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6,513 Research products

  • European Marine Science
  • 2014-2023
  • Research data
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  • FR
  • European Marine Science

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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: Trouche, Blandine;

    Anvi'o databases of the 47 ammonia-oxidizing archaea MAGs from abyssal and hadal surface sediments presented in Trouche et al, 2023 (https://doi.org/10.1038/s43705-023-00341-6). 

    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/ ZENODOarrow_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/
    ZENODO
    Other ORP type . 2023
    License: CC BY
    Data sources: ZENODO
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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/
      ZENODO
      Other ORP type . 2023
      License: CC BY
      Data sources: ZENODO
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  • Authors: Diaz-Arce, Natalia; Gagnaire, Pierre-Alexandre; Richardson, David E.; Walter III, John F.; +15 Authors

    The commercially important Atlantic bluefin tuna (Thunnus thynnus), a large migratory fish, has experienced notable recovery aided by accurate resource assessment and effective fisheries management efforts. Traditionally, this species has been perceived as consisting of eastern and western populations, spawning respectively in the Mediterranean Sea and the Gulf of Mexico, with mixing occurring throughout the Atlantic. However, recent studies have challenged this assumption by revealing weak genetic differentiation and identifying a previously unknown spawning ground in the Slope Sea used by Atlantic bluefin tuna of uncertain origin. To further understand the current and past population structure and connectivity of Atlantic bluefin tuna, we have assembled a unique dataset including thousands of genome-wide single-nucleotide polymorphisms (SNPs) from 500 larvae, young of the year and spawning adult samples covering the three spawning grounds and including individuals of other Thunnus species. Our analyses support two weakly differentiated but demographically connected ancestral populations that interbreed in the Slope Sea. Moreover, we also identified signatures of introgression from albacore (Thunnus alalunga) into the Atlantic bluefin tuna genome, exhibiting varied frequencies across spawning areas, indicating strong gene flow from the Mediterranean Sea towards the Slope Sea. We hypothesize that the observed genetic differentiation may be attributed to increased gene flow caused by a recent intensification of westward migration by the eastern population, which could have implications for the genetic diversity and conservation of western populations. Future conservation efforts should consider these findings to address potential genetic homogenization in the species.

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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: Ballantyne, John;

    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.

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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: Wang, Siyuan; Zhang, Futing; Koedooder, Coco; Qafoku, Odeta; +8 Authors

    The uploaded file contains three separate Python scripts aimed at modeling the sinking velocity of natural Trichodesmium colonies loaded with dust particles. Two scripts have been developed to calculate the dust influencing factor (K), and one script is dedicated to calculating the sinking velocity of particle-free Trichodesmium colonies (v0). All Python scripts are available on GitHub (https://github.com/Zhanzhu1110/Trichobuoyancy.git) and can be processed using the "Codespaces" function on GitHub. The file 'K given values' is a specialized script designed to simulate the dust factor (K), assuming seawater and dust densities of 1028 kg/m3 and 2500 kg/m3, respectively, with a colony radius of 1 mm.

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    ZENODO
    Model . 2023
    License: CC BY
    Data sources: ZENODO
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      ZENODO
      Model . 2023
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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: Muller, Veleda;

    This is an apatite and zircon (U-Th)/He dataset from the Fitz Roy and Torres del Paine regions in Southern Patagonia. The AHe data were analysed in the University of Arizona and University of Berkeley, USA and the ZHe data were analysed in the GEOPS Laboratory in the Paris-Saclay University, France. This data support the study “Geodynamic and climatic forcing on late-Cenozoic exhumation of the Southern Patagonian Andes (Fitz Roy and Torres del Paine massifs)” by Muller, V.A.P. et al., 2023 (DOI: 10.22541/essoar.168332179.93378898/v1).

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    Mendeley Data
    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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      Mendeley Data
      Dataset . 2023
      License: CC BY
      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/
    Authors: Zhen, Yicun; Resseguier, Valentin; chapron, bertrand;

    This is the document for the code mentioned in "On a generalization of Optical Flow algorithms for geophysical applications: a differential geometry perspective". (To save time, steps 1,2,3,4 can be skipped since the data is already saved in the corresponding filefolder) 1,GENERATE ENSEMBLE MEMBERS : run getens_doublevortex_256.py 2,GENERATE THE TRUTH : run gettruth_doublevortex_256.py 3,BEFORE MORPHING : run exp/get_dataens.py and exp/get_dataobs.py 4,MORPH THE ENSEMBLE : run exp/get_morphed.py 5,BEFORE DA : run exp/get_ens_LR.py and exp/get_truth_LR.py 6,DA : run exp/EnKF_direct.py and exp/EnKF_morphed.py 7,PLOT DA RESULTS : run exp/plt_comparemean.py and exp/plt_compare_member.py 8,MORPH WITH PLAIN T#(10000 steps) : run exp/get_morphed_noDiffGeo.py 9,MORPH WITH PLAIN T#(6000 steps) : run exp/get_morphed_noDiffGeo2.py 10,PLOT MORPHED ENSEMBLE MEMBERS : run exp/ensemble_morphed/figs/plt_main.py 11,PLOT MORPHED ENSEMBLE MEMBER WITH PLAIN T# : run exp/ensemble_morphed_noDiffGEo/figs/plt_main.py and exp/ensemble_morphed_noDiffGEo2/figs/plt_main.py

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    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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      ZENODO
      Dataset . 2023
      License: CC BY
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      ZENODO
      Dataset . 2023
      License: CC BY
      Data sources: Datacite
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    Authors: Koseki, Shunya; Vasquez, Ruben; Cabos, William; Gutierrez, Caludia; +2 Authors
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    Dataset . 2023
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    Dataset . 2023
    License: CC BY
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      Dataset . 2023
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      Dataset . 2023
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    Authors: Daniel Moreno-Parada; Alexander Robinson; Marisa Montoya; Jorge Alvarez-Solas;

    We present the ice-sheet model Nix, an open-source project intended for collaborative development. Nix is a 2D thermomechanical model written in C/C++ that simultaneously solves for the momentum balance equations, mass conservation and temperature evolution.

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    Model . 2023
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    Authors: Ballantyne, John;

    Combined quantum mechanical and molecular mechanical (QM/MM) methods play an important role in multiscale modeling and simulations. QMMM 2023 is a general-purpose program for single-point calculations, geometry optimizations, transition-state optimizations, and molecular dynamics (MD) at the QM/MM level. It calls a QM package and an MM package to perform the required single-level calculations and combines them into a QM/MM energy by a variety of schemes. QMMM 2023 supports GAMESS-US, Gaussian, and ORCA as QM packages and Tinker as the MM package. Four types of treatments are available for embedding the QM subsystem in the MM environment: mechanical embedding with gas-phase calculations of the QM region, electronic embedding that allows polarization of the QM region by the MM environment, polarizable embedding for mutual polarization of the QM and MM regions, and flexible embedding for both mutual polarization and partial charge transfer between the QM and MM regions. Boundaries between QM and MM regions that pass through covalent bonds can be treated by several methods, including the redistributed charge (RC) scheme, redistributed charge and dipole (RCD) scheme, balanced-RC scheme, balanced-RCD scheme, screened charge scheme that takes account of charge penetration effects, and smeared charge scheme that delocalizes the MM charges near the QM–MM boundary. Geometry optimization can be done using the optimizer implemented in QMMM 2023 or the Berny optimizer in Gaussian through external calls to Gaussian. Molecular dynamics simulations can be performed at the pure-MM level, pure-QM level, fixed-partitioning QM/MM level, and adaptive-partitioning QM/MM level. The adaptive-partitioning treatments permit on-the-fly relocation of the QM–MM boundary by dynamically reclassifying atoms or groups into the QM or MM subsystems.

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    Authors: Martínez Moreno, Josué;

    This dataset includes the NEMO 4.0.2 configuration used and analysed in the paper titled "Eddy-driven heterogeneity in sea ice during the ice-growth season". The output data is approximately 4TB for the 3 idealised configuration used in the manuscript, thus we opted to distribute the configuration. Note: The initial conditions for each simulation are compressed into the file `init_cond.zip` The configuration for one of the simulations is compressed in the file `config.zip` In order to reproduce all the runs, it's only required to change the initial conditions in the file namelist_cfg and namelist_ice_cfg. Further information and scripts to reproduce the result of the manuscript can be found at: https://github.com/josuemtzmo/Ice_formation

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    ZENODO
    Model . 2023
    License: CC BY
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6,513 Research products
  • 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: Trouche, Blandine;

    Anvi'o databases of the 47 ammonia-oxidizing archaea MAGs from abyssal and hadal surface sediments presented in Trouche et al, 2023 (https://doi.org/10.1038/s43705-023-00341-6). 

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    Other ORP type . 2023
    License: CC BY
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  • Authors: Diaz-Arce, Natalia; Gagnaire, Pierre-Alexandre; Richardson, David E.; Walter III, John F.; +15 Authors

    The commercially important Atlantic bluefin tuna (Thunnus thynnus), a large migratory fish, has experienced notable recovery aided by accurate resource assessment and effective fisheries management efforts. Traditionally, this species has been perceived as consisting of eastern and western populations, spawning respectively in the Mediterranean Sea and the Gulf of Mexico, with mixing occurring throughout the Atlantic. However, recent studies have challenged this assumption by revealing weak genetic differentiation and identifying a previously unknown spawning ground in the Slope Sea used by Atlantic bluefin tuna of uncertain origin. To further understand the current and past population structure and connectivity of Atlantic bluefin tuna, we have assembled a unique dataset including thousands of genome-wide single-nucleotide polymorphisms (SNPs) from 500 larvae, young of the year and spawning adult samples covering the three spawning grounds and including individuals of other Thunnus species. Our analyses support two weakly differentiated but demographically connected ancestral populations that interbreed in the Slope Sea. Moreover, we also identified signatures of introgression from albacore (Thunnus alalunga) into the Atlantic bluefin tuna genome, exhibiting varied frequencies across spawning areas, indicating strong gene flow from the Mediterranean Sea towards the Slope Sea. We hypothesize that the observed genetic differentiation may be attributed to increased gene flow caused by a recent intensification of westward migration by the eastern population, which could have implications for the genetic diversity and conservation of western populations. Future conservation efforts should consider these findings to address potential genetic homogenization in the species.

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    Authors: Ballantyne, John;

    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.

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    Authors: Wang, Siyuan; Zhang, Futing; Koedooder, Coco; Qafoku, Odeta; +8 Authors

    The uploaded file contains three separate Python scripts aimed at modeling the sinking velocity of natural Trichodesmium colonies loaded with dust particles. Two scripts have been developed to calculate the dust influencing factor (K), and one script is dedicated to calculating the sinking velocity of particle-free Trichodesmium colonies (v0). All Python scripts are available on GitHub (https://github.com/Zhanzhu1110/Trichobuoyancy.git) and can be processed using the "Codespaces" function on GitHub. The file 'K given values' is a specialized script designed to simulate the dust factor (K), assuming seawater and dust densities of 1028 kg/m3 and 2500 kg/m3, respectively, with a colony radius of 1 mm.

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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: Muller, Veleda;

    This is an apatite and zircon (U-Th)/He dataset from the Fitz Roy and Torres del Paine regions in Southern Patagonia. The AHe data were analysed in the University of Arizona and University of Berkeley, USA and the ZHe data were analysed in the GEOPS Laboratory in the Paris-Saclay University, France. This data support the study “Geodynamic and climatic forcing on late-Cenozoic exhumation of the Southern Patagonian Andes (Fitz Roy and Torres del Paine massifs)” by Muller, V.A.P. et al., 2023 (DOI: 10.22541/essoar.168332179.93378898/v1).

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    Dataset . 2023
    License: CC BY
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