Find research datasets worth reusing

Dataset to article "Distinct traits of structural and regulatory evolutional conser-vation of human genes with specific focus on major cancer mo-lecular pathways"

Abstract: Evolution of protein coding genes has both structural and regulatory components. The first can be assessed by measuring the ratio of non-synonymous to synonymous nucleotide sub-stitutions. The second component can be measured as the normalized proportion of transposable elements that used as the regulatory elements. For the first time, we characterized in parallel the regulatory and structural evolutionary profiles for 10,890 human genes and 2,972 molecular pathways. We observed ~0.1 correlation between the structural and regulatory metrics at the gene level, which appeared much higher (~0.4) at the pathway level. We deposited the data in the publicly available database RetroSpect accessible at https://retrospect.oncobox.com. We also analyzed evolutionary dynamics of six cancer pathways of two major axes: Notch/WNT/Hedgehog and AKT/mTOR/EGFR. The Hedgehog pathway had both components slower, whereas the Akt pathway had clearly accelerated structural evolution. In particular, the major hub nodes Akt and beta-catenin showed both components strongly decreased, whereas two major regulators of Akt TCL1 and CTMP had outstandingly high evolutionary rates. We al-so noticed structural conservation of serine/threonine kinases and the genes related to guanosine metabolism in cancer signaling: GPCRs, G proteins, and small regulatory GTPases (Src, Rac, Ras); however, this was compensated by the accelerated regulatory evolution.

The dataset and results for the article "More people might face severe water scarcity this century than previously estimated"

The dataset presents the values of each parameter and the parameters of different SSP scenarios. In addition, the results provide information about predicted values.

Pateto charts for the article "Biomass composition of Nephroselmis sp. under different ex-perimental conditions of nitrogen, salinity, and light: optimiza-tion of lipids accumulation (including EPA)"

Pareto charts for the statistical significance of the nitrogen concentration, salinity level and illuminance, regarding the derived equations for (a) proteins, (b) carbohydrates, (c) pigments, (d)fatty acids and (e) EPA production.

openother-openMay 2023View details →

ESIPFed/CRYO-Harmonization: Data for DSJ article

Trying to get the DOI thing with Zenodo to work...

Article dataset: Taxonomy of Open Science: revised and expanded

Conjunto de dados do artigo: Taxonomia da Ciência Aberta: revisada e ampliada

Italian and US news articles on COVID-19

Sample of Italian and US news  1/1/2020-20/10/2021obtqained searching: convalescent plasma, hydroxychloroquine, ivermectin, lockdown, mask, vaccine and vitamin D combined in a Boolean AND search with “covid AND  (published OR publication OR journal)”. (In Italian,: plasma convalescenti, idrossiclorochina, ivermectina, lockdown, mascherine, vaccino, vitamina D AND “covid AND (ricerca OR pubblicato OR pubblicazione)

Publication data for article "Scientific and technological knowledge grows linearly over time"

This dataset includes metadata for academic publications used in the article Scientific and technological knowledge grows linearly over time. The dataset contains citation relationships, publication dates, and academic fields for 213,715,816 publications from 1800 to 2020. These publications cover 292 secondary subjects in 19 major disciplines, including Economics, Biology, Computer Science, Physics, and more. The data are requested from Acemap (https://www.acemap.info, Shanghai Jiao Tong University) and sourced from the last snapshot of Microsoft Academic Graph (MAG) as of December 31, 2021. The dataset includes two gzip-compressed files, which contain all data in CSV format after decompression. Sample data is presented below: <ol> <li>paper_date_refs.csv (paper_date_refs.tar.gz) <ol> <li>paper_id</li> <li>date</li> <li>reference_ids (separated by comma)</li> </ol> </li> <li>field_paper (field_paper.tar.gz) <ol> <li>field_paper/Computer science.csv <ol> <li>paper_id</li> </ol> </li> <li>field_paper/Biology.csv <ol> <li>paper_id</li> </ol> </li> <li>...</li> </ol> </li> </ol>

Supplementary data as part of the article "Comparing the reaction profiles of single-iron catalytic sites in enzymes and in reticular frameworks for methane-to-methanol oxidation" (https://doi.org/10.1016/j.xcrp.2023.101422)

Cartesian coordinates in the *.XYZ format for all the structures optimized at the M06-L/def2-TZVP in the reactivity study as part of the article "Comparing the reaction profiles of single-iron catalytic sites in enzymes and in reticular frameworks for methane-to-methanol oxidation" (<a href="https://doi.org/10.1016/j.xcrp.2023.101422">https://doi.org/10.1016/j.xcrp.2023.101422</a>)

Output data for the article "Climate variability in 2030 European power systems"

Model outputs for the paper "Climate variability on Fit for 55 European power systems"

Dataset for the article "Alnus viridis: an encroaching species with valuable nutritional value reducing livestock greenhouse gas emissions"

Both files provide the data used for the article "Alnus viridis: an encroaching species with valuable nutritional value reducing livestock greenhouse gas emissions"   <ol> <li>"Data_file_1" provides the measured components of A. viridis, i.e. the chemical composition (micro/macro-elements, fibre fractions, ash), the phenolic content and the functional traits. </li> <li>"Data_file_2" provides the results of the in vitro measurements on organic matter digestibility and gas production.</li> </ol>

Data set for the article 'Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria'

This dataset contains data that support the manuscript Schmidt et al () "Gold-FISH enables targeted NanoSIMS analysis of plant-associated bacteria", The New Phytologist, accepted on 14.06.2023. It contains the following data: NanoSIMS imaging data, which was used for Fig. 2-3, as well as for Fig. S1-4. Data are provided as the original NanoSIMS images (.im) as well as their associated checkfiles (.chk_im).

opencc-by-4.0Feb 2023View details →

Inputs, output and animation files related to the article titled "A computational framework for crack propagation along contact interfaces and surfaces under load" submitted to CMAME.

Here you can find input mesh files, parameter files, output files and animations for numerical examples considered in the paper entitled "A computational framework for crack propagation along contact interfaces and surfaces under load" submitted to Computer Methods in Applied Mechanics and Engineering.

Raw data for the article 'Revisiting power-law distributions in empirical outage data of power systems'

Raw data for the article 'Revisiting power-law distributions in empirical outage data of power systems' (see the manuscript preprint https://arxiv.org/abs/2303.12714 for more details).

Supplementary materials for the article: "Where and when the mesopelagic carbon budget balances, if at all", Oliver et al., 2023

This is the supplementary materials for the article: "Where and when the mesopelagic carbon budget balances, if at all", Oliver et al., 2023 This folder contains: MLD.mat - The annual maximum of monthly-averaged mixed layer depth (m) in ECCO: 1992-2001 mean (data retrieved from ECCO Consortium et al., 2023). The mixed layer depth is determined by the depth where waters are first 0.8◦ C colder than the surface, as per the Kara Formula (Kara et al., 2000) FBGC3mm.mat - Sinking detrital flux [mmol P/m3/d], produced by MOPS (Kriest et al., 2015), monthly average FBGC4mm.mat - Detritus removal via remineralisation and denitrification [mmol P/m3/d], produced by MOPS (Kriest et al., 2015), monthly average FBGC7mm.mat - Detritus creation [mmol P/m3/d], produced by MOPS (Kriest et al., 2015), monthly average DETmm.mat - Sinking Detritus [mmol P/m3/d], produced by MOPS (Kriest et al., 2015), monthly average NPP.mat - Primary production [mmol P/m3/d], produced by MOPS (Kriest et al., 2015), annual average export.mat   - Export production [mmol P/m3/d], produced by MOPS (Kriest et al., 2015), annual average grid.mat - model grid information for ECCO transport matrix (see Khatiwala, S. (2018): https://zenodo.org/record/1246300 463doi: 10.5281/ZENODO.1246300) cmap5.mat - matlab colormap             bluewhitered.mat  - matlab colormap        cmap12.mat - matlab colormap PlotPaperFigures.m - matlab script for plotting journal paper figures for "Where and when the mesopelagic carbon budget balances, if at all", Oliver et al., 2023 findClosest.m - matlab script to find the closest value in a list of values to a specified value

Dataset to the article 'Redox-zoning in high-energy subterranean estuaries as a function of storm floods, temperatures, seasonal groundwater recharge and morphodynamics'

This repository contains model input files, and pre- and post-processing scripts for the research article: Janek Greskowiak, Stephan L. Seibert, Vincent E.A. Post, Gudrun Massmann (2023), Redox-zoning in high-energy subterranean estuaries as a function of storm floods, temperatures, seasonal groundwater recharge and morphodynamics, Estuarine, Coastal and Shelf Science, https://doi.org/10.1016/j.ecss.2023.108418 Data: The folder Laserascannerdata_top_and_hydr_heads contains five cross-shore topography profiles of a high energy beach on Spiekeroog Island, Germany, including a python-script that assembles them to a daily times-series over one year and that calculates the tide-averaged hydraulic heads in the intertidal zone as detailed in Greskowiak and Massmann (2021), The impact of morphodynamics and storm floods on pore water flow and transport in the subterranean estuary, Hydrological Processes, 35:e14050, https://doi.org/10.1002/hyp.14050 Model input: The file Dynamod_1_redox_basecase.zip contains a folder with the model input textfiles (SEAWAT and PHT3D) for the case that considers all dynamic influence factors investigated in the paper, i.e., seasonal meteoric groundwater recharge, stormfloods, temperature-dependence of reaction rates and morphodynamics. The files pht3d_ph.dat and pht3d_datab.dat are PHT3D model specific files defining the reacants and reactions, and have to be copied into the model folder before PHT3D is started. Run models: First the SEAWAT model needs to be run with the name file 'Dynamod_1_redox_basecase.nam'. This creates the mt3d link file 'mt3d_link.ftl'. After that, PHT3D has to be started with the name file 'pht3d.nam' Note that running the models will generate 22 Gybte output. Pre-processing: All model input files were generated with the python-script Dynamod_1_redox_basebase.py using Flopy, a python-based groundwater modelling user-interface: https://www.usgs.gov/software/flopy-python-package-creating-running-and-post-processing-modflow-based-models Post-processing: For the figures 3,4 and S1, S2 in the paper, the corresponding python scripts are provided in this database. Note that with respect to Figures 5 and S3, only the results for the case with all dynamic influence factors (Figure S3_h) are being plotted.   Other model output: Animation_A1_Dynamod_redox.mp4 is a video animation showing the dynamic modelled salinity and temperature distribution, and redox zoning in the subterranean estuary all dynamic influence factors investigated in the paper, i.e., seasonal meteoric groundwater recharge, stormfloods, temperature-dependence of reaction rates and morphodynamics.

Raw NMR data for the article "Photochemical [2+2] Cycloaddition of Alkynyl Boronates"

Raw NMR  data  for the article "Photochemical [2+2] Cycloaddition of Alkynyl Boronates" published in Chemistry A European Journal, DOI:  <a href="https://doi.org/10.1002/chem.202301650">https://doi.org/10.1002/chem.202301650</a> The number of the folders either correspond to compounds numbers in the article or the name of the folder is self-describing. All details concerning conditions and equipment for measurements can be found in the supporting information of the article.

opencc-by-4.0Jul 2023View details →

Supporting dataset for the article "Fostering Agroforestry - Lessons from Côte d'Ivoire"

This dataset has been used to produce Figure 1 of the paper. The data come from the Cocoa4Future project for which 150 permanent plots have been set up throughout Côte d'Ivoire's cocoa production zone. From these 150 plots, we retained agroforestry plots only, i.e. plots were filtered to keep only those with a basal area of trees greater than 10m2.ha-1. MetaData plotID - unique identifier of the plot clus - unique identifier of the cluster the plot belongs to type - plot number within cluster area - surface of the plot BA_remnant - Basal area of all remnant trees (in m2) BA_new - Basal area of all non-remnant trees (in m2) BA - Total basal area prop - % of the total basal area that is due to remnant trees

opencc-by-4.0Jul 2023View details →

Data set for the journal article "Hydrogen dissociation sites on indium-based ZrO2-supported catalysts for hydrogenation of CO2 to methanol"

Raw data for the article " Hydrogen dissociation sites on indium-based ZrO2-supported catalysts for hydrogenation of CO2 to methanol", already published in Catalysis Today, DOI: https://doi.org/10.1016/j.cattod.2021.04.010 Folder names describe the type of data content. All details concerning conditions and equipment for measurements can be found in the  main text and supporting information of the article.

opencc-by-4.0Aug 2023View details →

Research data from the article "The Populist Ambivalence. Presidents and Democracy in Latin America"

Research data from the article "The Populist Ambivalence. Presidents and Democracy in Latin America": dataset, truth table, prime implicants and list of populist presidents with sources supporting that they are populist