Find research datasets worth reusing

opencc-by-4.0Dec 2022View details →

Microscopy data (2/2): interaction of the gene iscub with RNA polymerase II clusters in inhibitor-treated zebrafish embryos

Microscopy image data containing fluorescently labeled gene loci, recruited RNA polymerase II, and elongating RNA polymerase II. This data set is for the gene iscub and is obtained from fixed zebrafish embryos, collected at the sphere stage of development. Embryos were treated for 30 minutes prior to collection with control media, flavopiridol (10 µM, 30 minutes), JQ-1 (10 µM, 30 minutes), or hexanediol (3% weight/volume, 5 minutes). Data were recorded using an instant-SIM microscope (iSIM, VisiTech UK) with a 100X TIRF oil immersion objective (Nikon, NA 1.49, CFI SR HP Apo TIRF 100XAC Oil). Two samples were prepared per inhibitor condition, and images were recorded from 3-4 embryos per sample, as indicated in the file names. The image data are in the ND2 format (Nikon proprietary) and can be imported using the BioFormats importer (Open Microscopy Environment).

Theoretical analysis of correlations between two quantum fields exciting a three-level system using the cluster-expansion approach

Dataset of the publication "Theoretical analysis of correlations between two quantum fields exciting a three-level system using the cluster-expansion approach" H. Rose, O. V. Tikhonova, T. Meier, and P. R. Sharapova, Proc. SPIE 11999, Ultrafast Phenomena and Nanophotonics XXVI, 1199905 (2022). (  https://doi.org/10.1117/12.2608528 ). The zip file includes the data on which the plots shown in figures 1, 2, and 3 are based.

ArMoR Cluster: 7 research projects fight Antimicrobial Resistance in livestock farming (updated version)

Supported by the European Commission, Horizon Dissemination Booster (HRB) contributes to an effective transfer of research and innovation project results to policy makers, industry and society by offering various services as dissemination, exploitation strategy and business plan development to projects. Within Horizon Results Booster programme (HRB), 7 research projects AMRILS, AVANT, BM-FARM, FARMCARE, DISARM, HealthyLivestock and ROADMAP have formed the "ArMoR Cluster" to develop a conceptual framework to improve understanding of AMR in livestock systems. The video is available on YouTube: <a href="https://www.youtube.com/watch?v=ACbnyu3PhOY">https://www.youtube.com/watch?v=ACbnyu3PhOY</a> For any further questions please contact us at: <ul> <li><a href="https://zenodo.org/record/avant@rtds-group.com">avant@rtds-group.com</a> (project AVANT)</li> </ul>

Intermediary and supplemental data for publication "Heterogenous circulating miRNA changes in ME/CFS converge on a unified cluster of target genes and may be a result of modulation by latent herpesviruses: A computational analysis"

Intermediary and supplemental data for publication "Heterogenous circulating miRNA changes in ME/CFS converge on a unified cluster of target genes and may be a result of modulation by latent herpesviruses: A computational analysis"

Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters, data part 6

Part 6 of data for the article Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters.

Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters, data part 4

Part 4 of data for the article Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters.

Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters, data part 3

Part 3 of data for the article Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters.

Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters, data part 5

Part 5 of data for the article Giant worm-shaped ESCRT-scaffolds surround actin-independent integrin clusters.

Dataset for Runaway and Hypervelocity Stars from Compact Object Encounters in Globular Clusters

The dataset used for Cabrera & Rodriguez 2023.  If building from the showyourwork-enabled GitHub, the file can be directly unzipped into the <code>src/data</code> folder. The top-level contains folders for <code>CMC</code> model- and Milky Way globular cluster-delineated data (<code>cmc</code> and <code>mwgcs</code>, respectively), and some auxiliary files, including the composite catalogs.  Within the two folders are subfolders for each of the <code>CMC</code> models and MWGCs.  The <code>CMC</code> model folders contain some of the output files from the <code>CMC Cluster Catalog</code> <a href="https://ui.adsabs.harvard.edu/abs/2020ApJS..247...48K">(Kremer+20</a>) (used in this project to examine GC evolution), and also two files <code>output_N-10.txt</code> (which has data for all <code>Fewbody</code> realizations for the model) and <code>output_N-10_ejections.txt</code> (which has data for all ejections from the model).  The columns in the former file are regrettably not labeled, but correspond to the following parameters, many of which are direct <code>Fewbody</code> arguments: <table align="center"> <thead> <tr> <th scope="col">#</th> <th scope="col">Parameter</th> <th scope="col">Description</th> <th scope="col">Units</th> </tr> </thead> <tbody> <tr> <td>1</td> <td>time</td> <td>Physical time of encounter in <code>CMC </code>model</td> <td>Myr</td> </tr> <tr> <td>2</td> <td>b</td> <td>Impact parameter</td> <td>a1</td> </tr> <tr> <td>3</td> <td>vinf</td> <td>Velocity of single object at infinity</td> <td>v_crit</td> </tr> <tr> <td>4</td> <td>a1</td> <td>Initial semi-major axis of binary</td> <td>AU</td> </tr> <tr> <td>5</td> <td>e1</td> <td>Initial binary eccentricity</td> <td>-</td> </tr> <tr> <td>6</td> <td>vesc</td> <td>Local escape velocity in <code>CMC </code>model</td> <td>km/s</td> </tr> <tr> <td>7</td> <td>m10</td> <td>Mass of first binary component</td> <td>Msun</td> </tr> <tr> <td>8</td> <td>m11</td> <td>Mass of second binary component</td> <td>Msun</td> </tr> <tr> <td>9</td> <td>m0</td> <td>Mass of single object</td> <td>Msun</td> </tr> <tr> <td>10</td> <td>r10</td> <td>Radius of first binary component</td> <td>Rsun</td> </tr> <tr> <td>11</td> <td>r11</td> <td>Radius of second binary component</td> <td>Rsun</td> </tr> <tr> <td>12</td> <td>r0</td> <td>Radius of single object</td> <td>Rsun</td> </tr> <tr> <td>13</td> <td>k10</td> <td>BSE k-type of first binary component</td> <td>-</td> </tr> <tr> <td>14</td> <td>k11</td> <td>BSE k-type of second binary component</td> <td>-</td> </tr> <tr> <td>15</td> <td>k0</td> <td>BSE k-type of single object</td> <td>-</td> </tr> <tr> <td>16</td> <td>s</td> <td>Random seed for <code>Fewbody</code></td> <td>-</td> </tr> <tr> <td>17</td> <td>type_i</td> <td> Index classifying initial system (see below) </td> <td>-</td> </tr> <tr> <td>18</td> <td>type_f</td> <td>Index classifying final system (see below)</td> <td>-</td> </tr> <tr> <td>19</td> <td>v_crit</td> <td>Critical velocity of encounter (<a href="https://ui.adsabs.harvard.edu/abs/2004MNRAS.352....1F/abstract">Fregeau+04</a>)</td> <td>km/s</td> </tr> <tr> <td>20</td> <td>a_fin</td> <td>Final semi-major axis of binary (0 if no binary is present)</td> <td>AU</td> </tr> <tr> <td>21</td> <td>e_fin</td> <td>Final binary eccentricity (identically 0 if no binary is present)</td> <td>-</td> </tr> <tr> <td>22</td> <td>Lx</td> <td>x-component of the initial angular momentum of the system</td> <td>code</td> </tr> <tr> <td>23</td> <td>Ly</td> <td>y-component of the initial angular momentum of the system</td> <td>code</td> </tr> <tr> <td>24</td> <td>Lz</td> <td>z-component of the initial angular momentum of the system</td> <td>code</td> </tr> <tr> <td>25</td> <td>Lbinx</td> <td>x-component of the angular momentum of the initial binary</td> <td>code</td> </tr> <tr> <td>26</td> <td>Lbiny</td> <td>y-component of the angular momentum of the initial binary</td> <td>code</td> </tr> <tr> <td>27</td> <td>Lbinz</td> <td>z-component of the angular momentum of the initial binary</td> <td>code</td> </tr> <tr> <td>28</td> <td>Ei</td> <td>Initial energy of the encounter</td> <td>code</td> </tr> <tr> <td>29</td> <td>DeltaEfrac</td> <td>Fractional change in energy by the time of termination</td> <td>-</td> </tr> <tr> <td>30/34/38</td> <td>vfin0/1/2</td> <td>Final velocity of the final top-level object with<code> Fewbody </code>index 0/1/2 (<a href="https://ui.adsabs.harvard.edu/abs/2004MNRAS.352....1F/abstract">Fregeau+04</a>)</td> <td>v_crit</td> </tr> <tr> <td>31/35/39</td> <td>kf0/1/2</td> <td>BSE k-type of the same</td> <td>-</td> </tr> <tr> <td>32/36/40</td> <td>Rmin0/1/2</td> <td>Minimum distance between this object and any other object during the encounter</td> <td>AU</td> </tr> <tr> <td>33/37/41</td> <td>Rmin_j0/1/2</td> <td><code>Fewbody </code>index of the other object at closest passage</td> <td>AU</td> </tr> </tbody> </table> The initial encounter classifying indices are as follows, where "C" denotes a compact object and "S" a star: <table align="center"> <thead> <tr> <th scope="col">type_i</th> <th scope="col">Configuration</th> </tr> </thead> <tbody> <tr> <td>1</td> <td>(C,C)+S</td> </tr> <tr> <td>2</td> <td>(C,S)+C</td> </tr> <tr> <td>3</td> <td>(C,S)+S</td> </tr> <tr> <td>4</td> <td>(S,S)+C</td> </tr> </tbody> </table> The final encounter classifying indices are as follows, using the initial <code>Fewbody </code>object indices to specify if objects end up in a binary ((a,b)) or if they merge (a:b) (note that <code>Fewbody</code> initializes all binary-single encounters in the <code>type_f=3</code> configuration, i.e. the object index 0 is assigned to the single): <table align="center"> <thead> <tr> <th scope="col">type_f</th> <th scope="col">Configuration</th> </tr> </thead> <tbody> <tr> <td>0</td> <td>0+1+2 (Ionization)</td> </tr> <tr> <td>1</td> <td>(0,1)+2</td> </tr> <tr> <td>2</td> <td>(0,2)+1</td> </tr> <tr> <td>3</td> <td>0+(1,2)</td> </tr> <tr> <td>4</td> <td>0:1+2</td> </tr> <tr> <td>5</td> <td>0:2+1</td> </tr> <tr> <td>6</td> <td>1:2+0</td> </tr> <tr> <td>7</td> <td>0:1:2</td> </tr> <tr> <td>-2</td> <td>binary</td> </tr> <tr> <td>-3</td> <td>hierarchical triple</td> </tr> </tbody> </table> The columns in <code>output_N-10_ejections.txt</code> are labeled, and use many of the same headers in the first table; the object indices for fields 30-41 are dropped because each row in this file corresponds to an escaper.  The two additions are <code>mf</code> and <code>rf</code>, which indicate the mass and radius of the ejected object. Each of the <code>mwgcs</code> folders contain the FITS files described in Appendix B of the text. There are also <code>output_N-10_ejections.txt</code> files similar to the ones for the <code>CMC</code> models; the MWGC versions contain the additional fields below: <table align="center"> <thead> <tr> <th scope="col">Parameter</th> <th scope="col">Description</th> <th scope="col">Units</th> </tr> </thead> <tbody> <tr> <td>vout</td> <td>Velocity of object at the time of ejection from the representative model</td> <td>km/s</td> </tr> <tr> <td>X/Y/Z</td> <td>Galactocentric X/Y/Z coordinate of object at the present day</td> <td>kpc</td> </tr> <tr> <td>U/V/W</td> <td>Galactocentric U/V/W velocity of object at the present day</td> <td>km/s</td> </tr> </tbody> </table>

Open clusters in LISC 2: high Galactic latitude ones

The basic information of 56 new cluster candidates and the colour-magnitude diagrams of some ones that were fitted are given here.

Quantum chemistry reference data set for random hydrogen clusters

This data set contains high-level quantum chemistry data (CCSD(T)/def2-QZVPP) for a set of 120,000 randomly-generated hydrogen clusters, along with data from other levels of theory (HF, MP2, CCSD), including 3 density functionals (PBE, B3LYP, omegaB97M-V) and 4 semiempirical models (AM1, PM7, GFN1, & GFN2). This entry also includes the workflow scripts used to generate the data and the post-processing scripts used to analyze and visualize it. By the standards of quantum chemistry data sets, this is a large and challenging test for electronic structure methods and models. These structures tend to have open-shell ground states that can be difficult to find.

Diurnal ejection of boulder clusters on comet 67P lasting beyond 3 AU

Dataset for manuscript "Diurnal ejection of boulder clusters on comet 67P lasting beyond 3 AU". Files descriptions: 01. bouder_statistics.txt contains results from the photometric analysis of all 268 boulders identified in all ejection events column 1 - boulder index column 2 - event time (yy-mm-ddThh) column 3 - local time of ejection (hour) column 4 - heliocentric distance (au) column 5 - equivalent radius (m) column 6 - projected speed (m/s) column 7 -  acceleration (exists when more than one observation of the same boulder was found) column 8 - modelled surface time at the source region at the ejection time) 02. ejection_source.txt contains the coordinates of the inferred source point and the direction vector of its surface normal. 03. ellipsoidal_boulder_shape.obj is the face-vertex representation of the modelled ellipsoidal boulder and its surroundings 04. ellipsoidal_boulder_thermal.txt contains the modelled thermal condition of the ellipsoidal boulder at the time of observation of the event on 2016-05-07. It is formated as follows: column 1 - facet number column 2 - insolation (W m^-2) column 3 - surface temperature (K) column 4 - water flux rate (kg m^-2 s^-1) column 5 - surface pressure (Pa)

Science meets industry: Joint ArMoR Cluster Meeting

The joint event took place in Wageningen, Netherlands on the 16th of February 2023.  Supported by the European Commission, Horizon Dissemination Booster (HRB) contributes to an effective transfer of research and innovation project results to policy makers, industry and society by offering various services as dissemination, exploitation strategy and business plan development to projects. Within Horizon Results Booster programme (HRB), 7 research projects AMRILS, AVANT, BM-FARM, FARMCARE, DISARM, HealthyLivestock and ROADMAP have formed the "ArMoR Cluster" to develop a conceptual framework to improve understanding of AMR in livestock systems. The video is available on YouTube: <a href="https://youtu.be/uSE20DHrE7E">https://youtu.be/uSE20DHrE7E</a> For any further questions please contact us at: <ul> <li><a href="https://zenodo.org/record/avant@rtds-group.com">avant@rtds-group.com</a> (project AVANT)</li> </ul>

opencc-by-4.0Mar 2023View details →

Morphometric Trends and Implications for the formation of Araneiform Clusters Supplementary Table

Table of araneiform morphometric measurements used to produce plots in Figure 3 of manuscript.

Data for "Revealing the sources and sinks of negative cluster ions in an urban environment through quantitative analysis"

This file consists of the detection efficiency of APi-TOF, the time series of total negative cluster ions and CS in urban Beijing, and the average spectrums of negative clusters ions measured by APi-TOF during haze and clean periods in urban Beijing, which have been analyzed in the manuscript "Revealing the sources and sinks of negative cluster ions in an urban environment through quantitative analysis". For more details, please contact the author (rujing.yin@helsinki.fi).

opencc-by-4.0Mar 2023View details →

Artificial Sphere Clusters Transported on a Conveyor Belt Simulated by a Discrete Element Method

This data set comprises sphere clusters that model particles of construction and demolition waste consisting of brick and sand lime brick while they were transported on a conveyor belt. The motion behavior of the sphere clusters was obtained by a discrete element method (DEM) model of the small-scale optical belt sorter Tablesort. The files contain mid-points, radii, and classes of spheres that build sphere clusters, with each cluster modeling a particle. Input images are generated by rendering the sphere clusters in the camera field of view of the simulated area-scan camera. The particles have diameters from 4 to 8 mm. The simulated mass flows were 70 g per s for sand-lime brick and 30 g per s for brick. The belt velocity is approximately 1.1 m per s. Data is recorded at 2000 fps and covers a simulated time period of 120 s. A detailed description of the DEM model can be found in <ul> <li>Albert Bauer, Georg Maier, Marcel Reith-Braun, Harald Kruggel-Emden, Florian Pfaff, Robin Gruna, Uwe Hanebeck, Thomas Längle, Towards a Feed Material Adaptive Optical Belt Sorter: A Simulation Study Utilizing a DEM-CFD Approach, Powder Technology, October 2022.</li> </ul>  A thorough description of the Tablesort system can be found in <ul> <li>Georg Maier, Florian Pfaff, Christoph Pieper, Robin Gruna, Benjamin Noack, Harald Kruggel-Emden, Thomas Längle, Uwe D. Hanebeck, Jürgen Beyerer, Experimental Evaluation of a Novel Sensor-Based Sorting Approach Featuring Predictive Real-Time Multiobject Tracking, Transactions on Industrial Electronics, February 2020.</li> <li>See also the <a href="https://www.iosb.fraunhofer.de/en/projects-and-products/inside-schuettgut.html">project website</a>.</li> </ul> To this date, publications that used this data include <ul> <li> Marcel Reith-Braun, Albert Bauer, Maximilian Staab, Florian Pfaff, Georg Maier, Robin Gruna, Thomas Längle, Jürgen Beyerer, Harald Kruggel-Emden, and Uwe D. Hanebeck, GridSort: Image-based Optical Bulk Material Sorting Using Convolutional LSTMs, 22nd IFAC World Congress, Yokohama, Japan, July 2023. </li> </ul> The used CSV format uses semicolons as separators. There is no header. The first three columns correspond to the x-, y-, and z-coordinate of each sphere in meters, with increasing x-coordinate in the transport direction. The fourth column contains the radii in meters, the fifth column the particle class (2 for sand-lime brick and 1 for brick), and the sixth column the particle ids to which the spheres belong. The file name encodes the simulated time in steps of 0.5 ms. Each file contains as many rows as spheres are visible in the respective time step. The field of view of the simulated camera is 0.442 m - 0642 m in the x-direction and 0.005 m - 0.145 m in the y-direction. Acknowledgment The IGF project 20354 N of the research association Forschungs-Gesellschaft Verfahrens-Technik e.V. (GVT) was supported via the AiF in a program to promote the Industrial Community Research and Development (IGF) by the Federal Ministry for Economic Affairs and Climate Action on the basis of a resolution of the German Bundestag.

Inferring neutral winds in the ionospheric transition region from AGW-TID observations with the EISCAT VHF radar and the Nordic Meteor Radar Cluster

[Dataset] Inferring neutral winds in the ionospheric transition region from AGW-TID observations with the EISCAT VHF radar and the Nordic Meteor Radar Cluster

Data from: Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians.

This repository contains genetic sequences obtained from Hybrid-Enrichment and RAD sequencing protocols of the amphibian genera Discoglossus, Lissotriton, Rana and Triturus, as well as phylogenetic trees inferred from the RADseq data. This data was generated for the manuscript "Exploring the impact of read clustering thresholds on RADseq-based systematics: an empirical example from European amphibians.", in which we tested the influence of the clustering threshold used to assemble RADseq data on downstream phylogenetic inferences. Details on the data generation and analyses can be found in the manuscript and related supplementary materials. The repository is organised as follow: -> Hybrid-Enrichment: alignments of the Hybrid-Enrichment markers in phylip/fasta format (with one subdirectory for each of the four datasets assembled: Discoglossus, Lissotriton, Rana, Triturus) --> RADseq: Assemblies and phylogenetic trees obtained from a RADseq protocol     --> Assemblies: RADseq assemblies (complete loci sequences and SNP matrices, spreadsheets with assembly metrics). Divided into "iCT" (assemblies produced with 23 different intra-sample Clustering Threshold [iCT] and a fixed between-samples Clustering Threshold [bCT]) and "bCT" (assemblies produced with a fixed iCT and 23 different bCT). Both iCT and bCT are further divided in four sub-directories corresponding to the four datasets: Discoglossus, Lissotriton, Rana, Triturus)     --> Trees: Phylogenetic trees inferred from the aforementionned assemblies. Divided into "iCT" (RAxML concatenation trees inferred from the assemblies with different iCTs) and "bCT" (RAxML concatenation trees and Tetrad species trees inferred from the assemblies with different bCTs).

Datasets used in Consensus Clustering Problem in Single-cell Transcriptome Data Analysis

20 benchmark scRNA-seq datasets used in Consensus Clustering Problem in Single-cell Transcriptome Data Analysis. In every datasets .zip files, it provided raw data files, the processed R code and the corresponding R objects. The datasets.xlsx file provided the detailed information of 20 datasets.