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92 results for “information structure”
Supporting Information for "Photothermal Laser Printing of Sub-micrometer Crystalline ZnO Structures"
<p>Supplementary information for the article <strong>"Photothermal Laser Printing of Sub-micrometer Crystalline ZnO Structures"</strong></p> <p>containing a video SEM-EBSD video of the rotating ZnO crystalline angles (mp4 file), raw and processed data of EDX and EBSD files (.bcf), raw and processed SEM and TEM images (.tif .emi .ser), processed images and plots (.svg .png .pdf), and evaluated data results (.txt .csv) .</p> <p> </p> <p>Link to publication: <a href="https://doi.org/10.1002/advs.202410771">https://doi.org/10.1002/advs.202410771</a></p> <p> </p> <p>An explanation of the data files can be found in the <em>Notes.docx </em>document</p>
Microevolutionary processes in a foundation tree inform macrosystem patterns of community biodiversity and structure
<p class="MDPI17abstract"><span>Despite an increased focus on multiscale relationships and interdisciplinary integration, few macroecological studies consider the contribution of genetic-based processes to landscape-scale patterns.<strong> </strong>We tested the hypothesis that tree genetics, climate, and geography jointly drive continental-scale patterns of community structure, using genome-wide SNP data from a broadly distributed foundation tree species (<a><em>Populus fremontii</em></a></span><span class="MsoCommentReference"><span> </span></span><span>S. Watson) and two dependent communities (leaf-modifying arthropods and fungal endophytes) spanning southwestern North America. Four key findings emerged: (1) Tree genetic structure was a significant predictor for both communities; however, the strength of influence was both scale- and community-dependent. (2) Tree genetics was the primary driver for endophytes, explaining 17% of variation in continental-scale community structure, whereas (3) climate was the strongest predictor of arthropod structure (24%). (4) Power to detect tree genotype<a><span>—</span></a></span><span>community phenotype associations changed with scale of genetic organization, increasing from individuals to populations to ecotypes, emphasizing the need to consider nonstationarity (i.e., changes in the effects of factors on ecological processes across scales) when inferring macrosystem properties. Our findings highlight the role of foundation tree species as drivers of macroscale community structure and provide macrosystems ecology with a theoretical framework for linking fine- and intermediate-scale genetic processes to landscape-scale patterns. Management of genetic diversity harbored within foundation species is a critical consideration for conserving and sustaining regional biodiversity.</span></p>
Data for: Population structure of a grassland songbird (Dolichonyx oryzivorus) to inform conservation units
<p>Understanding the patterns and processes driving population structure is crucial for conservation planning. Spatial conservation units (CUs) for one or more species have been defined using similarities in communities, habitats, and resource management concerns. Additionally, CU boundaries can be informed by population genetic structure. Here, we determined the population structure of the Bobolink (<em>Dolichonyx</em> <em>oryzivorus</em>), a migratory grassland bird. Its breeding range spans longitudinally across most of North America in the northern U.S. and southern Canada, and its population has declined by 59% from 1971 to 2014. We sampled blood from Bobolinks at seven breeding sites and used a ddRAD sequencing approach to identify 3236 SNPs for population genetic analyses. Using the Bayesian clustering approach, STRUCTURE, we found low levels of genetic differentiation across the breeding range. F st values ranged from 0.002 to 0.036 among all population pairs, and genetic structure followed an isolation-by-distance model. Despite low levels of genetic differentiation, we found evidence for four genetic groupings— breeding populations in Oregon and British Columbia were distinct from each other as well as from Central and eastern North American breeding populations. Investigating the demographic history of the populations using approximate Bayesian computation, we found evidence that western Bobolink populations are not relict populations but instead were founded during a recent westward range expansion, possibly enabled by agricultural expansion. We identify four genetics-based CUs that may serve as a complementary spatial framework, broader in scale compared to the commonly-used Bird Conservation Regions, for defining and achieving population objectives.</p>
Microevolutionary processes in a foundation tree inform macrosystem patterns of community biodiversity and structure
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Data for: Population structure of a grassland songbird (Dolichonyx oryzivorus) to inform conservation units
Open the record for dataset details and reuse information.
Seedling planting information: Interactive Effects of Fertility and Distribution on Plant Community Diversity and Structure
There are four levels of nitrogen, corresponding to treatments A, C, F and G in E001, applied at the same time as in that experiment. For a description of fertilizer added to E052, see file fertilization details. There are four levels of soil disturbance designated 1, 2, 3 and 4. Level 1: undisturbed Level 2: 1 pass with a 7 HP Honda rear-tined rototiller with the elevator set to till to a depth of 9 inches Level 3: 2 passes or however many required to produce about 50% bare ground Level 4: 3 passes or however many required to produce 100% bare ground. This requires 3 passes in some plots but 5 or 6 in others. In addition, all woody vegetation not destroyed by tilling is cut at the base. Rototilling is applied in late April. Each fertilization treatment receives each disturbance treatment, for a total of sixteen treatments. There are four replicates of each of the sixteen treatments. In addition, the four extreme ends (lowest N, lowest disturbance; highest N, lowest disturbance, etc. ) are replicated an additional ten times. Treatments are applied in a completely randomized design. Each of the 104 plots is 5m x 5m. Measurements taken at E052 will include: 1) species abundances, 2) community biomass allocation to leaves/roots/stems/flowers, 3) above and below ground net primary production and 4) rates of nitrogen mineralization. For a list of treatments, see the treatment layouts in file trmte52. The plots in E052 are enclosed by a fence to exclude mammalian herbivores. Galvanized welded-wire hardware cloth with 6mm x 6mm openings was buried to a depth of 50cm. Additional hardware cloth extends 60cm above the ground and poultry netting extends to 2m above the ground. In 1990, ten plots of each of four treatments (N1D1, N1D4, N4D1, N4D4, where N is the level of nitrogen added and D is the disturbance treatment) were randomly selected for the competition experiment. The above and belowground effects of neighbors on transplanted grass seedlings were measured using three
Improving early estimates of large earthquake's final fault lengths and magnitudes leveraging source fault structural maturity information - supplementary data
<p>Supplementary dataset for <em>Improving early estimates of large ea­­rthquake’s final fault lengths and magnitudes leveraging source fault structural maturity information. </em>This contains individual performance test results for the algorithm discussed in this publication for each earthquake included in the study</p>
Data from: Genotyping-in-Thousands by sequencing reveals marked population structure in Western Rattlesnakes to inform conservation status
<p>Delineation of units below the species level is critical for prioritizing conservation actions for species at-risk. Genetic studies play an important role in characterizing patterns of population connectivity and diversity to inform the designation of conservation units, especially for populations that are geographically isolated. The northernmost range margin of Western Rattlesnakes (<em>Crotalus oreganus</em>) occurs in British Columbia, Canada, where it is federally classified as threatened and restricted to five geographic regions. In these areas, Western Rattlesnakes hibernate (den) communally, raising questions about connectivity within and between den complexes. At present, Western Rattlesnake conservation efforts are hindered by a complete lack of information on genetic structure and degree of isolation at multiple scales, from the den to the regional level. To fill this knowledge gap, we used Genotyping-in-Thousands by sequencing (GT-seq) to genotype an optimized panel of 362 single nucleotide polymorphisms (SNPs) from individual samples (n = 461) collected across the snake's distribution in western Canada and neighboring Washington (USA). Hierarchical STRUCTURE analyses found evidence for population structure within and among the five geographic regions in BC, as well as in Washington. Within these regions, 11 genetically distinct complexes of dens were identified, with some regions having multiple complexes. No significant pattern of isolation-by-distance and generally low levels of migration were detected among den complexes across regions. Additionally, snakes within dens generally were more related than those among den complexes within a region, indicating limited movement. Overall, our results suggest that the single, recognized designatable unit for Western Rattlesnakes in Canada should be re-assessed to proactively focus conservation efforts on preserving total genetic variation detected range wide. More broadly, our study demonstrates a novel application of GT-seq for investigating patterns of diversity in wild populations at multiple scales to better inform conservation management.</p>
Quantifying range structure to inform management in invaded landscapes - Dataset
<p>This data set was collected in Table Mountain National Park, South Africa and comprises count and location data for invasive woody plant species for the genera <em>Acacia</em>, <em>Pinus,</em> and <em>Eucalyptus</em>. The data were collected between 2013 and 2015 and span 10 058 sample plots, uniformly distributed across the protected area. Further details of the dataset are provided in the attached meta-data document.</p>
Supplementary information for 'Structural and chemical properties of superconducting Co-doped BaFe2As2 thin films grown on CaF2'
<p>This repository contains supplementary information for the journal article '<a href="https://iopscience.iop.org/article/10.1088/1361-6668/abcecf">Structural and chemical properties of superconducting Co‑doped BaFe<sub>2</sub>As<sub>2</sub> thin films grown on CaF<sub>2</sub></a>'.</p> <p>The Jupyter notebooks (.ipynb) demonstrate data treatment for Fig. 4b (folder "HyperSpy EDXS Analysis") and Fig. 10a (folder "Atomap"). The notebooks can be run with the provided datasets. HTML files are also provided for quick inspection of the used procedures in a web browser. Supplementary video files (.mp4) show electron-beam-induced radiation damage at the BaFe<sub>2</sub>As<sub>2</sub>-CaF<sub>2</sub> interface.</p> <p>Please visit the websites of the <a href="https://hyperspy.org/">HyperSpy</a> and <a href="https://atomap.org/">Atomap</a> projects for more information.</p> <p>If there are any questions or bugs, please contact me under lukas.gruenewald_at_kit.edu.</p> <p> </p> <p> </p>
Supplementary information for: Using networks to identify structure in phylogenetic tree sets
<p>Modern phylogenomic studies produce large sets of trees that can represent variation in inferred phylogenies across genes, uncertainty in estimated phylogenies for a given gene, or both. Standard practice is to condense this variation down to a small set of point estimates or consensus trees in order to facilitate display and interpretation. However, doing so results in the loss of enormous amounts of information about the structure of the underlying tree set. Here, we propose new approaches to explore and detect structure in the tree set itself. These approaches rely on the well-developed mathematical foundations of community detection in networks and leverage two different network types. The first type uses nodes to represent trees and connects these nodes with edges whose weights are determined by the similarity (affinity) of the trees. The second type uses nodes to represent bipartitions and connects nodes with edges whose weights represent the covariance in bipartition presence/absence across trees in the set. These two network types carry information that is complementary, but not identical. A variety of methods may be applied to both networks in order to identify interesting community structure. These community detection approaches provide a rich view of the information contained in phylogenomic data sets and facilitate investigation into the forces driving inferred phylogenetic variation across genomes.</p>
Microbial structures in the surface sediments of Shenhu Area, South China Sea-Appendix A. Supporting information
<p>Microbial structures in the surface sediments of Shenhu Area, South China Sea-Appendix A. Supporting information</p>
Data from: Building genetic networks using relatedness information: a novel approach for the estimation of dispersal and characterization of group structure in social animals
Natal dispersal is an important life history trait driving variation in individual fitness and, therefore, a proper understanding of the factors underlying dispersal behaviour is critical to many fields including population dynamics, behavioural ecology and conservation biology. However, individual dispersal patterns remain difficult to quantify despite many years of research using direct and indirect methods. Here, we quantify dispersal in a single intensively-studied population of the cooperatively breeding chestnut-crowned babbler (Pomatostomus ruficeps) using genetic networks created from the combination of pairwise relatedness data and social networking methods and compare this to dispersal estimates from re-sighting data. Not only does this novel approach identify movements between social groups within our study sites but also provides an estimation of immigration rates of individuals originating outside the study site. Both genetic and re-sighting data indicated that dispersal was strongly female-biased, but the magnitude of dispersal estimates was much greater using genetic data. This suggests that many previous studies relying on mark-recapture data may have significantly underestimated dispersal. An analysis of spatial genetic structure within the sampled population also supports the idea that females are more dispersive, with females having no structure beyond the bounds of their own social group while male genetic structure expands for 750 meters from their social group. Although the genetic network approach we have used is an excellent tool for visualising the social and genetic microstructure of social animals and identifying dispersers, our results also indicate the importance of applying them in parallel with behavioural and life history data.
Data from: Resolving patterns of population genetic and phylogeographic structure to inform control and eradication initiatives for brown rats Rattus norvegicus on South Georgia
The control and eradication of invasive species is a common management strategy to protect or restore native biodiversity. On South Georgia in the Southern Ocean, the brown rat Rattus norvegicus was brought onto the island with the onset of whaling and sealing activity in the 1800s and has had a significant detrimental impact on key bird species of conservation concern. Efforts to eradicate rats from South Georgia using poisoned bait are ongoing. Despite the South Georgia rat eradication programme being the geographically largest and most ambitious eradication initiative to date, its success is facilitated by the potential that rat populations are effectively isolated by glacial barriers. This allows for localized eradication effort at manageable scales, leading to sequential eradication of individual populations with minimal risk of incursion from neighbouring areas. Here, we use the levels of population genetic divergence estimated from 299 single nucleotide polymorphism (SNP) loci and DNA sequence variation across 993 base pairs of the mitochondrial DNA cytochrome B locus to examine whether rat populations from nine glacially isolated areas on South Georgia are genetically distinct and so can be treated as independent eradication units. Bayesian clustering of individuals based on SNP similarity identified seven different genetic groups, which were confirmed using analyses based on pairwise genetic distance estimates and ordination of individuals using principal coordinate analysis. From a management perspective, these seven groups represent individual targets in baiting operations. Two mtDNA haplotypes were resolved across South Georgia, with a distinct geographical separation between the north-western and south-eastern populations. Approximate Bayesian computation (ABC) was used to identify that this divergence was a consequence of two separate historical colonization events. Synthesis and applications. We illustrate that molecular markers are a valuable tool in species management and pest eradication given that the spatial distribution of genetic diversity can: (i) identify demographically and genetically independent populations on which local eradication effort can be focussed, (ii) distinguish between incomplete eradication and immigration in situations where individuals remain after eradication has been attempted and (iii) identify the source of migrants when dispersal occurs over large spatial scales.
Supplementary information for: "A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling".
<p>This is supplementary data for F1000Research article: A voltage-dependent fluorescent indicator for optogenetic applications, archaerhodopsin-3: Structure and optical properties from in silico modeling.</p> <p>Here are files for modeling archaerhodopsin-3 with I-TASSER, Medeller and RosettaCM algorithms, structure postprocessing and spectra calculations.</p> <p>Please, refer to the readme.txt for the description.</p>
SUPPORTING INFORMATION FOR: Stochastic dynamic mass spectrometric 3D structural analysis of caffeine metabolites
<p>Supporting information for the entitled contribution.</p><p>It contains:</p><p>Static quantum chemical and high accuracy molecular dynamics computational data on protomers, tautomers, zwitterions, and isotopomers of caffeine (CAFF), paraxanthine (PARAXAN), theobromine (THEOBR), theophylline (THEOPH), and guanine (GUA), uric acid (UA), and xantine (XAN), as well as their derivatives.</p><p>The content includes data on characteristic parent and product ions of the analytes in ion mobility spectrometric and mass spectrometric experimental conditions. Tautomers, charge transfer processes, and intramolecular rearrangement; if any, are accounted for considering. </p><p>Molecular mechanics/molecular dynamics data are shown as *.txt files. </p><p>High accuracy molecular dynamics includes adiabatic computations using Born-Oppenheimer approach.</p><p>High accuracy static ground state and transition state computations use M062X/SDD level of theory. </p><p>Figures in color, illustrating the entitled contribution shown as *.pdf files.</p><p>The experimental ion mobility spectrometry and mass spectrometry data are according to reference [1].</p><p>[1] H. Sepman, A. Kruve, S. Tshepelevitsh, H. Hupatz, Experimental IMS and MS/MS data of caffeine metabolites (2022). Zenodo, [https://doi.org/10.5281/zenodo.6637393][ https://zenodo.org/record/6637393] (Accessible for 04.04.2022.)</p><p>They have been used and processed via the following software:</p><p>[2] ProteoWizard 3.0.11565.0 (2017) [https://proteowizard.sourceforge.io/download.html];</p><p>[3] mMass 5.0.0 [http://www.mmass.org/download/old.php];</p><p>[4] AMDIS 2.71 (2012) software [https://chemdata.nist.gov/mass-spc/amdis/downloads/AMDIS_Installer-17.zip]; and</p><p>[5] NIST Search Software 2.0 [https://chemdata.nist.gov/dokuwiki/lib/exe/fetch.php?media=chemdata:nist17:nist17demo.zip], respectively.</p><p> </p><p> </p>
Supporting information file of paper [Crystallographic and theoretical study of the atypical distorted octahedral geometry of the metal chromophore of zinc(II) bis((1R,2R)-1,2-diaminocyclohexane) dinitrate (Journal of Molecular Structure 1248 (2022) 131488)]
<p>Supporting information file of third revision of an already accepted and published paper [Crystallographic and theoretical study of the atypical distorted<br>octahedral geometry of the metal chromophore of zinc(II) bis((1R,2R)-1,2-diaminocyclohexane) dinitrate (Journal of Molecular Structure 1248 (2022) 131488)].</p>
Geographic Information System of structural elements in the Niobe-Aphrodite Map Area of Venus: a tool for structural and geologic analysis.
<p>The Niobe Aphrodite Map Area covers over 25% of the surface of Venus and extends from 57N to 57S and 60E to 180E. The structural-element map presented here is derived from the1:10 M-scale geologic maps of Niobe Planitia, U.S. Geological Survey I-2467 and Aphrodite Terra, U.S. Geological Survey I-2476. Both maps are in various stages of review and revision overseen by the U.S. Geological Survey on behalf of NASA.</p> <p>Here we present a Geographic Information System (GIS) that contain the different structural elements of the area (deformation structures and lithodemic units), that can be used to analyze relationships between and among suites of structural elements across this large portion of Venus’ surface.</p> <p>Base images and data on which determination of the structural element determination is based can be accessed and downloaded directly in GIS-ready formats through the USGS Map a Planet website (https://astrogeology.usgs.gov/tools/map-a-planet-2).</p>
Genetic diversity and population structure of two endangered neotropical parrots inform In Situ and Ex Situ conservation strategies
<p></p><p>A key aspect in the conservation of endangered populations is understanding patterns of genetic variation and structure, which can provide managers with critical information to support evidence-based status assessments and management strategies. This is especially important for species with small wild and larger captive populations, as found in many endangered parrots. We used genotypic data to assess genetic variation and structure in wild and captive populations of two endangered parrots, the blue-throated macaw, Ara glaucogularis, of Bolivia, and the thick-billed parrot, Rhynchopsitta pachyrhyncha, of Mexico. In the blue-throated macaw, we found evidence of weak genetic differentiation between wild northern and southern subpopulations, and between wild and captive populations. In the thick-billed parrot we found no signal of differentiation between the Madera and Tutuaca breeding colonies or between wild and captive populations. Similar levels of genetic diversity were detected in the wild and captive populations of both species, with private alleles detected in captivity in both, and in the wild in the thick-billed parrot. We found genetic signatures of a bottleneck in the northern blue-throated macaw subpopulation, but no such signal was identified in any other subpopulation of either species. Our results suggest both species could potentially benefit from reintroduction of genetic variation found in captivity, and emphasize the need for genetic management of captive populations.</p><p></p>
Matrix aggregation of species of Phyla Annelida (Polychaeta), Mollusca, Arthropoda (Decapoda, Stomatopoda, Amphipoda, and Chelicerata), and Echinodermata registered of the Caribbean Sea and Gulf of Mexico region by Ocean Biodiversity Information Systems of the research "Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) for capturing the biological diversity of two coral reefs in the Yucatán Península, México"
<p>This database consists of an aggregation matrix of species from Ocean Biodiversity Information Systems using as geographic filters the Caribbean Sea region (ID 34287) and the Gulf of Mexico region (ID 34287) nomenclature and hierarchical classification of each Phyla from World Register of Marine Species used for the calculation of average taxonomic distinction of species belonging to the Phyla Annelida (Polychaeta), Mollusca, Arthropoda (Decapoda, Stomatopoda, Amphipoda, and Chelicerata), and Echinodermata associated to Autonomous Reefs Monitoring Structures from the research “Evaluation of the use of Autonomous Reef Monitoring Structures (ARMS) to estimate cryptic diversity in two coral reefs of the Yucatan Península, México”</p> <p><strong>*Corresponding autor: </strong>edlinguerra@gmail.com</p> <p>BIS Ocean Biodiversity Information System. Available online: <a href="http://www.iobis.org/">www.iobis.org</a>.</p> <p>Horton, T.; Gofas, S.; Kroh, A.; Poore, G.C.B.; Read, G.; Rosenberg, G.; Stöhr, S.; Bailly, N.; Boury-Esnault, N.; Brandão, S.N.; et al. Improving nomenclatural consistency: A decade of experience in the World Register of Marine Species. <em>Eur. J. Taxon.</em> <strong>2017</strong>, <em>2017</em>, doi:10.5852/ejt.2017.389.</p> <p><span lang="EN-US">was produced in collaboration with the Biodiversidad Marina de Yucatán project. </span><a href="https://www.bdmy.org.mx/carteles-publicaciones/" target="_blank" rel="noopener">https://www.bdmy.org.mx/,</a> Universidad Nacional Autonoma de México and Escuela Nacional de Estudios Superiores</p>
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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.