Éditeur(s) : HAL CCSD Wiley
Résumé : A standardized rapid inventory method providing information on both tree species diversity and aboveground carbon stocks in tropical forests will be an important tool for evaluating efforts to conserve biodiversity and to estimate the carbon emissions that result from deforestation and degradation (REDD). Herein, we contrast five common plot methods differing in shape, size, and effort requirements to estimate tree diversity and aboveground tree biomass (AGB). We simulated the methods across six Neotropical forest sites that represent a broad gradient in forest structure, tree species richness, and floristic composition, and we assessed the relative performance of methods by evaluating the bias and precision of their estimates of AGB and tree diversity. For a given sample of forest area, a several small' (<1ha) sampling strategy led to a smaller coefficient of variation (CV) in the estimate of AGB than a few large' one. The effort (person-days) required to achieve an accurate AGB estimate (<10% CV), however, was greater for the smallest plots (0.1ha) than for a compromise approach using 0.5ha modified Gentry plots, which proved to be the most efficient method to estimate AGB across all forest types. Gentry plots were also the most efficient at providing accurate estimates of tree diversity (<10% CV of Hill number). We recommend the use of the 0.5ha modified Gentry plot method in future rapid inventories, and we discuss a set of criteria that should inform any choice of inventory method.
ISSN: 0006-3606

hal-01032408
https://hal.archives-ouvertes.fr/hal-01032408
DOI : 10.1111/btp.12006

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 Springer Verlag (Germany) Springer Verlag
Résumé : Direct numerical simulations of flow through two millimeter-scale rock samples of limestone and sandstone are performed using three diverse fluid dynamic simulators. The resulting steady-state velocity fields are compared in terms of the associated empirical probability density functions (PDFs) and key statistics of the velocity fields. The pore space geometry of each sample is imaged at 5.06−μm voxel size resolution using X-ray microtomography. The samples offer contrasting characteristics in terms of total connected porosity (about 0.31 for the limestone and 0.07 for the sandstone) and are typical of several applications in hydrogeology and petroleum engineering. The three-dimensional fluid velocity fields within the explicit pore spaces are simulated using ANSYS® FLUENT® ANSYS Inc. (2009), EULAG Prusa et al. (Comput. Fluids 37, 1193–1207 2008), and SSTOKES Sarkar et al. (2002). These computational approaches are highly disperse in terms of algorithmic complexity, differ in terms of their governing equations, the adopted numerical methodologies, the enforcement of internal no-slip boundary conditions at the fluid-solid interface, and the computational mesh structure. As metrics of comparison to probe in a statistical sense the internal similarities/differences across sample populations of velocities obtained through the computational systems, we consider (i) integral quantities, such as the Darcy flux and (ii) main statistical moments of local velocity distributions including local correlations between velocity fields. Comparison of simulation results indicates that mutually consistent estimates of the state of flow are obtained in the analyzed samples of natural pore spaces despite the considerable differences associated with the three computational approaches. We note that in the higher porosity limestone sample, the structures of the velocity fields obtained using ANSYS FLUENT and EULAG are more alike than either compared against the results obtained using SSTOKES. In the low-porosity sample, the structures of the velocity fields obtained by EULAG and SSTOKES are more similar than either is to the fields obtained using ANSYS FLUENT. With respect to macroscopic quantities, ANSYS FLUENT and SSTOKES provide similar results in terms of the average vertical velocity for both of the complex microscale geometries considered, while EULAG tends to render the largest velocity values. The influence of the pore space structure on fluid velocity field characteristics is also discussed.
ISSN: 1420-0597

hal-01174152
https://hal.archives-ouvertes.fr/hal-01174152
DOI : 10.1007/s10596-015-9486-7

Éditeur(s) : HAL CCSD Springer Verlag
Résumé : International audience
Purpose The objective of this article was to estimate the social cost of respiratory cancer cases attributable to occupational risk factors in France in 2010. Methods According to the attributable fraction method and based on available epidemiological data from the lit- erature, we estimated the number of respiratory cancer cases due to each identified risk factor. We used the cost- of-illness method with a prevalence-based approach. We took into account the direct and indirect costs. We estimated the cost of production losses due to morbidity (absenteeism and presenteeism) and mortality costs (years of production losses) in the market and nonmarket spheres. Results The social cost of lung, larynx, sinonasal and mesothelioma cancer caused by exposure to asbestos, chromium, diesel engine exhaust, paint, crystalline silica, wood and leather dust in France in 2010 were estimated at between 917 and 2,181 million euros. Between 795 and 2,011 million euros (87-92 %) of total costs were due to lung cancer alone. Asbestos was by far the risk factor representing the greatest cost to French society in 2010 at between 531 and 1,538 million euros (58-71 %), ahead of diesel engine exhaust, representing an estimated social cost of between 233 and 336 million euros, and crystalline silica (119-229 million euros). Indirect costs represented about 66 % of total costs. Conclusion Our assessment shows the magnitude of the economic impact of occupational respiratory cancers. It allows comparisons between countries and provides valu- able information for policy-makers responsible for defining public health priorities.
ISSN: 1618-7598

halshs-00922838
https://halshs.archives-ouvertes.fr/halshs-00922838
DOI : 10.1007/s10198-013-0528-6
PUBMED : 23974964

Éditeur(s) : HAL CCSD
Résumé : International audience
STUDY QUESTION: Do freezing and in vitro culture procedures enhance the expression of proteins involved in apoptotic or autophagic pathways in murine pre-pubertal testicular tissue? SUMMARY ANSWER: IVM strongly modified apoptosis- and autophagy-related relative protein levels in mice testicular tissue whereas the impact of cryopreservation procedures was minimal at the end of the culture. WHAT IS KNOWN ALREADY: In vitro spermatogenesis remains a challenging technical issue as it imposes to find a very close balance between survival and death of germ cell natural precursors (i.e. gonocytes and spermatogonia), which will eventually undergo a complete spermatogenesis close to in vivo conditions. The establishment of efficient culture conditions coupled with suitable cryopreservation procedures (e.g. controlled slow freezing [CSF] and solid surface vitrification [SSV]) of pre-pubertal testicular tissue is a crucial step in the fields of fertility preservation and restoration to improve the spermatic yield obtained in vitro. STUDY DESIGN, SIZE, DURATION: Here, we study cryopreservation procedures (i.e. CSF or SSV) and the impact of culture media compositions. A first set of 66 mouse pre-pubertal testes were directly cultured during 30, 36, 38 and 60 days (D) from 2.5 to 6.5-day-old CD-1 mice to evaluate the impact of time-aspect of culture and to endorse the reverse phase protein microarrays (RPPM) technique as an adapted experimental tool for the field of in vitro spermatogenesis. Ninety others fresh, slow-frozen and vitrified pre-pubertal testes were cultured during 30 days for the principal study to evaluate the impact of cryopreservation procedures before and after culture. Thirty-four testes dissected from 2.5, 6.5, 36.5, 40.5, 42.5 and 62.5 days postpartum (dpp) mice, corresponding to the time frames of spermatogenesis orchestrated in vitro, were used as in vivo controls. PARTICIPANTS/MATERIALS, SETTING, METHODS: After in vitro culture, testicular tissue samples originated from 2.5 or 6.5-day-old CD-1 male mice were analyzed using RPPM. This targeted proteomic technique allowed us to assess the expression level of 29 apoptosis- and autophagy-related factors by normalizing blank-corrected signal values. In addition, morphological analyses (e.g. HES, PAS, TRA98 and CREM) and DNA fragmentation in intra-tubular cells (i.e. terminal deoxynucleotidyl transferase dUTP nick end labeling; TUNEL) were assessed for the distinct experimental conditions tested as well as for in vivo control mouse testes. MAIN RESULTS AND THE ROLE OF CHANCE: A validation of the RPPM procedure in the field of in vitro spermatogenesis was completed with assay and array robustness before a principal study concerning the evaluation of the impact of in vitro culture and cryopreservation procedures. The proportion of elongated spermatids and the total cell number per seminiferous tubule tended to be very different between the in vivo and in vitro conditions (P < 0.05), suggesting the presence of a beneficial regulation on the first spermatogenesis wave by intrinsic apoptosis (Caspase₉) and autophagy (Atg5) factors (P < 0.0003 and r2 = 0.74). Concerning the impact of culture media compositions, a basic medium (BM) composed of αMEM plus 10% KnockOut™ serum replacement and gentamicin supplemented with retinol (Rol) and vitamin E (Vit. E) was selected as the best culture medium for fresh 6.5 dpp tissue cultured during 30D with 27.7 ± 8.10% of seminiferous tubules containing elongated spermatids. Concerning the impact of cryopreservation procedures, SSV did not have any impact on the morphological parameters evaluated after culture in comparison to fresh tissue (FT) controls. The proportion of tubules with elongated spermatids on testicular explants cultured with BMRol+Vit. E was not different between SSV (6.6 ± 1.6%) and CSF (5.3 ± 1.9%); however, round spermatids were observed more frequently for SSV (19 ± 6.2%) than CSF (3.3 ± 1.9%, P = 0.0317). Even if the proportion of TUNEL-positive cells for BMRol+Vit. E was higher at D30 after SSV (4.12 ± 0.26%) than CSF (1.86 ± 0.12%, P = 0.0022) and FT (2.69 ± 0.33%, P = 0.0108), the DNA damages observed at the end of the culture (i.e. D30) were similar to respective 6.5 dpp controls. In addition, the relative protein level expression ratio of an apoptotic factor, the phosphorylated FADD on Fas, was reduced by 64-fold in vitrified testes cultured with BMRol+Vit. E. Furthermore, we found in this study that the StemPro®-34 SFM culture medium supplemented with growth factors (e.g. EGF, bFGF, GDNF and LIF) prevented the differentiation of spermatogonial stem cells in favor of a significant proliferation with a better architectural pattern than in vivo 6.5 dpp controls with an increase of seminiferous tubules area for FT (P = 0.0357) and CSF (P = 0.0317). LIMITATIONS REASONS FOR CAUTION: Despite our promising results, the evaluation of apoptotic- and autophagic-related proteins was studied for a limited amount of proteins and on global testicular tissue. WIDER IMPLICATIONS OF THE FINDINGS: The data presented herein will help to improve apoptotic and autophagic understanding during the first spermatogenic wave. Moreover, our findings illustrate for the first time that, using finely-tuned experimental conditions, a testicular in vitro culture combined with proteomic technologies may significantly facilitate the study of cryopreservation procedures and in vitro culture evaluations. This study may also contribute to improve work on testicular tissues from pre-pubertal and adolescent cancer survivors. STUDY FUNDING/COMPETING INTEREST(S): This study was supported by a Ph.D. grant from the Rouen Normandie Université and a financial support from 'la Ligue nationale contre le cancer' (both awarded to L.D.), funding from Institute for Research and Innovation in Biomedicine (IRIB), Agence de la Biomédecine, and co-supported by European Union and Région Normandie. Europe gets involved in Normandie with European Regional Development Fund (ERDF). The authors declare that there is no conflict of interest.
Molecular Human Reproduction

hal-01647081
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01647081
DOI : 10.1093/molehr/gax054
PUBMED : 29040674

Éditeur(s) : HAL CCSD IWA Publishing
Résumé : International audience
UV spectrophotometry is largely used for water and wastewater quality monitoring. The measurement/estimation of specific and aggregate parameters such as nitrate and dissolved organic carbon (DOC) is possible with UV spectra exploitation, from 2 to multi wavelengths calibration. However, if nitrate determination from UV absorbance is known, major optical interferences linked to the presence of suspended solids, colloids or dissolved organic matter limit the relevance of UV measurement for DOC assessment. A new method based on UV spectrophotometric measurement of raw samples (without filtration) coupling a dual pathlength for spectra acquisition and the second derivative exploitation of the signal is proposed in this work. The determination of nitrate concentration is carried out from the second derivative of the absorbance at 226 nm corresponding at the inflexion point of nitrate signal decrease. A short optical pathlength can be used considering the strong absorption of nitrate ion around 210 nm. For DOC concentration determination the second derivative absorbance at 295 nm is proposed after nitrate correction. Organic matter absorbing slightly in the 270-330 nm window, a long optical pathlength must be selected in order to increase the sensitivity. The method was tested on several hundred of samples from small rivers of two agricultural watersheds located in Brittany, France, taken during dry and wet periods. The comparison between the proposed method and the standardised procedures for nitrate and DOC measurement gave a good adjustment for both parameters for ranges of 2-100 mg/L NO3 and 1 30 mg/L DOC. (C) 2016 Elsevier Ltd. All rights reserved.
ISSN: 0043-1354

hal-01460742
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01460742
DOI : 10.1016/j.watres.2016.11.010
PUBMED : 27838025

Éditeur(s) : Université des Antilles Études caribéennes
Résumé : À quelques kilomètres d’Oran, la zone côtière d’Aïn el Turck connue auparavant pour ses belles plages, a subi depuis quelques décennies une urbanisation incontrôlée touchant essentiellement son domaine public maritime (DPM). Actuellement, sur les parties hautes des plages comme Saint Roch, Paradis, Bouisseville ou Trouville s’alignent des villas de un à deux étages, des garages à bateaux et de grands hôtels. L’empiètement sur ces espaces pourtant protégés par plusieurs lois a participé à l’érosion de la bande sableuse et à la régression de l’activité touristique balnéaire. Une situation qui reflète une nette difficulté dans la gestion et la protection de cet espace convoité et fragile.Notre étude de la zone côtière d’Aïn el Turck va aborder quatre points : la relation entre la « bétonisation » du rivage et le changement du trait de côte, l’évolution de l’urbanisation et les stratégies d’occupations, les types de concurrence qui existent entre différents usagers sur l’appropriation du foncier littoral et enfin, les difficultés éprouvées dans la protection du domaine public maritime par les services gestionnaires. La méthode du travail est basée essentiellement sur deux approches : la première est la comparaison entre plusieurs photos aériennes, à différentes dates, pour l’identification des changements naturels affectant le rivage en relation avec l’évolution de l’urbanisation de la côte. La seconde est la réalisation d’entretiens avec les principaux acteurs du territoire et l’analyse des discours formulés par les différents groupes d’intérêts, souvent en situation de conflit.
A few kilometres from Oran, the coastal area of Ain el Turck previously known for its beautiful beaches, has suffered in recent decades uncontrolled urbanization affecting mainly the maritime public domain (DPM). Currently, the upper parts of beaches like St. Roch, Paradis, Trouville, Bouisseville or lined with villas from one to two floors, garages for boats and large hotels. Encroachment on these areas yet protected by several laws, participated in the erosion of the sandbank and the decline of seaside tourism. This reflected a marked difficulty in managing and protecting this fragile and coveted space.Our study of the coastal area of Ain el Turck will address four points: the relationship between 'concretisation' of shoreline and shoreline change, the evolution of urbanization and occupation strategies, types of competition between different users on the ownership of coastal land and finally, the difficulties in protecting the maritime public by managing services.The method of work is essentially based on two approaches:the first is the comparison between several aerial photographs at different dates, for identifying changes affecting the natural shoreline in relation to the evolution of the urbanization of the coast. The second is conducting interviews with stakeholders in the area and analysis of speeches made by various interest groups, often in conflict.
Algérie
Aïn el Turck

Droits : info:eu-repo/semantics/openAccess
urn:doi:10.4000/etudescaribeennes.4431
http://journals.openedition.org/etudescaribeennes/4431

Éditeur(s) : EDP Sciences
Résumé : The necessity to move from a traditional fishery management to an ecosystem approach is now acknowledged. Indicators are required to support the development of this approach. For example, community indicators have been proposed to assess the impact of fishing. We tested here the applicability of one such community indicator, the abundance-biomass comparison (ABC method), as a measure of the impact of bottom trawling (years of sampling: 2001 and 2003) on the benthic invertebrates-typically starfishes, crabs, squat lobsters, shrimps and large hard-shelled molluscs-of "Grande Vasiere", a major French fishing zone, in the Bay of Biscay. The ABC method is generally used as an impact indicator for different types of physical, biological and anthropogenic disturbances on benthic communities. This method is based on the assumption that increasing disturbance shifts communities from dominance by large-bodied species with low turnover rates toward dominance by small-bodied species with high turnover rates. At less disturbed areas the average biomass of individuals is greater than at more heavily disturbed areas. The ABC method measures this effect by comparing the ranked distributions of abundance and biomass within a given community. We applied the ABC method and compared the size structure and the species diversity at two areas exposed to moderate and high bottom trawl effort. Species diversity was lower in the most exploited area. The highly trawled area was dominated by opportunistic organisms, mainly one species of swimming crab Liocarcinus depurator, one species of squat lobster Munida rugosa and Norway lobsters Nephrops norvegicus, which are large-bodied species. Consequently, the results of the ABC method were inconsistent with the theoretical expectation for these particular macrofaunal communities and the measured levels of fishing intensity.
La nécessité de passer d'une gestion monospécifique des pêches à une approche écosystémique est largement reconnue. Pour mettre en place une telle approche, des indicateurs ont été proposés afin d'estimer l'impact de la pêche sur les communautés. Nous avons testé l'efficacité de l'un de ces indicateurs, la comparaison abondance-biomasse (méthode ABC), pour mesurer l'impact du chalutage de fond (année d'échantillonnage : 2001 et 2003) sur les communautés de la macrofaune benthique de la Grande Vasière, golfe de Gascogne (typiquement des crabes, étoiles de mer, des galathées, de gros mollusques à coquille dure). La méthode ABC est généralement utilisée comme un indicateur d'impact de différents types de perturbations physiques, biologiques et anthropiques sur les communautés benthiques. Cette méthode est basée sur l'hypothèse qu'un régime de perturbation croissant entraîne une modification de la structure des communautés qui deviennent graduellement dominées par des espèces opportunistes de petite taille caractérisées par un renouvellement rapide. Dans une communauté modérément perturbée, la biomasse moyenne des individus est ainsi plus grande que dans une communauté fortement perturbée. La méthode ABC mesure cet effet en comparant les distributions en biomasse et densité dans chaque communauté. Nous avons appliqué la méthode ABC et étudié la structure en taille et la diversité spécifique des communautés benthiques en comparant deux zones, l'une soumise à un effort de pêche modéré et l'autre à un important effort de pêche. La diversité spécifique était plus faible sur les sites fortement chalutés. Ces sites étaient dominés par des organismes opportunistes de grande taille, principalement une espèce de crabe nageur Liocarcinus depurator, une espèce de galathée Munida rugosa et des langoustines Nephrops norvegicus. Dans ces conditions, les résultats de la méthode ABC n'étaient pas cohérents avec la théorie pour ces communautés de macro-invertébrés benthiques et les efforts de pêche mesurés.
Aquatic Living Resources (0990-7440) (EDP Sciences), 2006-07 , Vol. 19 , N. 3 , P. 219-228

Droits : 2006 EDP
http://archimer.ifremer.fr/doc/2006/publication-2133.pdf
DOI:10.1051/alr:2006022
http://archimer.ifremer.fr/doc/00000/2133/

Éditeur(s) : HAL CCSD American Society for Microbiology
Résumé : International audience
This study aimed to evaluate the repeated sequence REP-529 compared to the B1 gene for the molecular diagnosis of toxoplasmosis by quantitative PCR (qPCR) in routine diagnosis.Over a ten-year period (2003-2013), all patients prospectively diagnosed with a positive REP-529 qPCR result for toxoplasmosis were included. All DNA samples (76 samples from 56 patients) were simultaneously tested using the two qPCR methods (REP-529 and B1).The mean Ct obtained with the B1 qPCR was significantly higher (+4.71 cycles) than that obtained with REP-529 qPCR (p<0.0001). Thirty-one out of 69 extracts (45.6%) positive with REP-529 qPCR were not amplified with the B1 qPCR (relative sensitivity 54.4%, compared to REP-529), yielding false negative results on 15/28 placentas, 5 cord blood, 2 amniotic fluids, 4 cerebrospinal fluids, 1 aqueous humor, 2 lymph node punctures and 1 abortion product. This defect in sensitivity would have left 20/56 patients undiagnosed, distributed as follows: 12/40 congenital toxoplasmosis, 4/5 cerebral toxoplasmosis, 2/8 patients with retinochoroiditis, and both patients with chronic lymphadenopathy. This poor performance of B1 qPCR could be related to low parasite loads, since the mean Toxoplasma quantification in extracts with B1 false negative results was 0.4 parasite/reaction.These results clearly show the superiority of the REP-529 sequence in the diagnosis of toxoplasmosis by PCR suggest that this target should be adopted as part of standardization of the PCR assay.
ISSN: 0095-1137

hal-01118293
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118293
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118293/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118293/file/A%2010-Year%20Retrospective%20Comparison%20of%20Two%20Target%20Sequences-belaz2015.pdf
PUBMEDCENTRAL : PMC4365238

Éditeur(s) : HAL CCSD Elsevier Masson
Résumé : Fire-free forest conversion with organic inputs as an alternative to slash-and-burn could improve agro-ecosystem sustainability. We assessed soil carbon mass changes in a sandy-clayey and well-drained soil in French Guiana after forest clearing by the chop-and-mulch method and crop establishment. At the experimental site of Combi, native forest was cut down in October 2008; woody biomass was chopped and incorporated into the top 20 cm of soil. After about one year of legume and grass cover, three forms of land management were compared: grassland (Urochloa ruziziensis), maize/soybean crop rotation with disk tillage and in direct seeding without tillage. There were four replicates. We measured 14.16 kg m(-2) of carbon in 2 mm-sieved soil down to 2 m depth for the initial forest. Forest clearing did not induce significant soil compaction; neither did any specific agricultural practice. In converted soils, C stocks were measured in the 0-30 cm layer after each crop for three years. Carbon mass changes for soil fractions <2 mm (soil C stock) and >2 mm (soil C pool) in the 0-5, 5-10, 10-20 and 20-30 cm soil layers were assessed on an equivalent soil mass basis. One year and 1.5 years after deforestation, higher C stocks (+0.64 to 1.16 kg C m(-2) yr(-1)) and C pools (+0.52 to 0.90 kg C m(-2) yr(-1)) were measured in converted soils, compared to those of the forest into the top 30 cm of soil. However, the masses of carbon in these converted soils declined later. The highest rates of carbon decrease were measured between 1.5 and 2 years after forest conversion in the <2 mm soil fraction, from 0.46 kg Cm-2 yr(-1) (in grassland soils) to 0.71 kg C m(-2) yr(-1) (in cropland under no tillage). The carbon pool declined during the third year at rates of 0.41 kg C m(-2) yr(-1) (cropland under disk tillage) to 0.76 kg C m(-2) yr(-1) (grassland soils). Three years after forest conversion, C masses in the top 30 cm of soils for grassland showed similar values than for forest. In comparison, the carbon stock in cropped soils managed under no tillage in direct seeding (without mulch) was significantly 17% and 16% lower than in forest and grassland soils, respectively. None of the studied agricultural practices succeeded in accumulating carbon from the chopped forest biomass.
ISSN: 0167-8809

hal-01032438
https://hal.archives-ouvertes.fr/hal-01032438
DOI : 10.1016/j.agee.2013.11.009

Éditeur(s) : Copernicus Gesellschaft Mbh
Résumé : Three methods for automatic detection of mesoscale coherent structures are applied to Sea Level Anomaly (SLA) fields in the South Atlantic. The first method is based on the wavelet packet decomposition of the SLA data, the second on the estimation of the Okubo-Weiss parameter and the third on a geometric criterion using the winding-angle approach. The results provide a comprehensive picture of the mesoscale eddies over the South Atlantic Ocean, emphasizing their main characteristics: amplitude, diameter, duration and propagation velocity. Five areas of particular eddy dynamics were selected: the Brazil Current, the Agulhas eddies propagation corridor, the Agulhas Current retroflexion, the Brazil-Malvinas confluence zone and the northern branch of the Antarctic Circumpolar Current (ACC). For these areas, mean propagation velocities and amplitudes were calculated. Two regions with long duration eddies were observed, corresponding to the propagation of Agulhas and ACC eddies. Through the comparison between the identification methods, their main advantages and shortcomings were detailed. The geometric criterion presents the best performance, mainly in terms of number of detections, duration of the eddies and propagation velocities. The results are particularly good for the Agulhas Rings, which have the longest lifetimes of all South Atlantic eddies.
Ocean Science (1812-0784) (Copernicus Gesellschaft Mbh), 2011 , Vol. 7 , N. 3 , P. 317-334

Droits : Author(s) 2011. This work is distributed under the Creative Commons Attribution 3.0 License. EGU
http://archimer.ifremer.fr/doc/00039/15051/12378.pdf
DOI:10.5194/os-7-317-2011
http://archimer.ifremer.fr/doc/00039/15051/

Éditeur(s) : HAL CCSD E Schweizerbart Science Publishers
Résumé : International audience
Mass balance calculations have been performed through a comparison of published graphical and statistical approaches applied to two contrasted geological settings: (i) the development of a greenschist-facies ductile shear-zone that recorded a weak volume change but significant mass transfers, and (ii) the formation of exoskarns in metacarbonate xenoliths that recorded a large volume decrease related to huge mass transfers. The comparison of the four mass-balance approaches shows that, if uncertainties are ignored, (1) they yield similar results concerning the mobile vs immobile behaviour of many components; (2) they yield similar mass-change values on bulk rock and on individual chemical elements (bulk-rock mass-change values differ by a maximum of ca. 15 % between graphical and statistical treatments of the metacarbonate xenolith evolution). The main difference concerns the uncertainties on mass changes (for bulk rocks and individual elements), which are much larger with the graphical than with the statistical approaches when uncertainties on chemical elements are taken into account, as they should be.The main advantage of the graphical methods is their rapid implementation and the clarity of the diagrams. Their main disadvantages are that uncertainties on each chemical element and bulk compositions are not taken into account and the difficulty in choosing an accurate immobility field to precisely define errors. Graphical methods need to be completed by a statistical treatment that gives absolute mass transfer results. The statistical approaches have the advantage of taking into account the chemical heterogeneities of the compared populations, in conjunction to a precise data treatment. The statistical treatment is an important and necessary step to decipher and to be pertinent in interpreting mobility/immobility of chemical elements, and, thus, in the absolute quantification of mass and volume changes.
ISSN: 0935-1221

hal-01260258
https://hal.archives-ouvertes.fr/hal-01260258
DOI : 10.1127/ejm/2015/0027-2475

Éditeur(s) : HAL CCSD
Résumé : The coastal intrusion of brine threatens populations. This is particularly prejudicial in carbonate environments. We have studied the Miocene coral reef of S-E Majorca for better understanding the relation between geological structure and intrusion. For that purpose, we have used multi-scalar and multi-disciplinary methods. The measurements in 25 boreholes over the whole coral platform have allowed defining the stratigraphic structure and some elements of the regional tectonic. The reef progrades in the NE-SW direction, starting from the Aquitanian to terminates at the Messinian. The Messinian Salinity Crisis involves a disappearance of the Mediterranean corals and results in a Terminal Carbonate Complex which overlays a great part of the previously living corals of Majorca. At the experimental site scale, the study of the mineral composition, the texture, and the diagenesis have allowed characterization of the carbonate sequence heterogeneity. Layers of mineralization accompanied by dolomitization and low porosity correspond to postdepositional eustatic levels. The causes for the existence and the orientation of fractures are studied. The permeability to porosity relation is approached. The porosity structure is studied by comparison between primary and secondary porosity. This study contributes to the knowledge of the world best documented site for the evolution of carbonate reef reservoirs, with applications for brine intrusion and for hydrocarbon extraction.
Les intrusions d'eau salée en zone côtière constituent une menace pour la population. Celles-ci sont particulièrement dommageables en contexte carbonaté. Nous avons étudié le récif corallien Miocène du sud-est de Majorque afin de comprendre la relation entre structure géologique et intrusion. Pour cela nous avons utilisé des méthodes multi-scalaires et multi-disciplinaires. Les mesures dans 25 forages sur l'ensemble de la plateforme corallienne ont permis de préciser la structure stratigraphique et certains éléments de la tectonique régionale. Le récif prograde dans la direction NE-SO, en partant de l'Aquitanien pour aboutir au Messinien. La Crise de Salinité Messinienne entraîne une disparition des coraux méditerranéens et se traduit par un Complexe Carbonaté Terminal qui s'étend sur une grande partie des coraux autrefois vivants de Majorque. A l'échelle du site expérimental, l'étude de la composition minérale, de la texture et de la diagenèse ont permis de caractériser l'hétérogénéité de la séquence carbonatée. Des couches de minéralisation accompagnées de dolomitisation et de faible porosité correspondent à différents niveaux eustatiques post-dépositionnels. Les causes de l'existence et de l'orientation des fractures sont étudiées. La relation de perméabilité à porosité est précisée. La structure de porosité est étudiée par comparaison entre la porosité primaire et la porosité secondaire. Cette étude contribue à la connaissance du site le mieux documenté au monde pour l'évolution des réservoirs carbonatés récifaux, avec applications pour les intrusions d'eau salée et l'extraction des hydrocarbures.
https://tel.archives-ouvertes.fr/tel-00440019

tel-00440019
https://tel.archives-ouvertes.fr/tel-00440019
https://tel.archives-ouvertes.fr/tel-00440019/document
https://tel.archives-ouvertes.fr/tel-00440019/file/thesemariasube.pdf

Éditeur(s) : Elsevier
Résumé : Because Vibrio aestuarianus is known to cause serious infections in Pacific oyster Crassostrea gigas, a real-time PCR assay was developed targeting the dnaJ gene of this bacterium. Only V. aestuarianus strains isolated from C. gigas mortality events in different geographic areas and the reference strain tested positive, whereas no amplification products was obtained with type strains belonging to 23 other species of Vibrio. Sensitivity and reproducibility of the method were assessed using either seawater or oyster homogenate samples spiked with one V aestuarianus strain. All these samples were stored at -20 degrees C in order to mimic retrospective or grouped natural sample analysis without quantification bias due to prolonged freezing. Analysis of standard curves revealed excellent correlation values between light microscopy cell enumerations and PCR Threshold Cycle (Ct) values, and acceptable PCR reaction efficiencies for all type of samples. Quantification curves of both sample types were equivalent, with a detection level as low as 1.6 V. aestuarianus cells in the PCR reaction tube, corresponding to 1.6.10(2) cells ml(-1) and 1.6.10(2) cells mg(-1) in seawater and entire oyster samples, respectively, taking into account the dilution factor used for appropriate template DNA preparation. Comparison of PCR assay reproducibility according to the complexity of samples revealed that seawater samples gave more reproducible quantification measures than samples from oyster homogenate, with precision of measured Ct values inferior to 0.4 and 0.6 respectively at 99% confidence. Use of the real-time PCR assay allowed us to monitor V. aestuarianus load in oysters naturally infected with this pathogen. Furthermore, we were able to detect V aestuarianus in samples of seawater in which oysters had been reared and in algal cultures used for feeding oysters. Because of the rapidity and reliability of the real-time PCR assay method used in this study, just a few hours are needed compared with the two days required using the classic culture method, this technique will be particularly valuable in mollusc pathology laboratories, for monitoring the source and course of infections by V. aestuarianus in pathogenesis and epidemiologic studies, as well as for designing appropriate prophylactic control measures. (C) 2009 Elsevier B.V. All rights reserved.
Journal of Microbiological Methods (0167-7012) (Elsevier), 2009-05 , Vol. 77 , N. 2 , P. 191-197

Droits : 2009 Elsevier B.V. All rights reserved.
http://archimer.ifremer.fr/doc/2009/publication-6447.pdf
DOI:10.1016/j.mimet.2009.01.021
http://archimer.ifremer.fr/doc/00000/6447/

Éditeur(s) : HAL CCSD Walter de Gruyter
Résumé :  
A method for measuring shrinkage resulting from drying in the three anisotropic directions is developed and tested. Measurements are performed on sawn discs, a technique which simplifies preparation and enables large numbers of measurements. Shrinkage values can be represented as a map of the disc surface. The results indicate that comparisons between shrinkage distribution and tension wood distribution on the discs show a clear relationship and can be measured with relatively high accuracy in reference to the "shrinkage map". In the long term, this method could be useful in the timber industry as a means for choosing the direction in which logs are cut depending on their type of wood composition.
Holzforschung

hal-01032055
https://hal.archives-ouvertes.fr/hal-01032055
DOI : 10.1515/HF.2003.100

Éditeur(s) : HAL CCSD EDP Sciences
Résumé : International audience
This paper presents a comparison of models for extreme rainfall and flood values. Based on a large set of thousands of rainfall and discharge data, the French ExtraFlo project showed that design estimate of extreme values based on the fitting of a distribution on a limited sample of maximum values is very inaccurate when only a few decades of observation are available. Some interesting alternatives are possible, using a regional approach, or historical data when available, or simulation methods, or sedimentological or geochemical signatures of flood deposits.
Cette communication présente les principaux résultats du projet ExtraFlo sur l'estimation des pluies et crues extrêmes. A partir d'un jeu de données conséquent de plusieurs milliers de stations, une procédure d'inter-comparaison a permis d'évaluer les performances d'une trentaine d'implémentations différentes issues de différentes combinaisons (modèle probabiliste, méthode d'estimation, cadre local / régional / mixte local et régional). Le projet ExtraFlo a permis de mettre en évidence le manque de robustesse des approches basées sur le traitement statistique d'une série de quelques dizaines d'années d'observation. Des alternatives intéressantes existent, basées sur l'exploitation des records de pluie et de débit à l'échelle d'une région, de la collecte de données historiques quand cela est possible, de méthodes de simulation basées sur le couplage d'un générateur d'averses avec un modèle hydrologique pour la transformation des pluies en débit, ou des traces morphologiques laissées par les crues anciennes.
ISSN: 0018-6368

hal-01128341
https://hal.archives-ouvertes.fr/hal-01128341
https://hal.archives-ouvertes.fr/hal-01128341/document
https://hal.archives-ouvertes.fr/hal-01128341/file/ly2014-pub00041933.pdf
DOI : 10.1051/lhb/2014010

Éditeur(s) : HAL CCSD Springer Verlag/EDP Sciences
Résumé : No efficient method is available to compare multi-locus estimates of diversity while taking into account inter-locus and inter-population stochastic variance. The advent of genome scan approaches makes the development of such tests absolutely necessary. We developed a method to compare genome-wide diversity estimates while taking into account-and factoring out-variation in census size and making use of inter-locus variance to assess significance of differences in diversity levels. An approach based on rarefaction with bootstrap re-sampling (RaBoT) was implemented into a test of multi-locus comparison of diversity coded in R. The properties of the test were studied by applying it to simulated populations with varying diversity levels and varying differences in diversity levels. The test was then applied to empirical data from disturbed and undisturbed populations of Virola michelii (Myristicaceae) genotyped at 693 amplified fragment length polymorphism (AFLP) markers. RaBoT was found to be rather conservative, with large numbers of false negatives when the diversity in the compared populations was similar, and false positives mostly associated to comparisons of populations with extremely high levels of diversity. When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult population, but it also revealed differences in diversity between subgroups within the disturbed and undisturbed plots. RaBoT is a sensitive method to compare multi-locus levels of diversity that can be applied both at the genotype level for dominant markers (e.g. AFLP) and at the allele level for biallelic codominant markers (e.g. single-nucleotide polymorphisms).
ISSN: 1286-4560

hal-01032413
https://hal.archives-ouvertes.fr/hal-01032413
DOI : 10.1007/s13595-013-0302-z

Éditeur(s) : Springer
Résumé : The light response curve methodology for microphytobenthic biofilms was studied by comparing the two most usual approaches used in pulse amplitude modulated (PAM) fluorometry. The non-sequential light curve (N-SLC) method is characterized by independent measures of the photosynthetic activity across a light gradient whereas the rapid light curve (RLC) method consists of successive measures on the same sample exposed to a stepwise increase of light intensities. Experiments were carried out on experimental microphytobenthic biofilms prepared from natural assemblages and acclimated to dark conditions. In preliminary experiments, N-SLCs were constructed from fluorescence induction curves performed at 12 different photon flux densities (PFDs). A minimum of 50 s of illumination was necessary to reach a stable light response curve; shorter illumination times resulted in underestimating the physiological parameters (alpha the light utilization coefficient in light-limited conditions and rETR(max) the maximum rate of photosynthesis efficiency) of the light response curve. For the comparison between N-SLCs and RLCs, the same time of illumination (50 s) was used for each light step of RLCs so that N-SLCs differed from RLCs only by the way the amount of light was delivered, i.e., a light dose accumulation for RLC. The experimental results showed the difference between the two photobiological response curves. In the lower range of PFDs, RLCs exhibited a larger value of alpha; in this light-limited part of the response curve the incremental increase of PFDs limited the development of NPQ and resulted in a better optimization of electron transport rate for RLC. In the higher range of PFDs, the trend was reversed and the RLC showed a lower value of rETR(max) than the N-SLC did; this is attributed to the light dose accumulation which likely led to a more efficient dispersion of energy, as illustrated by a higher non-photochemical quenching (NPQ). In conclusion, these results confirm that parameters derived from both methods differ in their value and do not bear the same physiological information.
Marine Biology (0025-3162) (Springer), 2007-11 , Vol. 153 , N. 1 , P. 91-101

Droits : 2007 Springer
http://archimer.ifremer.fr/doc/2007/publication-3331.pdf
DOI:10.1007/s00227-007-0787-9
http://archimer.ifremer.fr/doc/00000/3331/

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Estimating how topography is maintained provides insights into the different factors responsible for surface deformations and their relative roles. Here, we develop a new and simple approach to assess the degree of isostatic compensation of continental topography at regional scale from GOCE gravity gradients. We calculate the ratio between the radial gradient observed by GOCE and that calculated from topography only. From analytical and statistical formulations, simple relationships between this ratio and the degree of compensation are obtained under the Airy–Heiskanen isostasy hypothesis. Then, a value of degree of compensation at each point of study area can be easily deduced. We apply our method to the Alaska-Canada Cordillera and validate our results by comparison with a standard isostatic gravity anomaly model and additional geophysical information for this area. Both our GOCE-based results and the isostatic anomaly show that Airy–Heiskanen isostasy prevails for the Yukon Plateau whereas additional mechanisms are required to support topography below the Northwest Territories Craton and the Yakutat collision zone.
ISSN: 0956-540X

hal-01467540
https://hal.archives-ouvertes.fr/hal-01467540
https://hal.archives-ouvertes.fr/hal-01467540/document
https://hal.archives-ouvertes.fr/hal-01467540/file/cadioGJI2016.pdf
DOI : 10.1093/gji/ggw281

Éditeur(s) : HAL CCSD
Résumé : National audience
INTRODUCTION: Pulmonary arterial hypertension (PAH) is a severe complication of systemic sclerosis and detecting PAH efficiently remains challenging. The DETECT study has offered in 2013 a composite screening tool for PAH. The objective of our study was to compare the indication of right heart catheterisation (RHC) as suggested by the DETECT algorithm with the decisions of a multidisciplinary team. METHODS: This prospective monocentric non-interventional study consecutively included systemic sclerosis patients when data required to apply DETECT algorithm were available. We evaluate the number of RHC as requested by this algorithm and confronted it with the indications of RHC suggested by a multidisciplinary group blinded for the result of DETECT algorithm. RESULTS: In total, 117 systemic sclerosis patients were included. When DETECT algorithm was applied to all patients, RHC was suggested by this algorithm for 70 patients, whereas only 15 indications were required by the multidisciplinary group; among those patients only 7 had PAH. When DETECT algorithm was applied only to the 42 patients with DLCO<60% and disease duration of more than 3 years, RHC was suggested for 31 patients whereas only 13 were indicated by the multidisciplinary group; among those patients only 7 had PAH. CONCLUSION: The DETECT algorithm is able to efficiently detect all PAH patients finally diagnosed by our multidisciplinary team. However, it increases by 3 the number of RHC that should be performed.
La Revue de Médecine Interne

hal-01579606
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01579606
DOI : 10.1016/j.revmed.2017.04.005
PUBMED : 28545856