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12,346 results for “derivatives”
GMATA derived ssr files containing Microsatellite data for 128 Phytophthora strains
<p>These 128 files are GMATA software-derived .ssr files, containing Microsatellite data for each Phytophthora strain.</p>
Exemplary landscape planning results using different qualities of LU/LC data to derive implications for practical planning.
<p>This Dataset consist of two GIS Shape files showing examples of common landscape planning activities, namely the an assessment of the climate protection function and planning towards locating environmental protection measures using different data basis. Using overlay operation it is possible to use descriptive statistics to assess uncertainties and inconsistencies between different land use / land cover data sets and highlight their implications for practical planning.</p> <p>Once published, the results of such analysis can be seen in the related publication "Uncertainties in land use data may have substantial effects on environmental planning recommendations: a plea for careful consideration. Submitted to PLOS ONE."</p>
Four historical tree-ring chronologies and underlying data derived from dendrochronological research on Batavia shipwreck timbers
<p>This dataset comprises four tree-ring chronologies and underlying tree-ring data derived from the dendrochronological research on the shipwreck timbers of the <em>Batavia</em> shipwreck. The undated tree-ring series have also been included.</p> <p>For context information about this dendrochronological dataset, please refer to the publication:</p> <p>Daly A, Domínguez-Delmás M, van Duivenvoorde W (2021) <em>Batavia</em> shipwreck timbers reveal a key to Dutch success in 17th-century world trade. PLOS ONE 16(10): e0259391. <a href="https://doi.org/10.1371/journal.pone.0259391">https://doi.org/10.1371/journal.pone.0259391</a> </p> <p> </p>
Landsat-derived annual maps of agricultural greenhouse in Shandong province, China from 1989 to 2018
<p>Using 8,450 Landsat images on the Google Earth Engine, we built the first Landsat-derived annual maps of agricultural greenhouse (AG) in Shandong province, China from 1989 to 2018. Two types of reference datasets, including AG and Non-AG, were labeled via visual inspection of high-resolution imagery available in Google Earth or Landsat imagery based on a 10 km grid sampling structure. The mapping window for each year was selected based on the vegetation growth and the phenological information. Classification for each year was carried out initially based on the random forest classifier after the feature optimization. A temporal consistency correction algorithm based on classification probability was then proposed to the classified AG maps for further improvement.</p>
7-Dehydrocholesterol-derived oxysterols cause neurogenic defects in Smith-Lemli-Opitz syndrome
<p>Defective 3beta-hydroxysterol-delta<sup>7 </sup>-reductase (DHCR7) in the developmental disorder, Smith-Lemli-Opitz syndrome (SLOS), results in deficiency in cholesterol and accumulation of its precursor, 7-dehydrocholesterol (7-DHC). Here, we show that loss of <i>DHCR7</i> causes accumulation of 7-DHC-derived oxysterol metabolites, premature neurogenesis, and perturbation of neuronal localization in developing murine or human cortical neural precursors, both <i>in vitro</i> and <i>in vivo</i>. We found that a major oxysterol, 3b,5a-dihydroxycholest-7-en-6-one (DHCEO), mediates these effects by initiating crosstalk between glucocorticoid receptor (GR) and neurotrophin receptor kinase TrkB. Either loss of <i>DHCR7</i> or direct exposure to DHCEO causes hyperactivation of GR and TrkB and their downstream MEK-ERK-C/EBP signaling pathway in cortical neural precursors. Moreover, direct inhibition of GR activation with an antagonist or inhibition of DHCEO accumulation with antioxidants rescues the premature neurogenesis phenotype caused by the loss of <i>DHCR7</i>. These results suggest that GR could be a new therapeutic target against the neurological defects observed in SLOS.</p>
Data and code to replicate: Diet analysis using generalized linear models derived from foraging processes using R package mvtweedie
<p>Diet analysis integrates a wide variety of visual, chemical and biological identification of prey. Samples are often treated as compositional data, where each prey is analyzed as a continuous percentage of the total. However, analyzing compositional data results in analytical challenges, e.g., highly parameterized models or prior transformation of data. Here, we present a novel approximation involving a Tweedie generalized linear model (GLM). We first review how this approximation emerges from considering predator foraging as a thinned and marked point process (with marks representing prey species and individual prey size). This derivation can motivate future theoretical and applied developments. We then provide a practical tutorial for the Tweedie GLM using new package <i>mvtweedie</i> that extends capabilities of widely used packages in R (<i>mgcv</i> and <i>ggplot2</i>) by transforming output to calculate prey compositions. We demonstrate this approach and software using two examples. Tufted puffins (<i>Fratercula cirrhata</i>) provisioning their chicks on a colony in the northern Gulf of Alaska show decadal prey switching among sand lance and prowfish (1980-2000) and then Pacific herring and capelin (2000-2020), while wolves (<i>Canis lupus ligoni</i>) in Southeast Alaska forage on mountain goats and marmots in northern uplands and marine mammals in seaward island coastlines. </p>
E-scape: consumer-specific landscapes of energetic resources derived from stable isotope analysis and remote sensing
<p>Energetic resources and habitat distribution are inherently linked. Energetic resource availability is a major driver of the distribution of consumers, but estimating how much specific habitats contribute to the energetic resource needs of a consumer can be problematic.</p> <p>We present a new approach that combines remote sensing information and stable isotope ecology to produce maps of energetic resources (<i>E</i>-scapes). <i>E</i>-scapes project species-specific resource use information onto the landscape to classify areas based on energetic importance.</p> <p>Using our <i>E</i>-scapes, we investigated the relationship between energetic resource distribution and white shrimp distribution and how the scale used to generate the <i>E</i>-scape mediated this relationship.</p> <p><i>E</i>-scapes successfully predicted the size, abundance, biomass, and total energy of a consumer in salt marsh habitats in coastal Louisiana, USA at scales relevant to the movement of the consumer.</p> <p>Our <i>E</i>-scape maps can be used alone or in combination with existing models to improve habitat management and restoration practices and have potential to be used to test fundamental movement theory. </p>
BridgeDb: Human and SARS-related corona virus gene/protein mapping database derived from Wikidata
<p>Gene/Protein mappings for human and SARS-related coronaviruses. Data is derived from Wikidata. Mappings from Wikidata to NCBI Gene, RefSeq, UniProt, and Guide to Pharmacology Target are provided in the .bridge file.</p> <ul> <li>179 Wikidata (Wd) identifiers</li> <li>82 Uniprot-TrEMBL (S) identifiers</li> <li>70 NCBI Gene (L) identifiers</li> <li>66 RefSeq (Q) identifiers</li> <li>9 Guide to Pharmacology Target (Gpt) identifiers</li> </ul> <p>Virus name was added as attribute ("virus") to Wikidata Xrefs.</p>
Monthly mean optical depth at 550 nm derived from AERONET data used for model evaluation in GMD-2021-357
<p>Climatological monthly means over 2000-2014 derived from Aerosol Robotic Network version 3 level 2.0 direct sun retrievals (monthly data) used for model evaluation in Myriokefalitakis et al. (2021), doi: 10.5194/gmd-2021-357</p> <p>The netCDF file includes the AOD at the 4 native AERONET wavelengths (440 nm, 670 nm, 870 nm and 1020 nm), as well as the interpolated values at 550 nm used for the evaluation. The statistics stored are calculated over the monthly values for the 15 year period and include: monthly mean, 5th, 50th, and 95th percentile, standard deviation, standard error, number of days available per station and month and number of days where coarse AOD dominates (used as proxy for dusty days). </p> <p>The AERONET retrievals of optical depth were downloaded through the AERONET data download tool (available at: https://aeronet.gsfc.nasa.gov/, last accessed March 28, 2020). We thank the principal investigators and their collaborators for their effort in establishing and maintaining all AERONET sites used in this compilation.</p> <p>The use of this dataset must follow the guidelines of the original data providers at AERONET, explained here: https://aeronet.gsfc.nasa.gov/new_web/data_usage.html</p>
Deriving population scaling rules from individual-level metabolism and life history traits - Code and Data
<p>Individual metabolism generally scales with body mass with an exponent around 3/4. From dimensional arguments it follows that maximum population growth rate (rmax) scales with a -1/4 exponent. However, the dimensional argument implicitly assumes that offspring size is proportional to adult size. Here we calculate rmax from metabolic scaling at the level of individuals within size-structured populations while explicitly accounting for offspring size. We identify four general patterns of how rmax scales with adult mass based on four empirical life-history patterns employed by groups of species. These life-history patterns are determined by how traits of somatic growth rate and/or offspring mass relate to adult mass. One life-history pattern -- constant adult:offspring mass ratio and somatic growth rate independent of adult mass -- leads to the classic -1/4 scaling of rmax. The other three life-history patterns lead either to non-metabolic population growth scaling with adult mass or do not follow a power-law relationship at all. Using life-history data of five marine taxa and terrestrial mammals, we identify species groups that belong to one of each case. We predict that elasmobranchs, copepods, and mammals follow standard -1/4 power-law scaling, whereas teleost fish and bivalves do not have a pure power-law scaling. Our work highlights how taxa may deviate from the classic -1/4 metabolic scaling pattern of maximum population growth. The approach is generic and can be applied to any taxa.</p>
Stacked cross correlation functions for the MeSO-net network and derived 3D Vs model
<p>This dataset contains two major types of data.</p> <p>1) The yearly stacked cross-correlation functions between 296 MeSO-net stations covering the Kanto basin, Japan.</p> <p>2) A 3D radially anisotropic Vs model for the Kanto basin. The grid increment for the longitude and latitude is 0.01 degrees and that for the depth is 0.1 km.</p> <p>The complete station list for the 296 MeSO-net stations can be found on the Github page of https://github.com/chengxinjiang/Jiang_Kanto_anisotropy. </p>
Materials for Design Open Repository. Polymer Derived Ceramics
<p>The current dataset is composed of a collection of Polymer Derived Ceramics (PDCs). It contains the number of chemical elements (NoE), PDC composition, used precursor, Pyrolysis temperature <em>T</em><sub>p</sub>, Pyrolysis time <em>t</em><sub>p</sub>, gas atmosphere, a set of columns containing the chemical elements and their corresponding fraction, and the references. This dataset was developed in the framework of the European project ACHIEF for the discovery of novel materials to be used in industrial processes.</p>
Patient breast MRI images and computational breast phantom data for research in patient-derived realistic breast modelling
<p>The data is comprised of two parts: 1) patient DICOM MRI images and 2) 3D matrix of a computational breast phantom.</p> <ol> <li>The DICOM images are anonymised patient breast MRI images of a female patient diagnosed with invasive ductal carcinoma. The obtaining of the patients’ DICOM images is approved by the Ethics Committee of Medical University of Varna. The acquisition was performed with GE Signa HDxt MRI scanner. The images are from a T1-weigthed Axial multi-phase VIBRANT (3-phase) sequence and with voxel size of 0.7 mm x 0.7 mm x 0.8 mm. Contrast agent is present. The image set can be opened with any standard DICOM reader.</li> <li>The computational breast phantom is derived from the above mentioned dataset. The phantom is in the form of a 3D matrix saved as a MATLAB data file (.mat file). Each voxel has an assigned Hounsfield Unit value depending on its classification: air = 0, adipose tissue = -152, glandular tissue = 42, tumour = 64, skin = 108. The data file can be opened with MATLAB or Octave.</li> </ol>
Tree-ring dataset derived from the 16th century Evangelistas altarpiece at Seville Cathedral (Spain)
<p>Tree-ring dataset in Heidelberg format of 29 oak (<em>Quercus</em> sp.) boards making up the panels of the Evangelistas altarpiece at Seville cathedral. This collaborative research and publication took place within the scope of the NWO-funded project <em>Filling in the blanks in European dendrochronology</em>. We also provide an excel sheet with metadata.</p>
A hifi testing dataset derived from SRR13128014 (zymo D6331)
<p>This is a small dataset subsampled from SRR13128014 which represents a mock community, zymoBIOMICS D6331.</p> <p> </p> <p>We extraced E.coli reads by alignment, then used `seqtk subseq read.fq.gz 0.1` to randomly pick 10% from them. This is created for testing if hifiasm-meta (https://github.com/xfengnefx/hifiasm-meta ) runs. For r57, it roughly needs 170s on 48 threads with peak memory of 18GB. Refer to the tar.gz file for expected results. Hicanu and metaflye should be able to successfully run on this dataset as well.</p>
Flowing days Derived from CubeSat Imagery and Ground Observations in Hassayampa River (HR), Arizona from 2019-2021 (Water Years)
<p>Flowing days derived from CubeSat imagery and ground observations in Hassayampa River (HR), Arizona from October 2018 to September 2021. This database supports the following paper:</p> <div> <div>Wang, Z., & Vivoni, E. R. (2022). Detecting streamflow in dryland rivers using CubeSats. <em>Geophysical Research Letters</em>, 49, e2022GL098729. <a href="https://doi.org/10.1029/2022GL098729">https://doi.org/10.1029/2022GL098729</a></div> </div> <div> <div> </div> </div> <p>This database includes three folders.</p> <ol> <li>GroundObservations: Ground observations along the HR retrieved from USGS website (https://waterdata.usgs.gov/nwis) and Flood Control District of Maricopa County using Single Sensor Data Reports tool (https://alert.fcd.maricopa.gov/showrpts_mc.html): <ol> <li><strong>Precip</strong>: Records of daily precipitation amount.</li> <li><strong>Stream</strong>: Records of daily streamflow amount.</li> </ol> </li> <li>GIS: GIS layers used in deriving flowing days. <ol> <li><strong>Subreach</strong>: Shapefiles of nine sub reaches along the HR.</li> <li><strong>Buffer segment</strong>: Buffer zones perpendicular to HR reaches at 90 m resolution. Column ID is sorted in ascending order along the HR.</li> <li><strong>Channel masks: </strong>Channel masks of HR derived from Planet data.</li> </ol> </li> <li>Results <ol> <li><strong>BufferSegment_Flowdays.xlsx:</strong> Days with flow determined using the NIR difference threshold for water years (WY) 2019 to 2021 for each 90 m buffer areas. The relative location of each buffer areas can be found in the Buffer Segment GIS layer. ‘NaN’ suggests no data.</li> </ol> </li> </ol> <div> <div> </div> </div>
Line-Source Model based Rapid Inversion for Deriving Large Earthquake Rupture Characteristics using High-rate GNSS Observations
<p>The high-rate GNSS data and GNSS-derived velocity waveforms of six large earthquakes (the 2016 Mw 6.6 Norcia earthquake, the 2010 Mw 7.2 EI Mayor-Cucapah earthquake, the 2016 Mw 7.8 Kaikoura earthquake, the 2019 Mw 7.1 Ridgecrest earthquake, the 2014 Mw 8.2 Iquique earthquake, and the 2015 Mw 8.3 Illapel earthquake) are included in this repository.</p>
raw data for the article "Synthesis of Polycyclic Aminal Heterocycles via Decarboxylative Cyclisation of Dipeptide Derivatives"
<p>Raw NMR, IR and MS data for the article "Synthesis of Polycyclic Aminal Heterocycles via Decarboxylative Cyclisation of Dipeptide Derivatives" published in Chemical Communications, DOI: </p> <p><a href="https://doi.org/10.1039/D2CC00167E">https://doi.org/10.1039/D2CC00167E</a></p> <p>The number of the folders correspond to compounds numbers in the article. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.</p>
Synthesis, Herbicidal Activity, Crop Safety and Soil Degradation of Pyrimidine- and Triazine-Substituted Chlorsulfuron Derivatives Supplementary Information
<p>The content include SI1-Melting points, 1H-NMR, 13C-NMR and HRMS of W103-W111, SI2-Crystal data of compound W110(CCDC number 2142702), SI3-Biological assay and crop safety, SI4-Soil degradation assay, SI5-Report of soil analysis in Chinese, and SI6-Report of soil analysis in English.</p>
Data publication for "First-principles derivation and properties of density-functional average-atom models"
<p>Data for the pre-print "First-principles derivation and properties of density-functional average-atom models", https://arxiv.org/abs/2103.09928.</p> <p>Each data folder is named according to the corresponding figure in the paper. For any questions, please contact the authors.</p>
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.