Find research datasets worth reusing

Data supporting the manuscript: Demonstrating the value of beaches for adaptation to future coastal flood risk

*Forcing hydrograms used to compute the flooding maps in .mat format. *Geodatabase of Pre-storm flooding maps  *Geodatabase of Post-storm flooding maps

Project files provided as supporting information to the manuscript "Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations"

README file to the project files provided as supporting information to the manuscript “Kinetics of radiation-induced DNA double-strand breaks through coarse-grained simulations" Authors: Manuel Micheloni, Lorenzo Petrolli, Gianluca Lattanzi and Raffaello Potestio ================================== The .zip file is structured as follows: ############## 0_DNA_Sequence ############## The folder contains: • DNAsequence.txt: the DNA molecule employed in the study.  • ecseq.txt: the structure of the DNA. Each nucleotide (LAMMPS residue ID) is associated with the chemical type of the nucleic base. ################### 1_DSB_MDSimulations ################### • MDSimulations:  The LAMMPS MD simulation scripts. The subfolders are structured and named after different DSB motifs (folders 0,1, …,3) providing different external forces (folders 1000, 1100, 1200 refers to the respective average end-to-end distance). The latter subfolders provides: I. LMP_script provides the LAMMPS input file. II. the local internal energy contributions from the nucleotides involved with the residual contact interface between broken DNA moieties (data/1.E);  III. coordinates of the nucleotides involved with the residual contact interface between the DNA moieties (data/2.POS); IV. the binary LAMMPS data file, employed as starting coordinates for the DSB MD simulation (/input_structure). • ScriptsAndAnalysis: The scripts employed to analyze the DSB process.  I. /00_GeneralScripts all the MATLAB functions employed for the analysis. II. /1_SigmoidalFitting provides the scripts from a sigmoidal fitting procedure [1] on the internal energy profile of the nucleotides between the strand breaks (Section 2 of the Supplementary Material).  [1] R P (2022). sigm_fit (https://www.mathworks.com/matlabcentral/fileexchange/42641-sigm_fit), MATLAB Central File Exchange. Retrieved July 2, 2022. ################## 2_DNAFreeDiffusion ################## • SIM: It contains the MD simulations of the freely-diffusing DNA. Namely, the MSD of the DNA molecule, the input structure, and the LAMMPS simulation scripts are reported in /data, /input_structure, and /LMP_scripts respectively. • ANALYSIS: It provides the script employed to estimate the diffusion coefficient of the DNA molecule and the time-scaling factor \Gamma(\zeta). ####################### 3_ForceAnalysis ####################### • data It contains the forces computed from the MD simulations of the intact DNA molecules subject to the external force of 0.42, 0.88 and 3.06 pN. All data are stored in pickle format. The README file contains additional information. NOTE1: Most data/scripts are saved according to the format .mat, employed by MATLAB Ⓡ, a numerical computing environment and proprietary programming language developed by MathWorks. NOTE2: For the force data manipulation, we acknowledge the use of LammpsFileManipulation package (https://pypi.org/project/LammpsFileManipulation/)

Dataset of manuscript "No detectable upper limit of mineral associated carbon in temperate agricultural soils"

Dataset of carbon fractions (mineral associated organic carbon and particulate organic carbon) detected in a subset of topsoil samples of the first German Agricultural Soil Inventory.

WRF model configuration and data used for the NHESS manuscript "Heat wave characteristics: evaluation of regional climate model performances for Germany"

The file contains: <ul> <li>the namelist.input document with the description of the WRF model configuration used in Warscher et al. (2019)</li> <li>WRF simulation outputs from the reanalysis run: daily values of maximum temperature for the time period 1980-2009 from the innermost (5 km grid resolution) and second innermost (15 km) domain; from both domains the same section, relevant for the study, was taken; the data was bilineraily interpolated to 12.5 km horizontal grid resolution to match the EUR-11 CORDEX format</li> </ul>

Supplementary material for the manuscript of G.E. Gus'kov "The first record of adult Boops boops (Perciformes, Sparidae) near the Caucasian coast of the Black sea".

Video and photographs confirming the record of Boops boops (Pisces: Perciformes: Sparidae) near the Caucasian coast of the Black sea (Russian sector)

CSV Dataset Files and JSON OpenRefine Recipes for Alignment of the Schoenberg Dataset of Manuscripts (SDBM) Name Authority with Wikidata

Dataset CSVs and JSON recipe files for OpenRefine for a project to align Name Authority records in the Schoenberg Dataset of Manuscripts (SDBM) with Wikidata Items

Pooled datasets for scover manuscript

These are scanpy objects of the pooled datasets associated with <a href="https://doi.org/10.1101/2020.11.26.400218">our recent work</a>. Please note the datasets are gzipped to save space. The original datasets were obtained through the following sources: <ul> <li>Human kidney data: <a href="https://www.kidneycellatlas.org/">https://www.kidneycellatlas.org/</a></li> <li>Tabula Muris data: <a href="https://figshare.com/articles/dataset/Single-cell_RNA-seq_data_from_Smart-seq2_sequencing_of_FACS_sorted_cells_v2_/5829687/8">https://figshare.com/articles/dataset/Single-cell_RNA-seq_data_from_Smart-seq2_sequencing_of_FACS_sorted_cells_v2_/5829687/8</a> (CC BY 4.0)</li> <li>Human brain data: <a href="https://github.com/GreenleafLab/brainchromatin">https://github.com/GreenleafLab/brainchromatin</a>  (data can also be found <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE162170">here</a>)</li> </ul> Please find more information in our pre-print about how the datasets were created. For more information about the method, please see the <a href="https://github.com/jacobhepkema/scover">associated github</a>.

Data for the manuscript 'Cover crop root morphology rather than quality controls the fate of root and rhizodeposition C into distinct soil C pools'

Data for manuscript The data provided in the present document corresponds to the manuscript: Engedal, T., Magid, J., Hansen, V., Rasmussen, J., Sørensen, H., Jensen, L. S. (2023): Cover crop root morphology rather than quality controls the fate of root and rhizodeposition C into distinct soil C pools. Global Change Biology, in press.   Short abstract In order to investigate the fate of cover crop-derived belowground C as rhizodeposition and, over time, into the distinct soil organic carbon pools of particulate- and mineral-associated organic carbon (POC and MAOC), a column trial was esblished with 0.25 m top soil and 0.25 m sub soil. Four cover crops were grown for 3 months and 14CO2-labelled twice a week. Four out of eight replicate columns were destructively harvested to quantify root C and the carbon lost via rhizodeposition in absolute (qClvR) and relative terms (%ClvR) in bulk soil and rhizosphere soil from top- and subsoil (t1). The other four replicate columns were harvested for undisturbed incubation for one year, before final sampling (t2). Bulk soil from both sampling times were subject to a simple fractionation protocol by size, where particles larger from 50 microns were assigned to POC and smaller than 50 microns assigned to MAOC after dispersion in NaHMP. All fractions were dried, weighed and analyzed for 14C activity as disintegrations per minute (DPM).   Further details Column ID 1-16 refer to columns sampled at t1, while column ID 17-32 refer to columns sampled at t2. Underlying assumptions and detailed descriptions of the different fractions are to be found in the manuscript.

openJun 2023View details →

Vortex project file for PVA of Southern Resident Killer Whale -- manuscript by Williams et al.

Project file for Vortex PVA scenarios used in Williams et al. manuscript.  Williams, R., R.C. Lacy, E. Ashe, L. Barrett-Lenard, T.M. Brown, J.K. Gaydos, F. Gulland, M. MacDuffee, B.W. Nelson, K.A. Nielsen, H. Nollens, S. Raferty, S. Reiss, P.S. Ross, M.S. Collins, R. Stimmelmayr, & P. Paquet. 2024. Warning sign of an accelerating decline in critically endangered killer whales (Orcinus orca). Communications Earth & Environment (in press).

opencc-by-4.0Jul 2023View details →

Data and code for the manuscript "An estimate of excess mortality resulting from air pollution caused by wildfires in the eastern and central Mediterranean basin in 2021"

Data and R code used for generating the manuscript "An estimate of excess mortality resulting from air pollution caused by wildfires in the eastern and central Mediterranean basin in 2021".

Supplementary information for the manuscript 'GFViz: A tutorial on creating interactive visualization of genomic features using R Tidyverse and plotly'

This is the supplementary information of the manuscript  'GFViz: A tutorial on creating interactive visualization of genomic features using R Tidyverse and plotly' published as a part of the thesis 'Annotating and making use of the Avena sativa cv. Sang reference genome' by Nikos Tsardakas Renhuldt.

Supplementary information for the manuscript 'Mutation in SHAGGY-like kinase AsGSK2.1 causes a short kernel phenotype in oat (Avena sativa)'

This is the supplementary information of the manuscript 'Mutation in SHAGGY-like kinase AsGSK2.1 causes a short kernel phenotype in oat (Avena sativa)' published as a part of the thesis 'Annotating and making use of the Avena sativa cv. Sang reference genome' by Nikos Tsardakas Renhuldt. SI.pdf contains supplementary figures 1-3. Supplementary figure 4.html contains supplementary figure 4. Supplementary tables.xlsx contains supplementary tables 1-5.

opencc-by-4.0Jul 2023View details →

Dataset for the Figure 2 in manuscript "Numerical study of coupled water and vapour flow, heat transfer, and solute transport in variably-saturated deformable soil during freeze-thaw cycles"

This dataset includes the gathered experimental measurements of a freezing test by Wu (2017) for the model's verification shown in Figure 2 of the manuscript entitled 'Numerical study of coupled water and vapour flow, heat transfer, and solute transport in variably-saturated deformable soil during freeze-thaw cycles'' by Huang, X., and Rudolph, D.L.

opencc-by-4.0Jul 2023View details →

Raw data accompanying the manuscript "Uptake of microplastics and impacts on plant traits of savoy cabbage"

These are the raw datasets used to generate Figure 1 for the manuscript entitled "Uptake of microplastics and impacts on plant traits of savoy cabbage". The folders contain all raw CARS and SRS data that are needed to reproduce Figure 1 (TIFF format).

opencc-by-4.0Aug 2023View details →

Date set for the manuscript: Exploring the temporal dynamics of methane ebullition in a subtropical freshwater reservoir

The dataset supports the findings of the manuscript entitled ‘Exploring the Temporal Dynamics of Methane Ebullition in a Subtropical Freshwater Reservoir’. The results of the manuscript are based on continuous in-situ measurements conducted at Passaúna Reservoir, located in the southern part of Brazil (South America). The monitoring was carried out from 2017 to 2020, during which a comprehensive set of environmental variables was obtained from various studies. The primary objective of the manuscript was to comprehend the temporal dynamics of ebullition flux in the reservoir. Therefore, time series data of ebullition and relevant environmental variables were analyzed across different time scales, ranging from minutes to daily resolutions. Statistical and data driven models were tested to predict ebullition at varying time scales, considering the influence of environmental variables. The findings are discussed in the manuscript. Here, xlsx files and Matlab scripts are provided. The xlsx files contain time series data for environmental variables ('Environmental_Variables_TimeSeries') and ebullition flux ('Ebullition_Flux_TimeSeries'). Separate sheets were utilized for different time intervals, namely 5 minutes (dt=5min), 10 minutes (dt=10min), 1 hour (dt=1hr), and 1 day (dt=1d). Explanations and units are provided within the column labels, while 'NaN' denotes missing data. Matlab scripts for all the empirical models that were tested, as outlined in the manuscript's supporting information (Tables S1 and S2), have been made available (detailed in the following table). These scripts were developed using MatLab R2023a. <table> <tbody> <tr> <td> File (.m) </td> <td> Description </td> </tr> <tr> <td> Main scripts </td> </tr> <tr> <td> TableS1_Empirical_Models_Literature </td> <td> Empirical models from the literature tested. (Table S1 in the manuscript) </td> </tr> <tr> <td> TableS2_FirstPart_Reffited_Models </td> <td> Empirical models from the literature refitted. (Table S2 in the manuscript) </td> </tr> <tr> <td> TableS2_SecondPart_New_Models </td> <td> New empirical models implemented. (Table S2 in the manuscript) </td> </tr> <tr> <td> TableS2_SecondPart_New_Models_GAM_Timescales </td> <td> Generalized additive models (GAM) applied to predict ebullition at different timescales. (Table S2 in the manuscript). </td> </tr> <tr> <td> PredictedR2_GAM_models </td> <td> Calculate the predicted R-squared for GAM. </td> </tr> <tr> <td> Functions (need for the main scripts) </td> </tr> <tr> <td> load_TimeSeries </td> <td> Import time series of environmental variables from excel sheets into MatLab. </td> </tr> <tr> <td> load_EbullitionTS </td> <td> Import time series of ebullition from excel sheets into MatLab. </td> </tr> <tr> <td> units_description </td> <td> Description containing units of the variables. </td> </tr> <tr> <td> Bin_xdata </td> <td> Creates data binning of X and Y based on X data. </td> </tr> <tr> <td> RelativeError </td> <td> Calculate the relative error of accumulated flux between measured and simulated. </td> </tr> <tr> <td> ANN5Neurons_Retrained_Deshmukh2014 </td> <td> Trained Artificial Neural Network based on the ANN proposed by Deshmukh et al. (2014). </td> </tr> <tr> <td> ANN_Passauna_20Neurons </td> <td> Trained Artificial Neural Network with the addition of more environmental variables. </td> </tr> </tbody> </table>   Financial support The field measurements were financed by the German Federal Ministry of Education and Research (BMBF, Grant 02WGR1431A), in the framework of the research project MuDak-WRM (https://www.mudak-wrm.kit.edu). This study was financed in part by the Coordenação de Aperfeiçoamento de Pessoal de Nível Superior – Brasil (CAPES) – Finance Code 001. Tobias Bleninger received productivity stipend from the National Council for Scientific and Technological Development (CNPq, grant no. 312211/2020-1, call no. 09/2020). Michael Männich received productivity stipend from the National Council for Scientific and Technological Development (CNPq, grant no. 308744/2021-7, call no. 04/2021). Andreas Lorke received financial support from the German Research Foundation (DFG, grant number LO1150/16-1).

Dataset and Python Scripts used in the manuscript "Global-MHD Simulations using MagPIE : Impact of Flux Transfer Events on the Ionosphere"

Dataset and Python Scripts used in the manuscript "Global-MHD Simulations using MagPIE : Impact of Flux Transfer Events on the Ionosphere". Authors: Arghyadeep Paul, Antoine Strugarek and Bhargav Vaidya Date: 21 May, 2023   <ul> <li>Figure 1 has been plotted from two data files named Bx_By_Bz_prs_t_4783_C0.vtk and Bx_By_Bz_prs_t_4783_C1.vtk using the visualisation toolkit VisIt. Visit can be freely downloaded from https://wci.llnl.gov/simulation/computer-codes/visit</li> <li>Figure 2 has been plotted using the ipython notebook named "figure_2.ipynb" and the associated data files have been uploaded alongwith.</li> <li>Figure 3 has been plotted using the data file named "visit_prs_Bx_By_Bz_t_4964s.vtk" and the visualisation toolkit VisIt.</li> <li>Figure 4 has been plotted using the associated data files and the visualisation toolkit VisIt.</li> <li>Figures 5 and 6 has been plotted using the ipython notebook named "new_fig_5_and_6.ipynb" and the associated data files have been uploaded alongwith.</li> <li>Figure 7 has been plotted using the ipython notebook named "figure_7.ipynb" and the associated data files have been uploaded alongwith.</li> <li>Figure 8 has been plotted using the ipython notebook named "figure_8.ipynb" and the associated data files have been uploaded alongwith.</li> <li>Figure 9 has been plotted using the ipython notebook named "figure_9.ipynb" and the associated data files have been uploaded alongwith. An example swarm CSV data file is added for the python script. The original SWARM data can be downloaded from <a href="https://swarm-diss.eo.esa.int/">https://swarm-diss.eo.esa.int/</a> and the FAC data from two spacecrafts, Swarm A and C, named SW_OPER_FAC_TMS_2F has been used. This data was first published in Dong et.al. 2023 [https://doi.org/10.1029/2022GL102460].</li> </ul>

opencc-by-4.0Aug 2023View details →

Data for the manuscript "Bridged Nucleic Acid ASOs over Locked Nucleic Acid ASOs and their impact on the structure and stability of ASO/RNA duplexes"

The dataset contains: DFT and MD Data for the manuscript "Bridged Nucleic Acid ASOs over Locked Nucleic Acid ASOs and their impact on the structure and stability of ASO/RNA duplexes".

opencc-by-4.0Aug 2023View details →

TBT exposure dataset of the manuscript "Assessment of endocrine disruptors effects on zebrafish (Danio rerio) embryos by untargeted LC-HRMS metabolomic analysis"

Raw LC-HRMS data of the TBT exposure of zebrafish embryos (for more details see https://doi.org/10.1016/j.scitotenv.2018.03.369) The exposure protocol involved zebrafish embryos exposed in groups of 20 to various concentrations of chemical compounds, with five replicates per treatment. The concentrations ranged from the lowest observed effect concentrations (LOECs) to control levels. After exposure, embryos were collected, washed, frozen, and stored. Metabolites were extracted from individual embryo pools using methanol and methionine sulfone. The extraction process included vortexing, sonication, and centrifugation, followed by addition of water and chloroform. The aqueous fraction was dried and reconstituted using acetonitrile-water solution. Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) was used for analysis. Chromatographic separations were carried out on a hydrophilic interaction liquid chromatography (HILIC) column. Mass spectrometry was performed using an Orbitrap mass spectrometer with electrospray ionization in positive and negative modes. The mass spectra were acquired at high resolution, and fragmentation scans were used for metabolite identification. The overall process aimed to analyze the metabolomic profile of zebrafish embryos exposed to different chemical concentrations. Data files <blockquote> TBT ESI+ (tbt_pos.rar) - CDF files - QC (4 replicates) - Control (5 replicates) - TBT 3 nM (5 replicates) - TBT 10 nM (5 replicates) - TBT 30 nM (5 replicates) - TBT 100 nM (5 replicates) </blockquote>   <blockquote> TBT ESI- (tbt_neg.rar) - CDF files - QC (6 replicates) - Control (5 replicates) - TBT 3 nM (5 replicates) - TBT 10 nM (5 replicates) - TBT 30 nM (5 replicates) - TBT 100 nM (5 replicates) </blockquote>

opencc-by-4.0Sep 2023View details →

Data for submitted manuscript "Connections between Sub-cloud Coherent Structures and the Life Cycle of Shallow Cumulus Clouds: Evidence from Large Eddy Simulation"

This is the dataset for a submitted manuscript "Connections between Sub-cloud Coherent Structures and the Life Cycle of Shallow Cumulus Clouds: Evidence from Large Eddy Simulation" for peer review. The NetCDF file includes masked objects for sub-cloud coherent structures and cloud for tracking.