bacterial species shared by six host species we observed an obvious bacterial strain diversity. This diversity is structured in function of the geographic location of the hosts and not in function of ecological parameters or host phylogeny. Interestingly at the local level (same seagrass bed environment), we observed an unexpected specificity in host species/bacterial strain association (i.e., all individuals of the same host species harbor the same symbiotic sequence type). This specificity of association implied that there was a control of symbiont strain acquisition by the host, which was confirmed by a cross-infection experiment of starved adults performed in our study. Based upon our results and other evidence from the literature, we hypothesize that this pattern may be due to a ``capture/escape'' type antagonist evolution of the two partners.
ISSN: 0025-3162

hal-01544753
https://hal.archives-ouvertes.fr/hal-01544753
DOI : 10.1007/s00227-016-2949-0

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
Background: The filamentous fungus Trichoderma reesei is the main industrial cellulolytic enzyme producer. Several strains have been developed in the past using random mutagenesis, and despite impressive performance enhancements, the pressure for low-cost cellulases has stimulated continuous research in the field. In this context, comparative study of the lower and higher producer strains obtained through random mutagenesis using systems biology tools (genome and transcriptome sequencing) can shed light on the mechanisms of cellulase production and help identify genes linked to performance. Previously, our group published comparative genome sequencing of the lower and higher producer strains NG 14 and RUT C30. In this follow-up work, we examine how these mutations affect phenotype as regards the transcriptome and cultivation behaviour. Results: We performed kinetic transcriptome analysis of the NG 14 and RUT C30 strains of early enzyme production induced by lactose using bioreactor cultivations close to an industrial cultivation regime. RUT C30 exhibited both earlier onset of protein production (3 h) and higher steady-state productivity. A rather small number of genes compared to previous studies were regulated (568), most of them being specific to the NG 14 strain (319). Clustering analysis highlighted similar behaviour for some functional categories and allowed us to distinguish between induction-related genes and productivity-related genes. Cross-comparison of our transcriptome data with previously identified mutations revealed that most genes from our dataset have not been mutated. Interestingly, the few mutated genes belong to the same clusters, suggesting that these clusters contain genes playing a role in strain performance. Conclusions: This is the first kinetic analysis of a transcriptomic study carried out under conditions approaching industrial ones with two related strains of T. reesei showing distinctive cultivation behaviour. Our study sheds some light on some of the events occurring in these strains following induction by lactose. The fact that few regulated genes have been affected by mutagenesis suggests that the induction mechanism is essentially intact compared to that for the wild-type isolate QM6a and might be engineered for further improvement of T. reesei. Genes from two specific clusters might be potential targets for such genetic engineering.
ISSN: 1754-6834

Droits : http://creativecommons.org/licenses/by/
hal-01112360
http://hal.upmc.fr/hal-01112360
http://hal.upmc.fr/hal-01112360/document
http://hal.upmc.fr/hal-01112360/file/Poggi-Parodi_2014_Kinetic.pdf
DOI : 10.1186/s13068-014-0173-z

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
The island of Taiwan is located on the convergent boundary between the Philippine Sea plate and the Chinese continental margin. It offers very active mountain building and collapsing processes well illustrated by the rugged topography, rapid uplift and denudation, young tectonic landforms, active faulting and numerous earthquakes. In this paper, using simple models, we have estimated vertical movements and associated absolute gravity variations which can be expected along a profile crossing the southern part of the island and probably suffering the highest rates of rising. The two different tectonic styles proposed for the island, thin-skinned and thick-skinned, were taken into account. Horizontal and vertical movements were modeled by an elastic deformation code. Gravity variations due to these deformations are then modeled at a second step. They are dominated by plate and free-air effects, i.e. elevation of the topography, with several mu Gal yr(-1). By comparison, gravity changes generated by mass transfers are weak: maximum 0.1 mu Gal yr(-1) with the thin-skinned tectonic and 0.3 mu Gal yr(-1) with the thick-skinned tectonic. Though elastic rheology has limitations, this modeling offers interesting results on what gravity signal can be expected from the AGTO project (Absolute Gravity in the Taiwanese Orogen), which proposes to study the dynamic of these mountain ranges using absolute gravimetry (AG) and also including relative gravimetry (RG) and GPS measurements.
ISSN: 0264-3707

hal-00456035
https://hal.archives-ouvertes.fr/hal-00456035
DOI : 10.1016/j.jog.2009.09.004

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
In the Gulf of Cadiz key segment of the Africa-Iberia plate boundary (North-East Atlantic ocean), three main different modes of tectonic interference between a recently identified wrench system (SWIM) and the Gulf of Cadiz Accretionary Wedge (GCAW) were tested through analog sand-box modeling: a) An active accretionary wedge on top of a pre-existent inactive basement fault; b) An active strike-slip fault cutting a previously formed, inactive, accretionary wedge; and c) Simultaneous activity of both the accretionary wedge and the strike-slip fault. The results we obtained and the comparison with the natural deformation pattern favor a tectonic evolution comprising two main steps: i) the formation of the Gulf of Cadiz Accretionary Wedge on top of inactive, Tethyan-related, basement faults (Middle Miocene to ~ 1.8 Ma); ii) subsequent reactivation of these basement faults with dextral strike-slip motion (~ 1.8 Ma to present) simultaneously with continued tectonic accretion in the GCAW. These results exclude the possibility of ongoing active SWIM wrench system cross-cutting an inactive GCAW structure. Our results also support a new interpretation of the SWIM wrench system as fundamentally resulting from strike-slip reactivation of an old (Tethyan-related) plate boundary.
ISSN: 0025-3227

insu-00643630
https://hal-insu.archives-ouvertes.fr/insu-00643630
https://hal-insu.archives-ouvertes.fr/insu-00643630/document
https://hal-insu.archives-ouvertes.fr/insu-00643630/file/Duarte_etal_2011_MS-1.pdf
DOI : 10.1016/j.margeo.2011.09.014