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2,960 results for “elements”
Double-stranded RNA structural elements holding the key to translational regulation in cancer: the case of editing in RNA Binding Motif Protein 8A
<p>Raw data supporting the manuscript</p> <p>Abukar, A.;Wipplinger, M.;<br> Hariharan, A.; Sun, S.; Ronner, M.;<br> Sculco, M.; Okonska, A.;<br> Kresoja-Rakic, J.; Rehrauer, H.; Qi, W.;<br> et al. Double-Stranded RNA<br> Structural Elements Holding the Key<br> to Translational Regulation in Cancer:<br> The Case of Editing in RNA-Binding<br> Motif Protein 8A. Cells 2021, 10, 3543.<br> https://doi.org/10.3390/<br> cells10123543</p>
Data from: Improving the Effectiveness of the Solid-Solution-Strengthening Elements Mo, Re, Ru and W in Single-Crystalline Nickel-Based Superalloys
<p>This dataset is the basis for the journal article "Improving the Effectiveness of the Solid-Solution-Strengthening Elements Mo, Re, Ru and W in Single-Crystalline Nickel-Based Superalloys" (<a href="https://doi.org/10.3390/met11111707">doi.org/10.3390/met11111707</a>). </p> <p>Differential Scanning Calorimetry (DSC), Electron-Probe Mirco-Analysis (EPMA equipped with WDS detectors), Compression Creep and CalPhaD calculation data are included in this dataset. In the resulting article the partitioning and solid solution strengthening behavior of the elements Mo, Re, Ru, and W are investigated in three different alloy collections:</p> <p>"Reference" alloys: ERBO/1 (based on the commercial alloy CMSX-4), ERBO/13 (optimized alloy: <a href="http://doi.org/10.1088/0965-0393/23/3/035004">doi.org/10.1088/0965-0393/23/3/035004</a>) and ERBO/15 (optimized alloy: <a href="http://doi.org/10.1002/9781119075646.ch4">doi.org/10.1002/9781119075646.ch4</a>)</p> <p>"Model" alloys: ERBO/17, ERBO/18, ERBO/19 and ERBO/32 - experimental SX Nickel-Based superalloys to investigate the influence of Ti and Ta on the partitioning behavior of W</p> <p>"Experimental" alloys: EXP10, EXP11, EXP12, EXP13, EXP14, EXP15, EXP16, EXP17, EXP18 - general investigation of the behavior of Mo, Re, Ru and W, in terms of partitioning and thermophysical properties.</p> <p>_________</p> <p> </p> <p>CalPhaD data: short meta data file included in the respective subdirectory</p> <p>DSC data: Meta data as header in each file</p> <p>EPMA data: For each alloy a directory includes a general meta data file "0.cnd", an element specific meta data file "*.cnd" and the actual mapping data of each element "*.txt" (element name is listed in the corresponding specific meta data file). All element compositions are given in wt.-% in the mapping data .txt files. Exceptions: "COMPO" maps represent the total amount of detector counts; The values correspond to counts if the mapping .txt files contain non-float (e.g. integer) values (usually this means that there is very little or none of that element present and should therefore not be quantified to a wt.-% value).</p> <p>Creep: short meta data file included in the respective subdirectory</p>
Analyses of human cancer driver genes uncovers evolutionarily conserved RNA structural elements involved in posttranscriptional control - associated datasets
<p>These datasets include raw data output and associated files from ScanFold and CMbuilder analyses of human cancer driver gene mRNA. ScanFold was used to predict RNA regions of unusual thermodynamic stability, and CMbuilder was used to evaluate covariation of the predicted structures in those regions. Please view the file <em>README_general_description_Zenodo_files.txt</em> for brief descriptions of the content.</p> <p>These data are associated with the manuscript entitled <em>Analyses of human cancer driver genes uncovers evolutionarily conserved RNA structural elements involved in posttranscriptional control</em>. The manuscript has currently been submitted for review in PLOS ONE.</p>
Global mapping of lunar refractory elements: multivariate regression vs. machine learning
<p>The quantitative estimation of elemental concentrations at the spatial resolution of hyperspectral near-infrared (NIR) images<br> of the lunar surface is an important tool for understanding the processes relevant for the origin and evolution of the Moon. The NIR reflectance of the lunar regolith is an integrated response to the presence of refractory elements and soil alteration processes. Our approach was to define a combination of spectral parameters that are robust with respect to the effects of soil maturity.<br> We calibrated the spectral parameters with respect to elemental abundances measured by the Lunar Prospector Gamma Ray Spectrometer (LP GRS) and the Kaguya GRS (KGRS). For this purpose, we compared a classical multivariate linear regression (MLR) approach and the machine learning based support vector regression (SVR) technique applied to M3 global observations. The M 3 -based global elemental maps are consistent in distribution and range with the LP GRS and KGRS elemental maps<br> and do not show artifacts in immature areas such as small fresh craters. The results derived using MLR and SVR are compared to<br> sample-based ground truth data of the Apollo and Luna sample-return sites, where the root-mean-square deviations obtained by the<br> two regression models are similar. The main advantage of the proposed new algorithm is its ability to minimize artifacts due to space-weathering effects. The elemental maps of Mg and Ca provide additional information and reveal structures not always visible in the Fe map. The global elemental abundance maps derived for the fully calibrated M 3 observations might thus serve as important tools to investigate the lunar geology and evolution.</p>
Regulatory spine RS3 residue of protein kinases: a lipophilic bystander or a decisive element in the small-molecule kinase inhibitor binding?
<p>Datasets related to publication: </p> <p>Shevchenko E, Pantsar T: Regulatory spine RS3 residue of protein kinases: a lipophilic bystander or a decisive element in the small-molecule kinase inhibitor binding?. <em><em>Biochem Soc Trans</em></em> 28 February 2022; 50 (1): 633–648</p> <p>https://doi.org/10.1042/bst20210837</p> <p> </p> <p> </p>
elemental composition of alloys - ReINTEGRA
<p>Open access to acquired data (analysed), generated by the ReINTEGRA project (GA 886609, H2020, European Union, through Clean Sky 2 JU) along the research of the End-of-Life of novel welded Al-Li aerostructures. Research pertaining to Task 1.1 (WP1), Deliverable D1. </p> <p>Acquired data on chemical composition limits of Al-Li alloys and alloys for welding wires, collected from the international registration records published by the Aluminum Association (TEAL sheets) and from publicly available MSDS of aluminium welding wires manufactured by SAFRA S.P.A. and AlcoTec Wire Co, have been processed and analysed. Data analysis:</p> <ul> <li>Graphical comparison of ranges of contents of main alloying elements and impurities in the alloy combined in FSW and LBW coupons</li> <li>Identify elements in welding wires alloys showing low-medium compatibility for Al-Li alloys</li> </ul> <p>The data, analysed as part of the technical survey and experimental screening approach in WP1, have been the basis for further research on compatibility for recycling in WP3 and on the selection of the best EOL routes in WP2</p>
Transposable element annotation Rhynchosporium commune isolate UK7
<p>To obtain a consensus sequence for each TE family, RepeatModeler v. open-4.0.7 (http://www.repeatmasker.org/RepeatModeler/) was run on the <em>R. commune</em> UK7 reference genome. The classification was based on the GIRI Repbase (v. 2018) using RepeatMasker v. open-4.0.7. (Smit, Hubley, and P. 2015; Bao, Kojima, and Kohany 2015). We used WICKERsoft to finalize the classification of TE consensus sequences (Breen et al. 2010). Specifically, we used WICKERsoft to screen for copies of known consensus sequences from other fungal species with blastn filtering for sequence identity > 80% and sequence length > 80%. (Altschul et al. 1997). Then, using WICKERsoft, flanks of 10000 bp were added and visually inspected for sequence similarity and terminal repeats with dot plots. Subsequent multiple sequence alignments were performed with 10-15 sequences using ClustalW (Thompson, Higgins, and Gibson 1994). Alignment boundaries were visually inspected in WICKERsoft and trimmed if necessary. Using WICKERsoft, consensus sequences were classified according to the presence and type of terminal repeats, as well as homology of the encoded proteins based on blastx against the NCBI protein database. Consensus sequences were named according to the three-letter classification system (Wicker et al. 2007). The reference genome was annotated with the curated consensus sequences using RepeatMasker v. open-4.0.7 with a cut-off value of 250 (Smit, Hubley, and P. 2015). Simple repeats, low complexity regions and annotated elements shorter than 100 bp were filtered out and adjacent identical TEs overlapping by more than 100 bp were merged as belonging to the same TE family. Different TE families overlapping by more than 100 bp were considered as nested insertions and were renamed accordingly. Identical elements separated by less than 200 bp are indicative of interrupted elements and were grouped into a single element. TEs overlapping genes were recovered using the bedtools v. 2.27.1 suite and the “overlap” function (Quinlan and Hall 2010).</p>
Maps of depths are created for the site of 50 m length. Flow types are turbulent, broken standing waves, unbroken standing waves, and rippled. The average width was 8 m and varied from 5.5 to 12 m. Bed elements included bars, rocks, and step/pools. The average depth was 0.35 m, with a maximum of 0.6 m. The average velocity was 0.4 m/s, with a maximum of 1.2 m/s (figs 10). Distribution of bottom habitats at the locations with the crayfish are as follows: megalital — 5 %, macrolithal — 30 %, mesolithal — 25 %, microlithal — 15 %, psammal — 15 %, CPOM — 10 %. Assessment by hydrobiological parameters showed that the presence of Lyngbya and Oscillatoria, as well as the increase of the number of Oligochae- in New Findings Of White Clawed Crayfish, Austropotamobius Pallipes (Decapoda, Astacidae), And Peculiarities Of Its Spatial Distribution In Neretvica (Bosnia And Herzegovina)
Maps of depths are created for the site of 50 m length. Flow types are turbulent, broken standing waves, unbroken standing waves, and rippled. The average width was 8 m and varied from 5.5 to 12 m. Bed elements included bars, rocks, and step/pools. The average depth was 0.35 m, with a maximum of 0.6 m. The average velocity was 0.4 m/s, with a maximum of 1.2 m/s (figs 10). Distribution of bottom habitats at the locations with the crayfish are as follows: megalital — 5 %, macrolithal — 30 %, mesolithal — 25 %, microlithal — 15 %, psammal — 15 %, CPOM — 10 %. Assessment by hydrobiological parameters showed that the presence of Lyngbya and Oscillatoria, as well as the increase of the number of Oligochae-
Elements of Style in Reproducible Workflow Creation and Analysis: An INCLUDE Training Event
<p><a href="https://github.com/NIH-NICHD/Elements-of-Style-Workflow-Creation-Maintenance/blob/main/README.md">Elements of Style Workflow Creation and Maintenance</a>: An INCLUDE Training Event</p> <p>The <a href="https://includedcc.org/">INCLUDE Data Hub</a> is a new resource that securely hosts human clinical, genomic, transcriptomic, proteomic, and other data providing a wealth of opportunities to study conditions that affect individuals with Down syndrome. Today, the approach to answering new scientific questions with these data often uses cloud-based methods accessible through web browsers.</p> <p>During a three-hour virtual training, users learn the know-how to ask scientific questions with these data using cloud platforms and workflows. Users will learn how to build and share processes that assure reproducibility, repurposablility regardless of the computational environment. While many things are possible, the user will be oriented to approaching their work in a modular, testable fashion. </p>
Finite Element model data for Academic Rotor bladed-disc system
<div> <div> <div> <p>A computational finite element based technique is proposed for developing a stochastic reduced order model for rotating bladed disc with spatial random inhomogeneities. The spatial inhomogeneities imply the system to be randomly mistuned. The formulation assumes the availability of a high fidelity finite element (FE) model for the tuned system. The corresponding FE matrices are antisymmetric on account of the Coriolis forces due to rotation. The spatial inhomogeneities, available from limited point measurements on the blades, are modelled as non-Gaussian random fields with arbitrary distributions. A low order stochastic computational model is developed by projecting the FE model onto a reduced dimensional state space defined in terms of specified observable nodal points and expressing the stochasticity through an arbitrary polynomial chaos (aPC) basis. This model enables probabilistic quantification of the variabilities in the system response and estimating failure probabilities. The methodology enables drastic reduction in the state space and stochastic dimensions, addresses the practical difficulties with having limited measurable data points, antisymmetric FE matrices, aPC representation in complex irregular geometries and carrying out probabilistic analyses on industrial systems, at significantly reduced computational costs. The methodology is illustrated through an academic rotor and an industrial rotor blade.</p> </div> </div> </div>
Scale dependent spatial structuring of mountain river large bed elements maximizes flow resistance - Data Revision
<p>Datasets and R code related to manuscript entitled, "Scale dependent spatial structuring of mountain river large bed elements maximizes flow resistance". See '0_READ_ME.rtf' file for additional description of available files.</p>
Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteremia.
<p>Insertion sequences (ISs) and other transposable elements are associated with the mobilization of antibiotic resistance determinants and the modulation of pathogenic characteristics. In this work, we aimed to investigate the association between ISs and antibiotic resistance genes, and their role in dissemination and modification of the antibiotic resistant phenotype. To that end, we leveraged fully resolved <em>Enterococcus faecium</em> and <em>Enterococcus faecalis</em> genomes of isolates collected over five days from an inpatient with prolonged bacteremia. Isolates from both species harbored similar IS family content but showed significant species-dependent differences in copy number and arrangements of ISs throughout their replicons. Here, we describe two inter-specific IS-mediated recombination events and IS-mediated excision events in plasmids of <em>E. faecium</em> isolates. We also characterize a novel arrangement of the ISs in a Tn1546-like transposon in <em>E. faecalis</em> isolates likely implicated in a vancomycin genotype-phenotype discrepancy. Furthermore, an extended analysis revealed a novel association between daptomycin resistance mutations in <em>liaSR</em> genes and a putative composite transposon in<em> E. faecium</em>, offering a new paradigm for the study of daptomycin resistance and novel insights into the dissemination of daptomycin resistance. In conclusion, our study highlights the role ISs and other transposable elements play in the rapid adaptation and response to clinically relevant stresses such as aggressive antibiotic treatment in enterococci.</p>
IODP Expedition 372A ICP-AES elemental analysis (interstitial water)
<p>Elemental concentration in interstitial water samples was measured by inductively coupled plasma - atomic emission spectroscopy (ICP-AES). Data are presented by element-wavelength pair (e.g., more than one calcium line may be reported). Elemental lines for which data do not exist for a particular expedition will not appear.</p>
IODP Expedition 372A Elemental analysis (CHNS)
<p>Fundamental elemental component (total carbon, hydrogen, nitrogen, and sulfur) fluctuations help define the origin, depositional environment, and diagenetic alteration of source materials. To determine C, H, N, and S, solid samples are reacted with a catalyst, separated by chromatography, and detected by thermal conductivity on a FlashEA 1112 CHNS elemental analyzer. Organic carbon can be directly measured on the elemental analyzer by acidification of the sample to drive off carbonate as carbon dioxide before analyzing. Total organic carbon on this report is measured rather than calculated.</p>
IODP Expedition 374 ICP-AES elemental analysis (interstitial water)
<p>Elemental concentration in interstitial water samples was measured by inductively coupled plasma - atomic emission spectroscopy (ICP-AES). Data are presented by element-wavelength pair (e.g., more than one calcium line may be reported). Elemental lines for which data do not exist for a particular expedition will not appear.</p>
IODP Expedition 374 Elemental analysis (CHNS)
<p>Fundamental elemental component (total carbon, hydrogen, nitrogen, and sulfur) fluctuations help define the origin, depositional environment, and diagenetic alteration of source materials. To determine C, H, N, and S, solid samples are reacted with a catalyst, separated by chromatography, and detected by thermal conductivity on a FlashEA 1112 CHNS elemental analyzer. Organic carbon can be directly measured on the elemental analyzer by acidification of the sample to drive off carbonate as carbon dioxide before analyzing. Total organic carbon on this report is measured rather than calculated.</p>
Long-term dynamics of trace elements concentrations in the organism of the shrews (Sorex) during the periods of high and reduction emissions from the copper smelter
<p>Data and code for mixed-model analysis for the article: </p> <p>Mukhacheva S.V. (2022) Long-term dynamics of trace elements concentrations in the organism of the shrews (Sorex) during the periods of high and reduction emissions from the copper smelter" // Russian Journal of Ecology. Vol. 5. </p> <p>Data provided by S.V. Mukhacheva</p> <p>Code provided by A.N. Sozontov</p>
Data from: Hybrid incompatibility between D. virilis and D. lumei is stronger in the presence of transposable elements
<p>Mismatches between parental genomes in selfish elements are frequently hypothesized to underlie hybrid dysfunction and drive speciation. However, because the genetic basis of most hybrid incompatibilities is unknown, testing the contribution of selfish elements to reproductive isolation is difficult. Here we evaluated the role of transposable elements (TEs) in hybrid incompatibilities between Drosophila virilis and D. lummei by experimentally comparing hybrid incompatibility in a cross where active TEs are present in D. virilis (TE+) and absent in D. lummei, to a cross where these TEs are absent from both D. virilis (TE-) and D. lummei genotypes. Using genomic data, we confirmed copy number differences in TEs between the D. virilis (TE+) strain and the D. virilis (TE-) strain and D. lummei. We observed F1 postzygotic reproductive isolation exclusively in the interspecific cross involving TE+ D. virilis but not in the cross involving TE- D. virilis. This precisely mirrors the intraspecies dysgenic phenotype where teste atrophy only occurs when TE+ D. virilis is the paternal parent. A series of backcross experiments, designed to account for alternative models of hybrid incompatibility, showed that both F1 hybrid incompatibility and intrastrain dysgenesis is consistent with the action of TEs rather than other, genic, interactions. A further Y-autosome interaction contributes to additional, sex-specific, inviability in one direction of this cross combination. These experiments demonstrate that TEs that cause intraspecies dysgenesis can increase reproductive isolation between closely related lineages, thereby adding to the processes that consolidate speciation.</p>
The pan-genome unearths gene content and transposable element variations in modern pigs
<p>Genes, gene annotations, proteins, and sequences identified in the non-reference genome of the pig pan-genome. Transposable insertion polymorphisms (TIP) indentified in the pig mobolome.</p>
Dataset from Experimental and Nonlinear Finite Element Modeling Investigating an Innovative Buckling Restrained Bracing System for Rehabilitation of Seismic Deficient Structures
<p>The data presented in this paper were collected experimentally and modeled using the finite element method. A total of six BRBs (i.e., duplicates of three types of BRB core bars) specimens were tested experimentally and verified numerically using the finite element method employing the commercial Software ABAQUS. Specific labeling was used to designate each BRB type. Three core bars were used in the tested BRBs: fully-threaded, threaded-notched, and smooth-shaved. The specimens are labeled according to their core bar type and diameter. i.e., BRB-12-Th stands for a full threaded core bar diameter of 12 mm, the threaded notched type was labeled BRB-12-Th-Nd, and the smooth shave one was labeled BRB-12-Sh.</p> <p>Further details of the tested BRBs are included in the excel file called dimensions and properties of BRBs. The worksheet provides details of the BRB components (i.e., core bar, restraining unit, and innovative end units). The dimensions and strength of the materials were obtained from coupon tests. The experimental data are presented in the second excel file labeled hysteresis with three embedded worksheets, one for each type of BRB. The excel sheets provide the cyclic loading data and plots showing the hysteresis behavior of tested BRBs. A sample of the loading protocol included in the second excel file is presented in Fig.1. The third excel file presents the analytical data extracted from experimental data that has two sheets: stiffness and energy dissipation. The sheet labeled stiffness has the secant stiffness versus deformation plot for the push-pull cycles (compression-tension). The second sheet labeled energy dissipation shows the cumulative energy dissipated.</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.