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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: David, Romain; Richard, Audrey S.; Connellan, Claire; Lauer, Katharina B.; +41 Authors

    THIS PAPER IS NOW PUBLISHED: https://doi.org/10.5334/dsj-2023-035 The Horizon Europe project ISIDORe is dedicated to pandemic preparedness and responsiveness research. It brings together 17 Research Infrastructures (RIs) and networks to provide a broad range of services to infectious disease researchers. An efficient and structured treatment of data is central to ISIDORe’s aim to furnish seamless access to its multidisciplinary catalogue of services, and to ensure that users’ results are treated FAIRly. ISIDORe therefore requires a data management plan (DMP) covering both access management and research outputs, applicable over a broad range of disciplines, and compatible with the constraints and existing practices of its diverse partners. We undertook an iterative, step-by-step, process to build a community-approved living document, identifying good practices and processes, on the basis of use cases, presented as proof of concepts. International fora such as the RDA and EOSC, and primarily the BY-COVID project, furnished registries, tools and online data platforms, as well as standards, and the support of data scientists. Together, these elements provide a path for building an umbrella, FAIR-compliant DMP, aligned as fully as possible with FAIR principles, which could also be applied as a framework for data management harmonisation in other large-scale, challenge-driven projects. Finally, we discuss how data management and reuse can be further improved through the writing of realistic DMPs using 'DMP profiles' and, in the future, the contribution of an inter RIs data steward network, to produce a Community of Practice that could be integrated into planned trans-RI competence centres. Preprint added on zenodo with the autorisation of DSJ Editor

    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/ Oxford University Re...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/
    Oxford University Research Archive
    Other literature type . 2023
    License: CC BY
    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 literature type . 2023
    License: CC BY
    Data sources: ZENODO
    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 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
    Preprint . 2023
    License: CC BY
    Data sources: ZENODO
    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/
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    ZENODO
    Preprint . 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/
    Data Science Journal
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
    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
    Preprint . 2023
    License: CC BY
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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
    Preprint . 2023
    License: CC BY
    Data sources: ZENODO
    ZENODO
    Conference object . 2023
    License: CC BY
    Data sources: Datacite
    DOAJ
    Article . 2023
    Data sources: DOAJ
    ZENODO
    Preprint . 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/ Oxford University Re...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/
      Oxford University Research Archive
      Other literature type . 2023
      License: CC BY
      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 literature type . 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/
      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
      Preprint . 2023
      License: CC BY
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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/
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      ZENODO
      Preprint . 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/
      Data Science Journal
      Article . 2023 . Peer-reviewed
      License: CC BY
      Data sources: Crossref
      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
      Preprint . 2023
      License: CC BY
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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
      Preprint . 2023
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      ZENODO
      Conference object . 2023
      License: CC BY
      Data sources: Datacite
      DOAJ
      Article . 2023
      Data sources: DOAJ
      ZENODO
      Preprint . 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: Susanne Seemann; Manuela Dubs; Dirk Koczan; Hernando S. Salapare; +8 Authors

    International audience; Increased life expectancy in industrialized countries is causing an increased incidence of osteoporosis and the need for bioactive bone implants. The integration of implants can be improved physically, but mainly by chemical modifications of the material surface. It was recognized that amino-group-containing coatings improved cell attachment and intracellular signaling. The aim of this study was to determine the role of the amino group density in this positive cell behavior by developing controlled amino-rich nanolayers. This work used covalent grafting of polymer-based nanocoatings with different amino group densities. Titanium coated with the positively-charged trimethoxysilylpropyl modified poly(ethyleneimine) (Ti-TMS-PEI), which mostly improved cell area after 30 min, possessed the highest amino group density with an N/C of 32%. Interestingly, changes in adhesion-related genes on Ti-TMS-PEI could be seen after 4 h. The mRNA microarray data showed a premature transition of the MG-63 cells into the beginning differentiation phase after 24 h indicating Ti-TMS-PEI as a supportive factor for osseointegration. This amino-rich nanolayer also induced higher bovine serum albumin protein adsorption and caused the cells to migrate slower on the surface after a more extended period of cell settlement as an indication of a better surface anchorage. In conclusion, the cell spreading on amine-based nanocoatings correlated well with the amino group density (N/C).

    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/ Moleculesarrow_drop_down
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    Molecules
    Article . 2023
    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/
    Molecules
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
    DOAJ
    Article . 2023
    Data sources: DOAJ
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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/ Moleculesarrow_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/
      Molecules
      Article . 2023
      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/
      Molecules
      Article . 2023 . Peer-reviewed
      License: CC BY
      Data sources: Crossref
      DOAJ
      Article . 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: Anita Kubiak; Martyna Pajewska-Szmyt; Martyna Kotula; Bartosz Leśniewski; +15 Authors

    Marine sponges of the subclass Keratosa originated on our planet about 900 million years ago and represent evolutionarily ancient and hierarchically structured biological materials. One of them, proteinaceous spongin, is responsible for the formation of 3D structured fibrous skeletons and remains enigmatic with complex chemistry. The objective of this study was to investigate the interaction of spongin with iron ions in a marine environment due to biocorrosion, leading to the occurrence of lepidocrocite. For this purpose, a biomimetic approach for the development of a new lepidocrocite-containing 3D spongin scaffold under laboratory conditions at 24 °C using artificial seawater and iron is described for the first time. This method helps to obtain a new composite as “Iron-Spongin”, which was characterized by infrared spectroscopy and thermogravimetry. Furthermore, sophisticated techniques such as X-ray fluorescence, microscope technique, and X-Ray diffraction were used to determine the structure. This research proposed a corresponding mechanism of lepidocrocite formation, which may be connected with the spongin amino acids functional groups. Moreover, the potential application of the biocomposite as an electrochemical dopamine sensor is proposed. The conducted research not only shows the mechanism or sensor properties of “Iron-spongin” but also opens the door to other applications of these multifunctional materials.

    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/ Marine Drugsarrow_drop_down
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    Marine Drugs
    Other literature type . Article . 2023 . Peer-reviewed
    License: CC BY
    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/
    Marine Drugs
    Article . 2023
    DOAJ
    Article . 2023
    Data sources: DOAJ
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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/ Marine Drugsarrow_drop_down
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      Marine Drugs
      Other literature type . Article . 2023 . Peer-reviewed
      License: CC BY
      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/
      Marine Drugs
      Article . 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: Jay Paul Morgan; Adeline Paiement; Christian Klinke;

    We explore different strategies to integrate prior domain knowledge into the design of graph neural networks (GNN). Our study is supported by a use-case of estimating the potential energy of chemical systems (molecules and crystals) represented as graphs. We integrate two elements of domain knowledge into the design of the GNN to constrain and regularise its learning, towards higher accuracy and generalisation. First, knowledge on the existence of different types of relations/graph edges (e.g. chemical bonds in our case study) between nodes of the graph is used to modulate their interactions. We formulate and compare two strategies, namely specialised message production and specialised update of internal states. Second, knowledge of the relevance of some physical quantities is used to constrain the learnt features towards a higher physical relevance using a simple multi-task learning (MTL) paradigm. We explore the potential of MTL to better capture the underlying mechanisms behind the studied phenomenon. We demonstrate the general applicability of our two knowledge integrations by applying them to three architectures that rely on different mechanisms to propagate information between nodes and to update node states. Our implementations are made publicly available. To support these experiments, we release three new datasets of out-of-equilibrium molecules and crystals of various complexities.

    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/ Cronfa at Swansea Un...arrow_drop_down
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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
    Neural Networks
    Article . 2023 . Peer-reviewed
    License: Elsevier TDM
    Data sources: Crossref
    https://doi.org/10.48550/arxiv...
    Article . 2022
    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/ Cronfa at Swansea Un...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/
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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
      Neural Networks
      Article . 2023 . Peer-reviewed
      License: Elsevier TDM
      Data sources: Crossref
      https://doi.org/10.48550/arxiv...
      Article . 2022
      License: CC BY
      Data sources: Datacite
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    Authors: Doret R. van Muilekom; Bertrand Collet; Henrike Rebl; Kristina Zlatina; +3 Authors

    NF-κB signalling is largely controlled by the family of ‘inhibitors of NF-κB’ (IκB). The relevant databases indicate that the genome of rainbow trout contains multiple gene copies coding for iκbα (nfkbia), iκbε (nfkbie), iκbδ (nkfbid), iκbζ (nfkbiz), and bcl3, but it lacks iκbβ (nfkbib) and iκbη (ankrd42). Strikingly, three nfkbia paralogs are apparently present in salmonid fish, two of which share a high sequence identity, while the third putative nfkbia gene is significantly less like its two paralogs. This particular nfkbia gene product, iκbα, clusters with the human IκBβ in a phylogenetic analysis, while the other two iκbα proteins from trout associate with their human IκBα counterpart. The transcript concentrations were significantly higher for the structurally more closely related nfkbia paralogs than for the structurally less similar paralog, suggesting that iκbβ probably has not been lost from the salmonid genomes but has been incorrectly designated as iκbα. In the present study, two gene variants coding for iκbα (nfkbia) and iκbε (nfkbie) were prominently expressed in the immune tissues and, particularly, in a cell fraction enriched with granulocytes, monocytes/macrophages, and dendritic cells from the head kidney of rainbow trout. Stimulation of salmonid CHSE-214 cells with zymosan significantly upregulated the iκbα-encoding gene while elevating the copy numbers of the inflammatory markers interleukin-1-beta and interleukin-8. Overexpression of iκbα and iκbε in CHSE-214 cells dose-dependently quenched both the basal and stimulated activity of an NF-κB promoter suggesting their involvement in immune-regulatory processes. This study provides the first functional data on iκbε—versus the well-researched iκbα factor—in a non-mammalian model species.

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    DOAJ
    Article . 2023
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    Authors: Timo Moritz; Jacqueline Walter; Bianka Grunow; Philipp Thieme;

    Abstract The distinctive caudal-fin skeleton of gadiforms has puzzled scientists for a long time, because of its many differences in comparison to other teleosts. Contradicting hypotheses interpreted this structure as (i) a highly derived teleostean caudal fin, (ii) a new formation with parts from the caudal, dorsal and anal fins, a so called pseudocaudal, or (iii) a complete evolutionary novelty, a so called neocaudal. To shed light on to this issue, the caudal-fin ontogeny of Lota lota was studied in detail. It differs from the development in non-gadiform teleostean taxa, e.g. by absence of a distinct and early notochord flexion. However, there are also many similarities with other teleosts, e.g. the caudal fin develops before the dorsal and anal fins. Furthermore, the morphology of adult caudal fins of all major gadiform families were studied and reviewed. Our results, in combination with the latest molecular phylogenies, allowed us to discuss the evolution of the gadiform caudal fin and resolve the origin of this highly debated character complex. Although their caudal-fin skeleton shows several derived apomorphies, the gadiform caudal fin is homologous to the caudal fins of other teleosts, without principal inclusion of dorsal- or anal-fin elements.

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    ZENODO; Zoological Journal of the Linnean Society
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: ZENODO; Crossref
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      ZENODO; Zoological Journal of the Linnean Society
      Article . 2023 . Peer-reviewed
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    Authors: Fischbach, Vivian; Finke, Annegret; Moritz, Timo; Polte, Patrick; +6 Authors

    AbstractAtlantic herring (Clupea harengus) plays a key role within temperate marine food webs and is targeted by a significant over‐regional fishery. Due to its high economic importance, dynamics in herring stock biomass and recruitment are closely monitored, forming the basis for fisheries management advice. As recruitment patterns translate into the adult stock biomass, early life stage ecology has been thoroughly addressed in fisheries research. Larval monitoring programs commonly focus on length measurements and abundance indices, rarely, information on larval developmental stages is given. As length is highly influenced by temperature, salinity and food availability, their size range can significantly vary between cohorts, populations, and ecotypes. Nowadays, a systematic staging system from the 1970s provides the standard guide for herring larval development, although it does not fully resolve important developmental stages. Here, we propose an improved staging system based on external morphology and skeletal development of herring larvae. The staging system has been developed and tested with herring larvae from different populations of the North and Baltic Sea to ensure applicability. The system comprises 15 stages (+substages) in 5 major developmental phases: the yolk sac phase, the dorsal fin development, the caudal fin development, the pelvic fin development, and the juvenile phase. This staging system aims to simplify herring larval staging to gain a more specific picture of early life dynamics. Because of the detailed description of the development, future studies are better equipped to identify stages which, for example, show high mortality rates and better link them to environmental circumstances. Universität Rostock http://dx.doi.org/10.13039/501100012688 Promotionsstipendium Universität Rostock

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    Limnology and Oceanography Methods
    Article . 2023 . Peer-reviewed
    License: CC BY NC ND
    Data sources: Crossref
    GEO-LEO e-docs
    Article . 2023
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      Limnology and Oceanography Methods
      Article . 2023 . Peer-reviewed
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      GEO-LEO e-docs
      Article . 2023
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    Authors: Benelli, Giovanni; Lucchi, Andrea; Anfora, Gianfranco; Bagnoli, Bruno; +17 Authors

    Though the European grapevine moth, Lobesia botrana (Denis & Schiffermüller) (Lepidoptera: Tortricidae) can feed on more than forty plant species, grapevine is the preferred crop worldwide. This moth is a western palearctic species that has recently spread to Chile, Argentina, and California. The possible further expansion in other regions of the Americas is greatly feared and should be monitored carefully in the near future. In this framework, we provide an updated review of the current knowledge on its taxonomy, morphology, biology, ecology, genomics, geographic distribution, and invasiveness. Then, in the last section, we develop a research agenda pointing out significant challenges for future investigations on bio-ecology and invasion biology, which are tightly connected with the prevention and management strategies Peer reviewed

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    DIGITAL.CSIC
    Article . 2023 . Peer-reviewed
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    Authors: D. Kraus; J. Vorberger; N. J. Hartley; J. Lütgert; +33 Authors

    We demonstrate a significantly simplified experimental approach for investigating liquid metallic hydrogen, which is crucial to understand the internal structure and evolution of giant planets. Plastic samples were shockcompressed and then probed by short pulses of X-rays generated by free electron lasers. By comparison with ab initio simulations, we provide indirect evidence for the creation of elemental hydrogen in shock-compressed plastics at ∼150GPa and ∼5,000K and thus in a regime where hydrogen is predicted to be metallic. Being the most common form of condensed matter in our solar system, and ostensibly the simplest of all elements, hydrogen is the model case for many theoretical studies and we provide a new possibility to benchmark models for conditions with extreme pressures and temperatures. Moreover, this approach will also allow to probe the chemical behavior of metallic hydrogen in mixture with other elements, which, besides its importance for planetary physics, may open up promising pathways for the synthesis of new materials.

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    ROBIS
    Article . 2023
    Data sources: ROBIS
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    Physical Review Research
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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      ROBIS
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      Physical Review Research
      Article . 2023 . Peer-reviewed
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    Authors: Mijail Mijares Bullaín-Galardis; Raúl Campos-Posada; Gloria Campos-Posada; Bettina Eichler- Löbermann; +3 Authors

    International audience; The salinity of soils and water for irrigation is a limitation that influences the productivity of crops that has increased worldwide and af fects the morphology and physiology of plants since it causes osmotic stress and ionic toxicity and impairs the absorption of water and nutrients. The ef fect of salt stress on some morphological and physiological traits in Coccoloba uvifera (L.) L. (sea grape) seedlings from dif ferent origins was evaluated and the traits whose behavior under salt stress could be used as an ef fective criterion of tolerance to salinity were determined. A completely randomized design experiment with ten repetitions was performed. The factors under study were salinity (0, 5, 15, and 25 dS m-1), which was maintained for a period of sixteen weeks, and the second factor was the origin of the plant material. The salinity level and the seedlings’ origin significantly influenced the morphological and physiological variables controlled. However, it is necessary to carry out in situ experiments to obtain more information related to the mechanisms used by sea grape to tolerate salinity conditions, because in the consulted sources no research focused on evaluating the ef fect of salinity and the origin on the morphology and physiology of C. uvifera seedlings in Cuba has been found. The results of the research provide preliminary information to understand the negative ef fect of salt stress on this type of plant. The behavior of some controlled traits under salt stress can be used as an ef fective criterion of tolerance to salinity.

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    Terra Latinoamericana
    Article . 2023 . Peer-reviewed
    Data sources: Crossref
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    Article . 2023
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      Terra Latinoamericana
      Article . 2023 . Peer-reviewed
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    Authors: David, Romain; Richard, Audrey S.; Connellan, Claire; Lauer, Katharina B.; +41 Authors

    THIS PAPER IS NOW PUBLISHED: https://doi.org/10.5334/dsj-2023-035 The Horizon Europe project ISIDORe is dedicated to pandemic preparedness and responsiveness research. It brings together 17 Research Infrastructures (RIs) and networks to provide a broad range of services to infectious disease researchers. An efficient and structured treatment of data is central to ISIDORe’s aim to furnish seamless access to its multidisciplinary catalogue of services, and to ensure that users’ results are treated FAIRly. ISIDORe therefore requires a data management plan (DMP) covering both access management and research outputs, applicable over a broad range of disciplines, and compatible with the constraints and existing practices of its diverse partners. We undertook an iterative, step-by-step, process to build a community-approved living document, identifying good practices and processes, on the basis of use cases, presented as proof of concepts. International fora such as the RDA and EOSC, and primarily the BY-COVID project, furnished registries, tools and online data platforms, as well as standards, and the support of data scientists. Together, these elements provide a path for building an umbrella, FAIR-compliant DMP, aligned as fully as possible with FAIR principles, which could also be applied as a framework for data management harmonisation in other large-scale, challenge-driven projects. Finally, we discuss how data management and reuse can be further improved through the writing of realistic DMPs using 'DMP profiles' and, in the future, the contribution of an inter RIs data steward network, to produce a Community of Practice that could be integrated into planned trans-RI competence centres. Preprint added on zenodo with the autorisation of DSJ Editor

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    Oxford University Research Archive
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    Authors: Susanne Seemann; Manuela Dubs; Dirk Koczan; Hernando S. Salapare; +8 Authors

    International audience; Increased life expectancy in industrialized countries is causing an increased incidence of osteoporosis and the need for bioactive bone implants. The integration of implants can be improved physically, but mainly by chemical modifications of the material surface. It was recognized that amino-group-containing coatings improved cell attachment and intracellular signaling. The aim of this study was to determine the role of the amino group density in this positive cell behavior by developing controlled amino-rich nanolayers. This work used covalent grafting of polymer-based nanocoatings with different amino group densities. Titanium coated with the positively-charged trimethoxysilylpropyl modified poly(ethyleneimine) (Ti-TMS-PEI), which mostly improved cell area after 30 min, possessed the highest amino group density with an N/C of 32%. Interestingly, changes in adhesion-related genes on Ti-TMS-PEI could be seen after 4 h. The mRNA microarray data showed a premature transition of the MG-63 cells into the beginning differentiation phase after 24 h indicating Ti-TMS-PEI as a supportive factor for osseointegration. This amino-rich nanolayer also induced higher bovine serum albumin protein adsorption and caused the cells to migrate slower on the surface after a more extended period of cell settlement as an indication of a better surface anchorage. In conclusion, the cell spreading on amine-based nanocoatings correlated well with the amino group density (N/C).

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    Molecules
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    Molecules
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    Authors: Anita Kubiak; Martyna Pajewska-Szmyt; Martyna Kotula; Bartosz Leśniewski; +15 Authors

    Marine sponges of the subclass Keratosa originated on our planet about 900 million years ago and represent evolutionarily ancient and hierarchically structured biological materials. One of them, proteinaceous spongin, is responsible for the formation of 3D structured fibrous skeletons and remains enigmatic with complex chemistry. The objective of this study was to investigate the interaction of spongin with iron ions in a marine environment due to biocorrosion, leading to the occurrence of lepidocrocite. For this purpose, a biomimetic approach for the development of a new lepidocrocite-containing 3D spongin scaffold under laboratory conditions at 24 °C using artificial seawater and iron is described for the first time. This method helps to obtain a new composite as “Iron-Spongin”, which was characterized by infrared spectroscopy and thermogravimetry. Furthermore, sophisticated techniques such as X-ray fluorescence, microscope technique, and X-Ray diffraction were used to determine the structure. This research proposed a corresponding mechanism of lepidocrocite formation, which may be connected with the spongin amino acids functional groups. Moreover, the potential application of the biocomposite as an electrochemical dopamine sensor is proposed. The conducted research not only shows the mechanism or sensor properties of “Iron-spongin” but also opens the door to other applications of these multifunctional materials.

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    Marine Drugs
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    Authors: Jay Paul Morgan; Adeline Paiement; Christian Klinke;

    We explore different strategies to integrate prior domain knowledge into the design of graph neural networks (GNN). Our study is supported by a use-case of estimating the potential energy of chemical systems (molecules and crystals) represented as graphs. We integrate two elements of domain knowledge into the design of the GNN to constrain and regularise its learning, towards higher accuracy and generalisation. First, knowledge on the existence of different types of relations/graph edges (e.g. chemical bonds in our case study) between nodes of the graph is used to modulate their interactions. We formulate and compare two strategies, namely specialised message production and specialised update of internal states. Second, knowledge of the relevance of some physical quantities is used to constrain the learnt features towards a higher physical relevance using a simple multi-task learning (MTL) paradigm. We explore the potential of MTL to better capture the underlying mechanisms behind the studied phenomenon. We demonstrate the general applicability of our two knowledge integrations by applying them to three architectures that rely on different mechanisms to propagate information between nodes and to update node states. Our implementations are made publicly available. To support these experiments, we release three new datasets of out-of-equilibrium molecules and crystals of various complexities.

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    Neural Networks
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      Neural Networks
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    Authors: Doret R. van Muilekom; Bertrand Collet; Henrike Rebl; Kristina Zlatina; +3 Authors

    NF-κB signalling is largely controlled by the family of ‘inhibitors of NF-κB’ (IκB). The relevant databases indicate that the genome of rainbow trout contains multiple gene copies coding for iκbα (nfkbia), iκbε (nfkbie), iκbδ (nkfbid), iκbζ (nfkbiz), and bcl3, but it lacks iκbβ (nfkbib) and iκbη (ankrd42). Strikingly, three nfkbia paralogs are apparently present in salmonid fish, two of which share a high sequence identity, while the third putative nfkbia gene is significantly less like its two paralogs. This particular nfkbia gene product, iκbα, clusters with the human IκBβ in a phylogenetic analysis, while the other two iκbα proteins from trout associate with their human IκBα counterpart. The transcript concentrations were significantly higher for the structurally more closely related nfkbia paralogs than for the structurally less similar paralog, suggesting that iκbβ probably has not been lost from the salmonid genomes but has been incorrectly designated as iκbα. In the present study, two gene variants coding for iκbα (nfkbia) and iκbε (nfkbie) were prominently expressed in the immune tissues and, particularly, in a cell fraction enriched with granulocytes, monocytes/macrophages, and dendritic cells from the head kidney of rainbow trout. Stimulation of salmonid CHSE-214 cells with zymosan significantly upregulated the iκbα-encoding gene while elevating the copy numbers of the inflammatory markers interleukin-1-beta and interleukin-8. Overexpression of iκbα and iκbε in CHSE-214 cells dose-dependently quenched both the basal and stimulated activity of an NF-κB promoter suggesting their involvement in immune-regulatory processes. This study provides the first functional data on iκbε—versus the well-researched iκbα factor—in a non-mammalian model species.

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    DOAJ
    Article . 2023
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      DOAJ
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    Authors: Timo Moritz; Jacqueline Walter; Bianka Grunow; Philipp Thieme;

    Abstract The distinctive caudal-fin skeleton of gadiforms has puzzled scientists for a long time, because of its many differences in comparison to other teleosts. Contradicting hypotheses interpreted this structure as (i) a highly derived teleostean caudal fin, (ii) a new formation with parts from the caudal, dorsal and anal fins, a so called pseudocaudal, or (iii) a complete evolutionary novelty, a so called neocaudal. To shed light on to this issue, the caudal-fin ontogeny of Lota lota was studied in detail. It differs from the development in non-gadiform teleostean taxa, e.g. by absence of a distinct and early notochord flexion. However, there are also many similarities with other teleosts, e.g. the caudal fin develops before the dorsal and anal fins. Furthermore, the morphology of adult caudal fins of all major gadiform families were studied and reviewed. Our results, in combination with the latest molecular phylogenies, allowed us to discuss the evolution of the gadiform caudal fin and resolve the origin of this highly debated character complex. Although their caudal-fin skeleton shows several derived apomorphies, the gadiform caudal fin is homologous to the caudal fins of other teleosts, without principal inclusion of dorsal- or anal-fin elements.

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    ZENODO; Zoological Journal of the Linnean Society
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: ZENODO; Crossref
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      ZENODO; Zoological Journal of the Linnean Society
      Article . 2023 . Peer-reviewed
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    Authors: Fischbach, Vivian; Finke, Annegret; Moritz, Timo; Polte, Patrick; +6 Authors

    AbstractAtlantic herring (Clupea harengus) plays a key role within temperate marine food webs and is targeted by a significant over‐regional fishery. Due to its high economic importance, dynamics in herring stock biomass and recruitment are closely monitored, forming the basis for fisheries management advice. As recruitment patterns translate into the adult stock biomass, early life stage ecology has been thoroughly addressed in fisheries research. Larval monitoring programs commonly focus on length measurements and abundance indices, rarely, information on larval developmental stages is given. As length is highly influenced by temperature, salinity and food availability, their size range can significantly vary between cohorts, populations, and ecotypes. Nowadays, a systematic staging system from the 1970s provides the standard guide for herring larval development, although it does not fully resolve important developmental stages. Here, we propose an improved staging system based on external morphology and skeletal development of herring larvae. The staging system has been developed and tested with herring larvae from different populations of the North and Baltic Sea to ensure applicability. The system comprises 15 stages (+substages) in 5 major developmental phases: the yolk sac phase, the dorsal fin development, the caudal fin development, the pelvic fin development, and the juvenile phase. This staging system aims to simplify herring larval staging to gain a more specific picture of early life dynamics. Because of the detailed description of the development, future studies are better equipped to identify stages which, for example, show high mortality rates and better link them to environmental circumstances. Universität Rostock http://dx.doi.org/10.13039/501100012688 Promotionsstipendium Universität Rostock

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    Limnology and Oceanography Methods
    Article . 2023 . Peer-reviewed
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    GEO-LEO e-docs
    Article . 2023
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      Limnology and Oceanography Methods
      Article . 2023 . Peer-reviewed
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    Authors: Benelli, Giovanni; Lucchi, Andrea; Anfora, Gianfranco; Bagnoli, Bruno; +17 Authors

    Though the European grapevine moth, Lobesia botrana (Denis & Schiffermüller) (Lepidoptera: Tortricidae) can feed on more than forty plant species, grapevine is the preferred crop worldwide. This moth is a western palearctic species that has recently spread to Chile, Argentina, and California. The possible further expansion in other regions of the Americas is greatly feared and should be monitored carefully in the near future. In this framework, we provide an updated review of the current knowledge on its taxonomy, morphology, biology, ecology, genomics, geographic distribution, and invasiveness. Then, in the last section, we develop a research agenda pointing out significant challenges for future investigations on bio-ecology and invasion biology, which are tightly connected with the prevention and management strategies Peer reviewed

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    DIGITAL.CSIC
    Article . 2023 . Peer-reviewed
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    Authors: D. Kraus; J. Vorberger; N. J. Hartley; J. Lütgert; +33 Authors

    We demonstrate a significantly simplified experimental approach for investigating liquid metallic hydrogen, which is crucial to understand the internal structure and evolution of giant planets. Plastic samples were shockcompressed and then probed by short pulses of X-rays generated by free electron lasers. By comparison with ab initio simulations, we provide indirect evidence for the creation of elemental hydrogen in shock-compressed plastics at ∼150GPa and ∼5,000K and thus in a regime where hydrogen is predicted to be metallic. Being the most common form of condensed matter in our solar system, and ostensibly the simplest of all elements, hydrogen is the model case for many theoretical studies and we provide a new possibility to benchmark models for conditions with extreme pressures and temperatures. Moreover, this approach will also allow to probe the chemical behavior of metallic hydrogen in mixture with other elements, which, besides its importance for planetary physics, may open up promising pathways for the synthesis of new materials.

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    ROBIS
    Article . 2023
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    Physical Review Research
    Article . 2023 . Peer-reviewed
    License: CC BY
    Data sources: Crossref
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      Physical Review Research
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    Authors: Mijail Mijares Bullaín-Galardis; Raúl Campos-Posada; Gloria Campos-Posada; Bettina Eichler- Löbermann; +3 Authors

    International audience; The salinity of soils and water for irrigation is a limitation that influences the productivity of crops that has increased worldwide and af fects the morphology and physiology of plants since it causes osmotic stress and ionic toxicity and impairs the absorption of water and nutrients. The ef fect of salt stress on some morphological and physiological traits in Coccoloba uvifera (L.) L. (sea grape) seedlings from dif ferent origins was evaluated and the traits whose behavior under salt stress could be used as an ef fective criterion of tolerance to salinity were determined. A completely randomized design experiment with ten repetitions was performed. The factors under study were salinity (0, 5, 15, and 25 dS m-1), which was maintained for a period of sixteen weeks, and the second factor was the origin of the plant material. The salinity level and the seedlings’ origin significantly influenced the morphological and physiological variables controlled. However, it is necessary to carry out in situ experiments to obtain more information related to the mechanisms used by sea grape to tolerate salinity conditions, because in the consulted sources no research focused on evaluating the ef fect of salinity and the origin on the morphology and physiology of C. uvifera seedlings in Cuba has been found. The results of the research provide preliminary information to understand the negative ef fect of salt stress on this type of plant. The behavior of some controlled traits under salt stress can be used as an ef fective criterion of tolerance to salinity.

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    Terra Latinoamericana
    Article . 2023 . Peer-reviewed
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    Article . 2023
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      Terra Latinoamericana
      Article . 2023 . Peer-reviewed
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