Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
8,924
datasets available to search
ShareScore release 0.9.0
Dataset results
8,924 results for “formation”
Computational modelling of metal soap formation in historical oil paintings: the influence of fatty acid concentration and nucleus geometry on the induced chemo-mechanical damage.
<p>Metal soap formation is one of the most wide-spread degradation mechanisms observed in historical oil paintings, affecting works of art from museum collections worldwide. Metal soaps develop from a chemical reaction between metal ions present in the pigments and saturated fatty acids, which are released by the oil binder. The presence of large metal soap crystals inside paint layers or at the paint surface can be detrimental for the visual appearance of artworks. Moreover, metal soaps can possibly trigger mechanical damage, ultimately resulting in flaking of the paint. This paper departs from a recently proposed computational model to predict chemo-mechanical degradation in historical oil paintings, as presented in Eumelen et al. (J Mech Phys Solids 132:103683, 2019). The model describes metal soap formation and growth, which are phenomena that are driven by the diffusion of saturated fatty acids and proceed by a nucleation process from a crystalline nucleus of small size. This results into a chemically-induced strain in the paint, which may promote crack nucleation and propagation. The proposed model is here used to investigate the effects of saturated fatty acid concentration and initial nucleus geometry on the amount of chemo-mechanical damage generated. Numerical simulations show that both factors have a marginal influence on the growth rate of the metal soap crystal, but play a significant role on the extent of fracture induced in the paint.</p>
Raw Data to "Density functional theory study of CO formation through reactions of polycyclic aromatic hydrocarbons with atomic oxygen (O(3P))"
<p>This data is a supplement to the publication <a href="https://doi.org/10.1016/j.fuel.2018.12.047">https://doi.org/10.1016/j.fuel.2018.12.047</a>. The data includes Turbomole input and output files. The calculations are performed using DFT/TPSSh-D3/TZVP method and Turbomole version 7.2. The equilibrium structures for the reactions of polyaromatics are named as following:<br> C<sub>X</sub>H<sub>Y</sub> (<strong>S1</strong>) + O -> C<sub>X</sub>H<sub>Y</sub>O (<strong>S2</strong>) -> C<sub>X</sub>H<sub>Y-1</sub>O (<strong>S3</strong>) + H (i) O addition and H abstraction<br> C<sub>X</sub>H<sub>Y-1</sub>O (<strong>S3</strong>) [-> <strong>S4</strong> -> <strong>S5</strong> ] -> CX-1HY-1 (<strong>S6</strong>) + CO (ii) Single, two, or three step CO elimination</p> <p>The transition state structures are named according to the naming of the corresponding reactant and product. For example, the transition state connecting the structure S3 to S5 is named as T35. Under some of the transition state directories, intrinsic reaction coordinate calculation output can be found under the directories named as "IRC".<br> <br> </p> <p><br> The LibreOffice Calc spreadsheet "SUPPINFO.ods" includes the activation and reaction energies to the reaction steps.</p>
Three reconstructions of the formation of large open ocean polynyas in the Southern Ocean using ice core records
<p>The dataset contains the indices for three reconstructions of open ocean polynya formation in the Southern Ocean over the period 1250-1990 and their uncertainties. See the associated publication</p> <p>Goosse H., Dalaiden Q., Cavitte M.G.P., Zhang L. Can we reconstruct the formation of large open ocean polynyas in the Southern Ocean using ice core records? Climate of the past 2020. <a href="https://doi.org/10.5194/cp-2020-91">https://doi.org/10.5194/cp-2020-91</a></p> <p>The data are included in a text file. The first column is the time (in years). The next six columns are the three reconstructions using data assimilation with SPEAR_AM2 (DA AM2), using data assimilation with SPEAR_LO (DA LO) and a simple average of standardized time series (Stat), each of them directly followed by their uncertainties. The uncertainties are estimated from the standard deviation of the seven reconstructions using different combinations of the available ice core records.</p> <p>Please contact <a href="mailto:hugues.goosse@uclouvain.be">Hugues Goosse</a>(hugues.goosse@uclouvain.be) for more information.</p>
Conversion of measurements of tree ring gains: Canada, Africa, Mexico, South America from RWL- files to JSON format.
<p>The International Tree Rings Data Bank (ITRDB) is the most comprehensive tree growth database (https://www1.ncdc.noaa.gov/pub/data/paleo/treering).</p> <p>Shoudong Zhao, et al. (2019, 2018) analyzes the representativity of dendrochronological data (ITRDB) and proposes a corrected database with error indications. One of the bottlenecks of data use (ITRDB) is that the data is loaded as a collection of separate files in the Tucson positional format.</p> <p>The purpose of our data presentation is to change the Tucson data format to JSON format and combine the separate files into one.</p> <p>We convert the initial data for the <strong>Canada</strong>, <strong>Africa</strong>, <strong>Mexico</strong> and <strong>Southamerica</strong> rwl-files into Json format of data on tree growth in four files: <strong>canada.json</strong>, <strong>africa.json</strong>, <strong>mexico.json</strong> and <strong>southamerica.json</strong>. The data was converted using the R programming language and the dplR program library Bunn, A. (2008)</p> <p>The experience of developing the structure of dendroclimatic data in JSON format is described in the works of Kachaev A. (2016, 2017, 2020).</p> <p>Description of the structure of JSON data format is attached in the files ReadMe.pdf</p> <p> </p> <p>References</p> <p>Bunn, A. G. (2008). A dendrochronology program library in R (dplR). Dendrochronologia, 26, 115-124. https://doi.org/10.1016/j.dendro.2008.01.002</p> <p>Kachaev, Alexander (2020), "Compact dataset of dendrochronological data of pri-mary metric characteristics of tree rings of Asia.", Mendeley Data, V1, doi: 10.17632 / p9zhpmzgtk.1</p> <p>Kachaev A. V. (2017) Model for describing the structure of dendroclimatic data In the collection: Regional problems of remote sensing of the Earth Materials of the IV international scientific conference. Siberian Federal University, Institute of Space and Information Technologies. p. 120-122. (Russia)</p> <p>Kachaev A. V. (2016) NOSQL Approach for Development of Dendroclimatic Data Bank. In the collection: Regional problems of remote sensing of the Earth. Materials of the III International Scientific Conference. p. 89-91. (Russia)</p> <p>Shoudong Zhao, et al. (2019). The International Tree-Ring Data Bank (ITRDB) revisited: Data availability and global ecological representativity. Journal of Biogeography, 46 (2), 355-368. doi: 10.1111 / jbi.13488</p> <p>Zhao, Shoudong et al. (2018), Data from: The International Tree-Ring Data Bank (ITRDB) revisited: data availability and global ecological representativity, Dryad, Dataset, https://doi.org/10.5061/dryad.kh0qh06</p>
DADA2 formatted taxonomy from GTDBr95
<p>DADA2 requires taxonomy files in a specific format. This datasets are the files required to assign taxonomy using Genome Taxonomy Database (GTDB) database.</p> <p>GTDB release 95.0 is the latest version of database released on July 17th, 2020. GTDB-r95 contains 30,238 bacterial and 1,672 archaeal species clusters which span 194,600 genomes. FASTA file of 16S rRNA gene sequences identified within the representative genomes of bacteria (21965) and Archaea (1126) were downloaded from this <a href="https://data.ace.uq.edu.au/public/gtdb/data/releases/release95/95.0/genomic_files_reps/">link</a> on 24-12-2020. The link provides resources for GTDB species representatives hence, limiting one sequence per organism. The sequence headers were modified according to DADA2 requirements using regular expression based replace in Notepad++ (I was too lazy to do the same through awk/sed). </p> <p>Files <a href="https://zenodo.org/api/files/8b1de4c7-ce83-488b-b399-cc27dbadfaed/GTDBr95-Genus.fna">GTDBr95-Genus.fna</a> and <a href="https://zenodo.org/api/files/8b1de4c7-ce83-488b-b399-cc27dbadfaed/GTDBr95-Species.fna">GTDBr95-Species.fna</a> are to be used with assignTaxonomy and addSpecies commands of DADA2, respectively.</p> <p>Prepared files were checked and found compatible when run on DADA2 v1.14.0 (R v3.6.3).</p>
Measurement and model data comparisons for the HALO-FAAM formation flight during EMeRGe on 17 July 2017
<p>Within the project “Effect of Megacities on the transport and transformation of pollutants on the Regional and Global scales” (EMeRGe), the measurement flight of 13 July 2017 was performed for comparison of the instrumentation onboard of the research aircraft HALO and FAAM. The aircraft flew for 1.6 h in close formation along a racetrack pattern at three flight levels in Southern Germany. The flight started in a rather dry and clean troposphere and ended in a more polluted convective boundary layer. 28 measurement pairs sampled on both aircraft were found suitable for comparison. 17 further pairs of data are available from sampling on either HALO or FAAM. In addition, observations obtained at the DWD Hohenpeissenberg and results from 6 models are included in the comparisons. Overall, about 30% of the measured data pairs show deviations within the combined error estimates. Some measurements deviate considerably from model results.</p> <p>This dataset contains a pdf of the report and a zip file of the comparison data as described in that report.</p>
Data from: A new tusked cistecephalid dicynodont (Therapsida, Anomodontia) from the upper Permian Upper Madumabisa Mudstone Formation, Luangwa Basin, Zambia
Cistecephalids are among the most distinctive Permian dicynodonts because of their highly derived skulls and postcrania, which indicate a fossorial ecology. Four cistecephalid species have been described from India, South Africa, and Tanzania; a fifth putative species has been reported from the Luangwa Basin of Zambia but never formally described. Here we present a detailed description of the Luangwa Basin cistecephalid, which we name Kembawacela kitchingi gen. et. sp. nov. The most obvious diagnostic character of K. kitchingi is the presence of caniniform tusks in most specimens. Other important characters include a pineal foramen located at the posterior end of the skull roof; an interparietal that has a pair of anterior processes that extend onto the dorsal surface of the skull, flanking the pineal foramen (but otherwise is restricted to the occipital surface); an undivided nuchal crest; and a trough on the ventral surface of the mid-ventral vomerine plate. Phylogenetic analysis reconstructs Kembawacela as a basal cistecephalid and confirms that Cistecephalidae is a well-supported clade. However, relationships within the clade received low branch support. Increased knowledge of cistecephalid diversity shows that they vary in functionally relevant characters, such as degree of inflation of the bony vestibule and the morphology of the scapula and humerus, indicating the need for a more nuanced approach to the relationship between form, function, and ecology in the clade. The highly allopatric distribution of cistecephalid species suggests that they experienced strong interspecific competition for limited resources and had limited dispersal ability, similar to extant subterranean mammals.
Anasillomos species descriptions in SDD format
<p>Natural-language species descriptions of <em>Anasillomos</em> species in XML SDD format exported from Lucid Builder 3.5.</p>
Protein secondary-structure description with a coarse-grained model: code and datasets in ActivePapers format
<p>This file contains the supplementary material for the publication</p> <p><em>Protein secondary-structure description with a coarse-grained model</em><br /> by Gerald R. Kneller and K. Hinsen<br /> http://dx.doi.org/10.1107/S1399004715007191<br /> Acta Cryst. (2015). D<strong>71</strong>, 1411-1422</p> <p><strong>Datasets in this file</strong></p> <p>1) ScrewFit and ScrewFrame parameters for ideal secondary-structure elements</p> <p> Scripts:<br /> /code/import_ideal_structures<br /> /code/analyze_ideal_structures</p> <p>1.1) The PDB files generated with Chimera</p> <p> /data/ideal_structures/3-10.pdb<br /> /data/ideal_structures/alpha.pdb<br /> /data/ideal_structures/beta-antiparallel.pdb<br /> /data/ideal_structures/beta-parallel.pdb<br /> /data/ideal_structures/pi.pdb</p> <p>1.2) The corresponding MOSAIC datasets</p> <p> /data/ideal_structures/3-10<br /> /data/ideal_structures/alpha<br /> /data/ideal_structures/beta-antiparallel<br /> /data/ideal_structures/beta-parallel<br /> /data/ideal_structures/pi</p> <p>1.3) The ScrewFit parameters</p> <p> /data/ideal_structures/screwfit/3-10<br /> /data/ideal_structures/screwfit/alpha<br /> /data/ideal_structures/screwfit/beta-antiparallel<br /> /data/ideal_structures/screwfit/beta-parallel<br /> /data/ideal_structures/screwfit/pi</p> <p>1.4) The ScrewFrame parameters</p> <p> /data/ideal_structures/screwframe/3-10<br /> /data/ideal_structures/screwframe/alpha<br /> /data/ideal_structures/screwframe/beta-antiparallel<br /> /data/ideal_structures/screwframe/beta-parallel<br /> /data/ideal_structures/screwframe/pi</p> <p><br /> 2) Statistics for ScrewFit and ScrewFrame parameters computed<br /> for the ASTRAL SCOPe subset with less than 40% sequence identity.</p> <p> Scripts:<br /> /code/astral_analysis<br /> /code/fit_rho_distributions<br /> /code/plot_histograms</p> <p>2.1) The ASTRAL database (link to published ActivePaper)</p> <p> /data/astral_2.04</p> <p>2.2) The histograms for the ScrewFit and ScrewFrame parameters<br /> for the all-alpha and all-beta subsets</p> <p> /data/histograms/astral_alpha/screwfit<br /> /data/histograms/astral_alpha/screwframe</p> <p> /data/histograms/astral_beta/screwfit<br /> /data/histograms/astral_beta/screwframe</p> <p>2.3) The Gaussians fitted to the peaks in the distributions for rho</p> <p> /data/fitted_rho_distributions/screwfit<br /> /data/fitted_rho_distributions/screwframe</p> <p>2.4) Plots</p> <p> /documentation/delta.pdf<br /> /documentation/delta_q.pdf<br /> /documentation/delta_r.pdf<br /> /documentation/p.pdf<br /> /documentation/rho-detail.pdf<br /> /documentation/rho.pdf<br /> /documentation/sigma.pdf<br /> /documentation/tau.pdf</p> <p><br /> 3) Comparison of secondary-structure identification between ScrewFrame<br /> and DSSP.</p> <p> Script:<br /> /code/compare_secondary_structure_assignments<br /> /code/plot_histograms</p> <p>3.1) The histograms of the lengths of secondary-structure elements</p> <p> /data/histograms/secondary_structure/length-alpha-dssp<br /> /data/histograms/secondary_structure/length-alpha-screwframe<br /> /data/histograms/secondary_structure/length-beta-dssp<br /> /data/histograms/secondary_structure/length-beta-screwframe</p> <p>3.2) The 2D histograms of the number of residues inside identified<br /> secondary-structure elements</p> <p> /data/histograms/secondary_structure/n-alpha<br /> /data/histograms/secondary_structure/n-beta</p> <p>3.3) The distribution of rho inside alpha helices</p> <p> /data/histograms/secondary_structure/rho-alpha-dssp</p> <p>3.3) Plots</p> <p> /documentation/lengths-alpha.pdf<br /> /documentation/lengths-beta.pdf<br /> /documentation/n-alpha.pdf<br /> /documentation/n-beta.pdf<br /> /documentation/rho-alpha-dssp.pdf</p> <p><br /> 4) Illustration for myoglobin and VADC-1</p> <p> Scripts:<br /> /code/import_myoglobin_vdac<br /> /code/analyze_myoglobin<br /> /code/analyze_vdac<br /> /code/perturbation_analysis</p> <p>4.1) Imported structures in MOSAIC format:<br /> PDB code 1A6G for myoglobin<br /> PDB code 2K4T for VDAC-1</p> <p> /data/myoglobin<br /> /data/VDAC-1</p> <p>4.2) Plots showing rho and delta</p> <p> /documentation/rho-myoglobin.pdf<br /> /documentation/delta-myoglobin.pdf</p> <p>4.3) Tube models for visualization with Chimera</p> <p> /documentation/myoglobin-tube.bld<br /> /documentation/VDAC-1-tube.bld</p> <p>4.4) Sensitivity to perturbations in the coordinates</p> <p> /documentation/rho-perturbed-myoglobin.pdf<br /> /documentation/delta-perturbed-VDAC-1.pdf<br /> /documentation/rho-perturbed-myoglobin.pdf<br /> /documentation/delta-perturbed-VDAC-1.pdf<br /> /documentation/myoglobin-perturbation.pdf<br /> /documentation/VDAC-1-perturbation.pdf</p> <p>5) Analysis of CA-only structures in the PDB</p> <p> Scripts:<br /> /code/ca_analysis<br /> /code/import_calpha_structures<br /> /code/plot_histograms</p> <p>5.1) Imported CA-only structures in MOSAIC format</p> <p> /data/pdb_ca_only_structures</p> <p>5.2) Histograms for ScrewFrame parameters</p> <p> /data/histograms/ca_only_structures</p> <p>5.3) Plots</p> <p> /documentation/delta_ca.pdf<br /> /documentation/delta_q_ca.pdf<br /> /documentation/delta_r_ca.pdf<br /> /documentation/p_ca.pdf<br /> /documentation/rho_ca.pdf<br /> /documentation/sigma_ca.pdf<br /> /documentation/tau_ca.pdf</p> <p> </p>
Plyomydas species descriptions in SDD format
<p>Natural-language species descriptions of Plyomydas species in SDD format exported from Lucid Builder 3.5.</p>
FIGURE 8. A and B in A new early dinosaur (Sauropodomorpha) from the Caturrita Formation (Late Triassic), Paraná Basin, Brazil
FIGURE 8. A and B, right tibia – astragalus in posterior view. C and D, right tibia in anterior view. E, lateral groove. F, distal view of tibia. For abbreviation, see appendix. Scale bar represents 50 mm.
FIGURE 6 in A new early dinosaur (Sauropodomorpha) from the Caturrita Formation (Late Triassic), Paraná Basin, Brazil
FIGURE 6. Right ulna in: A and B, lateral view; C and D, medial view. For abbreviation, see appendix. Scale bar represents 50 mm.
FIGURE 5 in A new early dinosaur (Sauropodomorpha) from the Caturrita Formation (Late Triassic), Paraná Basin, Brazil
FIGURE 5. Right humerus in: A and B, Lateral view; C and D, medial view. For abbreviation, see appendix. Scale bar represents 50 mm.
FIGURE 4 in A new early dinosaur (Sauropodomorpha) from the Caturrita Formation (Late Triassic), Paraná Basin, Brazil
FIGURE 4. Right scapulocoracoid in: A and B, lateral view; C and D, medial view. For abbreviation, see appendix. Scale bar represents 50 mm.
FIGURE 2 in A new early dinosaur (Sauropodomorpha) from the Caturrita Formation (Late Triassic), Paraná Basin, Brazil
FIGURE 2. Skull of the prosauropod Unaysaurus tolentinoi gen. et sp. nov, in A, left lateral reconstruction of the bones; B, left lateral premaxilla, maxilla, nasal, and dentary (splenial bone [= spl] is
FIGURE 3 in A new early dinosaur (Sauropodomorpha) from the Caturrita Formation (Late Triassic), Paraná Basin, Brazil
FIGURE 3. Skeletal reconstruction of the prosauropod Unaysaurus tolentinoi gen. et sp. nov., showing A, preserved bones and individuals bones; B, axis; C, most anterior dorsal vertebrae; D, most posterior dorsal vertebrae with the infradiapophysial cavities; E, medial caudal vertebra; F, right digital manus I in dorsal view; G, left digital pes I in dorsal view and; H, preserved left metatarsals in proximal view. For abbreviations, see appendix. Scale bar equals 10 mm.
FIGURE 1 in A new early dinosaur (Sauropodomorpha) from the Caturrita Formation (Late Triassic), Paraná Basin, Brazil
FIGURE 1. Map showing the central portion of the Rio Grande do Sul State and the Água Negra outcrop, between Santa Maria and São Martinho da Serra cities (source Leal et al. 2001); Carnian Norian (c. 220 Ma) Upper Triassic paleogeographic map, the black cross indicates the fossiliferous exposures of southern Brazil (modified from Lucas 1998); Lithostratigraphic subdivision of the Upper Triassic rocks in the Rio Grande do Sul state, with the fossiliferous level of Unaysaurus tolentinoi gen. et sp. nov., shown in grey (modified from Da Rosa and Leal 2002).
FIGURE 8 in Anticyphon gen. nov., a new genus of Scirtidae (Coleoptera: Scirtoidea) inhabiting high altitude Andean cloud forests and páramo formation
FIGURE 8. Anticyphon oyonensis sp. nov., male genitalia. A) penis, B) tegmen, C) sternite VIII, D) sternite IX, E) tergite VIII, F) tergite IX. Scale bar = 0.5 mm.
FIGURE 4 in Anticyphon gen. nov., a new genus of Scirtidae (Coleoptera: Scirtoidea) inhabiting high altitude Andean cloud forests and páramo formation
FIGURE 4. Anticyphon paramoensis sp. nov., ventrum, SEM micrograph. Abbreviations: mf—mesoventral fossa, mpmesoventral process, sgr—subgenal ridge.
FIGURE 7 in Anticyphon gen. nov., a new genus of Scirtidae (Coleoptera: Scirtoidea) inhabiting high altitude Andean cloud forests and páramo formation
FIGURE 7. Anticyphon ecuadorensis sp. nov., male genitalia. A) penis (right parameroid broken), B) tegmen, C) sternite VIII, D) sternite IX, E) tergite VIII, F) tergite IX. Scale bar = 0.5 mm.
ScienceDex guides
Understand access before you commit
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.