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337 Research products

  • European Marine Science
  • 2014-2023
  • Open Access
  • Research data
  • Other research products
  • Wellcome Trust
  • 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: 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
      DRYAD
      Dataset . 2022
      License: CC 0
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    Authors: Chen, Christine; Kahanamoku, Sara; Tripati, Aradhna; Alegado, Rosanna; +3 Authors

    Concerns about systemic racism at academic and research institutions have increased over the past decade. Here, we investigate data from the National Science Foundation (NSF), a major funder of research in the United States, and find evidence for pervasive racial disparities. In particular, white principal investigators (PIs) are consistently funded at higher rates than most non-white PIs. Funding rates for white PIs have also been increasing relative to annual overall rates with time. Moreover, disparities occur across all disciplinary directorates within the NSF and are greater for research proposals. The distributions of average external review scores also exhibit systematic offsets based on PI race. Similar patterns have been described in other research funding bodies, suggesting that racial disparities are widespread. The prevalence and persistence of these racial disparities in funding have cascading impacts that perpetuate a cumulative advantage to white PIs across all of science, technology, engineering and mathematics. All data were collated from publicly available annual merit review reports published by the National Science Foundation, which can be accessed online at the following link: https://www.nsf.gov/nsb/publications/pubmeritreview.jsp

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    ZENODO
    Dataset . 2022
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    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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    This is the dataset pertaining to the article "Macrophage Innate Training Induced by IL-4 and IL-13 Activation Enhances OXPHOS Driven Anti-Mycobacterial Responses". To interpret and follow the data, please refer to the linked article, as each excel sheet corresponds with each named graph/figure.Abstract: Macrophages are a highly adaptive population of innate immune cells. Polarization with IFNγ and LPS into the “classically activated” M1 macrophage enhances pro-inflammatory and microbicidal responses, important for eradicating bacteria such as Mycobacterium tuberculosis. By contrast, “alternatively activated” M2 macrophages, polarized with IL-4, oppose bactericidal mechanisms and allow mycobacterial growth. These activation states are accompanied by distinct metabolic profiles, where M1 macrophages favor near exclusive use of glycolysis, whereas M2 macrophages up-regulate oxidative phosphorylation (OXPHOS). Here we demonstrate that activation with IL-4 and IL-13 counterintuitively induces protective innate memory against mycobacterial challenge. In human and murine models, prior activation with IL-4/13 enhances pro-inflammatory cytokine secretion in response to a secondary stimulation with mycobacterial ligands. In our murine model, enhanced killing capacity is also demonstrated. Despite this switch in phenotype, IL-4/13 trained murine macrophages do not demonstrate M1-typical metabolism, instead retaining heightened use of OXPHOS. Moreover, inhibition of OXPHOS with oligomycin, 2-deoxy glucose or BPTES all impeded heightened pro-inflammatory cytokine responses from IL-4/13 trained macrophages. Lastly, this work identifies that IL-10 attenuates protective IL-4/13 training, impeding pro-inflammatory and bactericidal mechanisms.In summary, this work provides new and unexpected insight into alternative macrophage activation states in the context of mycobacterial infection. 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

    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; NARCI...arrow_drop_down
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    Mendeley Data; NARCIS
    Dataset . 2022
    License: CC BY
    Data sources: Datacite; NARCIS
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    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/
    DANS-EASY
    Dataset . 2022
    Data sources: B2FIND
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    DANS-EASY
    Dataset . 2022
    Data sources: B2FIND
    Mendeley Data
    Dataset . 2022
    License: CC BY
    Data sources: Datacite
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      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 . 2022
      License: CC BY
      Data sources: Datacite; NARCIS
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      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 . 2022
      Data sources: B2FIND
      Mendeley Data
      Dataset . 2022
      License: CC BY
      Data sources: Datacite
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    Authors: Varma, S;

    All the tissues, cell lines, yeast, and bacteria samples, unless differently stated, were extracted using Genomic Tip-20 kit (Qiagen) following the manufacturer's instructions.References1. Allen, G. C., M. A. Flores-Vergara, S. Krasynanski, S. Kumar, and W. F. Thompson. 2006. “A Modified Protocol for Rapid DNA Isolation from Plant Tissues Using Cetyltrimethylammonium Bromide.” Nature Protocols 1 (5): 2320–25.2. Gossmann, Toni I., Achchuthan Shanmugasundram, Stefan Börno, Ludovic Duvaux, Christophe Lemaire, Heiner Kuhl, Sven Klages, et al. 2019. “Ice-Age Climate Adaptations Trap the Alpine Marmot in a State of Low Genetic Diversity.” Current Biology: CB 29 (10): 1712–20.e7. 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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    Mendeley Data; NARCIS
    Dataset . 2022
    License: CC BY
    Data sources: Datacite; NARCIS
    Mendeley Data
    Dataset . 2022
    License: CC BY
    Data sources: Datacite
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      DANS-EASY
      Dataset . 2022
      Data sources: B2FIND
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      Mendeley Data; NARCIS
      Dataset . 2022
      License: CC BY
      Data sources: Datacite; NARCIS
      Mendeley Data
      Dataset . 2022
      License: CC BY
      Data sources: Datacite
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    Authors: Ivanov, Aleksandar; King, Andrew; Willmore, Ben; Walker, Kerry; +1 Authors

    In almost every natural environment, sounds are reflected by nearby objects, producing many delayed and distorted copies of the original sound, known as reverberation. Our brains usually cope well with reverberation, allowing us to recognize sound sources regardless of their environments. In contrast, reverberation can cause severe difficulties for speech recognition algorithms and hearing-impaired people. The present study examines how the auditory system copes with reverberation. We trained a linear model to recover a rich set of natural, anechoic sounds from their simulated reverberant counterparts. The model neurons achieved this by extending the inhibitory component of their receptive filters for more reverberant spaces, and did so in a frequency-dependent manner. These predicted effects were observed in the responses of auditory cortical neurons of ferrets in the same simulated reverberant environments. Together, these results suggest that auditory cortical neurons adapt to reverberation by adjusting their filtering properties in a manner consistent with dereverberation. We have provided our Matlab scripts for generating our figures on Github: https://github.com/PhantomSpike/DeReverb Spike data were recorded using Neuropixels electrodes in the auditory cortex of anaesthetised ferrets.

    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
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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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      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
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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: Prete Jr, Carlos A.; Buss, Lewis F.; Whittaker, Charles; Salomon, Tassila; +41 Authors

    The COVID-19 situation in Brazil is complex due to large differences in the shape and size of regional epidemics. Here we tested monthly blood donation samples for IgG antibodies from March 2020 to March 2021 in eight of Brazil’s most populous cities. The inferred attack rate of SARS-CoV-2 adjusted for seroreversion in December 2020, before the Gamma VOC was dominant, ranged from 19.3% (95% CrI 17.5% - 21.2%) in Curitiba to 75.0% (95% CrI 70.8% - 80.3%) in Manaus. Seroprevalence was consistently smaller in women and donors older than 55 years. The age-specific infection fatality rate (IFR) differed between cities and consistently increased with age. The infection hospitalisation rate (IHR) increased significantly during the Gamma-dominated second wave in Manaus, suggesting increased morbidity of the Gamma VOC compared to previous variants circulating in Manaus. The higher disease penetrance associated with the health system’s collapse increased the overall IFR by a minimum factor of 2.91 (95% CrI 2.43 – 3.53). These results highlight the utility of blood donor serosurveillance to track epidemic maturity and demonstrate demographic and spatial heterogeneity in SARS-CoV-2 spread. This repository contains four datasets:1) Bloodbank.csv: The longitudinal cohort containing the tested blood samples used to estimate the seroprevalence in the eight cities.2) repeat_blood_donors.csv: The cohort of repeat blood donors used to estimate the probability distribution of the time-to-seroreversion.3) convalescent_plasma_longitudinal_roche.csv: Convalescent plasma donors used to estimate the sensitivity of the assay.4) prepandemic_cohort.csv: The pre-pandemic blood donors cohort, containing samples tested in February 2020 in São Paulo.In all files, each row represents a tested blood sample. Information as exact age, education level and declared race were removed to ensure data are anonymized. For the same reason, dates of sample collection were substituted by the corresponding week numbers, and the date of onset was substituted by the time interval between the date of sample collection and the date of onset in the convalescent plasma donors dataset. See data_dictionary.pdf for the data dictionary. We tested 97,950 blood donation samples for anti-SARS-CoV-2 IgG antibodies using the anti-N Abbott chemiluminescent microparticle immunoassay (CIMA). Tests were performed from March 2020 to March 2021 in eight Brazilian capitals: São Paulo, Manaus, Belo Horizonte, Curitiba, Fortaleza, Recife, Rio de Janeiro.We also tested blood samples from convalescent plasma donors to estimate the sensitivity of the assay. To estimate test specificity, we tested blood donation samples from São Paulo collected in February 2020, before the beginning of the SARS-CoV-2 epidemic in Brazil. In order to estimate the time-to-seroreversion distribution (used to correct for antibody waning), we also tested samples from repeat blood donors.Please see "Methods" section in the manuscript for more detailed information on this dataset.

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    ZENODO
    Dataset . 2022
    License: CC 0
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    DRYAD
    Dataset . 2022
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      ZENODO
      Dataset . 2022
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      Dataset . 2022
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    Authors: Jaworska, Katarzyna; Yan, Yuening; van Rijsbergen, Nicola; Ince, Robin; +1 Authors

    A key challenge in neuroimaging remains to understand where, when and now particularly how human brain networks compute over sensory inputs to achieve behavior. To study such dynamic algorithms from mass neural signals, we recorded the magnetoencephalographic (MEG) activity of participants who resolved the classic XOR, OR and AND functions as overt behavioral tasks (N = 10 participants/task, N-of-1 replications). Each function requires a different computation over the same inputs to produce the task- specific behavioral outputs. In each task, we found that source-localized MEG activity progresses through four computational stages identified within individual participants: (1) initial contra-lateral representation of each visual input in occipital cortex, (2) a joint linearly combined representation of both inputs in midline occipital cortex and right fusiform gyrus, followed by (3) nonlinear task-dependent input integration in temporal-parietal cortex and finally (4) behavioral response representation in post-central gyrus. We demonstrate the specific dynamics of each computation at the level of individual sources. The spatio-temporal patterns of the first two computations are similar across the three tasks; the last two computations are task specific. Our results therefore reveal where, when and how dynamic network algorithms perform different computations over the same inputs to produce different behaviors. This dataset includes source data and the related manuscript codes involved in the research Different Computations over the Same Inputs Produce Selective Behavior in Algorithmic Brain Networks published at eLife. Specifically, we provide all analyzed data reported in the paper including: Figure 1&3 related – Source Data in FigureSource1.mat. 1_DistancePattern.m 2_LinearRep.m 3_NonLinRep.m Figure 2 related – Source Data in FigureSource2.mat 4_DynaCoord.m

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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
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      DRYAD
      Dataset . 2022
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      Data sources: Datacite
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    Authors: Leibold, Sandra; Lakshminarasimha, Amrutha Bagivalu; Gremse, Felix; Hammerschmidt, Matthias; +1 Authors

    Obesity is a world wide problem and evidence suggests, that early lifetime undernourishment of caloric restirction predispose an organism for obesity and metabolic syndrome. We have raised two cohorts of zebrafish in an obesogenic environment (DIO) and compared several metabolic markers with fish raised under caloric restriction (CR) or fish shifted from CR to DIO at different periods in their life. We have looked morphologically at standard length and weight and found that fish on DIO grow faster in both axes. Fish shifted from CR to DIO show catch-up growth and not compensatory growth when shifted at one month, 3 months or 9 months of age. We have further characterized central agrp expression and hyperphagia, adipose tissue by histology as well as uCT imaging, hepatic histology, metabolic rate mitochondrial function as well as feeding induced glucose levels. We find that fish in an obesogenic environment develop markers of obesity which are not exacerbated by ealry lifetime food restriction.

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    PANGAEA
    Dataset . 2022
    Data sources: B2FIND
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      PANGAEA
      Dataset . 2022
      Data sources: B2FIND
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    Authors: Canedo, Aryelle; Saiki, Patrícia; Santos, Andressa Liberal; Carneiro, Karla da Silva; +5 Authors

    Abstract Zebrafish (Danio rerio) is a tropical fish species widely used in research, worldwide. The development of genetically modified animals and the increasing number of zebrafish breeding facilities due to their emerging use in several research fields, opened room for new ethical challenges for research carried out with this species. It is necessary to raise the scientific community’s awareness of the ethical standards and laws in force, on animal research. Thus, the aim of the current study is to describe 10 Rs ethical principles by using zebrafish as model system in research. The classical 3 Rs concerning animal welfare, namely replacement, reduction and refinement; and the added 7 Rs related to scientific (registration, reporting, robustness, reproducibility and relevance) and conduct principles (responsibility, and respect) in zebrafish research are herein presented and critically discussed. The use of these 10 Rs by researchers, institutions and the Animal Ethics Committee is recommended to support regulations, decision-making about and the promotion of zebrafish health and welfare in research.

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    figshare
    Dataset . 2022
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    Data sources: Datacite
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    figshare
    Dataset . 2022
    License: CC BY
    Data sources: Datacite
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      figshare
      Dataset . 2022
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    Authors: Leibold, Sandra; Lakshminarasimha, Amrutha Bagivalu; Gremse, Felix; Hammerschmidt, Matthias; +1 Authors

    For µCT imaging, adult zebrafish were fixed and decalcified in Bouin's solution at room temperature for 7 days, stored in PBS and imaged using a micro-computed tomography (µCT) device (SkyScan1272, Bruker BioSpin GmbH, Ettlingen, Germany). Zebrafish were placed individually in 1.5ml Eppendorf tubes using and an ultra-focus scan over the whole body was performed in a full-rotation in step-and-shoot mode. 322 projections (1008x672 pixels, 4x4 binning) were acquired per subscan with an x-ray tube voltage of 60 kV, power 0.166 mA, aluminum filter 0.25 mm,exposure time of 363 ms, 6 averages and a object-source distance of 86 mm. All CT images were reconstructed at an isotropic voxel size of 18 µm using a Feldkamp type algorithm (filtered back-projection). Fat-containing regions were appear hypo intense in µCT data and were segmented using Imalytics Preclinical (Gremse-IT GmbH, Aachen, Germany (Gremse et al., 2016; doi:10.7150/thno.13624). The volumetric fat percentage was calculated as the ratio of subcutaneous adipose tissue (SAT) or visceral adipose tissue (VAT) fat volume compared to the entire volume of the body cavity anterior of the anal fin and expressed per skeletal segment. Fish were raised as previously reported (Leibold and Hammerschmidt, 2015) for the following conditions:CG1: compensatory or catch up growth shifted at 1 month of ageCG3: compensatory or catch up growth shifted at 3 months of ageCG9: compensatory or catch up growth shifted at 9 months of ageCR: caloric restrictionDIO: diet induced obesityThe CT .nii files correlate to the groups as follows: Group 2: CG1; Group 3: DIO1; Group 6: CG3; Group 7 DIO3; Group 10: CG9; Group 11: DIO9; Group 1: CR1; Group 5: CR3; Group 9: CR9

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    PANGAEA
    Dataset . 2022
    Data sources: B2FIND
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      Dataset . 2022
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337 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: 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
    Dataset . 2022
    License: CC 0
    Data sources: ZENODO
    DRYAD
    Dataset . 2022
    License: CC 0
    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/ ZENODOarrow_drop_down
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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: Chen, Christine; Kahanamoku, Sara; Tripati, Aradhna; Alegado, Rosanna; +3 Authors

    Concerns about systemic racism at academic and research institutions have increased over the past decade. Here, we investigate data from the National Science Foundation (NSF), a major funder of research in the United States, and find evidence for pervasive racial disparities. In particular, white principal investigators (PIs) are consistently funded at higher rates than most non-white PIs. Funding rates for white PIs have also been increasing relative to annual overall rates with time. Moreover, disparities occur across all disciplinary directorates within the NSF and are greater for research proposals. The distributions of average external review scores also exhibit systematic offsets based on PI race. Similar patterns have been described in other research funding bodies, suggesting that racial disparities are widespread. The prevalence and persistence of these racial disparities in funding have cascading impacts that perpetuate a cumulative advantage to white PIs across all of science, technology, engineering and mathematics. All data were collated from publicly available annual merit review reports published by the National Science Foundation, which can be accessed online at the following link: https://www.nsf.gov/nsb/publications/pubmeritreview.jsp

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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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    This is the dataset pertaining to the article "Macrophage Innate Training Induced by IL-4 and IL-13 Activation Enhances OXPHOS Driven Anti-Mycobacterial Responses". To interpret and follow the data, please refer to the linked article, as each excel sheet corresponds with each named graph/figure.Abstract: Macrophages are a highly adaptive population of innate immune cells. Polarization with IFNγ and LPS into the “classically activated” M1 macrophage enhances pro-inflammatory and microbicidal responses, important for eradicating bacteria such as Mycobacterium tuberculosis. By contrast, “alternatively activated” M2 macrophages, polarized with IL-4, oppose bactericidal mechanisms and allow mycobacterial growth. These activation states are accompanied by distinct metabolic profiles, where M1 macrophages favor near exclusive use of glycolysis, whereas M2 macrophages up-regulate oxidative phosphorylation (OXPHOS). Here we demonstrate that activation with IL-4 and IL-13 counterintuitively induces protective innate memory against mycobacterial challenge. In human and murine models, prior activation with IL-4/13 enhances pro-inflammatory cytokine secretion in response to a secondary stimulation with mycobacterial ligands. In our murine model, enhanced killing capacity is also demonstrated. Despite this switch in phenotype, IL-4/13 trained murine macrophages do not demonstrate M1-typical metabolism, instead retaining heightened use of OXPHOS. Moreover, inhibition of OXPHOS with oligomycin, 2-deoxy glucose or BPTES all impeded heightened pro-inflammatory cytokine responses from IL-4/13 trained macrophages. Lastly, this work identifies that IL-10 attenuates protective IL-4/13 training, impeding pro-inflammatory and bactericidal mechanisms.In summary, this work provides new and unexpected insight into alternative macrophage activation states in the context of mycobacterial infection. 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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    Mendeley Data; NARCIS
    Dataset . 2022
    License: CC BY
    Data sources: Datacite; NARCIS
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    Mendeley Data; NARCIS
    Dataset . 2022
    License: CC BY
    Data sources: Datacite; NARCIS
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    DANS-EASY
    Dataset . 2022
    Data sources: B2FIND
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    DANS-EASY
    Dataset . 2022
    Data sources: B2FIND
    Mendeley Data
    Dataset . 2022
    License: CC BY
    Data sources: Datacite
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