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Auteur De Wit, R.; Gautret, P.; Bettarel, Y.; Roques, C.; Marlière, C.; Ramonda, M.; Nguyen Thanh, T.; Tran Quang, H.; Bouvier, T. url  doi
openurl 
  Titre Viruses Occur Incorporated in Biogenic High-Mg Calcite from Hypersaline Microbial Mats Type Article scientifique
  Année 2015 Publication Revue Abrégée PLoS ONE  
  Volume 10 Numéro 6 Pages e0130552  
  Mots-Clés  
  Résumé Using three different microscopy techniques (epifluorescence, electronic and atomic force microscopy), we showed that high-Mg calcite grains in calcifying microbial mats from the hypersaline lake “La Salada de Chiprana”, Spain, contain viruses with a diameter of 50–80 nm. Energy-dispersive X-ray spectrometer analysis revealed that they contain nitrogen and phosphorus in a molar ratio of ~9, which is typical for viruses. Nucleic acid staining revealed that they contain DNA or RNA. As characteristic for hypersaline environments, the concentrations of free and attached viruses were high (>1010 viruses per g of mat). In addition, we showed that acid treatment (dissolution of calcite) resulted in release of viruses into suspension and estimated that there were ~15 × 109 viruses per g of calcite. We suggest that virus-mineral interactions are one of the possible ways for the formation of nano-sized structures often described as “nanobacteria” and that viruses may play a role in initiating calcification.  
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  Numéro d'Appel MARBEC @ alain.herve @ collection 1283  
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Auteur Joo, R.; Bertrand, S.; Tam, J.; Fablet, R. url  doi
openurl 
  Titre Hidden Markov Models: The Best Models for Forager Movements? Type Article scientifique
  Année 2013 Publication Revue Abrégée PLoS ONE  
  Volume 8 Numéro 8 Pages  
  Mots-Clés  
  Résumé One major challenge in the emerging field of movement ecology is the inference of behavioural modes from movement patterns. This has been mainly addressed through Hidden Markov models (HMMs). We propose here to evaluate two sets of alternative and state-of-the-art modelling approaches. First, we consider hidden semi-Markov models (HSMMs). They may better represent the behavioural dynamics of foragers since they explicitly model the duration of the behavioural modes. Second, we consider discriminative models which state the inference of behavioural modes as a classification issue, and may take better advantage of multivariate and non linear combinations of movement pattern descriptors. For this work, we use a dataset of \textgreater200 trips from human foragers, Peruvian fishermen targeting anchovy. Their movements were recorded through a Vessel Monitoring System (∼1 record per hour), while their behavioural modes (fishing, searching and cruising) were reported by on-board observers. We compare the efficiency of hidden Markov, hidden semi-Markov, and three discriminative models (random forests, artificial neural networks and support vector machines) for inferring the fishermen behavioural modes, using a cross-validation procedure. HSMMs show the highest accuracy (80%), significantly outperforming HMMs and discriminative models. Simulations show that data with higher temporal resolution, HSMMs reach nearly 100% of accuracy. Our results demonstrate to what extent the sequential nature of movement is critical for accurately inferring behavioural modes from a trajectory and we strongly recommend the use of HSMMs for such purpose. In addition, this work opens perspectives on the use of hybrid HSMM-discriminative models, where a discriminative setting for the observation process of HSMMs could greatly improve inference performance.  
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  Numéro d'Appel LL @ pixluser @ collection 260  
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Auteur Durand, J.-D.; Guinand, B.; Dodson, J.J.; Lecomte, F. url  doi
openurl 
  Titre Pelagic Life and Depth: Coastal Physical Features in West Africa Shape the Genetic Structure of the Bonga Shad, Ethmalosa fimbriata Type Article scientifique
  Année 2013 Publication Revue Abrégée PLoS ONE  
  Volume 8 Numéro 10 Pages  
  Mots-Clés  
  Résumé <p>The bonga shad, <italic>Ethmalosa fimbriata</italic>, is a West African pelagic species still abundant in most habitats of its distribution range and thought to be only recently affected by anthropogenic pressure (habitat destruction or fishing pressure). Its presence in a wide range of coastal habitats characterised by different hydrodynamic processes, represents a case study useful for evaluating the importance of physical structure of the west African shoreline on the genetic structure of a small pelagic species. To investigate this question, the genetic diversity of <italic>E. fimbriata</italic> was assessed at both regional and species range scales, using mitochondrial (mt) and nuclear DNA markers. Whereas only three panmictic units were identified with mtDNA at the large spatial scale, nuclear genetic markers (EPIC: exon-primed intron-crossing) indicated a more complex genetic pattern at the regional scale. In the northern-most section of shad’s distribution range, up to 4 distinct units were identified. Bayesian inference as well as spatial autocorrelation methods provided evidence that gene flow is impeded by the presence of deep-water areas near the coastline (restricting the width of the coastal shelf), such as the Cap Timiris and the Kayar canyons in Mauritania and Senegal, respectively. The added discriminatory power provided by the use of EPIC markers proved to be essential to detect the influence of more subtle, contemporary processes (e.g. gene flow, barriers, etc.) acting within the glacial refuges identified previously by mtDNA.</p>  
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  Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 778  
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Auteur Masseret, E.; Banack, S.; Boumédiène, F.; Abadie, E.; Brient, L.; Pernet, F.; Juntas-Morales, R.; Pageot, N.; Metcalf, J.; Cox, P.; Camu, W.; the French Network on, A.L.S.C.D.; Investigation url  doi
openurl 
  Titre Dietary BMAA Exposure in an Amyotrophic Lateral Sclerosis Cluster from Southern France Type Article scientifique
  Année 2013 Publication Revue Abrégée PLoS ONE  
  Volume 8 Numéro 12 Pages  
  Mots-Clés  
  Résumé <sec sec-type=“headed”><title>Background</title><p>Dietary exposure to the cyanotoxin BMAA is suspected to be the cause of amyotrophic lateral sclerosis in the Western Pacific Islands. In Europe and North America, this toxin has been identified in the marine environment of amyotrophic lateral sclerosis clusters but, to date, only few dietary exposures have been described.</p></sec><sec sec-type=“headed”><title>Objectives</title><p>We aimed at identifying cluster(s) of amyotrophic lateral sclerosis in the Hérault district, a coastal district from Southern France, and to search, in the identified area(s), for the existence of a potential dietary source of BMAA.</p></sec><sec sec-type=“headed”><title>Methods</title><p>A spatio-temporal cluster analysis was performed in the district, considering all incident amyotrophic lateral sclerosis cases identified from 1994 to 2009 by our expert center. We investigated the cluster area with serial collections of oysters and mussels that were subsequently analyzed blind for BMAA concentrations.</p></sec><sec sec-type=“headed”><title>Results</title><p>We found one significant amyotrophic lateral sclerosis cluster (p = 0.0024), surrounding the Thau lagoon, the most important area of shellfish production and consumption along the French Mediterranean coast. BMAA was identified in mussels (1.8 µg/g to 6.0 µg/g) and oysters (0.6 µg/g to 1.6 µg/g). The highest concentrations of BMAA were measured during summer when the highest picocyanobacteria abundances were recorded. </p></sec><sec sec-type=“headed”><title>Conclusions</title><p>While it is not possible to ascertain a direct link between shellfish consumption and the existence of this ALS cluster, these results add new data to the potential association of BMAA with sporadic amyotrophic lateral sclerosis, one of the most severe neurodegenerative disorder.</p></sec>  
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Auteur Le Manach, F.; Chaboud, C.; Copeland, D.; Cury, P.; Gascuel, D.; Kleisner, K.M.; Standing, A.; Sumaila, U.R.; Zeller, D.; Pauly, D. url  doi
openurl 
  Titre European Union’s Public Fishing Access Agreements in Developing Countries Type Article scientifique
  Année 2013 Publication Revue Abrégée PLoS ONE  
  Volume 8 Numéro 11 Pages  
  Mots-Clés  
  Résumé The imperative to increase seafood supply while dealing with its overfished local stocks has pushed the European Union (EU) and its Member States to fish in the Exclusive Economic Zones of other countries through various types of fishing agreements for decades. Although European public fishing agreements are commented on regularly and considered to be transparent, this is the first global and historical study on the fee regime that governs them. We find that the EU has subsidized these agreements at an average of 75% of their cost (financial contribution agreed upon in the agreements), while private European business interests paid the equivalent of 1.5% of the value of the fish that was eventually landed. This raises questions of fisheries benefit-sharing and resource-use equity that the EU has the potential to address during the nearly completed reform of its Common Fisheries Policy.  
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  Numéro d'Appel LL @ pixluser @ collection 269  
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