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  • European Marine Science
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  • Mémoires en Sciences de l'Informati...

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Mark D. Goodsell; Ari Joury;

    We introduce BSMArt, a python program for the exploration of parameter spaces of theories Beyond the Standard Model. Especially designed for use with the SARAH family of tools, it is also sufficiently flexible to be used with a wide variety of external codes. BSMArt contains the first public release of the Active Learning scan by the same authors; but contains several additional scanning algorithms, ranging from the very simple to MultiNest and Diver. A BSMArt scan can be set up in a matter of minutes with only minimal editing of configuration files; installation scripts for all relevant tools and examples are provided. Comment: 33 pages; no figures. Code available at https://goodsell.pages.in2p3.fr/bsmart/

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ arXiv.org e-Print Ar...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Computer Physics Communications
    Article . 2024 . Peer-reviewed
    License: Elsevier TDM
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    https://doi.org/10.48550/arxiv...
    Article . 2023
    License: arXiv Non-Exclusive Distribution
    Data sources: Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ arXiv.org e-Print Ar...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Computer Physics Communications
      Article . 2024 . Peer-reviewed
      License: Elsevier TDM
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      https://doi.org/10.48550/arxiv...
      Article . 2023
      License: arXiv Non-Exclusive Distribution
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    Authors: Aiello, S; Albert, A; Garre, S. Alves; Aly, Z; +201 Authors

    Article signat per 266 autors/es:S. Aiello, A. Albert, S. Alves Garre, Z. Aly, A. Ambrosone, F. Ameli, M. Andre, E. Androutsou, M. Anghinolfi, M. Anguita, L. Aphecetche, M. Ardid, S. Ardid, H. Atmani, J. Aublin, C. Bagatelas, L. Bailly-Salins, Z. Bardačová, B. Baret, S. Basegmez du Pree, Y. Becherini, M. Bendahman, F. Benfenati , M. Benhassi, D.M. Benoit, E. Berbee, V. Bertin, V. van Beveren, S. Biagi, M. Boettcher, J. Boumaaza, M. Bouta, M. Bouwhuis, C. Bozza, R.M. Bozza, H. Brânzaş, F. Bretaudeau, R. Bruijn, J. Brunner, R. Bruno, E. Buis, R. Buompane, J. Busto, B. Caiffi, D. Calvo, S. Campion, A. Capone, F. Carenini, V. Carretero, T. Cartraud, P. Castaldi, V. Cecchini, S. Celli, L. Cerisy, M. Chabab, M. Chadolias, A. Chen, S. Cherubini , T. Chiarusi, M. Circella, R. Cocimano, J.A.B. Coelho, A. Coleiro, R. Coniglione, P. Coyle, A. Creusot, A. Cruz, G. Cuttone, R. Dallier, Y. Darras, A. De Benedittis, B. De Martino, V. Decoene, R. Del Burgo, L.S. Di Mauro, I. Di Palma, A.F. Díaz, D. Diego-Tortosa, C. Distefano, A. Domi, C. Donzaud, D. Dornic, M. Dörr, E. Drakopoulou, D. Drouhin, R. Dvornický, T. Eberl, E. Eckerová, A. Eddymaoui, T. van Eeden, M. Eff, D. van Eijk, I. El Bojaddaini, S. El Hedri, A. Enzenhöfer, G. Ferrara, M.D. Filipović, F. Filippini, L.A. Fusco, O. Gabella, J. Gabriel, S. Gagliardini, T. Gal, J. García Méndez, A. Garcia Soto, C. Gatius Oliver, N. Geißelbrecht, H. Ghaddari, L. Gialanella, B.K. Gibson, E. Giorgio, A. Girardi, I. Goos, D. Goupilliere, S.R. Gozzini, R. Gracia, K. Graf, C. Guidi, B. Guillon, M. Gutiérrez , H. van Haren, A. Heijboer, A. Hekalo, L. Hennig, J.J. Hernández-Rey, F. Huang, W. Idrissi Ibnsalih, G. Illuminati, C.W. James, P. Jansweijer, M. de Jong, P. de Jong, B.J. Jung, P. Kalaczyński, O. Kalekin, U.F. Katz, N.R. Khan Chowdhury, A. Khatun, G. Kistauri, C. Kopper, A. Kouchner, V. Kulikovskiy, R. Kvatadze, M. Labalme, R. Lahmann, G. Larosa, C. Lastoria, A. Lazo, S. Le Stum, G. Lehaut, E. Leonora, N. Lessing, G. Levi, M. Lindsey Clark, F. Longhitano, J. Majumdar, L. Malerba, F. Mamedov, J. Mańczak, A. Manfreda, M. Marconi, A. Margiotta, A. Marinelli, C. Markou, L. Martin, J.A. Martínez-Mora, F. Marzaioli, M. Mastrodicasa, S. Mastroianni, S. Miccichè, G. Miele, P. Migliozzi, E. Migneco, S. Minutoli, M.L. Mitsou, C.M. Mollo, L. Morales-Gallegos, C. Morley-Wong, A. Mosbrugger, A. Moussa, I. Mozun Mateo, R. Muller, M.R. Musone, M. Musumeci, L. Nauta, S. Navas, A. Nayerhoda, C.A. Nicolau, B. Nkosi, B. Ó Fearraigh, V. Oliviero, A. Orlando, E. Oukacha, J. Palacios González, G. Papalashvili, E.J. Pastor Gomez, A.M. Păun, G.E. Păvălaş, S. Peña Martínez, M. Perrin-Terrin, J. Perronnel, V. Pestel, R. Pestes, P. Piattelli, C. Poirè, V. Popa, T. Pradier, S. Pulvirenti, G. Quéméner, C. Quiroz, U. Rahaman, N. Randazzo, S. Razzaque, I.C. Rea, D. Real, S. Reck, G. Riccobene, J. Robinson y, A. Romanov aq j, A. Saina c, F. Salesa Greus c, D.F.E. Samtleben at s, A. Sánchez Losa c ak, M. Sanguineti aq j, C. Santonastaso bb e, D. Santonocito x, P. Sapienza x, Y. Scarpetta J. Schnabel, M.F. Schneider, J. Schumann, H.M. Schutte, J. Seneca, B. Setter, I. Sgura, R. Shanidze, Y. Shitov, F. Šimkovic, A. Simonelli, A. Sinopoulou, M.V. Smirnov, B. Spisso, M. Spurio, D. Stavropoulos, I. Štekl, M. Taiuti, Y. Tayalati, H. Tedjditi, H. Thiersen I. Tosta e Melo, B. Trocme, S. Tsagkli, V. Tsourapis, E. Tzamariudaki, A. Vacheret, V. Valsecchi, V. Van Elewyck, G. Vannoye, G. Vasileiadis, F. Vazquez de Sola, C. Verilhac, A. Veutro, S. Viola, D. Vivolo, H. Warnhofer, J. Wilms, E. de Wolf, H. Yepes-Ramirez, G. Zarpapis, S. Zavatarelli, A. Zegarelli, D. Zito, J.D. Zornoza, J. Zúñiga, N. Zywucka The authors acknowledge the financial support of the funding agencies: Agence Nationale de la Recherche (contract ANR-15-CE31-0020), Centre National de la Recherche Scientifique (CNRS), Commission européenne (FEDER fund and Marie Curie Program), Labex UnivEarthS (ANR-10-LABX-0023 and ANR-18-IDEX-0001), Paris Île-de-France Region, France; Shota Rustaveli National Science Foundation of Georgia (SRNSFG, FR-22-13708), Georgia; The General Secretariat of Research and Innovation (GSRI), Greece Istituto Nazionale di Fisica Nucleare (INFN), Ministero dell'Università e della Ricerca (MIUR), PRIN 2017 program (Grant NAT-NET 2017W4HA7S) Italy; Ministry of Higher Education, Scientific Research and Innovation, Morocco, and the Arab Fund for Economic and Social Development, Kuwait; Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO), the Netherlands; The National Science Centre, Poland (2021/41/N/ST2/01177); The grant “AstroCeNT: Particle Astrophysics Science and Technology Centre”, carried out within the International Research Agendas programme of the Foundation for Polish Science financed by the European Union under the European Regional Development Fund; National Authority for Scientific Research (ANCS), Romania; Grants PID2021-124591NB-C41, -C42, -C43 funded by MCIN/AEI/ 10.13039/501100011033 and, as appropriate, by “ERDF A way of making Europe”, by the “European Union” or by the “European Union NextGenerationEU/PRTR”, Programa de Planes Complementarios I+D+I (refs. ASFAE/2022/023, ASFAE/2022/014), Programa Prometeo (PROMETEO/2020/019) and GenT (refs. CIDEGENT/2018/034, /2019/043, /2020/049. /2021/23) of the Generalitat Valenciana, Junta de Andalucía (ref. SOMM17/6104/UGR, P18-FR-5057), EU: MSC program (ref. 101025085), Programa María Zambrano (Spanish Ministry of Universities, funded by the European Union, NextGenerationEU), Spain; The European Union's Horizon 2020 Research and Innovation Programme (ChETEC-INFRA - Project no. 101008324). The KM3NeT Collaboration is building and operating two deep sea neutrino telescopes at the bottom of the Mediterranean Sea. The telescopes consist of latices of photomultiplier tubes housed in pressure-resistant glass spheres, called digital optical modules and arranged in vertical detection units. The two main scientific goals are the determination of the neutrino mass ordering and the discovery and observation of high-energy neutrino sources in the Universe. Neutrinos are detected via the Cherenkov light, which is induced by charged particles originated in neutrino interactions. The photomultiplier tubes convert the Cherenkov light into electrical signals that are acquired and timestamped by the acquisition electronics. Each optical module houses the acquisition electronics for collecting and timestamping the photomultiplier signals with one nanosecond accuracy. Once finished, the two telescopes will have installed more than six thousand optical acquisition nodes, completing one of the more complex networks in the world in terms of operation and synchronization. The embedded software running in the acquisition nodes has been designed to provide a framework that will operate with different hardware versions and functionalities. The hardware will not be accessible once in operation, which complicates the embedded software architecture. The embedded software provides a set of tools to facilitate remote manageability of the deployed hardware, including safe reconfiguration of the firmware. This paper presents the architecture and the techniques, methods and implementation of the embedded software running in the acquisition nodes of the KM3NeT neutrino telescopes. Peer Reviewed

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ UPCommons. Portal de...arrow_drop_down
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    Other literature type . 2024 . Peer-reviewed
    License: CC BY NC
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    https://doi.org/10.48550/arxiv...
    Article . 2023
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    Authors: Hugo Iteney; Javier Antonio Gonzalez Joa; Christophe Le Bourlot; Thomas W. Cornelius; +2 Authors

    Natural samples are characterized by surface roughness which is intrinsically multi-scale as depicted by the well known concept of fractal dimension. Nevertheless, surface asperities are barely taken into account in simulations and modelling where flat surfaces and sharp corners or edges are generally preferred for the sake of simplicity. In this context, we propose here a versatile Python program called Pyrough that aims at building virtual samples characterized by configurable surface roughness for numerical applications such as atomistic and finite-element simulations. The program is open source and relies on the classical roughness theory that integrates the concept of self-affine surface. Several basic shapes including basic blocks, spheres, grains and wires with self-affine surface asperities are implemented and the object-oriented structure of the program simplifies the implementation of more complex objects. Virtual sample design is improved using Pyrough, which enables more realistic simulations to be made. Several application examples including e.g., the design of wavy grain boundaries or nanoindentation testing using a roughened indenter tip are presented.

    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Computer Physics Com...arrow_drop_down
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Computer Physics Communications
    Article . 2024 . Peer-reviewed
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Computer Physics Com...arrow_drop_down
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Computer Physics Communications
      Article . 2024 . Peer-reviewed
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Akihiro Koide; Sara Rabouli; Pierre Le Meur; Sylvain Tricot; +3 Authors

    International audience; We present the MsSpec Atomic Scattering Amplitude Package (MASAP), composed of a computation program and graphical interface to generate atomic scattering amplitude (ASA) an atom, either isolated or embedded in environment, at any chosen energy impinging electron up ≈15 KeV. The ASA is calculated using effective, complex optical potential which provides damping effects process fully relativistic framework. Optionally, scalar non-relativistic approximations are also available assess their applicability given problem. In order describe propagation solids we suggest replace ASA's based on Plane Waves (PW) with effective curved Spherical (SW) truncated-overlapped potentials Muffin-Tin (MT) type constructed according Mattheiss prescription. user generates not only data files providing Differential Cross Sections (DCS) but related quantities such as total Section (CS), both elastic inelastic, tl-matrices phase shifts. found general that imaginary part enhances DCSs forward direction compared same without part, feature theorem, gives rise lower intensity all other directions expected due effect potential. show differential transport for aluminum gold atoms isolation crystals Face-Centered-Cubic (FCC) structure.

    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Computer Physics Com...arrow_drop_down
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Computer Physics Communications
    Article . 2024 . Peer-reviewed
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Computer Physics Com...arrow_drop_down
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Computer Physics Communications
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  • image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Authors: Sardenne, Fany; Le Loc'h, François; Bodin, Nathalie; Mve-Beh, Jean-Hervé; +6 Authors

    International audience; Akanda National Park (ANP) is composed of mangrove ecosystems bordering Libreville, Gabon's capital. The contamination of aquatic resources from the ANP by persistent organic pollutants (POPs) and trace metals (TMs) was never evaluated. To provide a basis for their monitoring in the ANP, five species (two fish, two mollusks, and one crustacean) were analyzed from three sampling sites in 2017. Contamination levels for POPs and TMs were below maximum acceptable limits for seafood, including Cd and Pb. No DDT was found in any sample. Inter-specific differences were more obvious than the differences among sites, although the results may be biased by an unbalanced sampling design. The oyster Crassostrea gasar was the most contaminated species, making this species a good candidate to assess environmental contamination in the area. The studied species also contained essential elements, such as Fe, Zn and Mn at interesting levels in a nutritional point of view.

    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Marine Pollution Bul...arrow_drop_down
    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Marine Pollution Bulletin
    Article . 2024 . Peer-reviewed
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      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Marine Pollution Bul...arrow_drop_down
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
      Marine Pollution Bulletin
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    Authors: Violette Silve; Henrique Cabral; Martin Huret; Hilaire Drouineau;

    International audience; For many fishes, their early life stages are transported (passively) by currents between spawning areas and coastal nurseries, but also potential dispersal towards new habitats. Therefore, species have developed strategies to enhance the recruitment success, including the selection of appropriate spawning grounds. However, increased temperature due to climate change may lead to changes in hydrodynamics, shorter larval drifts, and earlier spawning, and consequently the location of the most suitable spawning grounds may change. We investigated whether the location of the most favourable spawning areas (allowing higher rates of larvae reaching coastal nurseries) was stable over time, and if differences could be found between environmentally contrasted years. We used a larval drift model taking into account hydrodynamics, larval characteristics and behaviour for three commercially exploited fish species (sole Solea solea, flounder Platichthys flesus and seabass Dicentrarchus labrax) in the Western Europe (encompassing the Bay of Biscay, the Celtic Sea and the English Channel). According to our model, we conclude that despite contrasting environmental conditions, the location of spawning grounds allowing the best chance of recruitment to nurseries for the offspring was fairly similar. However, even if the location of the main spawning grounds is stable over time, their relative effectiveness varies greatly between years. This would suggest that natural selection may favour the emergence of homing behaviour. This stability in this fish essential habitat location could facilitate protection measures. Going further, it could be interesting to study the variations occurring in spawning grounds (in terms of recruitment success, and retention/dispersion) during the course of a spawning season.

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    Estuarine Coastal and Shelf Science
    Article . 2024 . Peer-reviewed
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      Estuarine Coastal and Shelf Science
      Article . 2024 . Peer-reviewed
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    Authors: Amandine Morot; François Delavat; Alexis Bazire; Christine Paillard; +2 Authors

    The Vibrio genus includes bacteria widely distributed in aquatic habitats and the infections caused by these bacteria can affect a wide range of hosts. They are able to adhere to numerous surfaces, which can result in biofilm formation that helps maintain them in the environment. The involvement of the biofilm lifestyle in the virulence of Vibrio pathogens of aquatic organisms remains to be investigated. Vibrio harveyi ORM4 is a pathogen responsible for an outbreak in European abalone Haliotis tuberculata populations. In the present study, we used a dynamic biofilm culture technique coupled with laser scanning microscopy to characterize the biofilm formed by V. harveyi ORM4. We furthermore used RNA-seq analysis to examine the global changes in gene expression in biofilm cells compared to planktonic bacteria, and to identify biofilm- and virulence-related genes showing altered expression. A total of 1565 genes were differentially expressed, including genes associated with motility, polysaccharide synthesis, and quorum sensing. The up-regulation of 18 genes associated with the synthesis of the type III secretion system suggests that this virulence factor is induced in V. harveyi ORM4 biofilms, providing indirect evidence of a relationship between biofilm and virulence.

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    Microorganisms
    Article . 2024 . Peer-reviewed
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    Article . 2024
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      Microorganisms
      Article . 2024 . Peer-reviewed
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    Authors: Tim Druitt; Steffen Kutterolf; Thomas A. Ronge; Christian Hübscher; +33 Authors

    AbstractLarge explosive volcanic eruptions from island arcs pour pyroclastic currents into marine basins, impacting ecosystems and generating tsunamis that threaten coastal communities and infrastructures. Risk assessments require robust records of such highly hazardous events, which is challenging as most of the products lie buried under the sea. Here we report the discovery by IODP Expedition 398 of a giant rhyolitic pumice deposit emplaced 520 ± 10 ky ago at water depths of 200 to 1000 m during a high-intensity, shallow submarine eruption of ancestral Santorini Volcano. Pyroclastic currents discharged into the sea transformed into turbidity currents and slurries, forming a >89 ± 8 km3 volcaniclastic megaturbidite up to 150 m thick in the surrounding marine basins, while breaching of the sea surface by the eruption column laid down veneers of ignimbrite on three islands. The eruption is one of the largest recorded on the South Aegean Volcanic Arc, and highlights the hazards from submarine explosive eruptions.

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    DOAJ
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    Authors: Baptiste Delaporte; Thomas Arsouze; Gunnar Keppel; Swen Jullien; +2 Authors

    StormR is an R package allowing the easy extraction of storm track data from a provided database and the generation of surface wind fields (speed and direction) as reconstructed from storm track data and a parametric cyclone model. Then StormR allows us to compute three summary statistics (the maximum sustained wind speed, the power dissipation index, and the duration of exposure to winds reaching a given wing speed along the cyclone life span) and to plot the results. We suggest to use the IBTrACS (International Best Track Archive for Climate Stewardship) database as input (Knapp et al., 2010, 2018). This database provides a fairly comprehensive record of tropical storms and cyclones with a 3-hours temporal resolution since 1841. However any storm track data can be used as long as the mandatory fields are provided. Storm track data can be extracted using a specified point location, a user defined spatial polygon shapefile, a country or a cyclone basin name. The main functions of the StormR package allow us to generate wind speed and direction fields as reconstructed from storm track data and a parametric cyclone model. Different models and models combinations can be chosen by the user. By default the spatial resolution is set to 2.5 min (~4.5 km at the equator), but a finer spatial resolution of 30 s (~1 km at the equator) and coarser spatial resolutions of 5 min (~9 km at the equator) or 10 min (~18.6 km at the equator) can be set. The temporal resolution is set to 1 hour by default but finer resolutions of 45 min, 30 min, or 15 min can be set. Once wind speed is generated for each cell or specific location and each time step, StormR functions can compute summary statistics on wind speed over the lifespan of a storm. Summary statistics encompass the maximum sustained wind speed, the power dissipation index or total power dissipated by a tropical storm (Emanuel, 1999, 2005), and the duration of exposure to winds reaching defined speed thresholds. By default the duration of exposure is computed for each Saffir-Simpson Hurricane Scale threshold values for tropical cyclone categories, i.e., 33, 43, 50, 58, and 70 𝑚.𝑠−1 (Simpson, 1974), but can be defined by the user.

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    Journal of Open Source Software
    Article . 2024 . Peer-reviewed
    License: CC BY
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      Journal of Open Source Software
      Article . 2024 . Peer-reviewed
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    Authors: Aina Astorch-Cardona; Giliane P. Odin; Valérie Chavagnac; Alain Dolla; +2 Authors

    ABSTRACT Zetaproteobacteria have been reported in different marine and terrestrial environments all over the globe. They play an essential role in marine iron-rich microbial mats, as one of their autotrophic primary producers, oxidizing Fe(II) and producing Fe-oxyhydroxides with different morphologies. Here, we study and compare the Zetaproteobacterial communities of iron-rich microbial mats from six different sites of the Lucky Strike Hydrothermal Field through the use of the Zetaproteobacterial operational taxonomic unit (ZetaOTU) classification. We report for the first time the Zetaproteobacterial core microbiome of these iron-rich microbial mats, which is composed of four ZetaOTUs that are cosmopolitan and essential for the development of the mats. The study of the presence and abundance of different ZetaOTUs among sites reveals two clusters, which are related to the lithology and permeability of the substratum on which they develop. The Zetaproteobacterial communities of cluster 1 are characteristic of poorly permeable substrata, with little evidence of diffuse venting, while those of cluster 2 develop on hydrothermal slabs or deposits that allow the percolation and outflow of diffuse hydrothermal fluids. In addition, two NewZetaOTUs 1 and 2 were identified, which could be characteristic of anthropic iron and unsedimented basalt, respectively. We also report significant correlations between the abundance of certain ZetaOTUs and that of iron oxide morphologies, indicating that their formation could be taxonomically and/or environmentally driven. We identified a new morphology of Fe(III)-oxyhydroxides that we named “corals.” Overall, our work contributes to the knowledge of the biogeography of this bacterial class by providing additional data from the Atlantic Ocean, a lesser-studied ocean in terms of Zetaproteobacterial diversity. IMPORTANCE Up until now, Zetaproteobacterial diversity studies have revealed possible links between Zetaproteobacteria taxa, habitats, and niches. Here, we report for the first time the Zetaproteobacterial core microbiome of iron-rich mats from the Lucky Strike Hydrothermal Field (LSHF), as well as two new Zetaproteobacterial operational taxonomic units (NewZetaOTUs) that could be substratum specific. We highlight that the substratum on which iron-rich microbial mats develop, especially because of its permeability to diffuse hydrothermal venting, has an influence on their Zetaproteobacterial communities. Moreover, our work adds to the knowledge of the biogeography of this bacterial class by providing additional data from the hydrothermal vent sites along the Mid-Atlantic Ridge. In addition to the already described iron oxide morphologies, we identify in our iron-rich mats a new morphology that we named corals. Finally, we argue for significant correlations between the relative abundance of certain ZetaOTUs and that of iron oxide morphologies, contributing to the understanding of the drivers of iron oxide production in iron-oxidizing bacteria.

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    Applied and Environmental Microbiology
    Article . 2024 . Peer-reviewed
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      Applied and Environmental Microbiology
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    Authors: Mark D. Goodsell; Ari Joury;

    We introduce BSMArt, a python program for the exploration of parameter spaces of theories Beyond the Standard Model. Especially designed for use with the SARAH family of tools, it is also sufficiently flexible to be used with a wide variety of external codes. BSMArt contains the first public release of the Active Learning scan by the same authors; but contains several additional scanning algorithms, ranging from the very simple to MultiNest and Diver. A BSMArt scan can be set up in a matter of minutes with only minimal editing of configuration files; installation scripts for all relevant tools and examples are provided. Comment: 33 pages; no figures. Code available at https://goodsell.pages.in2p3.fr/bsmart/

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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    Computer Physics Communications
    Article . 2024 . Peer-reviewed
    License: Elsevier TDM
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    https://doi.org/10.48550/arxiv...
    Article . 2023
    License: arXiv Non-Exclusive Distribution
    Data sources: Datacite
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      Computer Physics Communications
      Article . 2024 . Peer-reviewed
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      https://doi.org/10.48550/arxiv...
      Article . 2023
      License: arXiv Non-Exclusive Distribution
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    Authors: Aiello, S; Albert, A; Garre, S. Alves; Aly, Z; +201 Authors

    Article signat per 266 autors/es:S. Aiello, A. Albert, S. Alves Garre, Z. Aly, A. Ambrosone, F. Ameli, M. Andre, E. Androutsou, M. Anghinolfi, M. Anguita, L. Aphecetche, M. Ardid, S. Ardid, H. Atmani, J. Aublin, C. Bagatelas, L. Bailly-Salins, Z. Bardačová, B. Baret, S. Basegmez du Pree, Y. Becherini, M. Bendahman, F. Benfenati , M. Benhassi, D.M. Benoit, E. Berbee, V. Bertin, V. van Beveren, S. Biagi, M. Boettcher, J. Boumaaza, M. Bouta, M. Bouwhuis, C. Bozza, R.M. Bozza, H. Brânzaş, F. Bretaudeau, R. Bruijn, J. Brunner, R. Bruno, E. Buis, R. Buompane, J. Busto, B. Caiffi, D. Calvo, S. Campion, A. Capone, F. Carenini, V. Carretero, T. Cartraud, P. Castaldi, V. Cecchini, S. Celli, L. Cerisy, M. Chabab, M. Chadolias, A. Chen, S. Cherubini , T. Chiarusi, M. Circella, R. Cocimano, J.A.B. Coelho, A. Coleiro, R. Coniglione, P. Coyle, A. Creusot, A. Cruz, G. Cuttone, R. Dallier, Y. Darras, A. De Benedittis, B. De Martino, V. Decoene, R. Del Burgo, L.S. Di Mauro, I. Di Palma, A.F. Díaz, D. Diego-Tortosa, C. Distefano, A. Domi, C. Donzaud, D. Dornic, M. Dörr, E. Drakopoulou, D. Drouhin, R. Dvornický, T. Eberl, E. Eckerová, A. Eddymaoui, T. van Eeden, M. Eff, D. van Eijk, I. El Bojaddaini, S. El Hedri, A. Enzenhöfer, G. Ferrara, M.D. Filipović, F. Filippini, L.A. Fusco, O. Gabella, J. Gabriel, S. Gagliardini, T. Gal, J. García Méndez, A. Garcia Soto, C. Gatius Oliver, N. Geißelbrecht, H. Ghaddari, L. Gialanella, B.K. Gibson, E. Giorgio, A. Girardi, I. Goos, D. Goupilliere, S.R. Gozzini, R. Gracia, K. Graf, C. Guidi, B. Guillon, M. Gutiérrez , H. van Haren, A. Heijboer, A. Hekalo, L. Hennig, J.J. Hernández-Rey, F. Huang, W. Idrissi Ibnsalih, G. Illuminati, C.W. James, P. Jansweijer, M. de Jong, P. de Jong, B.J. Jung, P. Kalaczyński, O. Kalekin, U.F. Katz, N.R. Khan Chowdhury, A. Khatun, G. Kistauri, C. Kopper, A. Kouchner, V. Kulikovskiy, R. Kvatadze, M. Labalme, R. Lahmann, G. Larosa, C. Lastoria, A. Lazo, S. Le Stum, G. Lehaut, E. Leonora, N. Lessing, G. Levi, M. Lindsey Clark, F. Longhitano, J. Majumdar, L. Malerba, F. Mamedov, J. Mańczak, A. Manfreda, M. Marconi, A. Margiotta, A. Marinelli, C. Markou, L. Martin, J.A. Martínez-Mora, F. Marzaioli, M. Mastrodicasa, S. Mastroianni, S. Miccichè, G. Miele, P. Migliozzi, E. Migneco, S. Minutoli, M.L. Mitsou, C.M. Mollo, L. Morales-Gallegos, C. Morley-Wong, A. Mosbrugger, A. Moussa, I. Mozun Mateo, R. Muller, M.R. Musone, M. Musumeci, L. Nauta, S. Navas, A. Nayerhoda, C.A. Nicolau, B. Nkosi, B. Ó Fearraigh, V. Oliviero, A. Orlando, E. Oukacha, J. Palacios González, G. Papalashvili, E.J. Pastor Gomez, A.M. Păun, G.E. Păvălaş, S. Peña Martínez, M. Perrin-Terrin, J. Perronnel, V. Pestel, R. Pestes, P. Piattelli, C. Poirè, V. Popa, T. Pradier, S. Pulvirenti, G. Quéméner, C. Quiroz, U. Rahaman, N. Randazzo, S. Razzaque, I.C. Rea, D. Real, S. Reck, G. Riccobene, J. Robinson y, A. Romanov aq j, A. Saina c, F. Salesa Greus c, D.F.E. Samtleben at s, A. Sánchez Losa c ak, M. Sanguineti aq j, C. Santonastaso bb e, D. Santonocito x, P. Sapienza x, Y. Scarpetta J. Schnabel, M.F. Schneider, J. Schumann, H.M. Schutte, J. Seneca, B. Setter, I. Sgura, R. Shanidze, Y. Shitov, F. Šimkovic, A. Simonelli, A. Sinopoulou, M.V. Smirnov, B. Spisso, M. Spurio, D. Stavropoulos, I. Štekl, M. Taiuti, Y. Tayalati, H. Tedjditi, H. Thiersen I. Tosta e Melo, B. Trocme, S. Tsagkli, V. Tsourapis, E. Tzamariudaki, A. Vacheret, V. Valsecchi, V. Van Elewyck, G. Vannoye, G. Vasileiadis, F. Vazquez de Sola, C. Verilhac, A. Veutro, S. Viola, D. Vivolo, H. Warnhofer, J. Wilms, E. de Wolf, H. Yepes-Ramirez, G. Zarpapis, S. Zavatarelli, A. Zegarelli, D. Zito, J.D. Zornoza, J. Zúñiga, N. Zywucka The authors acknowledge the financial support of the funding agencies: Agence Nationale de la Recherche (contract ANR-15-CE31-0020), Centre National de la Recherche Scientifique (CNRS), Commission européenne (FEDER fund and Marie Curie Program), Labex UnivEarthS (ANR-10-LABX-0023 and ANR-18-IDEX-0001), Paris Île-de-France Region, France; Shota Rustaveli National Science Foundation of Georgia (SRNSFG, FR-22-13708), Georgia; The General Secretariat of Research and Innovation (GSRI), Greece Istituto Nazionale di Fisica Nucleare (INFN), Ministero dell'Università e della Ricerca (MIUR), PRIN 2017 program (Grant NAT-NET 2017W4HA7S) Italy; Ministry of Higher Education, Scientific Research and Innovation, Morocco, and the Arab Fund for Economic and Social Development, Kuwait; Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO), the Netherlands; The National Science Centre, Poland (2021/41/N/ST2/01177); The grant “AstroCeNT: Particle Astrophysics Science and Technology Centre”, carried out within the International Research Agendas programme of the Foundation for Polish Science financed by the European Union under the European Regional Development Fund; National Authority for Scientific Research (ANCS), Romania; Grants PID2021-124591NB-C41, -C42, -C43 funded by MCIN/AEI/ 10.13039/501100011033 and, as appropriate, by “ERDF A way of making Europe”, by the “European Union” or by the “European Union NextGenerationEU/PRTR”, Programa de Planes Complementarios I+D+I (refs. ASFAE/2022/023, ASFAE/2022/014), Programa Prometeo (PROMETEO/2020/019) and GenT (refs. CIDEGENT/2018/034, /2019/043, /2020/049. /2021/23) of the Generalitat Valenciana, Junta de Andalucía (ref. SOMM17/6104/UGR, P18-FR-5057), EU: MSC program (ref. 101025085), Programa María Zambrano (Spanish Ministry of Universities, funded by the European Union, NextGenerationEU), Spain; The European Union's Horizon 2020 Research and Innovation Programme (ChETEC-INFRA - Project no. 101008324). The KM3NeT Collaboration is building and operating two deep sea neutrino telescopes at the bottom of the Mediterranean Sea. The telescopes consist of latices of photomultiplier tubes housed in pressure-resistant glass spheres, called digital optical modules and arranged in vertical detection units. The two main scientific goals are the determination of the neutrino mass ordering and the discovery and observation of high-energy neutrino sources in the Universe. Neutrinos are detected via the Cherenkov light, which is induced by charged particles originated in neutrino interactions. The photomultiplier tubes convert the Cherenkov light into electrical signals that are acquired and timestamped by the acquisition electronics. Each optical module houses the acquisition electronics for collecting and timestamping the photomultiplier signals with one nanosecond accuracy. Once finished, the two telescopes will have installed more than six thousand optical acquisition nodes, completing one of the more complex networks in the world in terms of operation and synchronization. The embedded software running in the acquisition nodes has been designed to provide a framework that will operate with different hardware versions and functionalities. The hardware will not be accessible once in operation, which complicates the embedded software architecture. The embedded software provides a set of tools to facilitate remote manageability of the deployed hardware, including safe reconfiguration of the firmware. This paper presents the architecture and the techniques, methods and implementation of the embedded software running in the acquisition nodes of the KM3NeT neutrino telescopes. Peer Reviewed

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    https://doi.org/10.48550/arxiv...
    Article . 2023
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    Authors: Hugo Iteney; Javier Antonio Gonzalez Joa; Christophe Le Bourlot; Thomas W. Cornelius; +2 Authors

    Natural samples are characterized by surface roughness which is intrinsically multi-scale as depicted by the well known concept of fractal dimension. Nevertheless, surface asperities are barely taken into account in simulations and modelling where flat surfaces and sharp corners or edges are generally preferred for the sake of simplicity. In this context, we propose here a versatile Python program called Pyrough that aims at building virtual samples characterized by configurable surface roughness for numerical applications such as atomistic and finite-element simulations. The program is open source and relies on the classical roughness theory that integrates the concept of self-affine surface. Several basic shapes including basic blocks, spheres, grains and wires with self-affine surface asperities are implemented and the object-oriented structure of the program simplifies the implementation of more complex objects. Virtual sample design is improved using Pyrough, which enables more realistic simulations to be made. Several application examples including e.g., the design of wavy grain boundaries or nanoindentation testing using a roughened indenter tip are presented.

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    Computer Physics Communications
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      Computer Physics Communications
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    Authors: Akihiro Koide; Sara Rabouli; Pierre Le Meur; Sylvain Tricot; +3 Authors

    International audience; We present the MsSpec Atomic Scattering Amplitude Package (MASAP), composed of a computation program and graphical interface to generate atomic scattering amplitude (ASA) an atom, either isolated or embedded in environment, at any chosen energy impinging electron up ≈15 KeV. The ASA is calculated using effective, complex optical potential which provides damping effects process fully relativistic framework. Optionally, scalar non-relativistic approximations are also available assess their applicability given problem. In order describe propagation solids we suggest replace ASA's based on Plane Waves (PW) with effective curved Spherical (SW) truncated-overlapped potentials Muffin-Tin (MT) type constructed according Mattheiss prescription. user generates not only data files providing Differential Cross Sections (DCS) but related quantities such as total Section (CS), both elastic inelastic, tl-matrices phase shifts. found general that imaginary part enhances DCSs forward direction compared same without part, feature theorem, gives rise lower intensity all other directions expected due effect potential. show differential transport for aluminum gold atoms isolation crystals Face-Centered-Cubic (FCC) structure.

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    Computer Physics Communications
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      Computer Physics Communications
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    Authors: Sardenne, Fany; Le Loc'h, François; Bodin, Nathalie; Mve-Beh, Jean-Hervé; +6 Authors

    International audience; Akanda National Park (ANP) is composed of mangrove ecosystems bordering Libreville, Gabon's capital. The contamination of aquatic resources from the ANP by persistent organic pollutants (POPs) and trace metals (TMs) was never evaluated. To provide a basis for their monitoring in the ANP, five species (two fish, two mollusks, and one crustacean) were analyzed from three sampling sites in 2017. Contamination levels for POPs and TMs were below maximum acceptable limits for seafood, including Cd and Pb. No DDT was found in any sample. Inter-specific differences were more obvious than the differences among sites, although the results may be biased by an unbalanced sampling design. The oyster Crassostrea gasar was the most contaminated species, making this species a good candidate to assess environmental contamination in the area. The studied species also contained essential elements, such as Fe, Zn and Mn at interesting levels in a nutritional point of view.

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    Marine Pollution Bulletin
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      Marine Pollution Bulletin
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    Authors: Violette Silve; Henrique Cabral; Martin Huret; Hilaire Drouineau;

    International audience; For many fishes, their early life stages are transported (passively) by currents between spawning areas and coastal nurseries, but also potential dispersal towards new habitats. Therefore, species have developed strategies to enhance the recruitment success, including the selection of appropriate spawning grounds. However, increased temperature due to climate change may lead to changes in hydrodynamics, shorter larval drifts, and earlier spawning, and consequently the location of the most suitable spawning grounds may change. We investigated whether the location of the most favourable spawning areas (allowing higher rates of larvae reaching coastal nurseries) was stable over time, and if differences could be found between environmentally contrasted years. We used a larval drift model taking into account hydrodynamics, larval characteristics and behaviour for three commercially exploited fish species (sole Solea solea, flounder Platichthys flesus and seabass Dicentrarchus labrax) in the Western Europe (encompassing the Bay of Biscay, the Celtic Sea and the English Channel). According to our model, we conclude that despite contrasting environmental conditions, the location of spawning grounds allowing the best chance of recruitment to nurseries for the offspring was fairly similar. However, even if the location of the main spawning grounds is stable over time, their relative effectiveness varies greatly between years. This would suggest that natural selection may favour the emergence of homing behaviour. This stability in this fish essential habitat location could facilitate protection measures. Going further, it could be interesting to study the variations occurring in spawning grounds (in terms of recruitment success, and retention/dispersion) during the course of a spawning season.

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    Estuarine Coastal and Shelf Science
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      Estuarine Coastal and Shelf Science
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    Authors: Amandine Morot; François Delavat; Alexis Bazire; Christine Paillard; +2 Authors

    The Vibrio genus includes bacteria widely distributed in aquatic habitats and the infections caused by these bacteria can affect a wide range of hosts. They are able to adhere to numerous surfaces, which can result in biofilm formation that helps maintain them in the environment. The involvement of the biofilm lifestyle in the virulence of Vibrio pathogens of aquatic organisms remains to be investigated. Vibrio harveyi ORM4 is a pathogen responsible for an outbreak in European abalone Haliotis tuberculata populations. In the present study, we used a dynamic biofilm culture technique coupled with laser scanning microscopy to characterize the biofilm formed by V. harveyi ORM4. We furthermore used RNA-seq analysis to examine the global changes in gene expression in biofilm cells compared to planktonic bacteria, and to identify biofilm- and virulence-related genes showing altered expression. A total of 1565 genes were differentially expressed, including genes associated with motility, polysaccharide synthesis, and quorum sensing. The up-regulation of 18 genes associated with the synthesis of the type III secretion system suggests that this virulence factor is induced in V. harveyi ORM4 biofilms, providing indirect evidence of a relationship between biofilm and virulence.

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    Microorganisms
    Article . 2024 . Peer-reviewed
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    Article . 2024
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      Microorganisms
      Article . 2024 . Peer-reviewed
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      Article . 2024
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    Authors: Tim Druitt; Steffen Kutterolf; Thomas A. Ronge; Christian Hübscher; +33 Authors

    AbstractLarge explosive volcanic eruptions from island arcs pour pyroclastic currents into marine basins, impacting ecosystems and generating tsunamis that threaten coastal communities and infrastructures. Risk assessments require robust records of such highly hazardous events, which is challenging as most of the products lie buried under the sea. Here we report the discovery by IODP Expedition 398 of a giant rhyolitic pumice deposit emplaced 520 ± 10 ky ago at water depths of 200 to 1000 m during a high-intensity, shallow submarine eruption of ancestral Santorini Volcano. Pyroclastic currents discharged into the sea transformed into turbidity currents and slurries, forming a >89 ± 8 km3 volcaniclastic megaturbidite up to 150 m thick in the surrounding marine basins, while breaching of the sea surface by the eruption column laid down veneers of ignimbrite on three islands. The eruption is one of the largest recorded on the South Aegean Volcanic Arc, and highlights the hazards from submarine explosive eruptions.

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    DOAJ
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    Authors: Baptiste Delaporte; Thomas Arsouze; Gunnar Keppel; Swen Jullien; +2 Authors

    StormR is an R package allowing the easy extraction of storm track data from a provided database and the generation of surface wind fields (speed and direction) as reconstructed from storm track data and a parametric cyclone model. Then StormR allows us to compute three summary statistics (the maximum sustained wind speed, the power dissipation index, and the duration of exposure to winds reaching a given wing speed along the cyclone life span) and to plot the results. We suggest to use the IBTrACS (International Best Track Archive for Climate Stewardship) database as input (Knapp et al., 2010, 2018). This database provides a fairly comprehensive record of tropical storms and cyclones with a 3-hours temporal resolution since 1841. However any storm track data can be used as long as the mandatory fields are provided. Storm track data can be extracted using a specified point location, a user defined spatial polygon shapefile, a country or a cyclone basin name. The main functions of the StormR package allow us to generate wind speed and direction fields as reconstructed from storm track data and a parametric cyclone model. Different models and models combinations can be chosen by the user. By default the spatial resolution is set to 2.5 min (~4.5 km at the equator), but a finer spatial resolution of 30 s (~1 km at the equator) and coarser spatial resolutions of 5 min (~9 km at the equator) or 10 min (~18.6 km at the equator) can be set. The temporal resolution is set to 1 hour by default but finer resolutions of 45 min, 30 min, or 15 min can be set. Once wind speed is generated for each cell or specific location and each time step, StormR functions can compute summary statistics on wind speed over the lifespan of a storm. Summary statistics encompass the maximum sustained wind speed, the power dissipation index or total power dissipated by a tropical storm (Emanuel, 1999, 2005), and the duration of exposure to winds reaching defined speed thresholds. By default the duration of exposure is computed for each Saffir-Simpson Hurricane Scale threshold values for tropical cyclone categories, i.e., 33, 43, 50, 58, and 70 𝑚.𝑠−1 (Simpson, 1974), but can be defined by the user.

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    Journal of Open Source Software
    Article . 2024 . Peer-reviewed
    License: CC BY
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      Journal of Open Source Software
      Article . 2024 . Peer-reviewed
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    Authors: Aina Astorch-Cardona; Giliane P. Odin; Valérie Chavagnac; Alain Dolla; +2 Authors

    ABSTRACT Zetaproteobacteria have been reported in different marine and terrestrial environments all over the globe. They play an essential role in marine iron-rich microbial mats, as one of their autotrophic primary producers, oxidizing Fe(II) and producing Fe-oxyhydroxides with different morphologies. Here, we study and compare the Zetaproteobacterial communities of iron-rich microbial mats from six different sites of the Lucky Strike Hydrothermal Field through the use of the Zetaproteobacterial operational taxonomic unit (ZetaOTU) classification. We report for the first time the Zetaproteobacterial core microbiome of these iron-rich microbial mats, which is composed of four ZetaOTUs that are cosmopolitan and essential for the development of the mats. The study of the presence and abundance of different ZetaOTUs among sites reveals two clusters, which are related to the lithology and permeability of the substratum on which they develop. The Zetaproteobacterial communities of cluster 1 are characteristic of poorly permeable substrata, with little evidence of diffuse venting, while those of cluster 2 develop on hydrothermal slabs or deposits that allow the percolation and outflow of diffuse hydrothermal fluids. In addition, two NewZetaOTUs 1 and 2 were identified, which could be characteristic of anthropic iron and unsedimented basalt, respectively. We also report significant correlations between the abundance of certain ZetaOTUs and that of iron oxide morphologies, indicating that their formation could be taxonomically and/or environmentally driven. We identified a new morphology of Fe(III)-oxyhydroxides that we named “corals.” Overall, our work contributes to the knowledge of the biogeography of this bacterial class by providing additional data from the Atlantic Ocean, a lesser-studied ocean in terms of Zetaproteobacterial diversity. IMPORTANCE Up until now, Zetaproteobacterial diversity studies have revealed possible links between Zetaproteobacteria taxa, habitats, and niches. Here, we report for the first time the Zetaproteobacterial core microbiome of iron-rich mats from the Lucky Strike Hydrothermal Field (LSHF), as well as two new Zetaproteobacterial operational taxonomic units (NewZetaOTUs) that could be substratum specific. We highlight that the substratum on which iron-rich microbial mats develop, especially because of its permeability to diffuse hydrothermal venting, has an influence on their Zetaproteobacterial communities. Moreover, our work adds to the knowledge of the biogeography of this bacterial class by providing additional data from the hydrothermal vent sites along the Mid-Atlantic Ridge. In addition to the already described iron oxide morphologies, we identify in our iron-rich mats a new morphology that we named corals. Finally, we argue for significant correlations between the relative abundance of certain ZetaOTUs and that of iron oxide morphologies, contributing to the understanding of the drivers of iron oxide production in iron-oxidizing bacteria.

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    Applied and Environmental Microbiology
    Article . 2024 . Peer-reviewed
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      Applied and Environmental Microbiology
      Article . 2024 . Peer-reviewed
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