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8,153 Research products

  • European Marine Science
  • 2013-2022
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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: Dixit, Tanmay; Choi, Gary P. T.; al-Mosleh, Salem; Lund, Jess; +4 Authors

    The persistence of imperfect mimicry in nature presents a challenge to mimicry theory. Some hypotheses for the existence of imperfect mimicry make differing predictions depending on how mimetic fidelity is measured. Here, we measure mimetic fidelity in a brood parasite–host system using both trait-based and response-based measures of mimetic fidelity. Cuckoo finches Anomalospiza imberbis lay imperfectly mimetic eggs that lack the fine scribbling characteristic of eggs of the tawny-flanked prinia Prinia subflava, a common host species. A trait-based discriminant analysis based on Minkowski functionals—that use geometric and topological morphometric methods related to egg pattern shape and coverage—reflects this consistent difference between host and parasite eggs. These methods could be applied to quantify other phenotypes including stripes and waved patterns. Furthermore, by painting scribbles onto cuckoo finch eggs and testing their rate of rejection compared to control eggs (i.e. a response-based approach to quantify mimetic fidelity), we show that prinias do not discriminate between eggs based on the absence of scribbles. Overall, our results support relaxed selection on cuckoo finches to mimic scribbles, since prinias do not respond differently to eggs with and without scribbles, despite the existence of this consistent trait difference. The dataset consists of pattern metrics extracted from egg images, and egg rejection data, from field experiments conducted from 2018-2020.

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    ZENODO
    Dataset . 2022
    License: CC 0
    Data sources: ZENODO
    DRYAD
    Dataset . 2022
    License: CC 0
    Data sources: Datacite
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      ZENODO
      Dataset . 2022
      License: CC 0
      Data sources: ZENODO
      DRYAD
      Dataset . 2022
      License: CC 0
      Data sources: Datacite
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    Authors: Schmechtig, Catherine; D'Ortenzio, Fabrizio; Carval, Thierry; Claustre, Hervé; +8 Authors

    Report providing recommendations for the data management and structure for the BGC extension at the European level.

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    ZENODO
    Other ORP type . 2022
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    Data sources: ZENODO
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      ZENODO
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    Authors: Castresana, Jose;

    ecently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (Galemys pyrenaicus). For this, we used the ddRADseq technique, which generated 1,421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research. Deutsche Forschungsgemeinschaft, Award: HA7255/1-1. MCIN/AEI/10.13039/501100011033, Award: PID2020-113586GB-I00, MCIN/AEI/10.13039/501100011033, Award: CGL2017-84799-P, "ERDF A way of making Europe", Award: CGL2017-84799-P. [Usage notes] ddRAD_reads.zip. Quality-filtered reads for each individual in FASTQ format. Peer reviewed

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    ZENODO
    Dataset . 2022
    License: CC 0
    Data sources: ZENODO
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    DRYAD
    Dataset . 2022
    License: CC 0
    Data sources: Datacite
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      ZENODO
      Dataset . 2022
      License: CC 0
      Data sources: ZENODO
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      DRYAD
      Dataset . 2022
      License: CC 0
      Data sources: Datacite
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    Supplementary Materials for 'A systematic evaluation of factors affecting referring expression choice in passage completion tasks'. This contains stimuli for Experiments 1, 2, and 3, and subset analyses for Experiments 1 and 2. THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOVE

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    DANS-EASY
    Dataset . 2022
    Data sources: B2FIND
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    DANS-EASY
    Dataset . 2023
    Data sources: B2FIND
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    Mendeley Data; NARCIS
    Dataset . 2022
    License: CC BY
    Data sources: Datacite; NARCIS
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    Mendeley Data; NARCIS
    Dataset . 2023
    License: CC BY
    Mendeley Data
    Dataset . 2023
    License: CC BY
    Data sources: Datacite
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      DANS-EASY
      Dataset . 2022
      Data sources: B2FIND
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      DANS-EASY
      Dataset . 2023
      Data sources: B2FIND
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      Mendeley Data; NARCIS
      Dataset . 2022
      License: CC BY
      Data sources: Datacite; NARCIS
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      Mendeley Data; NARCIS
      Dataset . 2023
      License: CC BY
      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: Santana Garçon, Julia; Bennett, Scott; Marbà, Núria; Vergés, Adriana; +2 Authors

    5 pages. -- Table S1. Summary table with description of sites and fish species studied at four locations across the Mediterranean Sea. -- Fig. S1 Trend in minimum (1st percentile of daily temperatures) and maximum (99th percentile of daily temperatures) sea surface temperatures from 1981 to 2019. -- Fig. S2 Ivlev’s electivity index for herbivorous fishes across the Mediterranean Sea. Ivlev’s index standardizes food consumed by food availability within the habitat and scales from -1 (extreme selection against food source) to 1 (extreme selection for food source) (Jones & Norman 1986) 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/ Recolector de Cienci...arrow_drop_down
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    Authors: Körtzinger, Arne; Steinhoff, Tobias; Wimart-Rousseau, Cathy; D'Ortenzio, Fabrizio;
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    ZENODO
    Other ORP type . 2022
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    Data sources: ZENODO
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      ZENODO
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    Authors: Gazert, Volker; Luedecke, Cornelia;
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    Authors: Bista, Iliana; Wood, Jonathan; Desvignes, Thomas; McCarthy, Shane; +17 Authors

    Phylogenetic analysis was performed using single copy ortholog genes identified with BUSCO, for the 24 newly sequenced notothenioid genomes and 17 previously published genomes of seven notothenioids and ten further species of percomorph fishes. BUSCO (v2) was run with lineage “actinopterygii_odb9”, and the sequences of single- opy orthologs identified in each assembly and extracted for use in further analysis. We used MAFFT v.7.453 to align 266 selected BUSCO genes that were single copy in our annotated gene sets. The 266 alignments were inspected by eye, and apparently misaligned sequence regions were set to missing data. A total of 1,141,524 amino acids were set to missing out of 6,410,688, including nine alignments that were excluded completely, leaving 257 alignments for further analysis. We then aligned nucleotide sequences of the same BUSCO genes according to the amino-acid alignments, ensuring that regions corresponding to the removed sequences were again set to missing data in the nucleotide sequence alignments. Sites with high entropy (entropy like score > 0.5) or high proportion of missing data (gap rate > 0.2) were removed with BMGE v.1.1 and alignments with more than three completely missing sequences, a minimum length below 500 bp, or a standard deviation of among-sequence GC-content variation greater than 0.03 were excluded. These filters were passed by 228 alignments. Each of these alignments was subjected to Bayesian phylogenetic analysis with BEAST 2 v.2.6.0, with an uncorrelated lognormal relaxed clock model and a Markov-chain Monte Carlo chain (MCMC) length of 25 million iterations. “Strict” and “permissive” sets of alignments were compiled based on estimates of the mutation rate and its among-species variation and contained 140 and 200 of the alignments, respectively. For the strict set of 140 alignments, the permissive set of 200 alignments, and the “full” set of 257 alignments, we performed maximum-likelihood phylogenetic analyses with IQ-TREE v.1.7 after alignment concatenation, maintaining separate partitions with unlinked instances of the GTR+Gamma substitution model for each of the original alignments. Node support was assessed with 1,000 ultrafast bootstrap replicates. Each of the three analyses was complemented with an estimation of gene- and site-specific concordance factors, and the three resulting sets of gene trees were used for separate species-tree analyses with ASTRAL v.5.7.3. Finally, we estimated the phylogeny and the divergence times of notothenioid species with BEAST 2 from a concatenated alignment combining all alignments of the strict set. The original data blocks were grouped in 12 positions selected with the rcluster algorithm of PartitionFinder v.2.1.1, assuming linked branch lengths, equal weights for all model parameters, a minimum partition size of 5,000 bp, and the GTR+Gamma substitution model. The same substitution model was also assumed in the BEAST 2 analysis, together with the birth-death model of diversification and the uncorrelated lognormal relaxed clock model. Time calibration of the phylogeny was based on four age constraints defined according to a recent timeline of teleost evolution inferred from genome and fossil information, at the most recent common ancestors of clades: Eupercaria, around 97.47 MYA (2.5–97.5 inter-percentile range: 91.3–104.0 MYA); the clade combining Eupercaria, Ovalentaria, and Anabantaria – around 101.79 MYA (95.4–109.0 MYA); the clade combining these four groups with Syngnatharia and Pelagiaria – around 104.48 MYA (97.3–112.0 MYA); and the clade combining those six groups with Gobiaria – around 107.08 MYA (100.0–114.0 MYA). All constraints were implemented as lognormal prior distributions with mean values as specified above and a standard deviation between 0.033 and 0.036. Additionally, we constrained the unambiguous monophyly of the groups Notothenioidei, Perciformes, Ovalentaria, Anabantaria, and the clade combining the latter two groups. We performed six replicate BEAST 2 analyses with 330 million MCMC iterations, and convergence among MCMC chains was confirmed by ESS values greater than 120 for all model parameters and greater than 270 for the likelihood and the prior and posterior probabilities. The posterior tree distribution was summarised in the form of a maximum-clade credibility tree with TreeAnnotator v.2.6.0. We attempted to repeat the BEAST 2 analyses with the permissive and full datasets, but these proved too computationally demanding to complete. Nevertheless, the preliminary results from these analyses supported the same tree topology as the analyses with the strict dataset. Numerous novel adaptations characterise the radiation of notothenioids, the dominant fish group in the freezing seas of the Southern Ocean. To improve understanding of the evolution of this iconic fish group, we generated and analysed new genome assemblies for 24 species covering all major subgroups of the radiation, including five long-read assemblies. We present a new estimate for the onset of the radiation at 10.7 million years ago, based on a time-calibrated phylogeny derived from genome-wide sequence data. We identify a two-fold variation in genome size, driven by expansion of multiple transposable element families, and use the long-read data to reconstruct two evolutionarily important, highly repetitive gene family loci. First, we present the most complete reconstruction to date of the antifreeze glycoprotein gene family, whose emergence enabled survival in sub-zero temperatures, showing the expansion of the antifreeze gene locus from the ancestral to the derived state. Second, we trace the loss of haemoglobin genes in icefishes, the only vertebrates lacking functional haemoglobins, through complete reconstruction of the two haemoglobin gene clusters across notothenioid families. Both the haemoglobin and antifreeze genomic loci are characterised by multiple transposon expansions that may have driven the evolutionary history of these genes.

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    ZENODO
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    DRYAD
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      ZENODO
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      Data sources: ZENODO
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    Authors: Ballantyne, J;

    We present an open-source software for simulation of observables in magnetic resonance experiments, including nuclear magnetic/quadrupole resonance NMR/NQR and electron spin resonance (ESR). Inspired by magnetic resonance protocols that emerged in the context of quantum information science (QIS), this software can assist experimental research in the design of new strategies for the investigation of fundamental quantum properties of materials. The package introduced here can simulate both standard NMR spectroscopic observables and the time-evolution of an interacting single-spin system subject to complex pulse sequences, i.e. quantum gates. The main purpose of this software is to facilitate the development of much needed novel NMR-based probes of emergent quantum order, which can be elusive to standard experimental probes. The software is based on a quantum mechanical description of nuclear spin dynamics in NMR/NQR experiments and has been widely tested on available theoretical and experimental results. Moreover, the structure of the software allows for basic experiments to be easily generalized to more sophisticated ones because it includes all the libraries required for the numerical simulation of generic spin systems. In order to make the program easily accessible to a large user base, we developed a user-friendly graphical interface, Jupyter notebooks, and fully-detailed documentation. Lastly, we portray several examples of the execution of the code that illustrate the prosepcts of a novel NMR paradigm, inspired by QIS, for efficient investigation of emergent phases in strongly correlated materials. THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOVE

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    Dataset . 2022
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      DANS-EASY
      Dataset . 2022
      Data sources: B2FIND
      Mendeley Data
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      Data sources: Datacite
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    Authors: Wesche, Christine; Regnery, Julia;
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8,153 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: Dixit, Tanmay; Choi, Gary P. T.; al-Mosleh, Salem; Lund, Jess; +4 Authors

    The persistence of imperfect mimicry in nature presents a challenge to mimicry theory. Some hypotheses for the existence of imperfect mimicry make differing predictions depending on how mimetic fidelity is measured. Here, we measure mimetic fidelity in a brood parasite–host system using both trait-based and response-based measures of mimetic fidelity. Cuckoo finches Anomalospiza imberbis lay imperfectly mimetic eggs that lack the fine scribbling characteristic of eggs of the tawny-flanked prinia Prinia subflava, a common host species. A trait-based discriminant analysis based on Minkowski functionals—that use geometric and topological morphometric methods related to egg pattern shape and coverage—reflects this consistent difference between host and parasite eggs. These methods could be applied to quantify other phenotypes including stripes and waved patterns. Furthermore, by painting scribbles onto cuckoo finch eggs and testing their rate of rejection compared to control eggs (i.e. a response-based approach to quantify mimetic fidelity), we show that prinias do not discriminate between eggs based on the absence of scribbles. Overall, our results support relaxed selection on cuckoo finches to mimic scribbles, since prinias do not respond differently to eggs with and without scribbles, despite the existence of this consistent trait difference. The dataset consists of pattern metrics extracted from egg images, and egg rejection data, from field experiments conducted from 2018-2020.

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    ZENODO
    Dataset . 2022
    License: CC 0
    Data sources: ZENODO
    DRYAD
    Dataset . 2022
    License: CC 0
    Data sources: Datacite
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      ZENODO
      Dataset . 2022
      License: CC 0
      Data sources: ZENODO
      DRYAD
      Dataset . 2022
      License: CC 0
      Data sources: Datacite
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    Authors: Schmechtig, Catherine; D'Ortenzio, Fabrizio; Carval, Thierry; Claustre, Hervé; +8 Authors

    Report providing recommendations for the data management and structure for the BGC extension at the European level.

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    ZENODO
    Other ORP type . 2022
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      ZENODO
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    Authors: Castresana, Jose;

    ecently, populations of various species with very low genetic diversity have been discovered. Some of these persist in the long term, but others could face extinction due to accelerated loss of fitness. In this work, we characterize 45 individuals of one of these populations, belonging to the Iberian desman (Galemys pyrenaicus). For this, we used the ddRADseq technique, which generated 1,421 SNPs. The heterozygosity values of the analyzed individuals were among the lowest recorded for mammals, ranging from 26 to 91 SNPs/Mb. Furthermore, the individuals from one of the localities, highly isolated due to strong barriers, presented extremely high inbreeding coefficients, with values above 0.7. Under this scenario of low genetic diversity and elevated inbreeding levels, some individuals appeared to be almost genetically identical. We used different methods and simulations to determine if genetic identification and parentage analysis were possible in this population. Only one of the methods, which does not assume population homogeneity, was able to identify all individuals correctly. Therefore, genetically impoverished populations pose a great methodological challenge for their genetic study. However, these populations are of primary scientific and conservation interest, so it is essential to characterize them genetically and improve genomic methodologies for their research. Deutsche Forschungsgemeinschaft, Award: HA7255/1-1. MCIN/AEI/10.13039/501100011033, Award: PID2020-113586GB-I00, MCIN/AEI/10.13039/501100011033, Award: CGL2017-84799-P, "ERDF A way of making Europe", Award: CGL2017-84799-P. [Usage notes] ddRAD_reads.zip. Quality-filtered reads for each individual in FASTQ format. Peer reviewed

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    ZENODO
    Dataset . 2022
    License: CC 0
    Data sources: ZENODO
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    DRYAD
    Dataset . 2022
    License: CC 0
    Data sources: Datacite
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      Dataset . 2022
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      DRYAD
      Dataset . 2022
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    Supplementary Materials for 'A systematic evaluation of factors affecting referring expression choice in passage completion tasks'. This contains stimuli for Experiments 1, 2, and 3, and subset analyses for Experiments 1 and 2. THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOVE

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    Dataset . 2022
    Data sources: B2FIND
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    DANS-EASY
    Dataset . 2023
    Data sources: B2FIND
    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/
    Mendeley Data; NARCIS
    Dataset . 2022
    License: CC BY
    Data sources: Datacite; NARCIS
    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/
    Mendeley Data; NARCIS
    Dataset . 2023
    License: CC BY
    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/ DANS-EASYarrow_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/
      DANS-EASY
      Dataset . 2022
      Data sources: B2FIND
      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/
      DANS-EASY
      Dataset . 2023
      Data sources: B2FIND
      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/
      Mendeley Data; NARCIS
      Dataset . 2022
      License: CC BY
      Data sources: Datacite; NARCIS
      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/
      Mendeley Data; NARCIS
      Dataset . 2023
      License: CC BY
      Mendeley Data
      Dataset . 2023
      License: CC BY
      Data sources: Datacite
      addClaim