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Simulated Ancient Genomic Kinship Dataset: BAM (5x run1-6) Files for Related (including inbred) Pairs
<p>Simulated Ancient Genomic Kinship Dataset: VCF and BAM (5x (run1-6)) Files for Related (including inbred) Pairs</p> <p><strong>Description:</strong></p> <p>This dataset comprises simulated pedigrees (VCF files containing 8,677,101 autosomal biallelic and 298,625 X chromosomal SNP positions) generated using Ped-sim (v1.3) and comprising pairs of diverse familial relationship types up to third-degree. The first-degree relationships are parent-offspring and siblings; the second-degree relationships are half-siblings, grandparent-grandchild, and avuncular pairs; and third-degree relationships are first cousins, great-grandparent-great-grandchild, and grand avuncular pairs. For each of these 8 relationship types, our dataset includes 48 pairs of individuals. It also contains unrelated pairs. Additionally, the dataset includes first- and second-degree relatives, with inbreeding (parent-offspring pairs where the parents of the offspring are the first cousins and grandparent-grandchild pairs where the grandchild is the offspring of first cousins). Our simulations encompass all combinations of kinship types regarding sex. The dataset was further enriched by simulating ancient DNA-like sequencing data (5x and 1x BAM files) of Ped-sim simulated individuals using the gargammel tool, employing procedures akin to standard paleogenomic sequencing libraries. Note that the BAM files contain only randomly chosen 200K autosomal SNP positions. Positions can be found in the "200K_positions" file. Details can be found in Aktürk, Mapelli and Güler et al. 2023.</p> <p><strong>Data Sources and Generation:</strong></p> <p>Founder genotypes for pedigree simulation were created from the Tuscany (TSI) population SNPs within the 1000 Genomes Dataset v3. Notably, the founder genotypes lack background relatedness or runs of homozygosity (ROH).</p> <p><strong>Description of File Naming Conventions:</strong></p> <p>The naming conventions of the BAM files in this dataset are designed to convey key information regarding the specifics of each file.</p> <p><strong>cov1x or cov5x:</strong> This segment denotes the coverage level of the BAM files, indicating whether the sequencing coverage for the individuals in the files is 1x or 5x.</p> <p><strong>run_*:</strong> Signifies the particular batch from which the pedigree and individuals are derived. This name segment also applies to VCF files.</p> <p><strong>parent-offspring_* or similar identifiers:</strong> Reflects the origin of the individual from the corresponding VCF file. For instance, "parent-offspring_1" corresponds to the individuals present in the "run_*_parent-offspring_1.vcf" file.</p> <p><strong>parent-offspring* or similar identifiers: </strong>Indicates the origin of the individual from the sets within the VCF files. For example, "parent-offspring1" signifies the first set of parent-offspring pedigrees within the VCF file. Note that parent-offspring, grandparent-grandchild, and great-grandparent-great-grandchild and the inbreeding VCFs contain only one set, so this identifier is always 1. This convention can be 1 or 2 for the rest of the pedigrees, as the VCF files contain two sets of related pairs.</p> <p><strong>_g*-b*-: </strong>Provides information about the individual's generational level within the VCF. This follows the Ped-sim syntax. For example, for parent-offspring type, "_g1-b1-" indicates the first parent (generation 1) within a specific pedigree, and "_g1-b2-" indicates the second parent (generation 1) while "_g2-b1-" represents the offspring (generation 2).</p> <p><strong>Example Naming Structure:</strong></p> <p>For instance, the file "cov1x_run1_parent-offspring_1_parent-offspring1_g1-b1-i1.all.hs37d5.cons.90perc.trimBAM.bam" signifies a BAM file with 1x coverage, originating from "run1," containing individuals from the "run_*_parent-offspring_1.vcf" file (first set of parent-offspring pairs) where "_g1-b1-" designates the first parent in the first generation. The latter half of the name "hs37d5.cons.90perc.trimBAM.bam" is the same across all files. </p> <p><strong>Note1:</strong> Segments such as <strong>parent-offspring*_g*-b*- </strong>can also be tracked in the naming of the genotype columns in the VCF.</p> <p><strong>Note2: </strong>Sexual information within the VCF files is discernible from the genetic data present at X chromosome positions. Individuals carrying two genotypes on the X chromosome are female, while those with a single genotype are male.</p> <p><strong>Note3: Some of the individuals from distinct pedigrees may</strong>,<strong> in fact</strong>,<strong> be related due to shared ancestry through common founders. To suit specific research objectives, researchers may need to identify and exclude such relatives if the full dataset is used for kinship estimation.</strong></p> <p>For more details about the dataset's generation process, unique characteristics, or any specific inquiries, our team is available for further information. We welcome and encourage inquiries, aiming to provide comprehensive support and additional details that might aid researchers in utilizing this dataset effectively. Please don't hesitate to contact us for any specific information you may need.</p> <p>This repository contains only cov5x BAM files (run1-6). The rest of the files can be found at <strong>10.5281/zenodo.10079625 </strong>and<strong> 10.5281/zenodo.10070958.</strong></p>
Auxiliary files and data to generate eddy flux and validate 2D model for MALTA
<p>This repository contains the following directories to accompany the manuscript 'A Zonally-Averaged Global Atmospheric Transport Model for Long-lived Trace Gases', submitted to JAMES:</p><p>1) <strong>GEOSChem </strong>This directory contains the run directory template and (slurm) runscript to generate the tracer fields used to generate the eddy fluxes. The GEOSChem model will have to be installed locally to run this, and the run directory built to your local area. It may be easiest to just copy the relevant bits in /Tracer_2D_template/ (i.e., the .rc files, /RestartFiles/, input.geos, reset_restart.py and species_database.yml) into a GEOSChem Transport run directory and change the directories in the copied files. If using slurm on an HPC, just change the directories in the runtracers_inputs.sh script to match that of your own HPC. Else, a different script will have to be written copying the slurm functionality.</p><p>2) <strong>GEOSChem_SF6 </strong>This directory contains the monthly mean SF6 mole fractions generated using GEOSChem used to validate the 2D model MALTA. Emissions come from the EDGAR v4.2 emissions inventory. Emissions after 2008 continue to use 2008 as the emissions value.</p><p>3) <strong>CFC11_inversion</strong> This directory contains the relevant script and files to quantify emissions of CFC-11 using an output mole fraction from the TOMCAT 3D model using MALTA, and compare these to the TOMCAT emissions used to generate the mole fractions. The directory paths at the beginning of the main script in CFC11_inversion.py must be changed to point to the remaining files in the /CFC11_inversion/ directory, and a save directory must be specified, before running locally. MALTA must be installed to run this.</p><p>4) <strong>singapore.dat </strong>This file contains the QBO winds above Singapore, taken from https://www.geo.fu-berlin.de/en/met/ag/strat/produkte/qbo/index.html</p><p> </p>
Europa Chaos Block Shapefiles and Geojson Files in Lower RegMap Images
<p>The included dataset includes the raw polygon shapefiles of the outlines for chaos blocks on Europa in the lower half of the RegMap images. The outlines were generated using the standard definitions of blocks and further subdivision in morphology of plates and knobs based on those previously published by Leonard et al. (2022) in which the author of this dataset is the same that created the majority of the Leonard et al. (2022) dataset. Images used to generate the outlines were the RegMap images within the Photogrammetrically Controlled Galileo Image Mosaics of Europa, produced by the USGS Astrogeology (Bland et al., 2021). The shapefiles do not include the entire metadata and will be uploaded at a later date, but information about chaos block morphology, area in sq km, lon/lat location of center, and chaos terrain location are included. Also included within this dataset are the Geojson files (produced by Marina Dunn) that complement the ArcMap shapefiles, so they could be implemented into other programs more easily. Both datasets have yet to be peer reviewed. </p><p> </p><p> </p><p><strong>References</strong></p><p>Leonard, E.J., Howel, S.M., Mills, A., Senske, D.A., Patthoff, D.A., Hay, H.C.F.C., and Pappalardo, R.T. (2022). Finding Order in Chaos: Quantitive Predictors of Chaos Terrain Morphology on Europa, Volume 49, Issue 8, doi: <a href="https://doi.org/10.1029/2021GL097309">10.1029/2021GL097309.</a></p><p>Bland, Michael T., Weller, Lynn A., Archinal, Brent A., Smith, Ethan, Wheeler, Benjamin H. (2021). Improving the Usability of Galileo and Voyager Images of Jupiter's Moon Europa, Earth and Space Science, Volume 8, Issue 12, doi: <a href="https://doi.org/10.1029/2021EA001935">10.1029/2021EA001935</a>.</p>
The Audio and Video Files of Handbook of Japanese Basic Verbs
<p>"KIHONDOUSHI HANDBOOK (Handbook of Japanese Basic Verbs) [基本動詞ハンドブッ ク] is a digital reference resource developed by the members of three collaborative research projects funded by the National Institute for Japanese Language and Linguistics (NINJAL), Tokyo, Japan during Oct. 2009 to March 2022. The reference work was developed with an aim to deepen the understanding of highly polysemous basic verbs in Japanese by way of providing detailed description of syntax and semantics of multiple meanings of the verb in question. To foster the ease of understanding, each meaning of a polysemous basic verb is illustrated with a couple of illustrative examples with audio and a few meanings, which are deemed to be difficult to understand, are illustrated with the help of audio-visual animations. The handbook consists of 190 headwords and includes 2,154 meanings, 12, 492 illustrative examples with audio and 521 audio-visual animations. On this site the audio and video files of the handbook is made available for researchers, teachers, and learners of Japanese language for the purpose of research on and education of Japanese polysemous basic verbs. Other data such as headword data will be available from the NINJAL repository site very soon.</p>
Ground truth and raw hyperspectral files of olive trees for plant stress detection
<p>This dataset contains raw hyperspectral images from Cubert S-185 collected on 13 May 2021 from an olive field in Halkidiki, Northern Greece. Included is also a matrix containing the id of each recorded olive tree (the samples) that also appears in the hyperspectral images. QGIS (ver.3.28.0) software plugin 'zonal statistics multiband' was used to compute zonal statistics for each of the 138 spectral bands available for each sample. Accompanying each sample is also the ground truthing data recorded, which addresses the present stress of 3 stressors (<i>Verticillium dahliae, Pleospora herbarum </i>and 'other stressors').</p>
Dataset and supplementary files - Behavioral response of chub (Squalius cephalus), barbel (Barbus barbus) and brown trout (Salmo trutta) to pulsed direct current electric fields and resulting optimal waveform for use at electrified bar racks
<p><strong>Behavior Library.zip: </strong>For each species and behavior observed during the experiments an exemplary video is provided. </p><p><strong>Behavior_all.pdf: </strong>Additional plots showing the thresholds for the first time each individual behavior was observed for all fish species and tested waveforms</p><p><strong>Species.pdf: </strong>Additional plot allowing direct comparison of observed thresholds for the tested species when subjected to different waveforms. </p><p><strong>data.csv:</strong> All data necessary to reevaluate the conducted experiments. The dataset consists of</p><ul><li>Experiment ID</li><li>waveform - indicating the set of electrical parameters used</li><li>fish species and fish id </li><li>behavior - observed behavior</li><li>time from and time to - time in s after the start of the experiment that a behavior was started and ended respectively</li><li>type - point or interval referring to whether a behavior is considered instantaneous or continuous</li><li>voltage - applied voltage at the start of the given behavior</li><li>experiment_timestamp - date and time of the start of the experiment</li><li>breathing rate start - breathing rate at the start of the experiment</li><li>water conductivity - water conductivity at a reference temperature of 25°C [muS/cm]</li><li>water temperature [°C]</li><li>breathing rate end - breathing rate at the end of the experiment</li><li>meta behavior - assigned category of meta behavior based on the observe behavior category</li><li>standard length, total length and height - standard length, total length and height of the tested fish in [mm]</li><li>volume - calculated fish volume based on the measured length and height and an assumed elliptical form of the fish</li><li>Fangdatum - Date of catch</li><li>t.Pulse - pulse length of the tested waveform [ms]</li><li>Frequency - Frequency of the tested waveform</li><li>N.Pulses.Group - Number of pulses per group of pulses for the waveform pattern</li><li>t.Gap - time between two pulses within a group of pulses [ms]</li><li>DutyCycle - Percentage of time current is flowing for a given waveform. Calculated based on the waveform parameters</li><li>usage - first, second or third time a fish was used in the experiments. </li><li>field strength - field strength at the time of this behavior calculated based on the applied voltage</li><li>c_w ambient water conductivity [muS/cm]</li><li>p_d - power density calculated based on the field strength and the ambient water conductivity</li><li>p_t - power transferred to the fish calculated based on the field strength, the ambient water conductivity and an assumed conductivity of the fish of 115 muS/cm</li></ul><p> </p><p> </p>
Supplementary files for: A dynamic 2000–540 Ma Earth history: From cratonic amalgamation to the age of supercontinent cycle
<p>Supplementary materials for the Earth-science Reviews paper 'A dynamic 2000–540 Ma Earth history: From cratonic amalgamation to the age of supercontinent cycle'. </p> <p>Supplementary Material 1 – Palaeomagnetic pole list for the ca. 2000–540 Ma interval.<br> Supplementary Material 2 – IGCP 440 pre-700 Ma geotectonic database (with minor corrections made) in shapefiles format<br> Supplementary Material 3 – Neoproterozoic sedimentary facies point data of Li et al. (2013) in shapefile format<br> Supplementary Material 4 – Generalised global large igneous province (LIP) database for 2010–0 Ma (after Ernst et al., 2021) in both shapefile and Excel formats<br> Supplementary Material 5 – Global passive margin database of (Bradley, 2008) in shapefile format<br> Supplementary Material 6 – Global orogen database of Condie et al. (2021) with minor modifications and in shapefile format<br> Supplementary Material 7 – Global 2000–540 Ma full-plate animation following the extended orthoversion principle, Scenario Ia (0-90W-0)<br> Supplementary Material 8 – Global 2000–540 Ma full-plate animation following the extended orthoversion principle, Scenario Ib (0-90E-0)<br> Supplementary Material 9 – 2000–540 Ma global animation highlighting the occurrence of LIP events in time and space, including possible plume centres.<br> Supplementary Material 10 – GPlates project files for the two alternative global 2000–540 Ma full-plate animations with associated geotectonic databases</p>
An efficient not-only-linear correlation coefficient based on clustering: Supplementary Files
<p>Supplementary Files for the manuscript "An efficient not-only-linear correlation coefficient based on machine learning" available at https://doi.org/10.1101/2022.06.15.496326</p> <ul> <li>Supplementary File 1: All pairwise gene correlations using Pearson, Spearman and CCC among the top 5,000 genes in GTEx’s whole blood with the largest variance. Columns indicates whether the gene pair was categorized in the top or bottom 30% of each coefficient, the correlation value, and the significance of the association. Significance is only present for the top 10 gene pairs of each intersection in the “Disagreements” group (Figure 3a, right) where CCC disagrees with Pearson, Spearman or both.</li> <li>Supplementary File 2: Percentiles of the coefficient values for the top 5,000 genes in GTEx’s whole blood.</li> <li>Supplementary File 3: Pearson, Spearman and CCC correlations values and their significance for two gene pairs (<em>UTY</em> - <em>KDM6A</em> and <em>DDX3Y</em> - <em>KDM6A</em>) across all tissues in GTEx.</li> </ul>
Data and configuration files for "Expansion of accreting main-sequence stars during rapid mass transfer"
<p>Data and configuration files that can be used to reproduce results from the paper <a href="https://ui.adsabs.harvard.edu/abs/2024ApJ...966L...7L/abstract">Expansion of Accreting Main-sequence Stars during Rapid Mass Transfer</a>. This directory contains MESA inlists and starting models used for calculations performed with MESA r15140, and YAML configuration files for calculations performed with COMPAS v02.41.04.</p> <p>See README.txt for a description of all files.</p> <p> </p> <p>Any work making use of these files should cite</p> <p>Lau, M., Hirai, R., Mandel, I., Tout, C., 2024, Expansion of Accreting Main-sequence Stars during Rapid Mass Transfer, ApJL, 966, 1</p> <div></div>
Design files for a low-cost high-resolution imaging device for hyphae in soil
<p>This dataset contains the stereolithography (STL) files for the 3D-printed and cut parts of a low-cost high-resolution imaging device for hyphae in soil called <em>Hyphascope</em>. The design of <em>Hyphascope</em> was adopted from the 3D printer i3 MK3S+ by Prusa Research, with a digital microscope camera (DMC; 600× magnification) replacing the filament extruder. Repeated imaging of a soil profile with the imaging device enables researchers to observe and quantify changes in the amount, distribution, and morphology of hyphae.</p> <p>The parts were created and modified using <a href="https://www.freecad.org">FreeCAD</a> (version 0.20). STL files for the original parts are distributed under the Creative Commons Attribution 4.0 International License, STL files for the remixed parts under the GNU General Public License v2.0. For a detailed description on how to prepare and assemble the parts see <a href="https://doi.org/10.17504/protocols.io.bp2l6xo3zlqe/v1">this protocol on protocols.io</a>. For information on the development, limitations, and expected outcomes of the protocol, see <a href="https://doi.org/10.1371/journal.pone.0318083">this article</a> published in PLOS ONE.</p> <p> </p> <div> <h2>STL files of 3D-printed parts</h2> <h3>Original parts</h3> </div> <div> <div> <ul> <li><em>dmc-attachment.stl</em></li> <li> <div><em>dmc-attachment-gear.stl</em></div> </li> <li><em>dmc-attachment-gear-wider.stl</em> (optional part)<em><br></em></li> <li><em>dmc-holder-back.stl</em></li> <li><em>dmc-holder-front.stl</em></li> <li><em>f-axis-motor-gear.stl</em></li> <li><em>f-axis-spring-end.stl</em></li> <li><em>f-axis-tighteners.stl</em></li> <li><em>frame-foot-inserts.stl</em></li> <li> <div><em>frame-foot-left.stl</em></div> </li> <li> <div><em>frame-foot-right.stl</em></div> </li> <li> <div><em>frame-hat.stl</em></div> </li> <li> <div><em>frame-hat-insert.stl</em></div> </li> </ul> </div> <h3>Remixed parts originally designed by Prusa Research</h3> <p><em>The five parts below are <strong>remi</strong></em><strong><em>xed from <a href="https://www.printables.com/model/57217-i3-mk3s-printable-parts">i3 MK3S+ printable parts</a> </em></strong><em>and </em><strong><em>re-distributed under the <a href="http://www.gnu.org/licenses/old-licenses/gpl-2.0.html">GNU General Public License v2.0</a></em></strong><em>.</em></p> </div> <ul> <li> <div><em>dmc-carriage-back.stl</em> (Remix of <em>x-carriage-back.stl</em>; the design was largely modified to fit the DMC including changes to the shape and screw hole placement; the inserts for the linear bearings have the most resemblence to the original part.)</div> </li> <li><em>dmc-carriage-front.stl </em>(Remix of <em>x-carriage.stl</em>; the design was largely modified to fit the DMC including changes to the shape and screw hole placement; the inserts for the linear bearings have the most resemblence to the original part.)</li> <li><em>x-end-idler-mod.stl</em> (Remix of <em>x-end-idler.stl</em>; the height was increased by 20 mm.)</li> <li><em>x-end-motor-mod.stl</em> (Remix of <em>x-end-motor.stl</em>; the height was increased by 20 mm and the counterbores of the three motor screws were moved to the opposite side.)</li> <li><em>z-axis-top-mod.stl </em>(Remix of <em>z-axis-top.stl</em>; 14.8 mm-long spacers were added.)</li> </ul> <h3>Parts designed by Prusa Research</h3> <ul> <li> <div><em>z-axis-bottom.stl</em> (available from <a href="https://www.printables.com/model/57217-i3-mk3s-printable-parts" target="_blank" rel="noopener">Printables</a>)</div> </li> <li> <div><em>z-screw-cover.stl</em> (available from <a href="https://www.printables.com/model/57217-i3-mk3s-printable-parts" target="_blank" rel="noopener">Printables</a>)</div> </li> </ul> <p> </p> <div> <h2>STL files of cut parts</h2> <h3>Original parts</h3> </div> <ul> <li><em>box-bottom.stl</em></li> <li><em>box-hook.stl</em></li> <li> <div><em>box-lid.stl</em></div> </li> <li> <div><em>box-lid-frame.stl</em></div> </li> <li><em>box-lid-valve-base.stl</em></li> <li><em>box-wall.stl</em></li> <li><em>box-wall-cables.stl</em></li> <li> <div><em>frame.stl</em></div> </li> </ul> <p> </p>
Supplemental Files for Schlegel et al., Nature (2024)
<p>This repository contains supplemental files for the paper "<strong>Whole-brain annotation and multi-connectome cell typing of Drosophila</strong>" - Schlegel <em>et al.</em>, Nature (2024).</p> <ul> <li><em>nblast_flywire_all_right_aba_comp.feather</em> contains all-by-all NBLAST score for all FlyWire neurons where neurons from the left hemisphere have been mirrored to the right</li> <li><em>nblast_flywire_hemibrain_min_comp.feather</em> <em> </em>contains NBLAST scores for FlyWire versus "hemibrain" neurons</li> <li><em>nblast_flywirre_mirrored_hemibrain_comp.feather</em> contains NBLAST scores for FlyWire versus "hemibrain" neurons where all FlyWire neurons have been mirrored</li> <li><em>sk_lod_783_healed_ds2.parquet</em> contains skeletons in SWC format for all FlyWire neurons (generated from lod 1 meshes and 2X downsampled, coordinates are in nanometres); the raw data can be read with e.g. the Python <a href="https://pypi.org/project/pyarrow/"><em>pyarrow</em></a> package (see <a href="https://arrow.apache.org/docs/python/parquet.html">documentation</a> for examples). Alternatively, you can use the <a href="https://github.com/navis-org/navis"><em>navis</em></a> Python package to read the contents into neuron objects (see <a href="https://navis-org.github.io/navis/reference/navis/#navis.read_parquet">navis.read_parquet).</a></li> </ul> <p>Additional notes:</p> <ul> <li>all root IDs refer to the 783 release of FlyWire</li> <li>for NBLAST files: <ul> <li>columns/indices for FlyWire neurons are given as "{root_id},{supervoxel_id}", where the supervoxel ID represents an anchor that can be used to map this neuron to different materialization versions</li> <li>scores were compressed by rounding to the 4th decimal and clipping values below 0</li> </ul> </li> </ul> <p>For neuron annotations and further details please see <a href="https://github.com/flyconnectome/flywire_annotations">https://github.com/flyconnectome/flywire_annotations</a>. </p> <p>The proofreading and FlyWire resource are described in our companion paper (Dorkenwald <em>et al.</em>, Nature, 2024).</p>
Bubble/Foam Simulations for Malej et al. 2023, source codes, input files, matlab files, data files
<p><i>.F are source codes, *.m are matlab scripts for analysis and postprocessing, .txt are data files including bathymetry and data from sensitivity tests</i></p>
Julia constitutive model integration replication files
<p>These files allow the user to check that their local version of Julia and the codes provided in the repository at <a href="https://github.com/nickcollins-craft/julia_constitutive_model_integration" target="_blank" rel="noopener">https://github.com/nickcollins-craft/julia_constitutive_model_integration</a> have successfully performed the integration and bifurcation analysis of a Cosserat Breakage Mechanics model. Each file is labelled with the integrator (h² or hyperplastic), the load condition (constant volume or constant confining stress) and whether it is an integration result (containing the mechanical information such as stresses and strains) or a localisation result (the wavelength corresponding to the largest value of the Lyapunov exponent, and a Boolean vector stating whether localisation has occurred or not). The files are in the jld2 format, which is read by Julia using the JLD2 and FileIO packages.</p>
Role of Volcano-Tectonic Interactions During Early-Phase Magma-Assisted Continental Rifting: Supplementary Model Files
<p>Input and output model files for the manual script titlted "Role of Volcano-Tectonic Interactions During Early-Phase Magma-Assisted Continental Rifting" submitted to Journal of Geophysical Research: Solid Earth.</p>
Supplementary Data Files for the paper "Intrinsically disordered compositional bias in proteins: Sequence traits, region clustering, and generation of hypothetical functional associations"
<div> <div> <div> <div> <p><strong>Supplementary data files relating to <a href="https://doi.org/10.1177/11779322241287485">https://doi.org/10.1177/11779322241287485. </a></strong></p> <p><strong><span>Suppl. File 1: Protein Family Clusters.</span></strong></p> <p><strong><span>Suppl. File 2: Cluster GO enrichments/depletions. </span></strong></p> <p><strong><span>Suppl. File 3: The raw ID-CBR data with annotations. </span></strong></p> <p><strong><span>Suppl. File 4: ­ID-CBR Cluster membership.</span></strong></p> <p><strong><span>Each file has an explanatory header. </span></strong></p> <p> </p> </div> </div> </div> </div>
Dataset and Input Files for the "Sustainability and Resilience Through Connection: The Economic Metacommunites of the Western USA" Manuscript
<p>Datasets and input files used for the Ecology and Society manusript "Sustainability and Resilience Through Connection: The Economic Metacommunites of the Western USA". </p>
Three Dimensional Multiscalar Neurovascular Nephron Connectivity Map of the Human Kidney Across the Lifespan - Supporting Movie Files
<p>This is a collection of movies related to the manuscript "Three Dimensional Multiscalar Neurovascular Nephron Connectivity Map of the Human Kidney Across the Lifespan" by McLaughlin et al to describe kidney organization using 3D light sheet fluorescence microscopy. The preprint manuscript associated with these movies is </p> <p>Three Dimensional Multiscalar Neurovascular Nephron Connectivity Map of the Human Kidney Across the Lifespan</p> <p>Liam McLaughlin, Bo Zhang, Siddharth Sharma, Amanda L. Knoten, Madhurima Kaushal, Jeffrey M. Purkerson, Heidy Huyck, Gloria S. Pryhuber, Joseph P. Gaut, Sanjay Jain</p> <p>bioRxiv 2024.07.29.605633; doi: <a href="https://doi.org/10.1101/2024.07.29.605633">https://doi.org/10.1101/2024.07.29.605633</a></p> <p>Movie Legends</p> <p>Movie 1: 3D view of the entire slice showing key structures.<br>3D light sheet fluorescence microscopy 5x movie of reference adult sample SK3, demonstrating glomeruli, collecting<br>ducts, nerves, and blood vessels. 0:00s — Raw signal. 0:10s — Segmentations. Annotations are in the movie.</p> <p><br>Movie 2: Relationship of nerves with glomeruli and juxtaglomerular apparatus.<br>The movie depicts innervation of glomeruli in 2D optical sections, containing glomeruli, Tuj1(labels TUBB3)-stained<br>nerves, and CGRP-stained sensory nerves. 0:22s — Innervation of the JGA. 0:33 s— Innervation of the Macula Densa.<br>0:47s — Innervation of the outer boundary of the Bowman’s Capsules.</p> <p><br>Movie 3: Neuro-nephron connectivity.<br>The movie explores innervation between different structures of the same nephron, and between nephrons in both 3D and<br>2D optical sections, containing glomeruli, Tuj1 (TUBB3)-stained nerves, CGRP-stained sensory nerves, proximal<br>(convoluted) tubule, thick ascending limb, distal convoluted tubule, and collecting duct. 0:00-1:53min — 3D<br>relationships. 0:38s — Innervation of glomerulus JGA. 1:02min — Post-JGA innervation of medullary ray structures.<br>1:54min-end — 2D relationships. 2:38min — Interglomerular/internephron innervation.</p> <p><br>Movie 4: Neurovascular – nephron patterns in the medulla.<br>The movie shows innervation pattern within the medulla. 0:00s—5x adult medullary innervation pattern in 3D;<br>0:34s—in 2D also showing Vasa Recta and Collecting Duct; 0:48s—in 3D at 20x resolution. 1:04min—20x adult<br>medullary innervation of proximal tubule, thick ascending limb, and Vasa Recta in 3D; 1:31min—view if the previous in<br>2D. 2:11min—5x adult medullary innervation pattern in 3D; 2:40min—in 2D also showing Vasa Recta and Collecting<br>Duct; 2:54min—in 3D at 20x resolution; 3:15—in 2D at 20x resolution.</p> <p><br>Movie 5: Network motifs.<br>Exploring 3D neuroglomerular networks at 5x and 20x resolution. 0:00s — Raw 5x signal from young adult sample SK2.<br>0:16s— Segmented 5x SK2 with 20x coregistrations. 0:26 — Exploring SK2 20x FOV. 0:38 — 20x network featuring<br>hourglass motif. 1:19 5x “Type I” network in SK2. 1:41 — Segmented 5x adult SK3 sample featuring a “Type 2” network<br>containing a lattice motif. 2:23 — Exploring SK3 20x FOV, featuring a network with a lattice motif.</p> <p><br>Movie 6: LSFM movie of pediatric kidney<br>3D lightsheet 5x image of neonatal sample SK414, containing glomeruli, collecting ducts, nerves, and blood vessels.<br>0:00s — Raw signal. 0:22s — Segmentations. 1:34min — Overlayed segmentations.</p> <p><br>Movie 7: Neuronephron connectivity time course<br>Exploring neuronephro-networks across a life time course in 1mm3 20x images. 0:00 — Raw neonatal. 0:17sec —<br>Segmented neonatal. 0:47 sec— Raw infant. 0:54 — Segmented infant with network. 1:13min — Raw young adult.<br>1:23min — Segmented young adult with network. 1:33min — Raw adult. 1:43min — Segmented adult featuring network<br>with keychain motif. 1:49min — Raw aged. 1:59min — Segmented aged with network featuring pyramid motif.</p> <p> </p> <p>Movie 8: Mother Glomeruli</p> <p>Evaluating distributions and innervation of mother glomeruli in neuroglomerular networks. 0:00 - Large 20x 3D Network sample SK1 FOV8. 0:13 - Sample SK1 5x Network in 2D. 0:36 - Mother glomerulus neural quantifications SK1. 0:41 Large 20x 3D Network sample SK3 FOV12. 0:56. Large 20x 2D Network sample SK3 FOV12. 1:21 - Mother glomerulus neural quantifications SK3.</p> <p> </p> <p>Movie 9: Segmentations</p> <p>Demonstrating accuracy of segmentations that combine supervised ML with manual validation in Sample SK2 FOV5. 0:00 - AQP2 labelled Collecting Duct and NPHS1 labelled Glomerulus. 0:26 - Tuj1 labelled nerve.</p> <p> </p> <p>metadata_analyzed_images:</p> <p>Metadata for images that were analyzed. Includes metadata .txt files for all stitched, downsampled samples, as well as .csv metadata for certain raw .czi files (pre-processing).</p>
Additional Phase Space Files of a Liac HWL linac
<p>Additional phase-space files (PSFs) calculated with <em>penEasy 2020</em> for the Liac HWL mobile accelerator (S.I.T.). This record complements the original record <a href="https://doi.org/10.5281/zenodo.14029134">https://doi.org/10.5281/zenodo.14029134</a> with the applicator diameters of 7, 9 and 12 cm.</p> <p><em>C7B0_12MeV</em> stands for applicator with a diameter of 7 cm, a 0º bevel ending and simulated with a beam energy of 12 MeV.</p> <p>NOTE: To recreate a realistic setup, the simulation should include a PMMA cylindrical applicator with the selected inner diameter and a wall thickness of 0.5 cm. This PSFs can be rotated to simulate beveled applicators.</p> <p>All files are provided in the IAEA PHSP format, including the corresponding header files, making them compatible with most Monte Carlo codes for radiation transport simulation.</p>
ABRomics genomic paired-end FASTQ data demo files
<p>This dataset contains the demo files for the <em>Genomic paired-end FASTQ</em> template of the ABRomics platform:</p> <ul> <li>Raw data: Paired-end Illumina sequencing files of sample ARDIG49.</li> <li>Metadata: Filled out <em>Genomic paired-end FASTQ</em> template for sample ARDIG49.</li> </ul>
Sensor Response Files for the Relativistic Proton Spectrometer aboard NASA's Van Allen Probes
<p>This data set provides the NASA Van Allen Probes Relativistic Proton Spectrometer (RPS) sensor response function files. These files provide the sensor’s response to protons and electrons as a function of energy and angle of incidence.</p>
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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.