Find research datasets worth reusing

opencc-by-4.0Apr 2024View details →

Supplemental data for the publication: "Algal methylated compounds shorten the lag phase of Phaeobacter inhibens bacteria"

Data S1: P. inhibens feature table (genes) with results from co-cultivation RNA-sequencing run. The dataset includes bacterial gene accession numbers, functional annotations, transcript abundances (TPM normalized read counts) and results of DESeq2 differential gene expression analysis. (Fig. 1, figs. S1A, S3-S4, tables S1-S2).  Data S2: P. inhibens feature table (genes) with results from lag phase RNA-sequencing run. The dataset includes bacterial gene accession numbers, functional annotations, transcript abundances (TPM normalized read counts) and results of DESeq2 differential gene expression analysis. (Fig. 4A, figs. S10-S13, tables S6-S7).  Data S3: Emiliania huxleyi CCMP3266 sGenome gene annotation file version 2 (GFF3 format). Data S4: Feature quantification obtained using Compound Discoverer. The table presents the output analysis using Compound Discoverer (v3.3) with a putative identification of metabolites. Each identified metabolite (each row) contains a sub-table under the + tab (on the left side) that specifies the feature quantification in each analyzed sample. Sample ID appears in the “Study File ID” column in each sub-table. Values in the columns “Exchange Rate [%]: 0” and “Exchange Rate [%]: 1” represent relative abundances of the molecules in their unlabeled form and with single 13C-label (M+1 isotopologue), respectively. Compounds marked with “1” in the “Tags” column were further validated using standards. The average M+1 isotope abundance [%] for S-Adenosylmethionine (SAM) and 5'-S-Methyl-5'-thioadenosine (MTA)—as reported in Fig. 4D—were calculated by averaging the values in the “Exchange Rate [%]: 1” column from samples supplemented with 13C-labeled and unlabeled DMSP, respectively. Detailed information regarding the isotope abundances of SAM and MTA can be found in the tab “SAM and MTA isotope abundance” in the table. In the tab “Features Positive Mode” samples F10, F12, F14, and F16 were supplemented with 13C-labeled DMSP and samples F2, F4, F6, F8 were supplemented with unlabeled DMSP. In the tab “Features Negative Mode” samples F2, F3, F4, and F5 were supplemented with 13C-labeled DMSP and samples F10, F11, F12, F13 were supplemented with unlabeled DMSP.

opencc-by-4.0Apr 2024View details →

Supplement to Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction

This repository contains the supplementary files for: Allen BJ, Volkova Oliveria MV, Stadler T, Vaughan TG, Warnock RCM. 2024. Mechanistic phylodynamic models do not provide conclusive evidence that non-avian dinosaurs were in decline before their final extinction. Cambridge Prisms: Extinction. Description of files This repository contains the cleaned tree files, tables of age constraints, XML files for running the analyses in BEAST2, and R code to process the datasets. Benson1clean.tree, Benson2clean.tree, Lloyd1clean.tree, Lloyd2clean.tree - the cleaned tree files containing the phylogenies inputted into BEAST2, with tip names matched to age data from the Paleobiology Database Tree modifications log.xlsx - a description of the modifications made to each input phylogeny compared to their state in the data supplement of their original papers dinosaur_ages.csv - the raw dinosaur age data downloaded from the Paleobiology Database tip_constraints.csv - the dinosaur age data converted into a format to input into BEAST2, to provide age constraints for tips change_times.txt - a text file describing the change times for the piecewise constant trajectories in the two phylodynamic analyses BDSKY.xml, PiecewiseCoalescent.xml - XML files describing the BEAST2 configuration for each of the two phylodynamic models BDSKY_logs.zip, BDSKY_trees.zip, Coalescent_logs.zip, Coalescent_trees.zip - compressed folders containing the output log files and inferred phylogenies for each of the 16 analysed phylogenies Supplementary_tables.zip - Tables containing summary statistics for each of the parameters inferred in each of the models Description of R code The R code is subdivided into the following files: Wrangle_trees.R - code for checking, cleaning, and splitting the phylogenies used in the analyses PBDB_tip_constraints.R - code for converting the raw age data from the Paleobiology Database into a format ready for input into BEAST2 as tip constraints BDSKY_post_processing.R, Coalescent_post_processing.R - code for cleaning and plotting data from the BEAST2 log files, for each of the two phylodynamic models

Projecting climate and socioeconomic contributions to global flood-induced displacements using a data-driven approach - Data Supplement

This contribution contains data and analysis scripts for the manuscript "Projecting climate and socioeconomic contributions to global flood-induced displacements using a data-driven approach" by Lenin Del Rio Amador, Mathieu Boudreault and David A. Carozza.

Supplemental Material for "Anomalous Shear Stress Variation in Wet Granular Medium: Implications for Landslide Lateral Faults"

Dataset and Constrained Parameters for "Anomalous Shear Stress Variation in Wet Granular Medium: Implications for Landslide Lateral Faults" by Chang et al. This dataset comprises 64 rheological experiments, which have been encapsulated in four experimental groups: Full Height, Half Height, Half Height & Load, and Ethanol-Water.  The experiments were conducted using a double-cylinder geometry on three-phase granular media to simulate the lateral faults of slow-moving landslides. The dataset includes Mechanical Data for time-evolution measurements of shear stress, fluid volume fraction under varying conditions, and Image Data for velocity fields derived from PIV (Particle Image Velocimetry) analysis. In addition, it provides constrained parameters, such as steady-state shear stress and the characteristics of the flow structure. Article information: <div> <div>Chang, C., Ohno, K., Schulz, W. H., & Yamaguchi, T. (2025). Anomalous Shear Stress Variation in Wet Granular Medium: Implications for Landslide Lateral Faults. Geophysical Research Letters, 52(7), e2024GL113816. <a href="https://doi.org/10.1029/2024GL113816">https://doi.org/10.1029/2024GL113816</a></div> </div>

opencc-by-4.0Dec 2022View details →

EvoWeaver Supplemental Datafiles

This dataset contains additional files related to EvoWeaver. The following are included: <ul> <li>ProteinComplexTrees.RData: All phylogenetic trees for Complexes benchmark. These are stored in a list object with one tree per gene group.</li> <li>ModulesEvoWeaver.RData: EvoWeaver object for Modules benchmark, containing phylogenetic trees for the Modules and Multiclass benchmark. `ModulePredAllPairs.RData` was made using this object.</li> <li>CORUM_Blast_Results.RData: All results from pairwise BLAST of proteomes against human reference genes.</li> <li>CORUM_proteomes.zip: all proteomes for all organisms used. Some of these are length 0, if an assembly could not be programatically found or retrieval failed to work.</li> <li>CORUMOrthogroupsWithIndices.RData: Orthogroups for the CORUM benchmark with gene index data included</li> <li>KOsWithPositions.RData: Gene index data for KO groups used in this study</li> <li>ModsWithPositions.RData: Gene index data for modules used in this study</li> <li>AllKEGGModules.RData: KEGG module taxonomy, names, and pathways for all modules used at time of download</li> <li>KEGGModuleComplexes.RData: All complexes in a KEGG module at time of download</li> <li>KEGGModuleDefinitions.RData: All KEGG module definitions at time of download</li> <li>ModulesPositionData.RData: Gene index information for Modules benchmark</li> <li>COG.links.detailed.v12.0.txt.tar.gz: STRING evidence streams between COGs (compressed, 1.44GB uncompressed)</li> <li>COG.mappings.v12.0.txt.tar.gz: STRING COG definitions (compressed, 5.80GB uncompressed)</li> <li>AllHumanGenes.fa: Human gene sequences used for BLASTing against in the CORUM benchmark</li> <li>AllKEGGCDSs.RData: all sets of available genes from all genomes used in KEGG.</li> <li>corum_bitscores.tsv: corum bitscores used as inputs to CladeOScope</li> <li>corum_npp.tsv: corum normalized phylogenetic profiles used as inputs to CladeOScope</li> <li>EukaryoteEWData.RData: Same as ModulesEvoWeaver.RData, but restricted to only eukaryotic sequences</li> </ul> Note that internal algorithm names may not exactly match those in published material due to computational requirements (e.g., difficulty naming functions/variables with special characters). See the <a href="https://github.com/WrightLabScience/EvoWeaver-ExampleCode/blob/1afeb5936470833a74cc2104994f54b363cc1103/README.md" target="_blank" rel="noopener">GitHub</a> page for a description of which internal names correspond to algorithms in the text.

Supplemental Material for Astrangia poculata genome assembly

Supplementary Table S5: GO annotations for the 143 terms enriched in the gene families unique to A. poculata relative to all other cnidarians included in this analysis (see Supplementary Table S2).   Supplementary Table S6: The gene annotations for all genes included in the gene families that were significantly different in size between A. poculata and A. millepora. Supplememtary Table S7: GO annotations for significantly enriched terms in the 73 gene families that were significantly larger in A. millepora relative to A. poculata. Supplememtary Table S8: GO annotations for significantly enriched terms in the 97 gene families that were significantly larger in A. poculata relative to A. millepora.

Supplemental Information on the Weighted Gene Co-expression Network Analysis performed for the work "Time-resolved oxidative signal convergence across the algae–embryophyte divide"

Supplemental Information on the Weighted Gene Co-expression Network Analysis (WGNCA) performed for the work "Time-resolved oxidative signal convergence across the algae–embryophyte divide" The results are sorted by the three species analysed: the two algae Zygnema circumcarinatum SAG 698-1b (Zygnema) and Mesotaenium endlicherianum SAG 12.97 (Mesotaenium); and the bryophyte Physcomitrium patens strain Gransden 2004 (Physcomitrium).

openother-pdFeb 2024View details →

PUDL Raw EIA Form 176 -- Annual Report of Natural and Supplemental Gas Supply and Disposition

The EIA Form 176, also known as the Annual Report of Natural and Supplemental Gas Supply and Disposition, describes the origins, suppliers, and disposition of natural gas on a yearly and state by state basis. Archived from <a href="https://www.eia.gov/naturalgas/ngqs/">https://www.eia.gov/naturalgas/ngqs/</a> This archive contains raw input data for the Public Utility Data Liberation (PUDL) software developed by <a href="https://catalyst.coop">Catalyst Cooperative</a>. It is organized into <a href="https://specs.frictionlessdata.io/data-package/">Frictionless Data Packages</a>. For additional information about this data and PUDL, see the following resources: <ul> <li><a href="https://github.com/catalyst-cooperative/pudl">The PUDL Repository on GitHub</a></li> <li><a href="https://catalystcoop-pudl.readthedocs.io">PUDL Documentation</a></li> <li><a href="https://zenodo.org/communities/catalyst-cooperative/">Other Catalyst Cooperative data archives</a></li> </ul>

opencc-by-4.0Mar 2024View details →

Supplemental Material: High serological barriers may contribute to restricted Influenza-A-virus transmission between pigs and humans

Human-to-swine (reverse zoonotic) transmission of seasonal and pandemic human influenza A viruses (IAV) to pigs primarily replenishes the vast reservoir of genetically and antigenically heterogeneous swine (sw) IAV maintained in domestic pigs worldwide. Sporadic but regularly observed cases of pig-to-human (zoonotic) infections with swIAV tend to be discovered by chance, with children being affected disproportionately often. Here, a total of 3070 porcine and 333 human nasal swab samples from 135 swine farms in Germany were investigated for IAV by real time RT-PCR and full genome sequencing. In addition, swIAV sequences generated in the frame of this study were analyzed to determine potential mutations for human MxA and BTN3A3 escape.  <div> 01_Table S1: Summary of information of swine holdings and RT-qPCR results. 1 indicates applicable; 0 indicates not applicable; n.d. indicates not determined. 02_Table S2: Summary of information about human samples and. 1 indicates applicable; 0 indicates not applicable; n.d. indicates not determined. 03_Table S3: A. Comparison of relevant mutations in the genome of MWP/21, swine-MWP/21, and NRW/22 generated by Flusurver (http://flusurver.bii.a-star.edu.sg). 1 indicates the presence of mutation(s), 0 indicates the absence of those mutation(s). B. Visualization of the AA differences of affected segments of the zoonotic case MWP/21 and the corresponding sequence (sw-MWP/21) generated from pigs of the related herd.  04_Table S4: Accession number (EPI_ISL) of sequences analyzed in the frame of this study. All sequences are available on GISAID EpiFLU. 05_Table S5: Amino acids on positions in the nucleoprotein (NP) sequence associated with MxA resistance and BTN3A3 resistance of selected swIAV NP sequences. "av) indicates genome segments phylogenetically associated with the avian-derived H1 (1C), "pdm" indicates those of the human pandemic A/H1N1 2009 lineage (1A).  06_Figure S1:  Phylogenic tree of swIAV H1 HA gene of the clades 1A, 1B and 1C annotated by global H1-lineage nomenclature by Anderson et al. (2016). Swine derived swIAV sequences generated in the frame of this study are colored in red, zoonotic cases MWP/21 and NRW/22 are colored in green.  The reverse-zoonotic case is highlighted in violet with its closest related human sequence colored in green. 07_Material and Methods: Description of material used and specification of applied methods in the frame of this study. 08_Questinonaire human participants: Questionaire used in the frame of this study. 09_Questinonaire swine farms: Questionaire used in the frame of this study. </div>

opencc-by-nc-nd-2.0Jun 2024View details →

Video Supplement for Himes et al. (2024): "Using neural networks for near-real-time aerosol retrievals from OMPS Limb Profiler measurements"

This archive contains the video supplement for Using neural networks for near-real-time aerosol retrievals from OMPS Limb Profiler measurements by Himes et al. (2024), submitted to Atmospheric Measurement Techniques.  The file contains an animation of the V2.1 and NRT average retrieved extinction coefficient between 19.5--21.5 km at 997 nm for the 2024 Ruang eruptions.

Supplement for "Mesoscopic hydrodynamic model for spreading, sliding and coarsening compound drops"

This repository contains the data sets and source code corresponding to the following publication   Diekmann, J. and Thiele, U. “Mesoscopic hydrodynamic model for spreading, sliding and coarsening compound drops” Phys. Rev. Fluids 10, 024002, 2025 DOI: <a href="https://doi.org/10.1103/PhysRevFluids.10.024002">https://doi.org/10.1103/PhysRevFluids.10.024002</a>   Please consider the README for more details.

Supplemental materials to "A quasi-2D model of convectively coupled vortices"

math_derivation_note: A hand-written note of key mathematical steps, mostly about section 4 and Appendix C.  quasi-2D model.zip: The package of the quasi-2D model code. postprocess_code_quasi2D.zip: The package of the postprocessing codes and intermediate files (.mat) related to the quasi-2D simulations. postprocess_code_CM1.zip: The package of the postprocessing codes and intermediate files (.mat) related to the CM1 simulation. Group_dh.avi: The Group-dh experiments with varying convective intermittency (dh/H). The first, second, and third column shows Group-dh-1, Ref, and Group-dh-2. Only the first member of each experimental ensemble is shown. The first row shows the raw vorticity normalized by f. The second shows the Gaussian-filtered vorticity (with a length scale of l=30 km) normalized by f. The black contour is the zero-value contour of the Gaussian-filtered vorticity. Group_dL.avi: The Group-l experiments with varying convective filter length l. The first, second, and third column shows Ref (l=30 km), Group-l-1 (l=45 km), and Group-l-2 (l=60 km). Only the first member of each experimental ensemble is shown. The first row shows the raw vorticity normalized by f. The second shows the Gaussian-filtered vorticity (with a length scale of l) normalized by f. The black contour is the zero-value contour of the Gaussian-filtered vorticity. Group_fE.avi: The Group-fE experiments with varying Coriolis parameter f and Ekman number E. They differ in the strength of the rotational flow. The first, second, and third column shows Group-fE-1 (f=1e-5 1/s), Ref (f=1e-4 1/s), and Group-fE-2 (f=2e-4 1/s). Only the first member of each experimental ensemble is shown. The first row shows the raw vorticity normalized by f. The second shows the Gaussian-filtered vorticity (with a length scale of l=30 km) normalized by f. The black contour is the zero-value contour of the Gaussian-filtered vorticity. Group_eta.avi: The Group-eta experiments with varying mesoscale feedback parameter eta. They differ in the strength of the mesoscale feedback. The first, second, and third column shows Group-eta-1 (eta=0), Group-eta-2 (eta=1.2), and Group-eta-3 (eta=1.4). Only the first member of each experimental ensemble is shown. The first row shows the raw vorticity normalized by f. The second shows the Gaussian-filtered vorticity (with a length scale of l=30 km) normalized by f. The black contour is the zero-value contour of the Gaussian-filtered vorticity. Please contact Dr. Hao Fu (haofu@uchicago.edu) if you have any questions!

Supplemental datasets for 'A near telomere-to-telomere phased reference assembly for the male mountain gorilla (Gorilla beringei beringei)'

The endangered mountain gorilla Gorilla beringei beringei faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for a male mountain gorilla generated using Pacbio HiFi and Oxford Nanopore Ultralong data. The resulting assembly exhibits exceptional contiguity, with contig N50 of ~ 95 Mbps for the combined pseudohaplotype (3,540,458,497 bps, and 56.5 Mbps (3.1 Gbps) and 51.0 Mbps (3.2 Gbps) for the maternal and paternal haplotypes and an average QV of 65.15 (error rate = 3.1 x 10-7). These represent substantial improvements over most other available primate genomes. This high-quality reference genome provides an invaluable resource for future studies on gorilla evolution, adaptation, and conservation, ultimately contributing to the long-term survival of this iconic species. A preprint for this work is available at bioRXiv, doi: https://doi.org/10.1101/2024.10.28.620258

Searching for non-English literature may be unnecessary for HTA Reports - supplemental material

Open the record for dataset details and reuse information.

opencc-by-4.0May 2024View details →

Supplemental materials to "A Laboratory Analogy for Mixing by Shallow Cumulus Convection"

These are the supplemental materials to the paper "A Laboratory Analogy for Mixing by Shallow Cumulus Convection" published in Journal of Fluid Mechanics. DOI: 10.1017/jfm.2025.173   <ul> <li>code_raw_data_video_temperature.zip  -  The MATLAB postprocessing code, raw video, and raw temperature profile data.</li> <li>reference_exp_S3_evolution_show.mp4  -  An introductory movie of the reference experiment (S3) with an illustration. </li> <li>change_heating_voltage_F1(speed_x_5.76)_F5.mp4  -  A movie about experiments that change the heating power. Experiment F1 (left panel) is accelerated with a factor of 5.76.</li> <li>change_initial_thickness_T2_T4_T5_(all_speed_x_16).mp4  -  A movie about experiments that change the initial thickness of the syrup layer. All experiments are accelerated with a factor of 16.</li> <li>change_syrup_concentration_S1_S3_S7_(all_speed_x_16).mp4   -  A movie about experiments that change the initial syrup concentration. All experiments are accelerated with a factor of 16. </li> <li>derivation_note.pdf  -  A math derivation note for some equations in the manuscript.</li> </ul> If you have any questions, please contact Dr. Hao Fu: haofu736@gmail.com; haofu@uchicago.edu

Evaluating Augmented Reality Light Probe Estimation Techniques using a Single Camera (Supplemental Material)

This repository contains the dataset for the paper "Evaluating Single Camera Augmented Reality Light Probe Estimation Techniques". The data archive includes: <ul> <li>The complete image set (3 scenes with 6 techniques and ground truth in 90 time points)</li> <li>SSIM data of the panoramas as a CSV file</li> <li>SSIM data of the rendered images as a CSV file</li> <li>Various graphs to visualize the data</li> <li>R files used to plot the graphs</li> </ul> The data archive includes additional plots that are not included in the paper.

CEA 2021-0486 Supplemental Data

Supplemental Data for CEA 2021-0486

Supplemental idf files used for paper "Refurbishmet Methodology to Attain Thermally Comfortable near-Zero Energy Buildings Using Customizable Solutions"

These are the idf files used to study different technology alternatives offered by the Reco2st project on an idealized dormitory room located in London, UK. The files are presented "as is" and were done for EnergyPlus v8.9. Includes files that might have not made it to the final paper. Geometry: One zone room with one external window. Materials: External construction is cavity wall, with bricks on both sides, gypsum plaster on internal side Internal walls brick single layer with gypsum plaster. Ceiling and floor reinforced concrete. Plaster finish on ceiling, nylon carpet on floor Double glazed window. Five panes available: one large central fixed, two small clerestory opening, and two large side opening. For simulation purposes a single equivalent area of all openings modelled. Material data sources: gov.scot, puravent.co.uk, nature.com. SHGC from LBL. This is part of work done for ReCO2ST - Residential Retrofit assessment platform and demonstrations for near zero energy and CO2 emissions with optimum cost, health, comfort and environmental quality. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 768576.

Integration-based Extraction and Visualization of Jet Stream Cores - Supplemental Video

Supplemental video for the publication "Integration-based Extraction and Visualization of Jet Stream Cores", which extracts jet stream core lines from ERA5 data using a predictor corrector algorithm.