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2,308 results for “repeatability”
Diffraction images of crystals of the spectrin repeats 7 and 8 (SR7-SR8) of the plakin domain of human plectin (PDB code 5J1G): native and Hg-derivative datasets for phasing by SIRAS
<p>Diffraction images of crystals of a fragment of the plakin domain of human plectin that includes the spectrin repeats 7 to 8 (SR7-SR8).</p> <p>Images correspond to the dataset used to solve and refine the pdb entry <strong>5J1G</strong> (http://www.rcsb.org/pdb/explore/explore.do?structureId=5J1G).</p> <p> </p> <p>The structure was phase by single isomorphous replacement with anomalous scattering (SIRAS) using two datasets: one from a native crystal and another one from a crystal derivatized with the mercurial compound ethylmercurithiosalicylate (EMTS).</p> <p> </p> <p>The <strong>Native dataset</strong> was collected on a single crystal at the beamline XALOC of the ALBA Synchrotron (Barcelona, Spain) using radiation of 0.9792 Å wavelength and a PILATUS 6M detector. The dataset consists of 4 wedges of 450 images each (0.2º oscillation per image). Each wedge was collected at a different position of the same crystal. The crystals belong to the space group P2<sub>1</sub> with approximate cell dimensions <em>a</em>=45.7 Å, <em>b</em>=115.9 Å, <em>c</em>=64.8 Å, beta=97.6 º.</p> <p> </p> <p>The data from a <strong>mercurial derivative</strong> (EMTS) was collected in house using a rotating anode X-ray generator (wavelength 1.54179 Å) and a mar345 image plate detector. The dataset consists of 360 images (1º oscillation per image). The crystal was isomorphic to the native crystal.</p> <p> </p> <p>In addition to the diffraction images the following files are included:</p> <p>a) Files for indexing with the program XDS and the HKL files containing the integrated intensities.</p> <p>b) Files for scaling using the program xscale (directory XSCALE_5J1G_Native_EMTS).<br> c) The directory “phasing_shelx” contains hkl files of the intensities of the native and EMTS datasets in a format suitable for analysis with Shelx. This directory also contains the files of the phasing by SIRAS using Shelx C/D/E.</p>
High-resolution, Decadal to Weekly Geomorphic Change Analysis of the Elbow River in Calgary, using Multi-temporal Lidar and Repeat Terrestrial Laser Scanning
<p>This directory contains files related to the scientific research project of Luc van Dijk at the Department of Earth, Energy, and Environment, University of Calgary. The project title is "High-resolution, Decadal to Weekly Geomorphic Change Analysis of the Elbow River in Calgary, using Multi-temporal Lidar and Repeat Terrestrial Laser Scanning". This project in the field of geomorphology was a collaboration between the University of Calgary and Utrecht University in the Netherlands. The project was completed on October 27, 2023. Below is a description of the files in this directory.</p><p> </p><p><strong>DisplacementVolumeDistributions_TLS.xlsx</strong></p><p>Excel file containing tabular data of the normalized sediment displacement volumes that were obtained using TLS. Each tab in the Excel file represents a period of interest in 2023. The data in this file were used to generate the 'histogram-like' figures in the report.</p><p> </p><p><strong>DoD_rasters.zip</strong></p><p>Folder containing the aerial lidar DEMs of Difference (DoDs) for each period of interest. The DoDs are 'waterless', i.e. the water surface is masked. The suffix of the file name before the file extension (e.g., ..._10cm.tif) indicates the maximum REM value that was used for the automated masking of the water surface extent (see report section 3.1.2). If the file name contains "large", it refers to the upstream greater area (see report section 3.1.3).</p><p>Within this folder is another folder called 'Clipped2AOIs'. This folder contains the same DoDs, but covering only the extents of the sites of interest ('AOIs' = Areas Of Interest).</p><p> </p><p><strong>FilteredPointClouds_TLS.zip</strong></p><p>Folder containing the processed and filtered point clouds that were acquired throughout the summer of 2023 using TLS. These point clouds have been pre-processed and filtered to remove vegetation (see report section 3.2). They are grouped in sub-folders per acquisition date. The filenames are numbered to location, i.e. 'elbow1', 'elbow2', 'elbow3' and 'elbow4'. These correspond to the sites of interest: Glenmore Dam, golf club, Sandy Beach and Riverdale, respectively.</p><p> </p><p><strong>PythonScripts_Discharge_Rainfall.zip</strong></p><p>Folder containing the Python scripts that were made to process the discharge and rainfall data that were sourced from Environment Canada and The City of Calgary (see report section 3.3). The scripts themselves contain descriptions of their purpose.</p><p> </p><p><strong>PythonScripts_DisplacementVolumeAnalysis.zip</strong></p><p>Folder containing the Python scripts that were made to process and analyze the aerial lidar DoDs and the TLS rasterized difference point clouds (M3C2 output). The 'convert2pickle' scripts converted the sizable rasters to smaller pickle files, which were easier and faster to work with. The 'chart' scripts load the data from the pickle files, analyze them and produce the 'histogram-like' figures in the report. The scripts themselves contain descriptions of their purpose.</p><p> </p><p><strong>RainfallDischargeData.xlsx</strong></p><p>Excel file containing the discharge and rainfall data from Environment Canada and The City of Calgary. The data came from different sources in different formats and were combined into this single table.</p><p> </p><p><strong>RasterizedDifferencedPointClouds_M3C2.zip</strong></p><p>Folder containing the rasterized results of the differenced TLS point clouds (M3C2 output) (see report section 3.2.4). The filenames are numbered to location, i.e. 'Elbow1', 'Elbow2', 'Elbow3' and 'Elbow4'. These correspond to the sites of interest: Glenmore Dam, golf club, Sandy Beach and Riverdale, respectively. The numeric sequence in the file name indicates the start and end date of the change analysis in a 'mm-dd' format. The suffixes '_dist', '_unc' and '_sig' refer to the three output layers of the M3C2 algorithm: distance, uncertainty and significance of change. The main files of interest are the '.tif' files. Files sharing the same name, but with different extensions (.tfw, .tif.aux.xml, .tif.xml) are supplementary/auxiliary files for the '.tif' file, generated by ArcGIS Pro.</p><p> </p><p><strong>ScarpsOfInterest_shapefile.zip</strong></p><p>Folder containing a polygon shapefile describing the extents and locations of the sites of interest. The main file of interest is the '.shp' file. The other files with the same name, but different extensions (.cpg, .dbf, .prj, .sbn, .sbx, .shp.xml, .shx) are supplementary/auxiliary files for the '.shp' file, generated by ArcGIS Pro.</p>
Coefficients for a Proxy Long-Wavelength Correction for the SWOT 1-Day Repeat Mission
<p>This archive contains NetCDF-formatted files containing the weighting coefficients which define the proxy long-wavelength correction (LWC) described in a manuscript submitted to AGU Earth and Space Science, "The Significance of the Long-Wavelength Correction for Studies of Baroclinic Tides with SWOT".</p>
Repeated and multivariate measures of perceived distance
<p>A dataset of repeated measures of distance perception at physical distances of 7, 8, 9, 10, and 11 meters. The data are also multivariate, with five dependent measures of distance perception. This is a 5 (physical distance) x 5 (dependent measure) within-participants design with a sample size of 46. Note data is missing for 15 trials due participant and experimenter errors.</p> <p>The csv file has 230 rows and 7 columns.</p> <p><em>Subject</em>: Unique identifier for each participant. <br> <em>Physical Distance</em>: Physical distance from the participant to the target cone, in meters.<br> <em>Blindwalk Away</em>: Participants put on the blindfold after viewing the target. Next, participants took one step to the left and turned 180 degrees to face the opposite direction. Participants were instructed to walk forward until they had walked the original distance to the target. <br> <em>Blindwalk Toward</em>: Participants put on the blindfold after viewing the target. Next, participants walked forward until they thought they had reached the target cone.<br> <em>Triangulated BW:</em> Participants put on the blindfold after viewing the target. Next, participants turned right 90 degrees and walked<br> forward 5 meters. The experimenter told participants when to stop walking. Finally, participants turned to face toward the target and walked forward two steps.<br> <em>Verbal:</em> Participants stated the distance between the target cone and themselves, in feet and inches. <br> <em>Visual Matching:</em> An experimenter stood next to the target cone and walked away from the cone in a straight line that was <br> perpendicular to the extent between the target and the participant. Participants instructed the experimenter to stop walking when they thought that the distance between the target and the experimenter was equal to the target distance.</p> <p> </p> <p> </p>
A comprehensive catalog of exact short tandem repeat regions on autosomes and sex chromosomes of the human genome GRCh38
<p>To obtain a general TR catalog across the human genome, we identified genomic intervals with a stretch of exact repetitions of a DNA motif ranging from 1-6bp on GRCh38 autosomes and sex chromosomes by using STRfinder (v1.0), and each STR region was annotated based on gencode.V38 (https://www.gencodegenes.org/human/release_38.html). To end up, we successfully found 1,233,959 TR intervals, covering 0.783306% (24.2 Mbp) of GRCh38 (https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/Homo_sapiens_assembly38.fasta). </p>
X-ray diffraction data for SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE)
<p>X-ray diffraction dataset for SARS-CoV2 spike glycoprotein N-terminal heptad repeat domain + SARS-CoV2(QEYKKEKE) collected at the AMX beamline (17-ID-1) at the National Synchrotron Lightsource II, Brookhaven National Laboratory, Upton, NY, USA.</p> <p>Final XDS.INP file generated by autoPROC.</p> <p>Serialized request document for vector collection from LSDC.</p> <p>KB mirrors</p> <p>Detector: EigerX9M (Si)</p> <p>Approx. photon flux at 13475eV: 4E12 ph/s</p> <p>Approx. beam size: 5 x 7 um</p>
Data from: Polymorphic tandem repeats shape single-cell gene expression across the immune landscape
<p>This dataset contains the association summary statistics (v0.1) for genome-wide tandem repeat (TR) expression quantitative trait (eQTL) analysis of TenK10K Phase 1 (https://doi.org/10.1101/2024.11.02.621562). </p> <p>Please access the README for a detailed description of file contents. </p> <p> </p>
PhasAGE Training School 1 - Structure and protein interactions of repeated and low complexity regions - LECTURE
<p>The Training School 1 <strong>“Computational Methods to Study Protein Phase Separation”</strong> is the first edition of a series of PhasAGE training activities.</p> <p>The goal of this course is to provide participants with the basic knowledge to understand the phenomenon of <strong>Phase Separation</strong>, its role in biological processes and diseases. In addition, the course will provide <strong>an overview of the available computational resources</strong> to navigate this knowledge. Participants will have <strong>hands-on training</strong> in tools and resources available for life sciences, to collect information from the literature on biomolecular phase transitions, identify features triggering phase transitions, mutations associated with diseases, known or predicted PTMs and molecular interaction sites.</p>
Catalog of Repeating Earthquakes for Northern California, 1984-2014
<p>This catalog includes 27,675 repeating earthquakes grouped in 7,713 sequences in northern California for the years 1984-2014. The repeating earthquakes were identified by a comprehensive analysis of waveform similarity, relative event location, and relative size of all earthquakes recorded by the Northern California Seismic Network (NCSN). Details can be found in:</p> <p>Waldhauser, F., & Schaff, D. P. (2021). A comprehensive search for repeating earthquakes in northern California: Implications for fault creep, slip rates, slip partitioning, and transient stress. Journal of Geophysical Research: Solid Earth, 126, e2021JB022495. https://doi.org/10.1029/2021JB022495</p> <p> </p>
An optimized buffer for repeatable Multicolor STORM Raw Data
<p>Raw microcopy data used to generate the figures in the paper "An optimized buffer for repeatable Multicolor STORM"</p> <p>Camera: Orca Fusion binning 2x2 readout speed 1</p> <p>Objective 100x/1.3 (Olympus) -> Effective pixel size 130x130 nm</p> <p>Expected Conversion factor according to spec sheet: 0.21 electrons/count</p> <p> </p> <p> </p> <p> </p>
Repeatability of energy metabolism and resistance to dehydration in the invasive slug Limax maximus
<p>Dataset from the paper "Repeatability of energy metabolism and resistance to dehydration in the invasive slug <em>Limax maximus"</em></p> <p>It contains metabolic rates and body mass assessed on 30 individuals of L. maximus in three different trials. Metabolic rates are in CO2 ml/m</p>
It takes Tau to tango : Investigating the fuzzy interaction between the Tau-R2 repeat domain and the C-terminal tails of tubulins
<p>The microtubule-associated protein (MAP) tau plays a key role in the regulation of microtubule assembly and spatial organisation. Tau hyperphosphorylation affects its binding on the tubulin surface and has been shown to be involved in several pathologies such as Alzheimer disease. As the tau binding site on the microtubule lays close to the disordered and highly flexible tubulin C-terminal tails (CTTs), these are likely to impact the tau-tubulin interaction. Since the disordered tubulin CTTs are missing from the available experimental structures, we used homology modeling to build two complete models of tubulin heterotrimers with different isotypes for the β-tubulin subunit (βI/αI/βI and βIII/αI/βIII). We then performed long timescale classical Molecular Dynamics simulations for the tauR2-tubulin assembly (in systems with and without CTTs) and analyzed the resulting trajectories to obtain a detailed view of the protein interface in the complex and the impact of the CTTs on the stability of this assembly. Additional analyses of the CTTs mobility in the presence, or in the absence, of tau also highlight how tau might modulate the CTTs activity as hooks that are involved in the recruitment of several MAPs.</p>
Dataset 2 for "Host-specificity and repeatability of haemosporidian infection parameters and potential consequences when testing host species-level hypotheses"
<p>Dataset with 154 host species (min 45 sampled individuals sampled at 1+ sites) for the second part of the analysis in "Host-specificity and repeatability of haemosporidian infection parameters and potential consequences when testing host species-level hypotheses". One file contains the data table. One file contains a table with descriptions of the columns in the data table.</p>
Do Repeat Yourself: Understanding Sufficient Conditions for Restricted Chase Non-Termination - Evaluation Material
<p>In this archive, we provide the (already normalized and translated) rule sets that we used for the evaluation<br> of RMFA2, DRPC, and RPC in our paper "Do Repeat Yourself: Understanding Sufficient Conditions for Restricted Chase Non-Termination" at KR 2023. We also provide the raw result files and some basic scripts that we used<br> to produce and count the results.<br> <br> Please refer to the provided README.md for more information.</p>
Annotation of inverted repeats displaying features of pble STIR or IR in the hg38 genome model
<p>Annotation of inverted repeats displaying features of pble STIR or IR in the hg38 genome model. The annotation of <em>pble</em>-like inner inverted repeats was done using Palindrome (EMBOSS package). The output file was then filtered using pal2gff (https://github.com/Leelouh/pal2gff/blob/main/pal2gff.py), using as parameters a repeat size between 5 and 15 nucleotides, a spacer between pairs of inverted repeats (IRs) of 2 to 10 nucleotides, and a number of mismatches within repeats ranging from 0 to 1. These parameters were chosen taking into account those of the inner IRs found at ends of invertebrate pbles.</p>
Repeat catalogs for TRGT
<p>This dataset contains various repeat catalogs for the <a href="https://github.com/pacificBiosciences/trgt/">Tandem Repeat Genotyping Tool</a> (TRGT):</p> <ul> <li>pathogenic_repeats.hg38.bed contains annotations of 56 known pathogenic repeats.</li> <li>polymorphic_repeats.hg38.bed contains 171,146 polymorphic repeats. The <a href="https://github.com/illumina/repeatcatalogs">original version of this catalog</a> was made for short reads and is distributed under CC BY-SA 4.0 license.</li> <li>adotto_repeats.hg38.bed contains 937,122 repeats originally released by the Genome in a Bottle tandem repeat benchmarking project <a href="https://doi.org/10.5281/zenodo.7226352">10.5281/zenodo.7226352</a>.</li> <li>adotto_hprc.tdb.tar is a TRGTdb file containing alleles of repeats from the adotto_repeats.hg38.bed catalog across 100 HPRC samples.</li> </ul> <p>Please consider citing <a href="https://www.biorxiv.org/content/10.1101/2023.05.12.540470v1.abstract">TRGT preprint</a> if you are using these data.</p> <p> </p> <p> </p>
ACCESS-OM2 1° resolution global repeat decade full forcing interannual simulation data for 1972-2018
<p>This data set contains the <strong>full forcing</strong> interannual simulation output from the global ocean-sea ice model ACCESS-OM2 in the 1° horizontal configuration over the period 1972-2018.</p> <p>This simulation was branched off from the repeat decade forcing spin-up and alongside the control simulation (see light blue and black lines in Fig. 1c in the publication linked below).</p> <p>The control simulation output can be found here: https://zenodo.org/record/8339578 The output here as well as in the control simulation is saved in sets of ten years (output200, output201, ...) in the ocean/ and ice/ folders as netcdf files.</p> <p>The last output folder contains the data for 2012-2018 with the last four years of this output folder (output204) are again the 1972-1975 period and should be omitted from any analysis.</p> <p>For more information on the spin-up and the model configuration, see the Methods section and Fig. 1 in Huguenin, M.F., Holmes, R.M. & England, M.H. Drivers and distribution of global ocean heat uptake over the last half century. <em>Nat Commun</em> 13, 4921 (2022). https://doi.org/10.1038/s41467-022-32540-51</p> <p> </p>
Repeat, ground-based photographs of microplots at the three Conmod Pilot study locations at Jornada Basin LTER, 2008-2016
This data package contains ground-based, repeat photographs taken at plots in the Connectivity Modifier (Conmod) Pilot study on the Jornada Experimental Range from 2008-2016. There were 3 sites for this study: Gravelly Ridges, Aeolian, and Dona Ana. Within each site, there were 8 study plots, 4 of which were treatment plots where connectivity modules (conmods) were installed to decrease gap sizes between perennial vegetation. The plots were 8 x 8 meters and had an 8 x 8 meter buffer zone on both sides of the plot (upwind and downwind). Beginning in 2008, photographs were taken once to twice per year at ten microplots located within the 8 study plots per site to document plant litter, plant germination and growth, and soil deposition/removal by wind and water transport. Five photos were taken of each microplot: One overhead (from directly over the microplot) and 4 lateral views at ground level from each cardinal direction. This data package only contains archives with the overhead photographs, but lateral view photos are available on request. Photo filenames are fully descriptive of the site, plot, microplot, photo view, and date taken (see Methods description for details). This study is complete (finished in 2016) and was the pilot study to the newer Cross Scale Interactions Study.
i2QTL HipSci Structural Variant and Short Tandem Repeat Genotypes
<p>Here we provide structural variant and short tandem repeat variant calls from 204 HipSci donors as described in the manuscript Jakubosky et al. "Discovery and quality analysis of a comprehensive set of structural variants and short tandem repeats". </p> <p><a href="https://www.biorxiv.org/content/10.1101/713198v2">https://www.biorxiv.org/content/10.1101/713198v2</a></p> <p>Jakubosky D, Smith EN, D’Antonio M, Bonder MJ, Young Greenwald WW, Matsui H, D’Antonio-Chronowska A, (Hipsci), Stegle O, Montgomery SB, DeBoever C, Frazer KA. Discovery and Quality Analysis of a Comprehensive Set of Structural Variants and Short Tandem Repeats. bioRxiv. January 2019:713198. doi:10.1101/713198.</p> <p> </p>
Three dimensional MRF obtains highly repeatable and reproducible multi-parametric estimations in the healthy human brain at 1.5T and 3.0T
<p>3D MR Fingerprinting T1/T2/M0 maps of twelve healthy volunteers obtained in eight different sites (1.5T and 3.0T scanners, single vendor). Each subject/site dataset includes two acquisitions (test-retest) to assess repeatability of the measurement.</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.