Find research datasets worth reusing

Supplementary data to Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022

ZIP folder containing supplementary files to the article entitled Analyzing and Modeling the Spread of SARS-CoV-2 Omicron Lineages BA.1 and BA.2, France, September 2021–February 2022 and published in Emerging Infectious Diseases with doi <a href="https://dx.doi.org/10.3201/eid2807.220033">10.3201/eid2807.220033</a> <ul> <li>Script_EID_1.R is the R script analysing the data_EID1.csv screening test data file (Figure 1 and Suppl Figure F1, and Tables 1 and 3).</li> <li>Script_EID_2.R is the R script analysing the data_EID2.csv screening test data file (Figures 2, 3, 5, and Suppl Figure F2, and Table 2).</li> <li>Script_EID_sequencing_raw.R is the R script analysing the data_EID_sequencing.csv sequencing data file (Figures 4, 5, and Suppl Figure F3).</li> </ul>

Supplementary Data for "Steric and electronic origins of fluorescence in GFP and GFP-like proteins"

Data accompanying "Steric and electronic origins of fluorescence in GFP and GFP-like proteins" under consideration at JACS.

Supplementary data for 'scROSHI - robust supervised hierarchical identification of single cells'

This record contains some of the supplementary files for the manuscript "scROSHI - robust supervised hierarchical identification of single cells" by Prummer et al. The file "scROSHI_Fig03_counts.zip" contains SingleCellExperiment R objects as RDS files, "sce_A.RDS", "sce_B.RDS", "sce_C.RDS", corresponding to the three samples shown in Figure 3. The 'assay' slot of the SingleCellExperiment objects contains the gene x cell raw count matrix, the 'colData' slot contains the description for each cell: barcode, celltype_major, celltype_final, cnv_status. Please see https://github.com/ETH-NEXUS/scROSHI for code generating the cell type labels.

Policy choices and outcomes for offshore wind auctions globally - Supplementary Data

This is the dataset to the academic paper with the title: "Policy choices and outcomes for offshore wind auctions globally" Please cite the dataset as follows: Jansen,M.; Beiter, P.;Riepin, I. Müsgens, Felix; Juarez Guajardo-Fajardo, Victor, Staffell, I.; Bulder, B.; Kitzing, L. (2022) Policy choices and outcomes for offshore wind auctions globally. Energy Policy. DOI: https://doi.org/10.1016/j.enpol.2022.113000

Supplementary Material. Radiogenic isotope data of K-feldspars from Sveconorwegian pegmatites and granites.

Supplementary Material Radiogenic isotope data of K-feldspars from Sveconorwegian pegmatites and granites as part of the part of the paper Lead isotopes and the sources of granitic magmas: The Sveconorwegian granite and pegmatite province of southern Norway by Rosing-Schow, N., Andersen, T., Müller, A. submitted to MDPI Minerals.

Data, scripts and supplementary information for analysis of the functioning of a three-species microcosm under cadmium pressure

Data files of different experiments conducted with a three-species microcosm + Rscript for infering paremeters from a mechanistic EDO based model describing the functioning of the microcosm and the effect of cadmium + JAGS script of the model + supplementary information

opencc-zeroJun 2022View details →

dryad36/100

Supplementary data for: From genomics to integrative taxonomy? The case study of Pocillopora corals

With the advent of genomics, sequencing thousands of loci from hundreds of individuals now appears feasible at reasonable costs, allowing complex phylogenies to be resolved. This is particularly relevant for cnidarians, for which insufficient data due to the small number of currently available markers, coupled with difficulties in inferring gene trees and morphological incongruences, encrypts species boundaries, thereby blurring the study and conservation of these organisms. Yet, can genomics alone be used to delimit species in an integrative taxonomic context? Here, focusing on the coral genus Pocillopora, which plays key roles in Indo-Pacific reef ecosystems but has challenged taxonomists for decades, we explored and discussed the usefulness of multiple criteria (genetics, morphology, biogeography and symbiosis ecology) to delimit species of this genus. Phylogenetic inferences, clustering approaches and species delimitation methods based on genome-wide single-nucleotide polymorphisms (SNPs) were first used to resolve Pocillopora phylogeny and propose genomic species hypotheses from 356 colonies sampled across the Indo-Pacific (western Indian Ocean, tropical southwestern Pacific and south-east Polynesia). These species hypotheses were then compared to previous genetic evidences, as well as to evidences based on morphology, biogeography and symbiosis. Genomics allowed to delimit 21 species hypotheses where only seven are currently recognised based on current taxonomy. Moreover, 13 species were strongly supported by all approaches, either confirming their currently recognised species status, or supporting the presence of new species that need to be formally described. Some of the other genomic species hypotheses were supported by biogeographic or symbiosis evidences, but additional investigations are needed to state on their species status. Altogether, our results support (1) the obsolescence of macromorphology (i.e., overall colony and branches shape) but the relevance of micromorphology (i.e., corallite structures) to refine Pocillopora species limits, (2) the need to identify molecularly species prior to their study, as morphology can blur species identification on the field, (3) the relevance of the mtORF (coupled with other markers in some cases) as a diagnostic marker of most species, and (4) the need for a taxonomical revision in the Pocillopora genus. These results give new insights into the usefulness of multiple criteria for resolving Pocillopora species limits and will ultimately provide helpful insights for the conservation of the species from this scleractinian genus.

opencc-by-4.0Jun 2022View details →

Chiral flow in a binary mixture of two-dimensional active disks - Supplementary Data

Supplementary data for the paper: "Chiral flow in a binary mixture of two-dimensional active disks"   <ol> <li>*_raw_trajectories.pkl.xz files contain tracking data for each experiment as a pickled Pandas DataFrame object (xz compression) in pixel units (particle diameter=77px)</li> <li>*_w.pkl.xz files contain self-rotation velocity for each experiment as a pickled Pandas DataFrame object (xz compression) in rad/s</li> <li>experiments_properties.dat is a summary table containing the average fields (including vorticity and kinetic energy) for all experiments. Also subdivided by species.</li> </ol>

opencc-by-nc-4.0Jun 2022View details →

Supplementary Data Files of the Greek Parliament Proceedings Dataset

The dataset includes supplementary files of the previous upload "<a href="https://zenodo.org/record/6626316">A Greek Parliament Proceedings Dataset for Computational Linguistics and Political Analysis</a>". Specifically, it includes the 5,355 sitting record files from which speeches were extracted in the form of the conversation that took place in the Greek Parliament as well as the previous versions of the tell_all_cleaned.csv before preprocessing and cleaning, namely tell_all.csv and tell_all_FILLED.csv. <ul> <li>original_data: A folder of the original record files downloaded from the website of the Greek Parliament (https://www.hellenicparliament.gr/Praktika/Synedriaseis-Olomeleias). The filenames are edited to follow the naming format "recordDate_id_periodNo_sessionNo_sittingNo.ext".</li> <li>_data: A folder of the record files converted to text format with filenames translated to English.</li> <li>tell_all.csv: The initial file of all extracted speeches before preprocessing and cleaning. The file includes the following columns: member_name, sitting_date, parliamentary_period, parliamentary_session, parliamentary_sitting, political_party, government, member_region, roles, member_gender, speaker_info, speech.</li> <li>tell_all_FILLED.csv: This file is an intermediate step of preprocessing of the tell_all.csv file. In this file, missing names of chairmen of various parliamentary sittings are filled. It includes the same columns as the tell_all.csv file.</li> </ul> ------------- Acknowledgments: This work was supported by the European Union’s Horizon 2020 research and innovation program ``FASTEN'' under grant agreement No 825328 and the non profit data journalism organization iMEdD.org.

openother-openJun 2022View details →

RoelMaas/Supplementary-Data-Files-Thesis: Supplementary Data Files D

Supplementary Data Files belonging to Thesis Roel J.M. Maas, titled: A microfluidic approach for forward design of modular cell-free genetic networks Supplementary Data 3.1: Derived parameter sets. Parameter sets used for the distributions and/or predictions grouped per fitting round. Which experiments are used to retrieve the parameter sets are specified in the sheet title. Supplementary Data 4.1: Pulse decoder predictions. Plots showing all 150 individual fits used to create the prediction cloud shown in figure 4.3c of the main text in chapter 4. Supplementary Data 4.2: Bistable switch predictions. Plots showing all 150 individual fits used to create the prediction cloud shown in figure 4.4c of the main text in chapter 4.

opencc-by-4.0Jun 2022View details →

Effect of different feeding substrates on the production of in-sect-derived frass fertilizers for effective alleviation of ammonium (NH4+) toxicity - Raw Data and Supplementary Materials

Raw data and Supplementary Materials for the submitted Article Titled: "Effect of different feeding substrates on the production of in-sect-derived frass fertilizers for effective alleviation of ammonium (NH4+) toxicity". Submitted to Agronomy-Basel MDPI.

opencc-by-4.0Jun 2022View details →

Electronic Supplementary Data to "Zika vector competence data reveals risks of outbreaks: the contribution of the European ZIKAlliance project"

Electronic Supplementary Data to "Zika vector competence data reveals risks of outbreaks: the contribution of the European ZIKAlliance project"

Supplementary table of PRIDE datasets analyzed for "FAVA: High-quality functional association networks inferred from scRNA-seq and proteomics data"

Our proteomics dataset comes from The PRoteomics IDEntifications (PRIDE) database, the world’s largest data repository of mass spectrometry-based proteomics data. Specifically, we used 633 human proteomics project experiments with a total of 32,546 runs and reanalyzed them using ionbot with an FDR threshold of 0.01 [16], resulting in a total of 154,885,151 peptide spectrum matches for 18,846 proteins. Here is the full list of projects, runs, and general statistics.

opencc-by-4.0Feb 2022View details →

Funding Covid-19 research: Insights from an exploratory analysis using open data infrastructures - Supplementary material

This dataset contains supplementary material for the paper 'Funding Covid-19 research: Insights from an exploratory analysis using open data infrastructures' by Alexis-Michel Mugabushaka, Nees Jan van Eck, and Ludo Waltman. <ul> <li>supplementary_material_1_dataset.ods: Dataset of Covid-19 publications.</li> <li>supplementary_material_2_sample.ods: Samples of publications used to assess the accuracy of funding data in the different databases.</li> <li>supplementary_material_3_tables_and_figures.ods: Statistics underlying the tables and figures presented in the paper.</li> </ul>

Supplementary data - "Learning Reduced Models for Large-Scale Agent-Based Systems"

This repository contains supplementary data on my PhD thesis "Learning Reduced Models for Large-Scale Agent-Based Systems". Chapters 1-3, 7 and A do not have supplementary data. Chapter 4 <ul> <li>Large_deviation_example.zip contains the trajectory for Figure 4.8.</li> <li>mean_exit_time* contains the raw data to compute the mean exit time and standard deviation for the ABM process (JP) and SDE process (CLE). It contains additionally a precomputed mean and standard deviation as well as the corresponding numbers of agents.</li> <li>transition_matrix* contain the computed box discretizations as MATLAB and Numpy files as used for Figures 4.2-4.4, 4.6 and Tables 4.1 and 4.2.</li> </ul> Chapter 5 <ul> <li>CVM_2021-07-09-15-53_training_data.npz contains the training data for Figure 5.7 a and b.</li> <li>CVM_2021-09-29-07-13_distribution.npz contains the raw data for Figure 5.7 c.</li> <li>The remaining data for Chapter 5 can be found in the related dataset <a href="https://doi.org/10.5281/zenodo.4522119">doi.org/10.5281/zenodo.4522119</a>.</li> </ul> Chapter 6 <ul> <li>CVM_pareto_estimate contains trajectory data required for Figure 6.6 b to estimate points in the Pareto Front using the civil violence model. </li> <li>CVM_training_data contains the training data to construct the surrogate model. Each data set consists of CVM_*_cops_train.npz as training set, CVM_*_cops_trajectory.npz as sample trajectory and CVM_*_cops.pkl to compute the training data.</li> <li>CVM_covering_iterations_8.mat Pareto set covering after 8 iterations for the civil violence model. Required for Figure 6.6 a.</li> <li>CVM_pareto_set+front.npz is required for Figure 6.6 b. </li> <li>CVM_surrogate_model.mat contains the surrogate model for the civil violence model</li> <li>Expl_iterations_* contains Pareto set coverings after 8 and 12 iterations for Example 6.1.4 and Figure 6.1.</li> <li>VM_covering_iterations_12.mat contains the Pareto set covering depicted in Figure 6.4 a.</li> <li>VM_ODE_covering_iterations_12_subset_front.mat contains the Pareto set covering depicted in Figure 6.5 and 6.5 c.</li> <li>VM_ODE_covering_iterations_12_subset.mat contains the Pareto set covering depicted in Figure 6.5 and 6.5 d.</li> <li>VM_ODE_covering_iterations_12.mat contains the Pareto set covering depicted in Figure 6.4 b.</li> <li>VM_surrogate_model.mat contains the surrogate model for the extended voter model.</li> <li>VM_test_points_non_pareto.npz contains Non-Pareto points in Figure 6.5 and 6.5 d.</li> <li>VM_test_points_pareto.npz contains Pareto points in Figure 6.5 and 6.5 c.</li> </ul>

opencc-zeroJul 2022View details →

dryad36/100

Supplementary data for: Surface damage of perpendicular and oblique bullet impacts in stone

Controlled experiments were conducted to investigate the surface damage caused by perpendicular and oblique impacts of bullets into sandstone and limestone targets. Individual bullets fired in conditions simulating modern rifles at typical combat distances excavated craters with diameters from 22 to 74 mm and depths from 4 to 24 mm. Limestone target craters were up to twice as large and deep as those in sandstone. These craters have a complex shape consisting of a central excavation surrounded by a shallow dish, compared to the simple bowl shape of most sandstone impacts. Radial fractures extending to the edge of the target block were common in limestone targets. Impacts at an angle of 45° to the surface in both rock types result in asymmetric craters. Two common types of ammunition were compared: the steel-tipped NATO projectile generally produced larger and deeper craters than the projectile that is commonly fired from AK-47 rifles, despite having approximately half the mass of the latter. These results characterise the sort of damage that can be expected at many sites of cultural significance involved in contemporary conflict zones, and have important implications for their conservation.

Supplementary data and code of the manuscript: "Strong evidence for the adaptive walk model of gene evolution in Drosophila and Arabidopsis"

This repository contains all data tables ad code to reproduce the analysis performed in "Strong evidence for the adaptive walk model of gene evolution in Drosophila and Arabidopsis".

Global offshore wind turbine analysis with Sentinel-1 - supplementary data

Gloabl offshore wind turbine analysis with Sentinel-1 - supplementary data The files are supplementary data of the publication: Global dynamics of the offshore wind energy sector monitored with Sentinel-1: Turbine count, installed capacity and site specifications which is currently under review in the International Journal of Applied Earth Observation and Geoinformation supplementary_data_B_OWT_height_capacity.csv holds 50 pairs of offshore wind turbine hub heights and the corresponding installed capacities along with the offshore wind farm project name, the number of turbines of this wind farm, and the source the information originates from. supplementary_data_B_DeepOWT_1_21_2_plus.geojson is the extended version of the DeepOWT data set (https://zenodo.org/record/5933967) with all of the derived attributes in the respective publication e.g. OWT hub height and installed capacity.

opencc-zeroJul 2022View details →

dryad36/100

Supplementary data for: Effects of thermal acclimation on the proteome of the planarian Crenobia alpina from an alpine freshwater spring

Species' acclimation capacities and their ability to maintain molecular homeostasis outside of ideal temperature ranges will partly predict their success following climate-change induced thermal regime shifts. Theory predicts that ectothermic organisms from thermally stable environments have muted plasticities, and that these species may be particularly vulnerable to temperature increase. Whether such species retained or lost acclimation capacities remains largely unknown. We studied proteome changes in the planarian Crenobia alpina, a prominent member of cold-stable alpine habitats that is considered to be cold-adapted stenotherm. We found that the species' CTmax is above its experienced habitat temperatures and that different populations exhibit differential CTmax acclimation capacities, whereby an alpine population showed reduced plasticity. In a separate experiment, we acclimated C. alpina individuals from the alpine population to 8, 11, 14, or 17°C over the course of 168 h and compared a comprehensively annotated species-specific proteome. Network analyses of 3399 proteins and protein set enrichment show that while the species' proteome is overall stable across these temperatures, protein sets functioning in oxidative stress response, mitochondria, protein synthesis and turnover are lower abundant following warm acclimation. Proteins associated with an unfolded protein response, ciliogenesis, tissue damage repair, development, and the innate immune system were higher abundant following warm acclimation. Our findings suggest that this species has not suffered DNA decay (e.g., loss of heat-shock proteins) during evolution in a cold-stable environment and retained plasticity in response to elevated temperatures, challenging the notion that stable environments necessarily result in muted plasticity.