The Rance Tidal Power Plant Model

Water Qualit

Egg production in the euryhaline tilapia, Sarotherodon melanotheron heudelotii, experimentally maintained in fresh, sea and hypersaline waters

Through the experiments presented here we wanted to test whether egg production of the black-chinned tilapia Sarotherodon melanotheron heudelotii under experimental conditions varies as a function of ambient salinity (fresh waters vs. sea waters vs. hypersaline waters, 0, 35 and 70, respectively) and whether these responses differ between fish acclimated within a few weeks from fresh water to saline and hypersaline environments (experiments E1 and E2, monitoring over 10 and 18 weeks), and individuals born and raised all life long at the experimental salinities (E3, monitoring over 18 weeks). In total, 233 spawns were collected. In each of the three experiments, the reproductive investment (gram of egg per gram of female over 2 weeks) did not differ between salinities of 0 and 35, whereas it was 2-3 times lower at 70 than at 0-35, because of lower spawning frequency (E1-E3), smaller clutch size (E1) and lower spawn mass (E1-E3). Finally, fish acclimated to salinity from fresh water over a few weeks and those maintained at a particular salinity all life long showed similar reproductive traits, thereby emphasizing the remarkable physiological plasticity of this species

Estimating the extended and hidden species diversity from environmental DNA in hyper-diverse regions

Species inventories are the building blocks of our assessment of biodiversity patterns and human impact. Yet, historical inventories based on visual observations are often incomplete, impairing subsequent analyses of ecological mechanisms, extinction risk and management success. Environmental DNA (eDNA) metabarcoding is an emerging tool that can provide wider biodiversity assessments than classical visual-based surveys. However, eDNA-based inventories remain limited by sampling effort and reference database incompleteness. In this study, we propose a new framework coupling eDNA surveys and sampling-theory methods to estimate species richness in under-sampled and hyper-diverse regions where some species remain absent from the checklist or undetected by visual surveys. We applied this framework to the coastal fish diversity in the heart of the coral triangle, the richest marine biodiversity hotspot worldwide. Combining data from 279 underwater visual censuses, 92 eDNA samples and an extensive custom genetic reference database, we show that eDNA metabarcoding recorded 196 putative species not detected by underwater visual census including 37 species absent from the regional checklist. We provide an updated checklist of marine fishes in the ‘Raja Ampat Bird's Head Peninsula' ecoregion with 2534 species including 1761 confirmed and 773 highly probable presences. The Chao lower-bound diversity estimator, based on the incidence of rare species, shows that the region potentially hosts an additional 123 fish species, including pelagic, cryptobenthic and vulnerable species. The extended and hidden biodiversity along with their asymptotic estimates highlight the ability of eDNA to expand regional inventories and species distributions to better guide conservation strategies

Nonsupervised Ranking of Different Segmentation Approaches: Application to the Estimation of the Left Ventricular Ejection Fraction From Cardiac Cine MRI Sequences

International audienceA statistical methodology is proposed to rank several estimation methods of a relevant clinical parameter when no gold standard is available. Based on a regression without truth method, the proposed approach was applied to rank eightmethods without using any a priori information regarding the reliability of each method and its degree of automation. It was only based on a prior concerning the statistical distribution of the parameter of interest in the database. The ranking of the methods relies on figures of merit derived from the regression and computed using a bootstrap process. The methodology was applied to the estimation of the left ventricular ejection fraction derived from cardiac magnetic resonance images segmented using eight approaches with different degrees of automation: three segmentations were entirely manually performed and the others were variously automated. The ranking of methods was consistent with the expected performance of the estimation methods: the most accurate estimates of the ejection fraction were obtained using manual segmentations. The robustness of the ranking was demonstrated when at least three methods were compared. These results suggest that the proposed statistical approach might be helpful to assess the performance of estimation methods on clinical data for which no gold standard is available

Comparison of different segmentation approaches without using gold standard. Application to the estimation of the left ventricle ejection fraction from cardiac cine MRI sequences.

International audienceA statistical method is proposed to compare several estimates of a relevant clinical parameter when no gold standard is available. The method is illustrated by considering the left ventricle ejection fraction derived from cardiac magnetic resonance images and computed using seven approaches with different degrees of automation. The proposed method did not use any a priori regarding with the reliability of each method and its degree of automation. The results showed that the most accurate estimates of the ejection fraction were obtained using manual segmentations, followed by the semiautomatic methods, while the methods with the least user input yielded the least accurate ejection fraction estimates. These results were consistent with the expected performance of the estimation methods, suggesting that the proposed statistical approach might be helpful to assess the performance of estimation methods on clinical data for which no gold standard is available

Improved estimation of the left ventricular ejection fraction using a combination of independent automated segmentation results in cardiovascular magnetic resonance imaging

—This work aimed at combining different segmenta-tion approaches to produce a robust and accurate segmentation result. Three to five segmentation results of the left ventricle were combined using the STAPLE algorithm and the reliability of the resulting segmentation was evaluated in comparison with the result of each individual segmentation method. This comparison was performed using a supervised approach based on a reference method. Then, we used an unsupervised statistical evaluation, the extended Regression Without Truth (eRWT) that ranks different methods according to their accuracy in estimating a specific biomarker in a population. The segmentation accuracy was evaluated by focusing on the left ventricular ejection fraction (LVEF) estimate resulting from the LV contour delineation using a public cardiac cine MRI database. Eight different segmentation methods, including three expert delineations, were studied, and sixteen combinations of the five automated methods were investigated. The supervised and unsupervised evaluations demonstrated that in most cases, STAPLE results provided better estimates of the LVEF than individual automated segmentation methods. In addition, LVEF obtained with STAPLE were within inter-expert variability. Overall, combining different automated segmentation methods improved the reliability of the segmenta-tion result compared to that obtained using an individual metho

Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity.

Some species responded successfully to prehistoric changes in climate [1, 2], while others failed to adapt and became extinct [3]. The factors that determine successful climate adaptation remain poorly understood. We constructed a reference genome and studied physiological adaptations in the Alpine marmot (Marmota marmota), a large ground-dwelling squirrel exquisitely adapted to the "ice-age" climate of the Pleistocene steppe [4, 5]. Since the disappearance of this habitat, the rodent persists in large numbers in the high-altitude Alpine meadow [6, 7]. Genome and metabolome showed evidence of adaptation consistent with cold climate, affecting white adipose tissue. Conversely, however, we found that the Alpine marmot has levels of genetic variation that are among the lowest for mammals, such that deleterious mutations are less effectively purged. Our data rule out typical explanations for low diversity, such as high levels of consanguineous mating, or a very recent bottleneck. Instead, ancient demographic reconstruction revealed that genetic diversity was lost during the climate shifts of the Pleistocene and has not recovered, despite the current high population size. We attribute this slow recovery to the marmot's adaptive life history. The case of the Alpine marmot reveals a complicated relationship between climatic changes, genetic diversity, and conservation status. It shows that species of extremely low genetic diversity can be very successful and persist over thousands of years, but also that climate-adapted life history can trap a species in a persistent state of low genetic diversity.This work was supported by the Francis Crick Institute which receives its core funding from Cancer Research UK (FC001134), the UK Medical Research Council (FC001134), and the Wellcome Trust (FC001134). CB and AC are supported by the Agence Nationale de la Recherche (project ANR-13-JSV7-0005) and the Centre National de la Recherche Scientifique (CNRS), CB is supported by the Rhône-Alpes region (Grant 15.005146.01). LD is supported by Agence Nationale de la Recherche (project ANR-12-ADAP-0009). TIG is supported by a Leverhulme Early Career Fellowship (Grant ECF-2015-453) and a NERC grant (NE/N013832/1). JMG is supported by a Hertha Finberg Fellowship (FWF T703). LDR is supported by the Diabetes UK RD Lawrence Fellowship (16/0005382)

Exploring the vertebrate fauna of the Bird’s Head Peninsula (Indonesia, West Papua) through DNA barcodes

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebratecommunities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.Fieldwork and laboratory activities were supported by the Lengguru 2014 Project (www.lengguru.org), conducted by the French National Research Institute for Sustainable Development (IRD), the Indonesian Institute of Sciences (LIPI) with the Research Centre for Biology (RCB), and the Politeknik KP Sorong, with the help of the Institut Français in Indonesia (IFI) and the French embassy in Jakarta, with corporate sponsorship from COLAS SA Company (Environment Department), Total Foundation, ABS, Wasco, Veolia Eau, SDV-Bolloré,Peer reviewe

1914 : La Guerre avant la guerre. Regards sur un conflit a venir

International audienceLes travaux de préparation à la guerre ont atteint, en France et en Allemagne, un degré de perfection qu'il semble difficile de dépasser", écrivait dès 1906 dans La Prochaine Guerre (librairie Chapelot) le général Henri Bonnal, expert reconnu en France comme à l'étranger, directeur de l'École de guerre jusqu'à 1902 et qui a occupé la chaire des cours militaires spéciaux de l'École jusqu'en 1897. À la veille de la conflagration, la guerre semble ainsi relever d'une pensée par anticipation, construite de longue date et qui serait selon la mémoire collective appuyée sur l'élaboration d'un sentiment de revanche constamment entretenu depuis 1870. Les textes réunis ici montrent combien, malgré les préparatifs effectifs, la guerre constitue, dans le court terme de l'été 1914, un temps paradoxal entre prévision et surprise. Les erreurs d'estimation ont été nombreuses, tant dans les registres civils que militaires. L'ouvrage reprend ainsi les contributions aux Journées d'études de Châlons en Champagne qui relisent les événements des années et des mois qui précèdent la guerre à la lumière de ce qu'elle fut vraiment. La ville de Châlons en Champagne n'a pas été choisie par hasard : placée au coeur de la guerre de 1914 à 1918, siège de l'état-major de la IV armée durant la majeure partie du conflit, elle est le lieu où fut choisi le corps du soldat inconnu américain

Estimation, Préservation, Reconstitution des bancs sauvages d’huîtres plates en Baie de Quiberon

L’huître plate, Ostrea edulis, est l’huître native des côtes européennes. Espèce emblématique de Bretagne, elle a subi deux épizooties successives dans les années 70 qui ont fait chuter sa production de 20 000 tonnes à moins de 2000 tonnes actuellement et disparaître de nombreux bancs naturels. Désormais l’espèce ne se reproduit plus que dans quelques baies et rias situées principalement en Bretagne et Normandie et le captage ne se pratique qu’en Baie de Quiberon et en Rade de Brest. Mais ce dernier est très variable d’une année à l’autre et a été particulièrement faible en Baie de Quiberon depuis 2010. De récentes études ont conclu que la diminution des stocks d’huîtres, notamment des bancs naturels de l’Ouest de la baie, pouvait être l’une des raisons à cette diminution du recrutement. Dans ce contexte, le syndicat des ostréiculteurs de la baie de Quiberon (SOBAIE) a souhaité, à partir de 2015, s’engager sur trois actions complémentaires : (1) Ré-actualiser les connaissances sur les densités d’huîtres plates des deux bancs sauvages de la baie de Quiberon, (2) restaurer le banc du milieu via des réensemencements en naissains d’huîtres plates natif de la baie et (3) restaurer le banc de Penthièvre par des mesures favorisant le recrutement. Ainsi, en collaboration avec les ostréiculteurs de la baie de Quiberon, l’Ifremer et Cochet Environnement, différentes opérations concrètes ont été menées en 2015. Ce rapport présente l’état d’avancement des opérations. Tout d’abord, une évaluation précise des densités et des stocks d’huîtres a été mise en œuvre sur les deux concessions du CRC de Bretagne Sud qui hébergent les deux bancs sauvages de la baie. Ces estimations de densités seront poursuivies au printemps 2016, mais il ressort déjà les résultats suivants: - Sur le banc de Penthièvre, les huîtres sauvages sont cantonnées exclusivement dans le nord du banc avec des densités relativement élevées (7-10 individus/m2) et la présence de petits récifs naturels d’huîtres. Cette zone à haute densité représente moins de 20 % de la surface totale du banc de Penthièvre. Sur tout le reste du banc, les densités en huîtres sont nulles et le recrutement récent a priori inexistant. Ces premières estimations confèrent donc un stock autour de 28 tonnes sur le banc de Penthièvre. - Sur le banc du milieu, trois zones ont fait l’objet de réensemencement régulier par des huîtres de Granville, de Penthièvre et de Cancale. Malgré tous ces transferts menés depuis quelques années (plus de 80 tonnes), les densités observées y restent faibles (maximum de 1.7 individus/m2) et les mortalités y sont très élevées (50 à 88 %), si bien que les stocks naturels sur ce banc ne s’élèvent qu’à 15 tonnes. En outre, du recrutement naturel a uniquement été observé au niveau du semis de Cancale, là où les huîtres sont en densité supérieure à 1 individu/m2. En parallèle de ces estimations, des actions collectives de restauration réalisées par les professionnels en 2015 (semis sur le banc du milieu de naissains natifs et hersage du banc de Penthièvre) montrent que la profession est en mesure de se fédérer pour contribuer à la reconstitution des bancs naturels de la baie de Quiberon. Un soutien et un suivi scientifique à ces opérations sont par contre essentiels pour valider ou non les mesures de restauration entreprises. Les connaissances acquises au cours de ce projet et dans les prochaines années aideront SOBAIE à proposer des actions et mesures de gestions adaptées permettant à moyen terme la reconstitution des bancs naturels d’huîtres plates, véritable patrimoine biologique de la baie de Quiberon