La Rochelle Université
  • La Rochelle, Poitou-Charentes, France
Recent publications
Background Scallops (Bivalvia: Pectinidae) present extraordinary variance in both mitochondrial genome size, structure and content, even when compared to the extreme diversity documented within Mollusca and Bivalvia. In pectinids, mitogenome rearrangements involve protein coding and rRNA genes along with tRNAs, and different genome organization patterns can be observed even at the level of Tribes. Existing pectinid phylogenies fail to resolve some relationships in the family, Chlamydinae being an especially problematic group. Results In our study, we sequenced, annotated and characterized the mitochondrial genome of a member of Chlamydinae, Mimachlamys varia— a species of commercial interest and an effective bioindicator—revealing yet another novel gene arrangement in the Pectinidae. The phylogeny based on all mitochondrial protein coding and rRNA genes suggests the paraphyly of the Mimachlamys genus, further commending the taxonomic revision of the classification within the Chlamydinae subfamily. At the scale of the Pectinidae, we found that 15 sequence blocks are involved in mitogenome rearrangements, which behave as separate units. Conclusions Our study reveals incongruities between phylogenies based on mitochondrial protein-coding versus rRNA genes within the Pectinidae, suggesting that locus sampling affects phylogenetic inference at the scale of the family. We also conclude that the available taxon sampling does not allow for understanding of the mechanisms responsible for the high variability of mitogenome architecture observed in the Pectinidae, and that unraveling these processes will require denser taxon sampling.
To reap the advantages of many continual growing cloud services, cloud industries should adopt smart and holistic resources scheduling strategies. By deploying efficient deep learning technologies, many chaotic cloud traffics’ potential issues may be solved. Toward efficient cloud instances rightsizing and scheduling, we adopt in this paper a new Bidirectional Gated Recurrent Unit predictor based on a power efficient Stacked Denoising Autoencoders to forecast simultaneously future hourly virtual CPU, memory, and storage utilizations. Using various data ranges of resources under three AWS instances families, the best forecasting results achieved so far [1,83,30,78,331,11] of mean RMSE values and [1,37,21,63,245,13] of mean MAE values while predicting respectively future vCPU, memory, and storage utilizations. In addition, the proposed model also proved its precision stability and outperformance over the three considered SDAE-GRU, SDAE-LSTM and BiGRU benchmark models. Given the neglected power consumption measurement noticed in most related studies, we eventually validated the proposed predictor’s power efficiency by measuring in addition its real time consumed power in watt and temperature throughout the training process duration. The proposed predictor decreased the average consumed power by 5% compared to a classical sparse AE-BiGRU.
This paper shows that the theory describing gas diffusion with no consideration of the total gas pressure leads to an underestimation of the water vapor diffusive permeability. This experimental method, called cup method, can be considered as one of the most popular tests in the domain of heat and mass transfer for building applications. Thus, it is likely that the water vapor permeability defined for most current building materials is underestimated. Thanks to the approach proposed in this paper, provided that there is an advective gas permeability, it is possible to know whether a given water vapor permeability has been underestimated or not. However, it is not possible to estimate the magnitude of this measurement error. In the last part, a new experimental procedure is proposed, integrating a total gas pressure measurement on both sides of the sample. This modified test method makes it possible to simultaneously determine the advective gas permeability and the diffusive vapor transfer coefficient.
Rammed earth (RE) construction is an ancient sustainable construction method, which offers various economic and environmental advantages such as the availability of local materials. However, RE construction is a very time-consuming and labor-intensive process due to the consolidation required to achieve the targeted performance. The use of self-consolidating earth concrete (SCEC) can facilitate casting and speed the construction process. However, developing SCEC is challenging due to the presence of clay in earth, which can significantly hinder flowability. Optimizing the paste matrix of SCEC, namely self-consolidating earth paste (SCEP), is essential for achieving targeted workability performance of SCEC. In this study, the Taguchi method was employed to evaluate the effect of various mixture parameters, including clay and admixture type, cement content, and water-to-powder (W/P) and cement-to-clay (Ce/Cl) ratios to proportion SCEP mixtures. These parameters form different binder compositions with various Atterberg limits and water contents to investigate the compatibility and efficiency of different admixture types on the workability and compressive strength of their corresponding SCEP mixtures. Adequate clay dispersion was achieved using sodium hexametaphosphate (NaHMP) whereas polycarboxylate ether (PCE) was only efficient on cement particles. Sodium silicate (NaSil) did not contribute to dispersion of single-powder systems, while sodium polynaphtalene (PNS) and non-esterified polycarboxylate (NE-PC) showed compatibility with both clay and cement particles. Signal-to-noise ratio (S/ N) analyses revealed that lower cement content and higher W/P and Ce/Cl resulted in lower admixture demand for targeted workability and marsh cone test (MCT) values. Regarding 1-day compressive strength, to facilitate the demolding process, PNS, PCE and NaSil showed the highest efficiency. As concluded from the analysis of variance (ANOVA), clay and admixture type had the highest contribution on workability, while cement content and W/P were significant on compressive strength. Several theoretical models were also established to predict the workability of SCEP mixtures from Atterberg limits of the corresponding soil. Finally, a new SCEP proportioning approach was proposed based on the established models and compressive strength contours to be used for different earth types.
Targeting tunas associated with drifting Fish Aggregating Devices (dFADs) raises questions on the sustainability of tropical tuna fisheries. To limit catches of juvenile tunas, multiple time-area dFADs-fishing moratoria have been implemented by ICCAT since 1998. In this study we assessed the effectiveness of two different dFADs time-area closures implemented for the protection of both bigeye and yellowfin tuna juveniles. Using Atlantic Ocean Tunas Tagging Program (AOTTP) data from 2016 to 2019, we estimated the relative risk for individuals tagged inside the moratorium strata to be recaptured inside in comparison to the recapture rate outside the spatio-temporal strata. AOTTP releases were not homogeneously distributed in terms of areas and school type, therefore to assess the effect of the moratorium without potential bias a matching procedure was used to rebalance the release areas. As a result of the matching procedure and subsequent filtering applied to the dataset, the number of bigeyes recaptures retained inside and outside the time-area closure were below the threshold from which any conclusion could be drawn. In contrast, our results show that a majority of yellowfin and skipjack tunas tagged within the closed area stayed within the closed area during the moratorium period. Consequently, the last moratorium can be considered as effective for these two species, at least during the months of fishing ban on dFADs.
Pollination is essential for many crops since 70% of the world's cultivated plants depend on pollinators for their production. Floral resources within cultivated areas, especially those produced by flowering crops such as oilseed rape, are known to have a positive effect on wild pollinators. Nevertheless, little is known about the contribution of other floral resources, such as weeds within cultivated areas, in supporting wild pollinator communities and subsequent pollination services. Here, we investigate the extent to which oilseed rape pollination benefits from floral resources produced within cultivated areas, either crops or associated weeds. Based on the Müller index, we analyzed, during four pairs of consecutive years, the potential for inter-annual indirect effects received by oilseed rape through shared wild pollinators from major crops, and their associated weeds, in a typical French intensive agricultural landscape. Our results show that most of the support for oilseed rape pollinating fauna came from alternative types of floral resources than itself. We also find that weeds support oilseed rape pollination as much as flowering crops. Finally, we show that weeds growing within cereal fields have a major contribution to the support of oilseed rape pollination, exceeding the contribution of other floral resources, except oilseed rape. Our results underline that oilseed rape pollination benefits from floral resources present within cultivated fields, whatever the type of crops, including those that do not depend on pollinators for their pollination. Management practices like herbicide reduction in non-pollinator-dependent crops such as cereals are thus likely to impact the pollination of pollinator-dependent crops.
Conventional farming has been implicated in global biodiversity loss, with many farmland birds in decline. Organic farming is often considered a more ecological alternative since it generally hosts greater faunal diversity. To date, the impact of conventional agriculture on the decline in avian species has mainly been assessed through the lens of biodiversity loss; few studies have examined the effects of conventional farming on individual life-history trait components. Behaviour represents the final integrated outcome of a range of biochemical and physiological pathways and can be considered a proxy of health as it is more sensitive than other life-history traits, potentially allowing environmental changes to be better tracked. The goal of this study was to understand how exposure to conventional versus organic farming affects the behaviour of passerine birds in real conditions. By sampling 6 species of passerine birds in 10 hedgerows in organic landscapes and 10 hedgerows in conventional landscapes during the breeding period, we found evidence that organic farming sharply increased the vitality of individuals, irrespective of species. This was measured through behaviour such as flee attempts, aggressivity, pecking and distress calls when captured, all of which were higher in birds caught in organic hedges than those caught in conventional landscapes. We posit that passerines living in organically farmed landscapes benefit from reduced pesticide exposure rather than a greater abundance of food, as body condition was identical in the two contexts. These findings suggest that the behaviour of passerines can be a useful indicator of the state of the environment and can thus serve as an early warning of specific environmental change in agricultural areas. Further studies assessing the life-history traits of farmland birds may be a valuable aid to understanding the impact of conventional agriculture on biodiversity.
The characterization of organic and inorganic environmental pollution in coastal ecosystems, such as port areas, is complex and difficult to carry out due to the effect of environmental variables, as well as anthropic activities. For this study, the objective was to define a statistical method, taking into account the confounding factors influence, to define reference values for biomarkers in the black scallop (Mimachlamys varia). Thus, for five biomarkers (SOD (Superoxyde Dismutase), GST (Glutathion-S Transferase), MDA (Malondialdehyde), AChE (Acetylcholinesterase) and LAC (Laccase)), reference data could be described for individuals placed on sites more or less strongly impacted by specific environmental contaminations in port areas for more than two years, which had never been done before. All these results enabled us to calibrate and validate our approach in terms of active biomonitoring for the evaluation of a good ecological status of the environment of a port located on the French Atlantic coast.
Our aim in this paper is to study a mathematical model for high grade gliomas, taking into account lactates kinetics, as well as chemotherapy and antiangiogenic treatment. In particular, we prove the existence and uniqueness of biologically relevant solutions. We also perform numerical simulations based on different therapeutical situations that can be found in the literature. These simulations are consistent with what is expected in these situations.
Sublethal dehydration can cause negative physiological effects, but recent studies investigating the sub-lethal effects of dehydration on innate immune performance in reptiles have found a positive correlation between innate immune response and plasma osmolality. To investigate if this is an adaptive trait that evolved in response to dehydration in populations inhabiting water-scarce environments, we sampled free-ranging cottonmouths (n=26 adult cottonmouths) from two populations inhabiting contrasting environments in terms of water availability: Snake Key (n=12), an island with no permanent sources of fresh water and Paynes Prairie (n=14), a flooded freshwater prairie. In addition to field surveys, we manipulated the hydration state of 17 cottonmouths (Paynes Prairie n=9, Snake Key n=8) in a laboratory setting and measured the response of corticosterone and innate immune performance to dehydration with the aim of identifying any correlation or trade-offs between them. We measured corticosterone of cottonmouths at a baseline level and then again following a 60-min stress test when at three hydration states: hydrated, dehydrated, and rehydrated. We found that innate immune performance improved with dehydration and then returned to baseline levels within 48 hours of rehydration, which agrees with previous research in reptiles. Despite the frequent exposure of cottonmouths on Snake Key to dehydrating conditions, we did not find cottonmouths inhabiting the island to show a greater magnitude or more prolonged immune response compared to cottonmouths from Paynes Prairie. We also found a positive association between dehydration and corticosterone values.
Several analysis pipelines are available to microbial ecologists to process amplicon sequencing data, yet to date, there is no consensus as to the most appropriate method, and it becomes more difficult for genes that encode a specific function (functional genes). Standardized approaches need to be adopted to increase the reliability and reproducibility of environmental amplicon-sequencing-based data sets.
1. Non-additive effects from multiple interacting stressors can have unpredictable outcomes on wildlife. Stressors that initially have negligible impacts may become significant if they act in synergy with novel stressors. Wildlife markers can be a source of physiological stress for animals and are ubiquitous in ecological studies. Their potential impacts on vital rates may vary over time, particularly when changing environments impose new stressors. 2. In this study, we evaluated the temporal changes in the combined impact of two stressors, one constant (collar-marking) and another one variable over time (hunting intensity), in greater snow geese (Anser caerulescens atlantica). Over a 30-year period (1990-2019), hunting regulations were liberalized twice, in 1999 and 2009, with the instauration of special spring and winter hunting seasons, respectively. We evaluated the effect of collars on goose survival through this period of changing hunting regulations. We compared annual survival of >20,000 adult females marked with and without neck collars using multievent capture-recapture models, and partitioned hunting from non-hunting mortality. 3. Survival of geese marked with or without collars was similar in 1990-1998, before hunting regulations were liberalized (average survival[95% C.I.]: 0.87[0.86, 0.89]). However, absolute survival of collared geese was 0.05[0.03, 0.07] lower than that of non-collared geese between 1999 and 2009, and 0.12[0.09, 0.15] lower after hunting regulations were liberalized further in 2009. Hunting and non-hunting mortality probabilities were both higher in collared birds compared to those without collars. 4. The interaction between the effects of collars and hunting was synergistic because collars affected survival only after the hunting pressure increased significantly. These cumulated stresses probably reduced goose body condition sufficiently to increase their vulnerability to multiple sources of mortality. 5. Synthesis and applications: Researchers relying on long-term marking programs should evaluate the effect of markers periodically rather than solely in the beginning, as interactions with changing environmental conditions may eventually affect conclusions of studies based on marked animals. Here, we provide a rare demonstration in a natural setting that a combination of stressors can push animals beyond a threshold where vital rates are affected, even when one stressor applied alone initially had no detectable impact.
This paper presents a numerical study of capillary interfaces using the Single Component Multi-Phase Shan–Chen model, which is based on the lattice Boltzmann method. Despite the simplicity of the model, it has been shown to be effective and the present study aims to test its ability to correctly reproduce the physics of multiphase systems. To this end, several benchmark simulations were carried out in the configurations of a drop on a flat wall and then on a spherical surface to characterize the wetting behavior and relate explicitly the contact angle to model parameters. In addition, the capillary forces induced by a liquid bridge between two spherical particles were numerically calculated. We show that the results obtained are in agreement with experimental and theoretical results from the literature. The model is thus accurate in addressing the wetting behavior and capillary interfaces in unsaturated granular soils despite the fact that surface tension and contact angles are not explicit parameters of the model. To this respect, explicit relationships with Shan–Chen parameters are provided. Graphic abstract
This paper takes place in improving the energy performance assessment of cob buildings, by evaluating the variability of its hygrothermal properties at the material scale, related to the traditional construction process. For so, we proposed and analyzed data to handle the variability of the hygrothermal properties. The specimens were manufactured using a moulding method representative of on-site cob wall manufacturing process, for three plants species (hemp shiv, flax yarn and hay stalk) and three fibre content (0, 1% and 3%). Using non-destructive tests and statistical analysis, the random variability of cob composites hygrothermal properties (density, thermal conductivity, specific heat capacity, water-vapour permeability, moisture buffering value and sorption isotherms) was found as well as the variability distribution. It has been shown that the variability of properties is sensitive to the plant fibres specie and the fibre content. Using the variability indicators, it has been found on thermal conductivity, a low coefficient of variation of 2.88% for 1%-flax fibred mixture (lower than unfibred material) and a high one for 3%-hemp composites of 10.88%. The variability of sorption isotherms was usually found to be high at lower humidity loads. It has been shown that increasing the fibre²content stabilizes the variability of properties. Moreover, some evolution trends of the variability according to mixes was proposed; two parameters were found: the first, either FCmax highlighting the fibre content for which the maximum of variability was achieved or FCmin for the opposite; the second is FCres highlighting the residual variability, for high fibre content. The distribution of properties were found to be generally centred.
Multiple initiatives have called for large-scale representative networks of marine protected areas (MPAs). MPAs should be ecologically representative to be effective, but in large, remote regions this can be difficult to quantify and assess. We present a novel bioregionalization for the Southern Ocean, which uses the modelled circumpolar habitat importance of 17 marine bird and mammal species. The habitat-use of these predators indicates biodiversity patterns that require representation in Southern Ocean conservation and management planning. In the predator habitat importance predictions, we identified 17 statistical clusters, falling into four larger groups. We characterized and contrasted these clusters based on their predator, prey and oceanographic characteristics. Under the existing Southern Ocean MPA network, some clusters fall short of 10 % representation, yet others meet or exceed these targets. Implementation of currently proposed MPAs can in some cases contribute to meeting even 30 % spatial coverage conservation targets. However, the effectiveness of mixed-use versus no-take MPAs should be taken into consideration, since some clusters are not adequately represented by no-take MPAs. These results, combined with previous studies in the Southern Ocean, can help inform the continued design, implementation, and evaluation of a representative system of MPAs for Southern Ocean conservation and management.
The seasonal pattern of microplastics (MPs) contamination of the French littoral area of the Pertuis Charentais, one of the main French shellfish production regions, was assessed for the first time, between May 2019 and May 2020 at four different sites. The reference site was located at “Ile de Ré” and the other sites were located in the estuaries of the Sèvre Niortaise, Charente and Seudre rivers. Both blue mussels (Mytilus edulis) and Pacific oysters (Magallana gigas), that are considered sentinel species for the quality of the marine environment were analysed, along with sediment and seawater samples. MPs were extracted from each sample, counted, measured and sorted by colour and type. Micro-Raman spectroscopy was used to determine the proportion of confirmed MPs and the polymer types. The results showed that the contamination of mussels by fibres and fragments (1.9 ± 2.1 MPs/g ww) was significantly higher than for oysters (0.4 ± 0.4 MPs/g ww). Specifically, the contamination by fibres in both species was significantly greater than the contamination by fragments. Significant variations of MPs contamination were observed across the seasons and sites in bivalves, and depended on the species and the type of MPs (fibres or fragments). Mean concentrations of MPs measured in water and sediment were 0.007 MPs/L and 210 MPs/kg dw, respectively. Finally, blue was the dominant colour for fibres (79 %) and fragments (81 %). Blue fragments were mainly made of PS (70 %) followed by PC (18 %) and PP, PA or PLA (3 %) whereas blue fibres were mainly made of PA (80 %) followed by PET (13 %) or PP (7 %). This rare environmental case study of long-term chronic exposure of farming areas to MPs provides new knowledge on in situ variations of plastic fibres and fragments contamination throughout the seasons.
Mercury is a pervasive environmental contaminant that can negatively impact seabirds. Here, we measure total mercury (THg) concentrations in red blood cells (RBCs) from breeding brown skuas (Stercorarius antarcticus) (n = 49) at Esperanza/Hope Bay, Antarctic Peninsula. The aims of this study were to: (i) analyse RBCs THg concentrations in relation to sex, year and stable isotope values of carbon (δ¹³C) and nitrogen (δ¹⁵N); and (ii) examine correlations between THg, body condition and breeding success. RBC THg concentrations were positively correlated with δ¹⁵N, which is a proxy of trophic position, and hence likely reflects the biomagnification process. Levels of Hg contamination differed between our study years, which is likely related to changes in diet and distribution. RBC THg concentrations were not related to body condition or breeding success, suggesting that Hg contamination is currently not a major conservation concern for this population.
The concentrations of 13 trace elements were determined in 1032 muscles of 54 small-scale fisheries species collected from the Seychelles waters between 2013 and 2019. Overall, profiles were dominated by zinc (Zn) > arsenic (As) > iron (Fe) > copper (Cu) > selenium (Se), with the spiny lobsters, spanner crab and octopus exhibiting the highest levels of As, Cu and Zn while fish had higher Fe concentrations. Both taxonomy-dependent processes and ecological factors explained the interspecific differences of trace element profiles observed. A benefit-risk assessment revealed that crustaceans and cephalopods were good sources of Cu and Zn. One portion of any fish could provide 30–100 % of daily Se needs, and one portion of demersal and pelagic teleost fish could bring 5–20 % of Cu, Fe and Zn needs, especially for young adult and adult women. Finally, our analysis showed that there was very low health risks associated with small-scale fisheries consumption for the Seychelles population.
CONTEXT Policies and strategies at EU and national level aim at a reduced use of pesticides in agriculture, such as the Farm to Fork Strategy of the EU Commission. Technological progress can lower pesticide application and contribute to a sustainable bioeconomy. As an example, the greenRelease technology increases the attachment of the active ingredient of plant protection products to the leaf surface and slowly releases the active ingredient from a microgel container. Experiments under both controlled and field conditions have demonstrated the potential of the greenRelease technology to reduce pesticide use. As a so-called platform technology, the greenRelease concept can be applied to various crops and plant protection chemicals. OBJECTIVE To guide further development, this study analyses the greenRelease technology regarding its economic potential and its possible contribution to the reduction of environmental and health risks from pesticide use. METHODS To do so, we use a bio-economic farm model to assess the technology potential for a typical farm and spraying sequences of various crops in northwestern Germany. RESULTS AND CONCLUSIONS The results reveal that the economic potential of the greenRelease technology is highest for systemic fungicides in all assessed crops as well as for herbicides for potato cultivation. It is lowest for insecticides in winter barley and potato as well as for contact fungicides, due to the small doses and low product costs. The potential to lower possible environmental and health risks of pesticide use, indicated by the Danish pesticide load indicator, is highest for fungicides in potato, winter wheat, and winter barley as well as for herbicides in sugar beet cultivation. Relative to overall costs in arable farming, the cost changes induced by the greenRelease technology are minor, such that the environmental benefits will be key for promoting its application. However, the economic competitiveness of the technology increases if agri-environmental policies progressively internalize the negative externalities of pesticides use. SIGNIFICANCE This research is the first comprehensive economic and environmental assessment of the technology greenRelease which can contribute to lower the environmental burden of pesticide use in agriculture.
Understanding the linkages within complex and evolving marine food webs is essential to comprehend marine ecosystem structure and dynamics. Carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotope signatures are recognized to be powerful descriptors of the trophic ecology and trophic relationships within marine communities. Apex predators such as seabirds can influence the structure of communities by predating in lower trophic levels. They also convey information both over a range of spatial and temporal scales due to their high mobility and longevity, respectively. For this reason, here, we studied the trophic ecology of northern gannets and the extent of niche overlap with other apex predators within the Bay of Biscay (North-East Atlantic), a key feeding area for numerous predatory species. Mixing models indicated that northern gannets fed primarily on European anchovy Engraulis encrasicolus and on a mixed group composed of European sardine Sardina pilchardus, European sprat Sprattus sprattus, juvenile hake Merluccius merluccius, Atlantic mackerel Scomber scombrus and Atlantic horse mackerel Trachurus trachurus. Within the apex predator community, the northern gannets trophic niche overlapped the most with common guillemots Uria aalge (15.58%, based on Stable Isotope Bayesian Ellipses (SIBER)) and overlapped to a lesser extent with cetacean species occupying shelf habitats (i.e., the harbour porpoise Phocoena phocoena (9.99%) and the short-beaked common dolphin Delphinus delphis (10.37%)). Overall, the overlap found was moderate indicating trophic similarities and dissimilarities between these species. Information on trophic interactions between co-existing species is necessary for holistic environmental management, particularly in areas where several megafauna species share their foraging grounds with fisheries activity.
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1,415 members
Thierry Bouwmans
  • Laboratoire MIA (Mathématiques, Image et Applications)
Christophe Saint-Jean
  • Laboratoire MIA (Mathématiques, Image et Applications)
Mickaël Coustaty
  • Laboratoire Informatique, Image et Interaction
Said Jabbouri
  • LIttoral ENvironnement et Sociétés (LIENSs)
Salagnac Patrick
  • Laboratoire des Sciences de l’Ingénieur pour l’Environnement - LaSIE
Avenue Michel Crépeau, 17042, La Rochelle, Poitou-Charentes, France
Head of institution
Jean-Marc Ogier
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