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1,048 results for “unveil”
Research data supporting: "Innate dynamics and identity crisis of a metal surface unveiled by machine learning of atomic environments"
<p>This repository contains the set of data shown in the paper <strong>"Innate dynamics and identity crisis of a metal surface unveiled by machine learning of atomic environments"</strong>, published on The Journal of Chemical Physics (DOI:10.1063/5.0139010)</p>
Dataset for Extensive programmed centriole elimination unveiled in C. elegans embryos
<p>Spreadsheets, confocal and wide field microscopy images and related scripts. Related to the publication "Extensive programmed centriole elimination unveiled in C. elegans embryos." For the complete dataset, please refer to https://doi.org/10.5075/epfl-upgon-305930 </p>
Code and data supplement for "Unveiling the transition from niche to dispersal assembly in ecology"
<p>This repository contains the data and code needed to reproduce the results and figures in the article “Unveiling the transition from niche to dispersal assembly in ecology” published in Nature.</p>
Genomic epidemiology unveils the dynamics and spatial corridor behind the Yellow Fever virus outbreak in Southern Brazil
<p>Despite the considerable morbidity and mortality of yellow fever virus (YFV) infections in Brazil our understanding of disease outbreaks is hampered by limited viral genomic data. Determining the timing and spatial corridors of YFV spread, as well as the geographic hotspots that link the endemic north of the country with epidemic extra-Amazonian regions, are central to predicting and preventing future outbreak and epidemics. Here, we tracked the recent spread of the virus by integrating genome sequences with both epidemiological and vector data. Through a combination of phylogenetic and epidemiological models we reconstructed the recent transmission history of YFV within different epidemic seasons in Brazil. A suitability index based on the highly domesticated <em>Aedes aegypti</em> was able to capture the seasonality of reported human infections. Spatial modelling revealed spatial hotspots with both past reporting and low vaccination coverage, which coincided with many of the largest urban centres in the Southeast. Phylodynamic analysis unravelled the circulation of three distinct YFV lineages, and provided proof of the directionality of a known spatial corridor of viral spread that connects the endemic North with the extra-Amazonian basin. This study illustrates that genomics linked with eco-epidemiology in a One Health framework can provide new insights into the landscape of YFV transmission, augmenting traditional approaches to infectious disease surveillance and control.</p>
Fig. 3 in Unveiling global species abundance distributions
Fig. 3 | The temporal change in our statistical understanding of gSADs. a, The final 20-year rolling window gSAD for each of ten example classes with the best fit overlaid for the log-series, negative binomial and Poisson log-normal distributions.b, Yearly goodness of fit (correlation) of each distribution for each 20-year rolling window gSAD.Example classes from top to bottom: Actinopterygii, Amphibia,Arachnida, Aves, Bivalvia, Cephalopoda, Cycadopsida, Insecta, Liliopsida and Mammalia.
Fig. 4 in Unveiling global species abundance distributions
Fig. 4 | How the relative position of the veil corresponds to species richness and the number of individuals in a class. a–c, The proportion of the gSAD uncovered,assuming a Poisson log-normal distribution, and its relationship to observed species richness/number of observations (a), number of observations (b) and species richness (c). To aid in visualizing the patterns, the red dashed line represents a fit from geom_smooth() and the shaded grey area represents the 95% confidence interval around that fit.
Fig. 1 in Unveiling global species abundance distributions
Fig. 1 | Conceptual scheme illustrating the Poisson sampling of a community with species abundances described by a gamma or a log-normal distribution. Two types of gSAD—gamma (left) and log-normal distribution (right) are shown at the top.Each distribution represents the probability f of a species having a given abundance λ, with the gamma distribution having parameters k (shape) and θ (scale) and the log-normal distribution having parameters μ (mean) and σ (standard deviation), and Γ() representing the gamma function.In the middle, sampling of the gSAD with the probability of each species having a given number of individuals sampled described by a Poisson distribution is illustrated. The mean abundance of each species sampled is randomly taken from the SAD.We exemplify two samples of different sizes, where different symbols denote individuals of different species. The bottom graphs show that: if the global abundances have a log-normal distribution, the mixture distribution of abundances in the sample is a Poisson log-normal; if the global abundances follow a gamma distribution the resulting mixture distribution is a negative binomial but in the limit k→0, we obtain the Fisher log-series.
Unveiling the Catalytic Mechanism of NADP+-Dependent Isocitrate Dehydrogenase with QM/MM Calculations
<p>Raw molecular dynamics simulations for the complexes simulated for 20 ns with the AMBER 12 software. Details can be found in the original manuscript (<a href="https://doi.org/10.1021/acscatal.5b01928">https://doi.org/10.1021/acscatal.5b01928</a>). Molecular topology in AMBER Parameter Topology format and Trajectories in NETCDF binary coordinate format.</p> <p>Two protonation states were simulated: non-charged state of catalytic Lys212/Asp275 (<strong>LYN626+ASH275+ASP666</strong>) and charged state of catalytic Lys212/Asp275 (<strong>LYS626+ASP275+ASP666</strong>)</p> <p>Production trajectories are included in the <strong>MM-MD</strong> folders. Input and restart coordinates files for reproducibility are located in folders <strong>inputs</strong> and <strong>rst</strong>.</p> <p>Instructions for the calculations are summarized in <em>amber_min-md.sh</em>.</p>
Resurrecting Ancient Antibiotics: Unveiling the Origins of Modern Lipid II Targeting Glycopeptides
<p>Data supporting the publication "Resurrecting Ancient Antibiotics: Unveiling the Origins of Modern Lipid II Targeting Glycopeptides"</p>
Unveiling the genetic networks: Exploring the dynamic interaction of photosynthetic phenotypes in woody plants across varied light gradients
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Single cell transcriptomics unveiled that early life BDE-99 exposure reprogrammed the gut-liver axis to promote a pro-inflammatory metabolic signature in male mice at late adulthood (Part 1/2)
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Unveiling the impact of soil methane sink on atmospheric methane concentrations in 2020
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Single cell transcriptomics unveiled that early life BDE-99 exposure reprogrammed the gut-liver axis to promote a pro-inflammatory metabolic signature in male mice at late adulthood (Part 2/2)
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Data from: Eco–enzymatic stoichiometry unveils resource limitations in soil microorganisms during subtropical vegetation restoration
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On the use of antibiotics in plasticity research: gastropod shells unveil a tale of caution
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Unveiling the impacts of land use on the phylogeography of zoonotic New World Hantaviruses
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Figure 1 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Fig. 1</strong> <strong>Phylogeny and cerebellar diversity of squamates.</strong> <strong>a</strong> Phylogenetic tree of all snake and lizard species used in morphological and volumetric analyses, adapted from the most inclusive phylogenetic study available for extant squamates. The seven major locomotor modes for snakes (coloured squares) and/or lizards (coloured circles), as defined based on anatomical features, habitat use, and movement type, are indicated by the same colour code throughout the entire manuscript (see bottom left corner): limbless or limb-reduced burrower (red squares and circles); limbless or limb-reduced facultative burrower (purple squares and circles); limbless or limb-reduced multi-habitat using lateral undulation (orange squares and circles); limbless or limb-reduced multi-habitat using other movements (yellow squares); quadrupedal arboreal (dark blue circles); quadrupedal terrestrial (light blue circles); quadrupedal facultative bipedal/aerial (green circles). <strong>b</strong>–<strong>o</strong> 3D-volume rendering and high-resolution whole-brain segmentation of iodine-stained adult heads (<strong>b</strong>–<strong>h</strong>) highlighting the cerebellum structure (<strong>b</strong>–<strong>o</strong>, red colour) of selected representative squamates at indicated position in the phylogenetic tree: <em>Pantherophis guttatus</em> (<strong>b</strong>, <strong>i</strong>), <em>Epicrates cenchria</em> (<strong>c</strong>, <strong>j</strong>), <em>Pogona vitticeps</em> (<strong>d</strong>, <strong>k</strong>), <em>Draco volans</em> (<strong>e</strong>,<strong> l</strong>), <em>Bradypodion pumilum</em> (<strong>f</strong>, <strong>m</strong>), <em>Anguis fragilis</em> (<strong>g</strong>, <strong>n</strong>), <em>Melanoseps loveridgei</em> (<strong>h</strong>, <strong>o</strong>). High magnifications of 3D-rendered cerebella (<strong>i</strong>–<strong>o</strong>) are shown in pial surface (left panels) and lateral (right panels) views for each selected species. Scale bars: 1mm (<strong>b</strong>–<strong>h</strong>), 500 μm (<strong>i</strong>–<strong>o</strong>).</p>
Figure 8 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Fig. 8 Comparative transcriptomics of the squamate cerebellum.</strong> <strong>a</strong> Two-way hierarchical clustering heat map showing three clusters of genes (rows) that behave similarly (clusters 1 and 2) or differently (cluster 3) across ten selected squamate species (columns). Z-score colour intensities reflect scaled gene expression values, ranging from low (blue) to high (yellow), for 630 one-to-one orthologous genes identified in all species. <strong>b</strong> Pie charts showing the distribution of orthologous genes (in %) among all significantly enriched gene ontology terms for biological processes (hypergeometric test with a false discovery rate multiple-hypothesis correction, p-value < 0.01) in clusters identified in <strong>a</strong>. c Hierarchical clustering of pairwise Pearson’s correlation coefficients for 630 orthologous genes identified across all squamate species. Colour intensities of individual tiles in the heat map depict pairwise correlation coefficient values, ranging from low (blue) to high (yellow), between selected species with indicated locomotor mode (see colour code and symbols on the right). Numbers at nodes in the cluster dendrogram represent approximately unbiased p-values (in percentage) obtained by multiscale bootstrap resampling.</p> <p> </p> <p> </p> <p> </p>
Figure 7 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Fig. 7</strong> <strong>Variability in the arrangement of Purkinje cells (PCs) in the squamate cerebellum.</strong> <strong>a</strong>, <strong>b</strong> Representative light-sheet microscopy imaging of cleared whole-cerebella showing the 3D distribution and arrangement of calbindin 1 (CALB1)-immunolabelled PCs in two representative species with different locomotor modes (see colour code and symbols in top left corner): <em>Pogona vitticeps </em>(<strong>a</strong>) and <em>Boaedon fuliginosus</em> (<strong>b</strong>). The boxed areas in the coronal 3Drendered cerebellar views (top panels) are shown at higher magnifications in coronal (left) and sagittal (right) views in the lower panels. <strong>c</strong>, Violin plot showing the quantitative distribution of CALB1-immunolabelled PCs in the cerebellar cortex of selected squamate species with similar or different locomotor modes (colour code and symbols as above). Due to intra- and interspecies heterogeneity in molecular layer (ML) thickness, the position of individual cells (n = 250–750 per species) was calculated as the distance (in %) from the granule cell layer (GCL) to the outer border (pial surface) of the ML, and error bars represent the standard deviation. Four major positioning patterns containing three or four squamate species and reflecting the increased scattering of PCs (from I to IV) were identified based on Kruskal-Wallis statistics. Immunohistochemistry with CALB1 marker (red staining) on sagittal sections of the cerebellar cortex in selected representative species are shown at low and high magnifications (insets) for each pattern: <em>Pogona vitticeps</em> (I), <em>Eryx colubrinus</em> (II), <em>Pseudopus apodus</em> (III), <em>Dasypeltis gansi</em> (IV). Scale bars: 30 μm (<strong>a</strong>, <strong>b</strong>), 100 μm (<strong>c</strong>).</p> <p> </p> <p> </p>
Figure 6 from "Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"
<p> </p> <p>Published as part of <a href="https://doi.org/10.1038/s41467-019-13405-w"><strong>Macrì, S <em>et al</em>., 2019, Nature Communications: 10(1):5560</strong></a></p> <p><strong>"Comparative analysis of squamate brains unveils multi-level variation in cerebellar architecture associated with locomotor specialization"</strong> DOI: https://doi.org/10.1038/s41467-019-13405-w</p> <p> </p> <p><strong>Fig. 6 Cerebellar size variation in squamates with different locomotor behaviours.</strong> <strong>a</strong> Scatter plot showing the correlation of cerebellum relative to wholebrain volume (in mm3) for selected representative squamate species (see colour code and symbols in bottom right corner). The coloured lines and shadings represent the phylogenetic generalized least squares (PGLS) regression lines and 95% confidence intervals for each locomotor mode, respectively. <strong>b</strong> Ridgeline plot showing the distribution of the cerebellum-to-whole-brain volume ratios (in percentage) for each indicated limbless or limbreduced (top panels) or quadrupedal (bottom) locomotor mode. Colour gradient, ranging from yellow to blue, reflects the tail distribution probability.</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.