Résumé : Herbácea, robusta, erguida, perenne. Culmos glabros, de 1 a 2 m de altura. Hojas de hasta 1 m de longitud, glabras, escabrosas en el margen. Panículas alargado-piramidales de hasta 30 cm; racimos individuales de hasta 5 cm; espiguillas purpúreas, sin cerdas.
Herbacée robuste, dressée, pérenne. Tiges glabres, de 1 à 2 m de haut. Feuilles pouvant atteindre 1 m de long, glabres, aux bords découpés. Panicules allongées-pyramidales pouvant atteindre 30 cm; grappes séparées pouvant atteindre 5 cm; petits épis pourpres, sans barbes.
Tufted perennial grass with aromatic roots.  Culms 1-2 m high.  Leaves linear, 30-100 cm x 4-10 mm, margins scabrous, blade glabrous. Panicles long-pyramidal up to 20-35 cm long with many branches in several whorls, spikelets awnless, 4-5 mm long no bristles.
Nativa de Asia tropical y subtropical, cultivada en las regiones tropicales.
Originaire d’;Asie tropicale et subtropicale, cultivée dans les régions tropicales.
Native to tropical and subtropical Asia, cultivated in tropical regions.

http://www.tramil.net/fototeca/plant358

Éditeur(s) : George A. Smathers Libraries, University of Florida George A. Smathers Libraries, University of Florida ( Gainesville, FL )
Résumé : UF leverages its robust technical infrastructure to support many collaborative projects and materials from many partner institutions in a variety of ways. UF supports the full technical workflow with online curation tools and hosting of all digital files. In some cases partners host their own materials and UF ingests the metadata to have all partner materials findable and linked/referenced from the collaborative digital library hosted at UF.

Droits : [cc0] The author dedicated the work to the Commons by waiving all of his or her rights to the work worldwide under copyright law and all related or neighboring legal rights he or she had in the work, to the extent allowable by law.
http://ufdc.ufl.edu/AA00017119/00035

Résumé : Herbácea de hasta 90 cm, con rizoma tuberoso. Hojas linear-lanceoladas, sésiles, ápice agudo, base cuneada, glabras, de hasta 20 cm de largo. Espigas florales largo-pedunculadas, elipsoides, densas, brácteas ovadas, cuspidadas, verde pálidas; cáliz crenado; corola verde-amarillenta, tubo de 2 cm. Cápsula de 3 valvas, abriendo irregularmente. Existen diferentes cultivares.
Herbacée pouvant atteindre 90 cm, avec rhizome tubéreux. Feuilles linéaires-lancéolées, sessiles, à pointe aiguë, à base cunéiforme, glabres, pouvant atteindre 20 cm de long. Epis floraux à longs pédoncules, ellipsoïdaux, denses, bractées ovées, munies d’une pointe, de couleur vert pâle; calice créné; corolle vert-jaunâtre, tube de 2 cm. Capsule à 3 valves, s’ouvrant irrégulièrement. Il existe plusieurs procédés de culture.
Herb 30-100 cm high, with robust, branched, rhizome near the surface of the soil. Leaves, 5-25 x 1-3 cm, linear-lanceolate, sessile, with acute apex and cuneate base, glabrous; inflorescence cylindrical, spikes 4-7 x 1.5-2.5 cm, corolla yellowish-green; flower produced in the axil of yellowish bracts; fruit a three-valved capsule with small black arillate seeds.
Originaria de Asia tropical, cultivada en las regiones tropicales y subtropicales.
Originaire d’;Asie tropicale, cultivée dans les régions tropicales et subtropicales.
Native to Asia tropical, cultivated in tropical and subtropical regions.

http://www.tramil.net/fototeca/plant363

Éditeur(s) : HAL CCSD BioMed Central
Résumé : International audience
BACKGROUND: Sampling design is a key issue when establishing species inventories and characterizing habitats within highly heterogeneous landscapes. Sampling efforts in such environments may be constrained and many field studies only rely on subjective and/or qualitative approaches to design collection strategy. The region of Cacao, in French Guiana, provides an excellent study site to understand the presence and abundance of Anopheles mosquitoes, their species dynamics and the transmission risk of malaria across various environments. We propose an objective methodology to define a stratified sampling design. Following thorough environmental characterization, a factorial analysis of mixed groups allows the data to be reduced and non-collinear principal components to be identified while balancing the influences of the different environmental factors. Such components defined new variables which could then be used in a robust k-means clustering procedure. Then, we identified five clusters that corresponded to our sampling strata and selected sampling sites in each stratum. RESULTS: We validated our method by comparing the species overlap of entomological collections from selected sites and the environmental similarities of the same sites. The Morisita index was significantly correlated (Pearson linear correlation) with environmental similarity based on i) the balanced environmental variable groups considered jointly (p = 0.001) and ii) land cover/use (p-value<0.001). The Jaccard index was significantly correlated with land cover/use-based environmental similarity (p-value = 0.001). CONCLUSIONS: The results validate our sampling approach. Land cover/use maps (based on high spatial resolution satellite images) were shown to be particularly useful when studying the presence, density and diversity of Anopheles mosquitoes at local scales and in very heterogeneous landscapes.
BMC Ecology

pasteur-00914104
https://hal-riip.archives-ouvertes.fr/pasteur-00914104
https://hal-riip.archives-ouvertes.fr/pasteur-00914104/document
DOI : 10.1186/1472-6785-13-45
PUBMED : 24289184

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

Résumé : Herbácea robusta de 1 a 3 m, anual o bianual; pegajoso-pubérula. Hojas ovadas a elípticas o lanceoladas, de 30 cm o más, las inferiores, sésiles, decurrentes y amplexicaules. Panículas con varias ramas; cáliz tubular con lóbulos más cortos que el tubo; corola tubular con el limbo súbitamente aplanado, rosada, roja o blanca, dos a tres veces el largo del cáliz. Cápsula subglobosa que se abre en dos valvas longitudinales con numerosas semillas.
Herbacée robuste de 1 à 3 m, annuelle ou bisannuelle; recouverte d&rsquo;un duvet court et poisseux. Feuilles ovées à elliptiques ou lancéolées, de 30 cm ou plus; feuilles inférieures sessiles, décurrentes, et pourvues d&rsquo;une large tige apparente. Panicules à plusieurs branches; calice tubulaire à lobes plus courts que le tube; corolle tubulaire avec limbe s&rsquo;affaissant brusquement, rosée, rouge ou blanche, deux à trois fois plus longue que le calice. Capsule presque sphérique s&rsquo;ouvrant en deux valves longitudinales qui contiennent de nombreuses graines.
Annual, glandular-pubescent, robust herb, 1-3 m high. Leaves sub-sessile, oblong, lanceolate to elliptic, 10-50 cm x 3-30 cm, base decurrent on stem, apex acute to acuminate, margins entire, membranous; inflorescence a terminal panicles to 30 cm long, corolla pink, 5 cm long; fruit an ovoid capsule, 15-20 mm long; seeds brown, ridged, globose or ellipsoid, 0.5 mm long.
Nativa de América tropical, ampliamente cultivada.
Originaire de l’;Amérique tropicale, cultivée sur des zones très étendues.
Native to tropical America, widely cultivated.

http://www.tramil.net/fototeca/plant244

Éditeur(s) : HAL CCSD
Résumé : Session "Articles"
National audience
Dans cet article, nous présentons une méthode robuste et précise pour détecter 17 points caractéristiques du visage sur des images expressives. Une nouvelle architecture multi-résolution basée sur les récents algorithmes multi-noyau est introduite. Les patches de faibles résolutions codent les informations globales du visage donnant lieu à une détection grossière mais robuste du point désiré. Les patches de grandes résolutions quant à eux utilisent les détails locaux afin d'affiner cette localisation. En combinant une détection indépendante de points et des informations a priori sur les distributions de points, nous proposons un détecteur robuste aux changements d'expressions ainsi qu'aux variations d'illuminations. Ce système a été évalué sur plusieurs bases de données de la littérature. Les résultats présentés améliorent les performances des détecteurs de l'état de l'art
Actes de la conférence RFIA 2012
Lyon, France

hal-00656522
https://hal.archives-ouvertes.fr/hal-00656522
https://hal.archives-ouvertes.fr/hal-00656522/document
https://hal.archives-ouvertes.fr/hal-00656522/file/rfia2012_submission_99.pdf

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Meconium is the first fecal excretion of newborns. This complex accumulative matrix allows assessing the exposure of the fetus to xenobiotics during the last 6 months of pregnancy. To determine the eventual effect of fetal exposure to micropollutants in this matrix, robust and sensitive analytical methods must be developed. This article describes the method development of liquid chromatography methods coupled to triple quadrupole mass spectrometry for relevant pollutants. The 28 selected target compounds had different physico-chemical properties from very polar (glyphosate) to non-polar molecules (pyrethroids). Tests were performed with three different types of columns: reversed phase, ion exchange and HILIC. As a unique method could not be determined for the simultaneous analysis of all compounds, three columns were selected and suitable chromatographic methods were optimized. Similar results were noticed for the separation of the target compounds dissolved in either meconium extract or solvent for reversed phase and ion exchange columns. However, for HILIC, the matrix had a significant influence on the peak shape and robustness of the method. Finally, the analytical methods were applied to “real” meconium samples.
ISSN: 0039-9140

hal-01141722
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01141722
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01141722/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01141722/file/Development%20of%20liquid%20chromatography%20%281%29.pdf
PUBMED : 25863396

Éditeur(s) : HAL CCSD Elsevier
Résumé : Vegetation phenology is the study of the timing of seasonal events that are considered to be the result of adaptive responses to climate variations on short and long time scales. In the field of remote sensing of vegetation phenology, phenological metrics are derived from time series of optical data. For that purpose, considerable effort has been specifically focused on developing noise reduction and cloud-contaminated data removal techniques to improve the quality of remotely-sensed time series. Comparative studies between time series composed of satellite data acquired under clear and cloudy conditions and from radiometric data obtained with high accuracy from ground-based measurements constitute a direct and effective way to assess the operational use and limitations of remote sensing for predicting the main plant phenological events. In the present paper, we sought to explicitly evaluate the potential use of MODerate resolution Imaging Spectroradiometer (MODIS) remote sensing data for monitoring the seasonal dynamics of different types of vegetation cover that are representative of the major terrestrial biomes, including temperate deciduous forests, evergreen forests, African savannah, and crops. After cloud screening and filtering, we compared the temporal patterns and phenological metrics derived from in situ NDVI time series and from MODIS daily and 16-composite products. We also evaluated the effects of residual noise and the influence of data gaps in MODIS NDVI time series on the identification of the most relevant metrics for vegetation phenology monitoring. The results show that the inflexion points of a model fitted to a MODIS NDVI time series allow accurate estimates of the onset of greenness in the spring and the onset of yellowing in the autumn in deciduous forests (RMSE <= one week). Phenological metrics identical to those provided with the MODIS Global Vegetation Phenology product (MDC12Q2) are less robust to data gaps, and they can be subject to large biases of approximately two weeks or more during the autumn phenological transitions. In the evergreen forests, in situ NDVI time series describe the phenology with high fidelity despite small temporal changes in the canopy foliage. However, MODIS is unable to provide consistent phenological patterns. In crops and savannah, MODIS NDVI time series reproduce the general temporal patterns of phenology, but significant discrepancies appear between MODIS and ground-based NDVI time series during very localized periods of time depending on the weather conditions and spatial heterogeneity within the MODIS pixel. In the rainforest, the temporal pattern exhibited by a MODIS 16-day composite NDVI time series is more likely due to a pattern of noise in the NDVI data structure according to both rainy and dry seasons rather than to phenological changes. More investigations are needed, but in all cases, this result leads us to conclude that MODIS time series in tropical rainforests should be interpreted with great caution. (C) 2013 Elsevier Inc. All rights reserved.
ISSN: 0034-4257

hal-01032407
https://hal.archives-ouvertes.fr/hal-01032407
DOI : 10.1016/j.rse.2013.01.010

Éditeur(s) : Agrocampus-ouest
Résumé : Quantitative evaluations of management measure impact on resource and fleet viability are required to provide diagnostics and feed decision process. Fisheries are complex systems where numerous dynamics interact at various spatial and temporal scales. This complexity and the difficulty to observe marine systems are responsible for the high uncertainty surrounding fishery functioning that makes it hard to identify adequate management measures. The increasing consideration of uncertainties in diagnostics argues in favor of robust management measures rather than optimal management measures. Identifying robust management measures requires the development of models that account for complexity and uncertainty in the description and prediction of management impact as well as the identification of synthetic descriptors (indicators) of the state and dynamic of the system. The aim of this work is to propose generic methodologies for developing such tools. The methodological developments are applied to the pelagic fishery of the bay of Biscay. This fishery mainly focused on anchovy and was highly impacted by fishing ban on this species since 2005. Causes for anchovy drop in biomass either environmental or due to fishing are poorly understood, making management decision much harder in a critical environmental and economic context. The adequacy of traditional management using TAC is questioned and additional spatial management measures are proposed.
Des évaluations quantitatives de l’impact de mesures de gestion sur les ressources et la viabilité des flottilles sont nécessaires pour établir des diagnostics et pour fournir des éléments d’orientation pour la gestion des pêcheries. Les pêcheries sont des systèmes complexes mettant en œuvre de nombreuses dynamiques à des échelles de temps et d’espace très variables et interagissant très fortement entre elles. Cette complexité et la difficulté d’observer les systèmes marins, conduit à une grande incertitude sur leur fonctionnement qui rend difficile la détermination des mesures de gestion adaptées. La reconnaissance de ces incertitudes, plaide de plus en plus en faveur d’une gestion robuste plutôt qu’optimale. Déterminer la robustesse des mesures de gestion nécessite le développement de modèles de description et de prédiction capable d’intégrer la complexité et l’incertitude du système, ainsi que d’outils de description synthétiques (indicateurs) de l’état et de la dynamique de la pêcherie à partir d’observations. L’objectif de ce travail est de proposer des méthodes génériques pour le développement de tels outils. Ces développements méthodologiques sont appliqués à la pêcherie pélagique du golfe de Gascogne. Cette pêcherie ciblant principalement l’anchois a été fortement perturbée par la fermeture de la pêche à cette espèce en 2005. Le déterminisme environnemental et le rôle de la pêche dans le déclin de la population d’anchois sont mal compris ce qui rend difficile la prise de décision dans un contexte économique et écologique critique. La gestion traditionnelle par TAC pourrait s’avérer insuffisante pour permettre l’exploitation durable et des mesures spatialisées sont envisagées en complément.

Droits : 2010 The Author, UEB
http://archimer.ifremer.fr/doc/00025/13630/10712.pdf
http://archimer.ifremer.fr/doc/00025/13630/

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
Cratons represent the oldest preserved lithospheric domains. Their lithosphere (lithospheric mantle welded to overlying Precambrian crystalline basement) is considered to be particularly robust and long-lived due to the protecting presence of buoyant and rigid “keels” made up of residual harzburgites. Although the cratons are mostly assumed to form in the Archaean, the timing of their formation remains poorly constrained. In particular, there are very few datasets describing concurrently the age of both the crustal and mantle portions of the lithosphere. In this study, we report new U–Pb ages and Hf isotope compositions for zircons in crustal xenoliths from the Udachnaya kimberlite in the central Siberian craton; this dataset includes samples from both the upper and lower portions of the crust. The zircon ages agree well with model melt-extraction Re–Os ages on refractory peridotite xenoliths from the same pipe; taken together they allow an integrated view of lithosphere formation. Our data reveal that the present day upper crust is Archaean, whereas both the lower crust and the lithospheric mantle yield Paleoproterozoic ages. We infer that the deep lithosphere beneath the Siberian craton was not formed in a single Archaean event, but grew in at least two distinct events, one in the late Archaean and the other in the Paleoproterozoic. Importantly, a complete or large-scale delamination and rejuvenation of the Archaean lower lithosphere (lower crust and lithospheric mantle) took place in the Paleoproterozoic. This further demonstrates that craton formation can be a protracted, multi-stage process, and that the present day crust and mantle may not represent complementary reservoirs formed through the same tectono-magmatic event. Further, deep cratonic lithosphere may be less robust and long living than often assumed, with rejuvenation and replacement events throughout its history.
ISSN: 0012-821X

hal-01467648
https://hal.archives-ouvertes.fr/hal-01467648
DOI : 10.1016/j.epsl.2016.09.046

Éditeur(s) : HAL CCSD
Résumé : Both short-term and long-term morphodynamics of sand barrier systems forced by moderate storm conditions have been studied significantly in the literature. However, the dynamics of the emerged beach -- from a seaside water depth of ~ 1.5 metres below the lowest tide to the back-barrier -- impacted by typhoons remain scarcely documented. This study focuses on the analysis and a better understanding of the morphologic changes of such an emerged beach, when it is forced by one typhoon, several typhoons or the combination of a summer season of typhoons and a winter season of Monsoon wave/ wind conditions. The monitoring of near-shore hydrodynamics and beach morphodynamics was performed in the Wan-Tzu-Liao sand barrier from November 2011 to August 2012. Waves, currents and water level were measured at an offshore buoy (Cigu buoy; 18 m of water depth; 1.5 km seaward the studied zone), a current profiler (4 m of water depth), and a serie of pressure sensors deployed along a cross-shore section from the lower intertidal zone up to the eolian dune. Tide was obtained from a tide gauge inside the lagoon and wind conditions were obtained respectively from an inland station and the offshore Cigu buoy. Morphodynamic changes were monitoring thanks to DGDPS surveys performed on a grid including a 300 meters long portion of sand barrier extending from the subtidal zone to the back-barrier, as well as along two cross-shore and two long-shore profiles located within the grid. Surveys were performed each week during winter and just before and after each storm during the typhoons summer season. This field methodology provided a new and very robust dataset in order to quantify sand barrier dynamics exposed to high-energy events at various time scales. Amongst the eight typhoons recorded, TALIM is the most significant and representative. Offshore wave height reached 10.34 m (Tp = 14.6 s) at Cigu buoy and 2.3 m in 4 m of water depth. Morphological changes recorded 6 m of retreat for the dune front, a 20 m large dune breaching and the occurence of a wash-over fan in the lagoon. These changes form a well-known morphodynamic responses to moderate storms. More surprisingly, TALIM drove a significant nourishment of the supratidal zone, as well as a positive sand balance on the whole sand barrier. Five other typhoons resulted in the same type of morphological responses while two typhoons resulted in a strong erosion of the whole emerged beach. During winter and spring (moderate wave conditions and strong Monsoon winds), sand moved from the beach front to the back-barrier. For the whole year, the sand barrier recorded a 12 m landward migration concomitantly with a 12 m widening without abrasion of the dune elevation.
American Geophysical Union, Fall Meeting 2013

hal-01012312
https://hal.archives-ouvertes.fr/hal-01012312

Éditeur(s) : HAL CCSD MDPI
Résumé : International audience
Malaria remains one of the most common vector-borne diseases in the world and the definition of novel control strategies can benefit from the modeling of transmission processes. However, data-driven models are often difficult to build, as data are very often incomplete, heterogeneous in nature and in quality, and/or biased. In this context, a knowledge-based approach is proposed to build a robust and general landscape-based hazard index for malaria transmission that is tailored to the Amazonian region. A partial knowledge-based model of the risk of malaria transmission in the Amazonian region, based on landscape features and extracted from a systematic literature review, was used. Spatialization of the model was obtained by generating land use and land cover maps of the cross-border area between French Guiana and Brazil, followed by computing and combining landscape metrics to build a set of normalized landscape-based hazard indices. An empirical selection of the best index was performed by comparing the indices in terms of adequacy with the knowledge-based model, intelligibility and correlation with P. falciparum incidence rates. The selected index is easy to interpret and successfully represents the current knowledge about the role played by landscape patterns in malaria transmission within the study area. It was significantly associated with P. falciparum incidence rates, using the Pearson and Spearman correlation coefficients (up to 0.79 and 0.75, respectively; p-value < 0.001), and the linear regression coefficient of determination (reaching 0.63; p-values < 0.001). This study establishes a spatial knowledge-driven, landscape-based hazard malaria index using remote sensing that can be easily produced on a regular basis and might be useful for malaria prediction, surveillance, and control. Keywords: remote sensing; land use and land cover; landscape metric; knowledge-based hazard modeling; malaria; cross-border area between French Guiana and Brazil
ISSN: 2072-4292

hal-01355255
https://hal.archives-ouvertes.fr/hal-01355255
https://hal.archives-ouvertes.fr/hal-01355255/document
https://hal.archives-ouvertes.fr/hal-01355255/file/010066865.pdf
IRD : fdi:010066865

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
We present new archaeointensity results from three Italian kilns situated at Ascoli Satriano, Vagnari and Fontanetto Po obtained with the Thellier modified by Coe double heating method. These data complement the directional results previously published. All sites are dated on the basis of archaeological information and/or thermoluminescence dating. The results are corrected for the anisotropy of the thermoremanent magnetization and the cooling rate effects. The new data are compared with previously published archaeointensity data from Italy and nearby countries within 900 km radius from Viterbo. An initial data set including archaeointesity data mainly coming from Italy, France, Switzerland, Czech Republic, Slovakia, Hungary, Greece and Bulgaria has been compiled. After the application of strict selection criteria, the most reliable data have been used for the calculation of a preliminary Italian intensity secular variation (SV) curve for the last 3000 yr. The new curve covers the 300 BC-400 AD and 1200-1900 AD periods. It is established by means of sliding windows of 200 yr shifted by 100 yr. The lack of reliable data for the 1000-200 BC and 400-1200 AD time intervals does not permit the calculation of a continuous curve. Clearly, more high-quality archaeointensity data from Italy and Europe are still needed to draw a robust intensity SV curve for the Italian Peninsula that could be used for archaeomagnetic dating in combination with the directional data.
ISSN: 0956-540X

hal-00828691
https://hal.archives-ouvertes.fr/hal-00828691
DOI : 10.1093/gji/ggs120

Éditeur(s) : European Geosciences Union (EGU)
Résumé : Barrier layers are defined as the layer between the pycnocline and the thermocline when the latter are different as a result of salinity stratification. We present a revisited 2-degree resolution global climatology of monthly mean oceanic Barrier Layer (BL) thickness first proposed by de Boyer Montegut et al. (2007). In addition to using an extended data set, we present a modified computation method that addresses the observed porosity of BLs. We name porosity the fact that barrier layers distribution can, in some areas, be very uneven regarding the space and time scales that are considered. This implies an intermittent alteration of air-sea exchanges by the BL. Therefore, it may have important consequences for the climatic impact of BLs. Differences between the two computation methods are small for robust BLs that are formed by large-scale processes. However, the former approach can significantly underestimate the thickness of short and/or localized barrier layers. This is especially the case for barrier layers formed by mesoscale mechanisms (under the intertropical convergence zone for example and along western boundary currents) and equatorward of the sea surface salinity subtropical maxima. Complete characterisation of regional BL dynamics therefore requires a description of the robustness of BL distribution to assess the overall impact of BLs on the process of heat exchange between the ocean interior and the atmosphere.
Ocean Science (1812-0784) (European Geosciences Union (EGU)), 2009-09 , Vol. 5 , N. 3 , P. 379-387

Droits : European Geosciences Union (EGU)
http://archimer.ifremer.fr/doc/2009/publication-6915.pdf
http://archimer.ifremer.fr/doc/2009/sup-6915.pdf
http://archimer.ifremer.fr/doc/00000/6915/

Résumé : Nous avons étudié les marqueurs hémorhéologiques, hématologiques et biochimiques chez des sujets drépanocytaires homozygotes SS (HbS/HbS) et hétérozygotes composites SC (HbS/HbC) dans deux cohortes, pédiatriques et adultes, de patients drépanocytaires, et ce, à travers 7 complications récurrentes de la drépanocytose : 2 appartenant au profil hémolytique (l’ulcère de jambes et la glomérulopathie) et 5 appartenant au phénotype visqueux/vaso-occlusif (l’hypertension artérielle, le syndrome thoracique aigu (STA), la crise vaso-occlusive (CVO), la rétinopathie et l’ostéonécrose). Nous avons montré que : 1) une viscosité sanguine et une déformabilité érythrocytaire élevées sont des facteurs de risques de CVO chez les enfants homozygotes ; 2) Une viscosité sanguine élevée est associée à une hypertension artérielle systémique relative chez des adultes SS ; 3) les enfants SC présente une fonction vasculaire mieux préservée que les enfants SS pour faire face à une augmentation de la viscosité sanguine ; 4) les patients adultes SS avec une ostéonécrose présentent une déformabilité érythrocytaire plus élevée que les patients sans ostéonécrose ; 5) une viscosité sanguine élevée est associée à la présence d’une rétinopathie chez les adultes SC mais pas chez les SS ; 6) les patients adultes SS présentant une glomérulopathie ont un taux d’hémolyse élevé, une déformabilité érythrocytaire réduite et des agrégats érythrocytaires très robustes ; 7) les patients adultes SS avec des ulcères de jambes récurrents ont un taux d’hémolyse accru et une déformabilité érythrocytaire réduite. De plus, nos travaux confirment que l’-thalassémie module les propriétés de déformabilité érythrocytaire, mais montrent pour la première fois qu’elle module aussi les propriétés d’agrégation érythrocytaire, et notamment la force des agrégats érythrocytaires. En conclusion, ces travaux permettent de préciser le rôle de la rhéologie sanguine dans un certain nombre de complications de la drépanocytose et d’enrichir le modèle préexistant divisant les complications de la drépanocytose selon 2 phénotypes : hémolytique versus visqueux/vaso-occlusif. Nous montrons pour la première fois que le phénotype hémolytique est caractérisé aussi par des anomalies de la rhéologie du globule rouge : rigidité accrue et agrégats érythrocytaire robustes.
Hemorheological, hemathological, and biochemical marquers of patients with sickle cell anemia (SS) and patients with sickle cell SC disease (SC) were studied in 2 cohorts: children and adults. We focused on 7 recurrent complications: 5 belonging to the viscosity/vaso-occlusion phenotype (systemic hypertension, acute chest syndrome (ACS), vaso-occlusive crisis (VOC), retinopathy and osteonecrosis) and 2 belonging to the hemolytic phenotype (leg ulcer and glomerulopathy). Our results show that 1) high viscosity is associated with increased risk for VOC in SS children; 2) blood viscosity is increased in SS adults with systemic relative hypertension; 3) SC children have preserved vascular function compared to SS children; 4) SS adults with osteonecrosis are characterized by higher red blood cell (RBC) deformability than SS adults without osteonecrosis; 5) high blood viscosity is associated with retinopathy in SC adults but not in SS adults; 6) SS adults affected by glomerulopathy have high hemolytic rate, low RBC deformability and increased RBC aggregates strenght; 7) SS adults with recurrent leg ulcers have high hemolytic rate and reduced RBC deformability. Moreover, our studies shows that alpha-thalassemia modulate RBC deformability and RBC aggregation properties. In conclusion, this work shows for the first time that the hemolytic phenotype is characterized by an abnormal RBC rheology which may play a role in several sickle cell complications.

http://www.theses.fr/2013AGUY0684/document

Éditeur(s) : HAL CCSD Elsevier
Résumé : International audience
This study addresses the mechanical and chemical behavior of allanite during shear zone formation under high-pressure metamorphism. Understanding physico-chemical processes related to the retention or resetting of Pb isotopes in allanite during geological processes is essential for robust petrochronology. Dating of allanite in meta-granodiorite showing variable amounts of strain (from an undeformed protolith to mylonite) at Monte Mucrone (Sesia Zone, NW Italy) gave surprising results. Based on structural and petrographic observations the shear zones at Mt Mucrone are Alpine, yet allanite located within an eclogite facies mylonite yielded Permian ages (208Pb/232Th average age: 287 ± 7 Ma). These mm-sized allanite grains are rimmed by an aggregate of coarse-grained garnet + phengite, thought to derive from former epidote. These aggregates were immersed in a weak matrix that experienced granular flow, and they were thus chemically and mechanically shielded during Alpine mylonitization. In undeformed samples (8a and 8b), two populations of epidote group minerals were found. Allanite forms either coronas around Permian monazite or individual grains with patchy zoning. Both types yield Permian ages (208Pb/232Th age: 291 ± 5 Ma). On the other hand, grains of REE-rich clinozoisite of Cretaceous age are found in undeformed rocks. These grains appear as small fragments with embayed surface outlines and minute satellites or rims around Permian allanite. These (re)crystallized grains are Sr-rich and show mosaic zoning. These results indicate that allanite crystals retained their chemical and isotopic characteristics, and thus their Permian age, as a result of strong strain partitioning between the epidote group porphyroclasts and the eclogite facies matrix in HP-mylonites. The observed partial mobilization of Pb isotopes, which lead to the Cretaceous-aged rims or grains in undeformed samples was facilitated by (re)crystallization of allanite and not by mere Pb diffusion alone under the HP conditions.
ISSN: 0024-4937

insu-00679730
https://hal-insu.archives-ouvertes.fr/insu-00679730
DOI : 10.1016/j.lithos.2011.01.005

Éditeur(s) : HAL CCSD Lambert Academic Publishing
Résumé : The Himalaya-Tibet system is considered as the classical case of continental collision. Nonetheless, some fundamental questions concerning its structure, as well as physical processes influencing its evolution are still pending. This book presents several advances in the subject matter. Based on new high-resolution geophysical data from the field, combined with robust imaging techniques, the structure of the collision is revealed in detail: the underplating of India beneath half of Tibet, as well as the geometry of the surface along which this happens. Various numerical modelling techniques allow to discuss physical processes at work in the collision zone, such as the rheology of the India plate whose strong mantle supports the Himalayas, or the metamorphic reactions at depth emphasizing the role of water. We recommend this book to Earth Scientists in a broader sense. While specialists in seismology or modelling can thumb technical details, all Readers can get an interdisciplinary overview of mountain building in the Himalayas, with a retrospective outlook on early day explorers and the dawn of some classical geological principles.
https://hal.archives-ouvertes.fr/hal-00854592

ISBN : 978-3838323534
hal-00854592
https://hal.archives-ouvertes.fr/hal-00854592

Éditeur(s) : Ecole Nationale Supérieure Agronomique de Rennes
Résumé : Long-line fishing has been growing on the island of La Réunion since the beginning of the 1990s. The target species is the swordfish (Xiphias gladius), fished mainly in the tropical waters surrounding the island between longitudes 45 degree E and 60 degree E, and latitudes 17 degree S and 27 degree S. From 1998 to 2000, a finalised research programme enabled the collection of precise data concerning the lines' positions and the parameters of the fishing efforts: 3,602 nettings were thus informed by the catches (in numbers of individuals caught) and 12 descriptive variables of the effort. In parallel with this collection effort, satellite maps that described the ocean's landscape of this region of the Indian Ocean exploited by La Réunion's fisheries were made available to sailors and scientists. Extractions from these environmental variables were made at the fishing lines' positions, which allowed us to propose 20 variables describing the environmental conditions of swordfish catches applied to the nettings. In an early part of this study, after a descriptive analysis and a first selection of the variables, we used several GAM (Generalised Additive Models) to model the respective effects of effort and environmental variables on the variability of swordfish catches. We thus highlighted the predominance of factors linked to fishermen (fishing effort) on oceanographic factors in the explanation of this variability. Following these results, a summary on the biology and ecology of the swordfish was proposed in order to draw up hypotheses on the characteristics of this species' population in the Indian Ocean. The aspects linked to the individual behaviour and movements of the population were particularly highlighted. In a latter part of this study and in order to complete the empirical approach by an exploratory constructivist approach, we proposed a modelling tool in order to simulate the possible movements of individuals within the oceanic landscape described by the available satellite maps. After reading in the literature about the various forms of modelling the movements of the large pelagics, we developed an original computer modelling architecture of the multi-agent type that made it possible to manipulate in a dynamic way the satellite maps (and derived products), the individual movements of "animats" whose behaviours were based on this environmental information, and agents that clarify the process of long-line fishing in a geographical way. The computer model that was implemented (MUFINS, for MUlti-Fish INdian ocean Simulator) was next used by calibrating the behaviour of the animats on the real data originally from the analysis of commercial catches proposed in the first part, using robust techniques based on fuzzy logic. The results of the simulations were compared, on the one hand, with the large-scale hypotheses of movement proposed in the first part, and, on the other hand, to swordfish catches both real and corrected for the effect of the fishing effort modelled by the GAM models. Even if the results of these simulations in this study do not allow for proposing convincing interpretations of the underlying processes, the MUFINS tool showed its ability to address questions associated with the swordfish's behaviour in the tropical oceanic landscape and to the effects of scale transfers between the individual level and the collective level. We now envisage its use in a more operational framework, as an interface for dialogue between fishermen and scientists with a goal of sustainable management of the resource.
La peche palangriere s'est developpee a l'ile de La Reunion depuis le debut des annees 1990. L'espece cible est l'espadon (Xiphias gladius), principalement exploite dans les eaux tropicales autour de l'ile entre les longitudes 45 degree E et 60 degree E, et les latitudes 17 degree S et 27 degree S. De 1998 a 2000, un programme de recherche finalisee a permis de collecter des informations precises concernant les positions des lignes et les parametres de l'effort de peche : 3602 filages sont ainsi renseignes par les captures (en nombre d'individus captures) et 12 variables descriptives de l'effort. En parallele de cet effort de collecte, des cartes satellitales ont pu etre mises a la disposition des marins et des scientifiques, decrivant le paysage oceanique de cette region de l'ocean Indien exploitee par la pecherie reunionnaise. Des extractions de ces variables environnementales ont ete effectuees aux positions des lignes de peche, nous permettant de proposer 20 variables descriptives des conditions environnementales de captures d'espadon appliquees aux filages. Dans une premiere partie de ce travail, apres une analyse descriptive et une premiere selection des variables, on a modelise par plusieurs modeles GAM (Generalized Additive Models) les effets respectifs des variables d'effort et des variables environnementales sur la variabilite des captures d'espadon. On a ainsi mis en evidence la predominance des facteurs lies aux pecheurs (effort de peche) sur les facteurs oceanographiques dans le caractere explicatif de cette variabilite. A la suite de ces resultats, une synthese sur la biologie et l'ecologie de l'espadon a ete proposee afin de degager des hypotheses sur les caracteristiques de la population de cette espece dans l'ocean Indien. Les aspects lies au comportement individuel et aux deplacements de la population ont ete particulierement mis en evidence. Dans une deuxieme partie de ce travail et afin de completer l'approche empirique par une approche constructiviste exploratoire, nous avons propose un outil de modelisation afin de simuler les deplacements possibles d'individus au sein du paysage oceanique decrit par les cartes satellitales disponibles. Apres avoir passe en revue dans la litterature les differentes formes de modelisation des deplacements des grands, pelagiques, nous avons developpe une architecture originale de modelisation informatique de type multi-agents permettant de manipuler de maniere dynamique les cartes satellitales (et les produits derives), les mouvements individuels < d'animats >, dont les comportements sont bases sur cette information environnementale, et des agents qui explicitent le processus de capture palangriere de maniere geographique. Le modele informatique ainsi implemente (MUFINS, pour MUlti-Fish INdian ocean Simulator) a ensuite ete utilise en calibrant les comportements des animats sur les donnees reelles issues de l'analyse des captures commerciales proposee en premiere partie, a partir de techniques robustes basee sur la logique floue. Les resultats des simulations ont ete confrontes d'une part aux hypotheses de deplacement a grande echelle proposees en premiere partie, et d'autre part aux captures d'espadon reelles et corrigees de l'effet de l'effort de peche modelise par les modeles GAM. Meme si les resultats de simulations presentes dans ce travail ne permettent pas de proposer d'interpretations convaincantes des processus sous-jacents, l'outil MUFINS a demontre son aptitude a aborder les questions liees au comportement de l'espadon dans le paysage oceanique tropical et aux effets des transferts d'echelle entre le niveau individuel et le niveau collectif. On envisage desormais son utilisation dans un cadre plus operationnel, comme interface de dialogue entre les pecheurs et les scientifiques a des fins de gestion durable de la ressource.

Droits : info:eu-repo/semantics/openAccess
http://archimer.ifremer.fr/doc/2005/these-2592.pdf
http://archimer.ifremer.fr/doc/00000/2592/

Éditeur(s) : HAL CCSD Oxford University Press (OUP)
Résumé : International audience
Motivation: Gene fusion is an important evolutionary process. It can yield valuable information to infer the interactions and functions of proteins. Fused genes have been identified as non-transitive patterns of similarity in triplets of genes. To be computationally tractable, this approach usually imposes an a priori distinction between a dataset in which fused genes are searched for, and a dataset that may have provided genetic material for fusion. This reduces the `genetic space' in which fusion can be discovered, as only a subset of triplets of genes is investigated. Moreover, this approach may have a high-false-positive rate, and it does not identify gene families descending from a common fusion event. Results: We represent similarities between sequences as a network. This leads to an efficient formulation of previous methods of fused gene identification, which we implemented in the Python program FusedTriplets. Furthermore, we propose a new characterization of families of fused genes, as clique minimal separators of the sequence similarity network. This well-studied graph topology provides a robust and fast method of detection, well suited for automatic analyses of big datasets. We implemented this method in the C++ program MosaicFinder, which additionally uses local alignments to discard false-positive candidates and indicates potential fusion points. The grouping into families will help distinguish sequencing or prediction errors from real biological fusions, and it will yield additional insight into the function and history of fused genes.
ISSN: 1367-4803

hal-01544795
https://hal.archives-ouvertes.fr/hal-01544795
DOI : 10.1093/bioinformatics/btt049