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388 results for “Data element”
Mg isotope and element data in silicate component for core NHX3 from upwelling area off the Vietnam coast
<p>Mg isotope and element data in silicate component for core NHX3 from upwelling area off the Vietnam coast</p>
The Data For Spatial Variations of Stellar Elemental Abundances in FIRE Simulations of Milky Way-Mass Galaxies: Patterns Today Mostly Reflect Those at Formation
<p>Spatial patterns of stellar elemental abundances encode rich information about a galaxy’s formation<br>history. We analyze the radial, vertical, and azimuthal variations of metals in stars, both today and at<br>formation, in the FIRE-2 cosmological simulations of Milky Way-mass galaxies, and we compare<br>with the Milky Way. Overall, spatial variations of stellar metallicities show only modest differences between formation and today; spatial variations today primarily reflect the conditions of stars at birth, with spatial redistribution of stars after birth contributing secondarily. </p> <p> </p> <p>This data abides by CC-BY.</p>
Source Data for the manuscript: General-purpose machine-learned potential for 16 elemental metals and their alloys
<p>***Source Data***<br>This folder contains multiple .txt files that provide the source data for the figures and tables presented in the paper: "General-purpose machine-learned potential for 16 elemental metals and their alloys."</p> <p>The source data are organized in the following folders and files:</p> <p>1) Fig2<br>2) Fig3<br>3) Fig4<br>4) Fig5<br>5) Fig6<br>6) FigS1<br>7) FigS2<br>8) FigS3<br>9) FigS4-6-pure<br>10) FigS7-9-binary<br>11) FigS10-12-ternany<br>12) FigS13-15-quaternary<br>13) FigS16-17-quinary<br>14) FigS18-20<br>15) FigS21<br>16) FigS22<br>17) FigS23<br>18) FigS26<br>19) Table1-Element-atoms-GPU-Speed.txt<br>20) Table-S1-DFT-EAM-UNEP-Elastic.txt<br>21) Table-S2-DFT-EAM-UNEP-Mono-vacanc.txt<br>22) Table-s3-Surface-100-110-111-DFT-EAM-UNEP.txt<br>23) Table-S4-Melting-EAM-UNEP-Exp.txt</p>
Data from: Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence
Active transposable elements (TEs) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky-Muller incompatibilities (DMI), thus contributing to the evolution of endogenous genetic barriers and eventually cause population divergence. We investigated differential TE abundance among conspecific populations of the non-biting midge Chironomus riparius and evaluated their potential role in causing endogenous genetic incompatibilities between these populations. We focussed on a Chironomus-specific TE, the minisatellite-like Cla-element, whose activity is associated with speciation in the genus. Using a newly generated and annotated draft genome for a genomic study with five natural C. riparius populations, we found highly population-specific TE insertion patterns with many private insertions. A significant correlation of the pairwise FST estimated from genome-wide single nucleotide polymorphisms (SNPs) and the FST estimated from TEs, is consistent with drift as the major force driving TE population differentiation. However, the significantly higher Cla-element FST level due to a high proportion of differentially fixed Cla-element insertions also indicates selection against segregating (i.e. heterozygous) insertions. With reciprocal crossing experiments and fluorescent in-situ hybridisation of Cla-elements to polytene chromosomes, we documented phenotypic effects on female fertility and chromosomal mispairings. We propose that the inferred negative selection on heterozygous Cla-element insertions may cause endogenous genetic barriers and therefore acts as DMI among C. riparius populations. The intrinsic genomic turnover exerted by TEs may thus have a direct impact on population divergence that is operationally different from drift and local adaptation.
Data from: High-throughput SNP genotyping of historical and modern samples of five bird species via sequence capture of ultraconserved elements
Sample availability limits population genetics research on many species, especially taxa from regions with high diversity. However, many such species are well represented in museum collections assembled before the molecular era. Development of techniques to recover genetic data from these invaluable specimens will benefit biodiversity science. Using a mixture of freshly preserved and historical tissue samples, and a sequence capture probe set targeting >5000 loci, we produced high-confidence genotype calls on thousands of single nucleotide polymorphisms (SNPs) in each of five South-East Asian bird species and their close relatives (N = 27–43). On average, 66.2% of the reads mapped to the pseudo-reference genome of each species. Of these mapped reads, an average of 52.7% was identified as PCR or optical duplicates. We achieved deeper effective sequencing for historical samples (122.7×) compared to modern samples (23.5×). The number of nucleotide sites with at least 8× sequencing depth was high, with averages ranging from 0.89 × 106 bp (Arachnothera, modern samples) to 1.98 × 106 bp (Stachyris, modern samples). Linear regression revealed that the amount of sequence data obtained from each historical sample (represented by per cent of the pseudo-reference genome recovered with ≥8× sequencing depth) was positively and significantly (P ≤ 0.013) related to how recently the sample was collected. We observed characteristic post-mortem damage in the DNA of historical samples. However, we were able to reduce the error rate significantly by truncating ends of reads during read mapping (local alignment) and conducting stringent SNP and genotype filtering.
Supplementary Data for: Life history in primate teeth is revealed by changes in major and minor element concentrations measured via field-emission SEM-EDS analysis
<p>Overcoming the non-specificity of histological accentuated growth lines in hard tissues is an ongoing challenge. Identifying season at death and reproductive events has profound implications for evolutionary, ecological and conservation studies. Dental cementum is a mineralized tissue with yearly periodicity that continues deposition from tooth formation until death, maintaining a record spanning almost the entire life of an individual. Recent work has successfully employed elemental analysis of calcified incremental tissues to detect changes in extrinsic conditions such as diet and climate and to identify two important life history milestones: weaning and sexual maturity. Here, we employ field-emission scanning electron microscopy and energy-dispersive X-ray analysis to measure the relative concentrations of calcium, phosphorous, oxygen, magnesium and sodium in the cementum of 34 teeth from seven male and female rhesus macaques with known medical and life history information. We find that changes in relative magnesium concentrations correspond with reproductive events in females and breastfeeding in infants. Additionally, we observe seasonal calcium patterns in 77.3% of the samples.</p>
Supplementary data Quantitative elemental mapping of chondritic meteorites using laser ablation-inductively coupled plasma-time of flight-mass spectrometry (LA-ICP-TOF-MS)
<p>Supplementary data Quantitative elemental mapping of chondritic meteorites using laser ablation-inductively coupled plasma-time of flight-mass spectrometry (LA-ICP-TOF-MS)English</p>
Sequencing data for "Identifying and tracking mobile elements..." by van Dijk et al. (2023)
<p>The dataset contains the following directories:</p> <p><strong>All_raw_MAGs</strong>: all cross-assembled MAGs per community, with a text file for their BAT annotation results. Cross-assembly was done by combining all time points. <br> <strong>Candidatus_Saccharibacterium_MAGs</strong>: identified nanobacterium MAGs from various communities. <br> <strong>Cellvibrio_MAGs</strong>: identified cellvibrio spp. across communities. <br> <strong>Cellvibrio_Plasmids:</strong> Cp plasmids belonging to Cellvibrio (C1) which transferred from communities 8 to 4, 6, 9, and 10 (in horizontal communities)<br> <strong>Interactive_Dataset:</strong> HTML5 (Plotly) graphs to explore all xenotypic sequences and MAG abundance plots<br> <strong>Rscript_mock_data</strong>: R script used to design the mock data for the benchmark set. </p> <p>And a single spreadsheet (<strong>Xenoseq_mastersheet.xlsx, </strong>Supplementary Table 1) of data discussed in the main text.</p>
Data for: A selfish genetic element and its suppressor causes abnormalities to testes in a fly
<p class="MsoNormal">Selfish genetic elements (SGEs), specifically X-chromosome meiotic drive (XCMD), create huge conflicts within a host's genome and can have profound effects on fertility. Suppressors are a common evolutionary response to XCMD to negate its costs. However, whether suppressors themselves can cause negative non-target effects remains understudied. Here, we examine whether the intragenomic conflicts created by XCMD and its suppressor affect gonad morphology in <em>Drosophila subobscura. </em>We found significant differences in testes, seminal vesicle, and accessory gland size depending on whether a male carried a non-driving X chromosome, an XCMD, and if the XCMD was suppressed. We also found the first evidence of abnormal testes development that is specifically associated with a suppressor of XCMD. Unlike other studies, our evidence suggests that XCMD in <em>D. subobscura </em>creates major abnormalities to male gonads. These abnormalities are most frequent if both XCMD and its suppressor are both present. While costs of suppression have importance in theoretical models, they have largely been ignored in empirical XCMD systems. Overall, this study highlights that genetic conflict, created by SGEs and their suppressors, is a potent evolutionary force that can have major impacts on gonad development and gametogenesis. <span><br></span></p>
Apatite trace element data for genetic type classification
<p>Apatite trace element data for genetic type classification, including porphyry, skarn, orogenic Au, iron-oxide copper gold (IOCG), and iron-oxide apatite (IOA or Kiruna type).</p>
Numerical results data of 'Impact of Injection Pressure and Polyaxial Stress on Hydraulic Fracture Propagation and Permeability Evolution in Greywacke: Insights from Discrete Element Models of a Laboratory Test'
<p>Numerical results data of '<strong>Impact of Injection Pressure and Polyaxial Stress on Hydraulic Fracture Propagation and Permeability Evolution in Greywacke: Insights from Discrete Element Models of a Laboratory Test</strong>'</p>
Data for the Journal article "Reduced whereas still noteworthy atmospheric pollution of trace elements in China"
<p>This dataset provides the trace elements emission inventory with 27km resolution for China in 2017, the model simulated concentrations of trace elements for China in 2017 and the associated health risks of trace elements for China in 2017.</p>
Detection of Ore-forming Elements Migrated from Rock and Soil to Vegetation Leaves using Hyperspectral Data
<p>In this paper we present the detection of ore-forming elements migrated from soil and rock to vegetation leaves using hyperspectral data. The rock, soil (C, B, A layer) and vegetation (root, stem, leaf) samples with the measurements of spectra and element concentrations in the vertical section of the abandoned pits were collected. The wavelet approach is applied to analyze the correlations between spectral features and element concentrations. The results show that the significant correlations are found at a lower order mother wavelets such as Haar. Moreover, the significant correlations are negative between Cu and Mo elements and the wavelet energy vector of the soil and rock to vegetation leaves spectrum. The results also show that ore-forming elements migrated from rock and soil to vegetation leaves can be detected using hyperspectral data in the study area.</p>
Data for the publication by Mouchi et al "A step towards measuring connectivity in the deep-sea: elemental fingerprints of mollusk larval shells discriminate hydrothermal vent sites"
<p>This is the elemental data collected by fsLA-ICP-MS-MS on 600 individual larval shells of the hydrothermal-vent limpet Shinkailepas tollmanni from 14 sites in the Southwest Pacific Ocean.</p> <p>The first column indicates the sample ID corresponding to onship sample during the scientific cruise CHUBACARC (Hourdez & Jollivet, 2019).</p> <p>The second column indicates the S. tollmanni sample ID from the publication of Mouchi et al.</p> <p>Columns 3 to 15 correspond to elemental abundances measured.</p> <p>Column 16 to 18 correspond to the region, area and hydrothermal sites, respectively, for each larval shell.</p> <p> </p> <p>Hourdez, S., Jollivet, D., 2019. CHUBACARC cruise, <em>L’Atalante R/V</em>. doi: 10.17600/18001111.</p>
EAMv2 anthropogenic aerosol emissions data in model-native spectral-element grid
<p>Anthropogenic aerosol emissions data from surface and elevated sources in E3SM Model-native grid. Data available for standard uniform resolution in EAMv2 (ne30pg2) and North America Regionally Refined Model (NA RRM). Data were prepared as a part of the improved emission treatment in E3SMv2 (available at: https://doi.org/10.5281/zenodo.7823633).</p>
Supplementary data to 'Coupling between cohesive element method and Node-to-segment contact algorithm : Implementation and application'
<p>This archive contains the data and the scripts for the simulations presented in the paper</p> <p>Pundir, M., Guillaume, A. "Coupling between cohesive element method and Node-to-segment contact algorithm : Implementation and application'" (2020)</p>
Supplementary Data for "The impetus for bloom of Mesozoic terrestrial ecosystems in northern China: Insights from volcanic nutrient and harmful element delivery" in GRL.
<p>Supplementary data tables for Ma et al. (2023) associated with the paper entitled "The impetus for bloom of Mesozoic terrestrial ecosystems in northern China: Insights from volcanic nutrient and harmful element delivery" published in <em>GRL</em>.</p>
Data for: Combining stable isotopes, trace elements, and distribution models to assess the geographic origins of migratory bats
<p>The expansion of industrial-scale wind-energy facilities has increased the production of low-carbon emission energy but has also resulted in mortality of wildlife, including migratory bats. Management decisions can be limited by a lack of understanding of the geographic impact of bats killed at wind-energy facilities. Several studies have leveraged stable hydrogen isotope ratios (δ<sup>2</sup>H) of bat fur to illuminate this issue but are limited in the precision of conclusion because δ<sup>2</sup>H values vary primarily across latitudinal and elevational bands. One approach to increase the precision of geographic assignment is to combine independent inferences about spatial location from additional biomarkers and other related information. To test this possibility, we assigned known-origin individuals of three bat species commonly killed at on-shore wind-energy facilities in North America (<em>Lasiurus</em> <em>borealis</em>, <em>L</em>. <em>cinereus</em>, and <em>Lasionycteris</em> <em>noctivagans</em>) to probable origin using δ<sup>2</sup>H values, trace element concentrations, and species distribution models. We used cross-validation calibrated combined model tuning to determine the degree to which assignment probabilities improved when combining datasets. We found that combining markers typically performed better than single approaches. For <em>L. borealis</em> and <em>L. cinereus</em>, combining all three data sources outperformed any single or other combined approach. With an accuracy set at 80%, an average of 39.7% and 36.0% of each species' total geographic range was considered a potential origin, respectively; stable hydrogen alone included 51.8% and 50.6% of the total geographic area. In contrast, for <em>L. noctivagans</em>, including trace elements did not increase precision, and adding distribution data to δ<sup>2</sup>H values only improved precision by 0.6%. Thus, we found that a combination of multiple biomarkers typically, but not always, outperforms single marker approaches, and optimized combinations of different markers outperform equal weighting of each marker. From a practical perspective, δ<sup>2</sup>H values performed better than trace elements alone; in cases where cost is a limiting factor, the stable hydrogen should be the single biomarker used in conjunction with species distribution models. Overall, these results highlight the importance of validating methods for each species they are applied to and show that combining information from intrinsic biomarker approaches is a useful tool to document bat movements.</p>
Data for the project: Climatic impacts on the availability and transfer of chemical elements through Arctic terrestrial food-chains: a pilot study
<p>Uploaded data contain trace element concentrations measured in various biological samples collected at Zackenberg Research station (northeast Greenland) in August 2021</p> <p>Fifty (50) sample plots were visited to collect invertebrates (using pitfalls) and sample soil, vegetation, muskox feces and wool.</p> <p>The sheet PlotInfo provides information on the sample plots, which were placed using a stratified random placement procedure across 5 vegetation types and the elevational gradient</p> <p>The sheet Soil contains trace element concentrations (ppm) as well as N and C (%) measured in the soil samples across all 50 sample plots</p> <p>The sheet Vegetation contains trace element concentrations (ppm) as well as N and C (%) measured in the vegetation samples across all 50 sample plots</p> <p>The sheet Insects contains trace element concentrations (ppm) measured in the various insect groups captured in pitfall traps in 9 sample plots</p> <p>The sheet Muskox feces contains trace element concentrations (ppm) measured in the feces samples collected at all 50 sample plots</p> <p>The sheet Muskox Wool contains trace element concentrations (ppm) measured in 25 wool samples collected throughout the sampling area (not at specific sample plots).</p> <p> </p> <p>Trace element concentrations were measured at the ICP-MS platform at the Observatoirie Midi-Pyrenees, Toulouse, France</p> <p>N and C analyses were done at Department of Biology, University of Copenhagen, Denmark</p> <p> </p> <p>For further information on the project, samples, methods used contact flbe@ecos.au.dk</p>
Supplemental information data from: "Alkali Trace Elements Observed by MarSCoDe LIBS at Zhurong Landing Area on Mars: Quantitative Analysis and Its Geological Implications"
<p>This dataset includes the normalized peak areas of MarSCoDe scietific targets used in Table 3 of the corresponding article. The specific peaks are listed below.</p> <p>Data Set S1: Li 670.97 nm, Fe 260.04 nm, Al 309.37 nm, Ca 318.03 nm, Mg 518.15 nm, K 766.70 nm, and Na 818.55/819.70 nm.</p> <p>Data Set S2: Sr 421.67 nm, Fe 260.04 nm, Al 309.37 nm, Ca 318.03 nm, Mg 518.15 nm, K 766.70 nm, and Na 818.55/819.70 nm.</p> <p>Data Set S3: S 564 nm, Fe 260.04 nm, Al 309.37 nm, Ca 612.39 nm, Mg 448.24 nm, K 766.70 nm, and Na 589.16/589.76 nm.</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.