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388 results for “Data element”
Data from: Flickers of speciation? Sympatric color morphs of the arc-eye hawkfish, Paracirrhites arcatus, reveal key elements of divergence-with-gene-flow
One of the primary challenges of evolutionary research is to identify ecological factors that favor reproductive isolation. Therefore, studying partially isolated taxa has the potential to provide novel insight into the mechanisms of evolutionary divergence. Our study utilizes an adaptive color polymorphism in the arc-eye hawkfish (Paracirrhites arcatus) to explore the evolution of reproductive barriers in the absence of geographic isolation. Dark and light morphs are ecologically partitioned into basaltic and coral microhabitats a few meters apart. To test whether ecological barriers have reduced gene flow among dark and light phenotypes, we evaluated genetic variation at 30 microsatellite loci and a nuclear exon (Mc1r) associated with melanistic coloration. We report low, but significant microsatellite differentiation among color morphs and stronger divergence in the coding region of Mc1r indicating signatures of selection. Critically, we observed greater genetic divergence between color morphs on the same reefs than between the same morphs in different geographic locations. We hypothesize that adaptation to the contrasting microhabitats is overriding gene flow and is responsible for the partial reproductive isolation observed between sympatric color morphs. Combined with complementary studies of hawkfish ecology and behavior, these genetic results indicate an ecological barrier to gene flow initiated by habitat selection and enhanced by assortative mating. Hence the arc-eye hawkfish fulfill theoretical expectations for the earliest phase of speciation-with-gene-flow.
Data from: Analysis of transposable elements in the genome of Asparagus officinalis from high coverage sequence data
Asparagus officinalis is an economically and nutritionally important vegetable crop that is widely cultivated and is used as a model dioecious species to study plant sex determination and sex chromosome evolution. To improve our understanding of its genome composition, especially with respect to transposable elements (TEs), which make up the majority of the genome, we performed Illumina HiSeq2000 sequencing of both male and female asparagus genomes followed by bioinformatics analysis. We generated 17 Gb of sequence (12×coverage) and assembled them into 163,406 scaffolds with a total cumulated length of 400 Mbp, which represent about 30% of asparagus genome. Overall, TEs masked about 53% of the A. officinalis assembly. Majority of the identified TEs belonged to LTR retrotransposons, which constitute about 28% of genomic DNA, with Ty1/copia elements being more diverse and accumulated to higher copy numbers than Ty3/gypsy. Compared with LTR retrotransposons, non-LTR retrotransposons and DNA transposons were relatively rare. In addition, comparison of the abundance of the TE groups between male and female genomes showed that the overall TE composition was highly similar, with only slight differences in the abundance of several TE groups, which is consistent with the relatively recent origin of asparagus sex chromosomes. This study greatly improves our knowledge of the repetitive sequence construction of asparagus, which facilitates the identification of TEs responsible for the early evolution of plant sex chromosomes and is helpful for further studies on this dioecious plant.
Processed data from "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"
<p>This is the processed data from our manscript "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"</p>
Processed data from "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"
<p>This is the processed data from our manscript "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"</p>
Processed data from "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"
<p>This is the processed data from our manscript "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"</p>
Processed data from "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"
<p>This is the processed data from our manscript "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"</p>
Processed data from "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"
<p>This is the processed data from our manscript "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"</p>
Processed data from "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"
<p>This is the processed data from our manscript "Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits"</p>
Data for Automatic recognition of element classes and boundaries in the birdsong with variable sequences
<p>Data for Automatic recognition of element classes and boundaries in the birdsong with variable sequences</p>
Supplementary material 1 from: Jasso-Martínez JM, Brady SG, Kula RR (2023) Phylogenetic affinities of the non-cyclostome subfamilies Amicrocentrinae and Dirrhopinae (Hymenoptera, Braconidae) confirmed by ultraconserved element data. Journal of Hymenoptera Research 96: 1017-1030. https://doi.org/10.3897/jhr.96.111012
Maximum likelihood tree resulting from the 50% complete matrix without collapsed clades and with full names of the terminal taxa
Collected data from finite element simulations to calculate the mechanical properties of innovative CLT using ABAQUS
<p>A dataset is collected from finite element computation using ABAQUS for different configurations of innovative CLT. In the dataset, we have the inputs (w, t1, t2, t3, t4, s, E_L, G_LZ, G_CZ) describing the microstructure of innovative CLT, and the elastic properties (Membrane stiffness: A11, A22, In-plane Poisson effect stiffness: A12, In-plane shear stiffness: A33, Bending stiffness: D11, D22, Out of plane Poisson effect stiffness: D12, Torsional stiffness: D33, out of plane Bending Gradient shear compliances: h11, h12, h16, h22, h26, h33, h34, h35, h44, h45, h55, h66) deriving from the FE computations. We have also the results of closed-form solutions that predicts these elastic properties of innovative CLT. </p>
Negative Muon Elemental Spectroscopy Data
<p>Training and test data associated with the DNN exercise notebook from: <a href="https://github.com/mdi-group/iisc-ml-school">https://github.com/mdi-group/iisc-ml-school</a></p> <p>This work was supported by EPSRC project EP/Y000552/1 and Royal Society project IES\R3\223036.</p>
Comparing ultraconserved elements and exons for phylogenomic analyses of Middle American cichlids: When data agree to disagree
<p>Choosing among types of genomic markers to be used in a phylogenomic study can have a major influence on the cost, design, and results of a study. Yet few attempts have been made to compare categories of next-generation sequence markers limiting our ability to compare the suitability of these different genomic fragment types. Here we explore properties of different genomic markers to find if they vary in the accuracy of component phylogenetic trees and to clarify the causes of conflict obtained from different datasets or inference methods. As a test case, we explore the causes of discordance between phylogenetic hypotheses obtained using a novel dataset of ultraconserved elements (UCEs) and a recently published exon dataset of the cichlid tribe Heroini. Resolving relationships among heroine cichlids has historically been difficult, and the processes of diversification and colonization of Middle America and the Greater Antilles are not yet well understood. Despite differences in informativeness and levels of gene tree discordance between UCEs and exons, the resulting phylogenomic hypotheses generally agree on most relationships. The independent datasets disagreed in areas with low phylogenetic signal that were overwhelmed by noise and non-phylogenetic signals. For UCEs, high levels of incomplete lineage sorting (ILS) seem to be a major cause of noise, whereas, for exons, non-phylogenetic signal may be caused by a reduced number of highly informative loci. This paucity of informative loci in exons might be due to heterogeneous substitution rates that are problematic to model (i.e., computationally restrictive) resulting in systematic errors that UCEs (being less informative individually but more uniform) are less prone to. These results generally demonstrate the robustness of phylogenomic methods to accommodate genomic markers with different biological and phylogenetic properties. However, we identify common and unique pitfalls of different categories of genomic fragments when inferring enigmatic phylogenetic relationships.</p>
the data of "High-pressure behavior of synthetic quenchable hydroxylbastnasite-(Sm): Implications for rare earth elements, carbon, and water transmission into the deep earth"
<p>This is the package of the Raman data of synthesized Sm(CO<sub>3</sub>)OH at high-pressure and ambient temperature and synchrotron radiation X-Ray data of synthesized Sm(CO<sub>3</sub>)OH at high-pressure and ambient temperature, they are in *.asc and *.chi respectively.</p>
Elemental and S isotopic composition data for "Sulfur isotopic fractionation of the youngest Chang'e-5 basalts: Constraints on the magma degassing and geochemical features of the mantle source"
<p>Data for "Sulfur isotopic fractionation of the youngest Chang'e-5 basalts: Constraints on the magma degassing and geochemical features of the mantle source".</p>
Data from: Using ultraconserved elements to reconstruct the termite tree of life
<p><span>The phylogenetic history of termites has been investigated using mitochondrial genomes and transcriptomes. However, both sets of markers have specific limitations. Mitochondrial genomes represent a single genetic marker likely to yield phylogenetic trees presenting incongruences with species trees, and transcriptomes can only be obtained from well-preserved samples. In contrast, ultraconserved elements (UCEs) include a great many independent markers that can be retrieved from poorly preserved samples. Here, we designed termite-specific baits targeting </span><span>50,616 UCE loci. We tested our UCE bait set on 42 samples of termites and three samples of <em>Cryptocercus</em>, for which we generated low-coverage highly-fragmented genome assemblies and successfully extracted <em>in silico</em> between 3,426 to 42,860 non-duplicated UCEs per sample. Our maximum likelihood phylogenetic tree, reconstructed using the 5,934 UCE loci retrieved from upward of 75% of samples, was congruent with transcriptome-based phylogenies, demonstrating that our UCE bait set is reliable and phylogenetically informative. Combined with non-destructive DNA extraction protocols, our UCE bait set provides the tool needed to carry out a global taxonomic revision of termites based on poorly preserved specimens such as old museum samples. The Termite UCE database is maintained at: </span><span><a href="https://github.com/oist/TER-UCE-DB/"><span>https://github.com/oist/TER-UCE-DB/</span></a></span><span>.</span></p>
Data From - TE Density: a tool to investigate the biology of transposable elements
<p><strong>Background</strong>: Transposable elements (TEs) are powerful creators of genotypic and phenotypic diversity due to theirinherent mutagenic capabilities and in this way they serve as a deep reservoir of sequences for genomic variation. As agents of genetic disruption, a TE's potential to impact phenotype is partially a factor of its location in the genome. Previous research has shown TEs' ability to impact the expression of neighboring genes, however our understanding of this trend is hampered by the exceptional amount of diversity in the TE world, and a lack of publicly availablecomputational methods that quantify the presence of TEs relative to genes.</p> <p><strong>Results: </strong>Here, we have developed a tool to more easily quantify TE presence relative to genes through the useof only a gene and TE annotation, yielding a new metric we call TE density. Briefly defined as the proportion of TE-occupied base-pairs relative to a window-size of the genome. This new pipeline reports TE density for each gene in the genome, for each type descriptor of TE (order and superfamily), and for multiple positions and distances relative to the gene (upstream, intragenic, and downstream) over sliding, user-defined windows. In this way, we overcome previous limitations to the study of TE-gene relationships by focusing on all TE types present in the genome, utilizing flexible genomic distances for measurement, and reporting a TE presence metric for every gene in the genome.</p> <p><strong>Conclusions: </strong>Together, this new tool opens up new avenues for studying TE-gene relationships, genome architecture,comparative genomics, along with the tremendous diversity present in the TE world.</p> <p><strong>Data Availability: </strong>TE Density is open-source and freely available at: https://github.com/sjteresi/TE_Density.</p>
Data from: The effect of the intensity of the element that distinguishes flavor on the memory and perception of Peruvian millennials and centennials
<p>Globalization has facilitated a lot the access to all kinds of products and brands from different parts of the world, which has increased consumer choice and also competition among packaged products. For this reason, the package design of a brand to attract<br> consumers must be able to stand out among so much supply, especially if it is a new product or a new flavor. The packaging of the product has a strong direct influence on consumers and therefore it becomes necessary to explore dimensions of packaging design that allow a high degree of differentiation or at least enough to differentiate from the competition and the same product line. In this line, there are very efficient strategies and approaches used in the literature to perform this exploration in packaging, such as evaluations of perception measured with attributes and the use of eye-tracking technology that records direct information about visual attention on the most distinctive elements. Thus, this study aims to determine the impact of the presentation of a new flavor on the packaging by varying the intensity of the stimulus that represents it according to the Weber-Fechner law, using the three main elements of the packaging: text, color and image. The experiment exposed three groups of participants (n=30) to 3 stimuli, which were based on the addition of an element as the intensity of the flavor description of three products from three different food categories was intended to increase. This study used the eye-tracking platform via RealEye webcam to measure attention, and a self-administered questionnaire was used to examine perception and recall.</p>
Data for J-PLUS: Beyond spectroscopy III. Stellar parameters and elemental-abundance ratios for five million stars from DR3
<p>The table contains stellar atmospehric parameters (Teff, logg, [Fe/H]), luminosity classification, element abundance ratios ([C/Fe], [Mg/Fe] and [alpha/Fe]), distance and age for over five million stars derived using J-PLUS DR3 + Gaia EDR3.</p><p>It includes the following parameters:</p><p>ra: Right Ascension from J-PLUS DR3 (J2000)</p><p>dec: Declination from J-PLUS DR3 (J2000)</p><p>gl: Galactic longitude derived from ICRS coordinates</p><p>gb: Galactic latitude derived from ICRS coordinates</p><p>mag[12]: Magnitudes of J-PLUS twelve bands (r, g, i, z, u, J0378, J0395, J0410, J0430, J0515, J0660, J0861)</p><p>err_mag[12]&Uncertainties of magnitudes of J-PLUS twelve bands (r, g, i, z, u, J0378, J0395, J0410, J0430, J0515, J0660, J0861)</p><p>gp1/rp1/ip1: Magnitudes from Pan-STARRS1</p><p>err_gp1/rp1/ip1: Uncertainties of magnitudes from Pan-STARRS1</p><p>G/BP/RP: Magnitudes for the Gaia three bands from EDR3; note G represents a calibration-corrected G magnitude</p><p>err_G/BP/RP: Uncertainties of magnitudes for the three Gaia bands from EDR3</p><p>ebv_sfd: Value of E(B - V) from the extinction map of SFD98, corrected for a 14% systematic</p><p>[Fe/H]: Photometric metallicity</p><p>err_[Fe/H]: Uncertainty of photometric metallicity</p><p>flg_[Fe/H]: Quality flag of [Fe/H]</p><p>[C/Fe]: Photometric carbon-to-iron abundance ratio</p><p>err_[C/Fe]:Uncertainty of photometric carbon-to-iron abundance ratio</p><p>flg_[C/Fe]: Quality flag of [C/Fe]</p><p>[Mg/Fe]: Photometric magnesium-to-iron abundance ratio</p><p>err_[Mg/Fe]: Uncertainty of photometric magnesium-to-iron abundance ratio</p><p>flg_[Mg/Fe]: Quality flag of [Mg/Fe]</p><p>[alpha/Fe]: Photometric alpha-to-iron abundance ratio</p><p>err_[alpha/Fe]: Uncertainty of photometric alpha-to-iron abundance ratio</p><p>flg_[alpha/Fe]: Quality flag of [alpha/Fe]</p><p>Teff: Effective temperature</p><p>err_Teff: Uncertainty of effective temperature</p><p>logg: Surface gravity</p><p>err_logg: Uncertainty of surface gravity</p><p>dist: Distance </p><p>err_dist: Uncertainty of distance</p><p>flg_dist: Flag to indicate the method used to derive distance, which takes the values ``parallax", ``CMF", and ``NO"</p><p>age: Stellar age</p><p>err_age: Uncertainty of stellar age</p><p>rv: Radial velocity</p><p>err_rv: Uncertainty of radial velocity</p><p>flg_rv: Flag to indicate the source of radial velocity, which takes the values ``GALAH", ``APOGEE'', ``Gaia",``RAVE", ``LAMOST", ``SEGUE"</p><p>parallax: Parallax from {it Gaia} EDR3</p><p>err_parallax: Uncertainty of parallax from {it Gaia} EDR3</p><p>pmra: Proper motion in Right Ascension direction from Gaia EDR3</p><p>err_pmra: Uncertainty of proper motion in Right Ascension direction from Gaia EDR3</p><p>pmdec: Proper motion in Declination direction from Gaia EDR3</p><p>err_pmdec&Uncertainty of proper motion in Declination direction from Gaia EDR3</p><p>ruwe: Renormalised unit weight error from Gaia EDR3</p><p>type: Flag to indicate classifications of stars, which takes the values ``dwarf" and ``giant" </p><p>subtype: Flag to indicate further sub-classifications of dwarf stars, which takes the values ``TO", ``MS" and ``Binary"</p>
Data Sets for: Trace elements in aerosol from Northwest Pacific marginal sea, Indian Ocean and South Pacific to Antarctica: Spatial variability and source identification
<p>This dataset includes the concentrations of trace elements in aerosols, along with location and time information, collected during a cruise from November 2021 to April 2022. The cruise covered the Pacific, the Indian Ocean, the Southern Ocean.</p>
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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.