Find research datasets worth reusing

Data to the manuscript 'Imperfect cross-linking of Xanthan for pH-responsive bio-based composite moist wound dressings by stencil printing'

Evaluation data for the manuscript stated above. For follow-up evaluation, files have to be arranged according to file designation in the scripts uploaded. There is no additional description of how to arrange. Please feel free to contact the first author for help and information.

Raw data files for the manuscript entitled "Hybridization of Synthetic Humins with a Metal–Organic Framework for Precious Metal Recovery and Reuse"

Datasets for the data presented in the manuscript entitled "Hybridization of Synthetic Humins with a Metal–Organic Framework for Precious Metal Recovery and Reuse" published in ACS Applied Materials and Interfaces.

Dataset for manuscript "Responses to single and multiple temperature-, medium-, and pH-stimuli triggering reversible shape shifts in hydrogel actuators"

The dataset includes data for the article "Responses to single and multiple temperature-, medium-, and pH-stimuli triggering reversible shape shifts in hydrogel actuators", https://doi.org/10.1016/j.matdes.2022.111511

opencc-by-4.0Dec 2022View details →

Data for manuscript "Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae"

Data and code for manuscript "Synteny identifies reliable orthologs for phylogenomics and comparative genomics of the Brassicaceae". Preprint available at bioRxiv: https://doi.org/10.1101/2022.09.07.506897.

Supplementary videos for the "Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture" manuscript

Supplementary videos for preprint manuscript:  Remote-refocusing light-sheet fluorescence microscopy enables 3D imaging of electromechanical coupling of hiPSC-derived and adult cardiomyocytes in co-culture Liuba Dvinskikh, Hugh Sparks, Liliana Brito, Kenneth T MacLeod, Sian E Harding, Christopher Dunsby bioRxiv 2023.01.28.526043; doi: https://doi.org/10.1101/2023.01.28.526043 All videos have been rendered with JPEG compression. Shortened video captions (Please see supplementary information document for full caption) Video 1: 3D LSFM timelapse of hiPSC-CM undergoing spontaneous calcium transients.   Video 2: Widefield transillumination timelapse of hiPSC-CM and adult-CM  Video 3: Widefield fluorescence timelapse of hiPSC-CM and adult CM with synchronized spontaneous calcium transients.  Video 4a: 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients.  Video 4b: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients.  Video 5a: 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture undergoing synchronized spontaneous transients in a sample without NBleb.  Video 5b: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture without NBleb undergoing synchronized spontaneous transients.  Video 6a: 3D LSFM timelapse of hiPSC-CM and adult-CM co-culture undergoing synchronized spontaneous transients in a sample treated with NBleb.  Video 6b: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 1 co-culture with NBleb undergoing synchronized spontaneous transients.  Video 7a: 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture undergoing synchronized spontaneous transients in a sample without NBleb.  Video 7b: Depth-encoded MIPs of the 3D LSFM timelapse of hiPSC-CM and adult-CM day 0 co-culture without NBleb.

opencc-by-4.0Dec 2022View details →

Part 1: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'

Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory. The file Data.One.Focb-2.tar contains 22 files of paired-end reads from F. oxysporum f.sp. cubense tropical race 1 isolate N2 (SRA accession: SRR550150, SRR550151), and F. oxysporum f.sp. cubense TR4 isolates Hainan.B2 (SRR550152), My-1 (SRR7226877), La-2 (SRR7226878), Vn-2 (SRR7226879), Leb1.2C (SRR7226880), JV11 (SRR7226881), Phi2.6C (SRR7226882), Pak1.1A (SRR7226883), UK0001 (SRR9733598).

opencc-by-4.0Dec 2022View details →

Part 2: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogens'

Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory. The file Data.One.Focb.tar contains 16 files of paired-end reads from F. oxysporum f.sp. cubense TR4 isolates II-5 (SRA accession: SRR10054446), S1B8 (SRR10054447), JV14 (SRR10054448), FOC.TR4-5 (SRR10054449), FOC.TR4-1 (SRR10054450), Col2 (SRR10103605), Col4 (SRR10125423), Col17 (SRR10747097).

Part 4: Dataset and script for a manuscript entitled 'Host-specific subtelomere: structural variation and horizontal transfer in asexual filamentous fungal pathogen

Datasets, scripts and instructions for reproducing some of the results in the manuscript. The file subtelomere.tar needs to be unpacked on a Linux system. After unpacking it, go to the directory subtelomere, which contains a number of subdirectories. One subdirectory is named data, which contains genome assemblies and is used to hold datasets of short reads; the datasets of short reads in the files Data.One.Focb.tar, Data.One.Focb-2.tar and reads.tar on the four-part depository need to be placed in the subdirectory subtelomere/data/reads/. The other subdirectories under the directory subtelomere contain instructions and scripts for reproducing some of the results in the manuscript. Please see the README and z.cmd files in each subdirectory. The file reads.tar contains 44 files of paired-end reads from F. oxysporum f.sp. lycopersici isolate Fol069 (SRA accession: SRR307106, SRR307107, SRR307113, SRR307115, SRR307123, SRR307257, SRR307266), isolate Fol072 (SRR307122, SRR307092, SRR307091, SRR307090, SRR307086, SRR307281, SRR307250), isolate Fol4287 (SRR7690004, SRR3139043), and F. oxysporum f.sp. radicis-cucumerinum isolate Forc016 (SRR3139027, SRR3139028), isolate Forc024 (SRR3139029, SRR3139030), isolate Forc031 (SRR3139031, SRR3139032).

opencc-by-3.0-usFeb 2023View details →

Final data used in GRL manuscript GRL65488 (DOI: 10.1029/2022GL102603)

Final processed data used to generate all figures in the article "Mesoscale Convective Systems in DYAMOND Global Convection-Permitting Simulations", published in the Geophysical Research Letter. All data are in self descriptive netCDF formats. <ul> <li>codes directory contains Python scripts/notebooks used to visualize the data.</li> <li>data directory contains final processed data used in the manuscript.</li> </ul>

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Secondary ion mass spectrometry, a powerful tool for revealing ink formulations and animal skins in medieval manuscripts

Book production by medieval scriptoria has gained growing interest in recent studies. In this context, identifying ink compositions and parchment animal species from illuminated manuscripts is of great importance. Here, we introduce time-of-flight secondary ion mass spectrometry (ToF-SIMS) as a non-invasive tool to identify both inks and animal skins in manuscripts, at the same time. For this purpose, both positive and negative ion spectra in inked and non-inked areas were recorded. Chemical compositions of pigments (decoration) or black inks (text) were determined by searching for characteristic ion mass peaks. Animal skins were identified by data processing of raw ToF-SIMS spectra using principal component analysis (PCA). In illuminated manuscripts from the fifteenth to sixteenth century, malachite (green), azurite (blue), cinnabar (red) inorganic pigments, as well as iron-gall black ink, were identified. Carbon black and indigo (blue) organic pigments were also identified. Animal skins were identified in modern parchments of known animal species by a two-step PCA procedure. We believe the proposed method will find extensive application in material studies of medieval manuscripts, as it is non-invasive, highly sensitive and able to identify both inks and animal skins at the same time, even from traces of pigments and tiny scanned areas.

opencc-zeroFeb 2023View details →

Supplementary materials of the manuscript "Establishing a new workflow in the study of core reduction intensity and distribution".

This repository hosts the R code scripts and datasets that allow reproducibility and replicability of the statistical analyses implemented in the paper: Lombao et al. (2022). Establishing a new workflow in the study of core reduction distribution. Journal of Lithic Studies.   The analytical and statistical protocols applied for this study were implemented in in R (version 3.6.3) (R Core Team, 2021). Contents: 1.    Script.txt: The R- Script with all the packages and functions used and all the steps followed in the statistical analyses. 2.   vrm_experiment_database.xlsx: the database with the data used in this manuscript. The data comes from an experiment presented in Lombao et al., 2020. A new approach to measure reduction intensity on cores and tools on cobbles: the Volumetric Reconstruction Method. Archaeological and Anthropological Sciences 12(9) DOI: 10.1007/s12520-020-01154-7 3.    Supplementary_table_S1.docx 4.    Supplementary_table_S2.docx 5.    Supplementary_table_s3.xlsx  This database is used in the R-script.

Assemblies and alignment data generated for NAHRwhals manuscript.

This repository contains 56 human assemblies used for a manuscript describing the NAHRwhals SV identifying tool (<a href="https://github.com/WHops/NAHRwhals" target="_new" rel="noreferrer">https://github.com/WHops/NAHRwhals</a>). All underlying raw data as well as half of the assemblies are directly taken from the Human Genome Structural Variation Consortium (HGSVC). Raw HiFi reads underlying the assemblies can be obtained from: <a href="http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/" target="_new" rel="noreferrer">http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/</a>. Assemblies were created with in two batches. Batch one (HG00512, HG00513, HG00514, HG00731, HG00732, HG00733, HG02818, HG03125, HG03486, NA12878, NA19238, NA19239, NA19240, NA24385) was created by the HGSVC (Ebert et al. 2021) and used in the NAHRwhals manuscript. Batch two (GM19129, GM19434, HG00171, HG00864, HG02018, HG02282, HG02769, HG02953, HG03452, HG03520, NA12329, NA19036, NA19983, NA20847) is based on HGSVC raw data but was created specifically for the manuscript by Tobias Rausch. For more information, please refer to the NAHRwhals paper "Impact and characterization of serial structural variations across humans and great apes" by Höps et al., 2024 for further details on assembly generation and intended usage. Contact: <a rel="noreferrer">wolfram.hoeps@gmail.com</a>

Colossal optical anisotropy from atomic-scale modulations: manuscript data

<ul> <li>Relevant data files for Main Text figures of "Colossal optical anisotropy from atomic-scale modulations"</li> <li>Relevant data files for Supplementary Information figures of "Colossal optical anisotropy from atomic-scale modulations"</li> </ul>

Dataset for the manuscript: Trap-and-Track for Characterizing Surfactants at Interfaces

This repository includes datasets supporting our manuscript that will be submitted to Molecules – Special issue "Surfactants with Specific Molecular Architecture as Building Blocks for Nanocarriers." <ul> <li>'rawdata.zip': Recordings of trapped particle motions, estimated trajectories, and calculated mean squared displacements (MSD). Each recording has a identification number (e.g., 1, 2, 3, etc.); the corresponding trajectories and MSDs have file names '(ID#)_traj.csv' and '(ID#)_msd.csv', respectively. </li> <li>'results_summary+figures.opju': This is a Origin file summarizing the raw data and containing data figures in the manuscript.</li> </ul> Typical particle recording has about 30 s duration. The MSDs are calculated for τ up to 30 seconds. For data analysis, MSDs up to τ = 10 s were used in order to avoid errors occurring at marginal τ. The data with cetyltrimethylammonium chloride (CTAC) can be found in a separate repository:  Kim, Jeonghyeon, & Martin, Olivier J. F. (2021). Dataset for the Manuscript: Surfactants Control Optical Trapping Near a Glass Wall [Data set]. Zenodo. https://doi.org/10.5281/zenodo.5557074

opencc-by-4.0Oct 2022View details →

Data for manuscript, "An optimized workflow for MS-based quantitative proteomics of challenging clinical bronchoalveolar lavage fluid (BALF) samples"

Clinical BALF samples are rich in biomolecules, including proteins, and useful for molecular studies of lung health and disease.  However, MS based proteomic analysis of BALF is impeded by the dynamic range of protein abundance, and potential for interfering contaminants.  We have developed a workflow that eliminates these challenges.  By combining high abundance protein depletion, protein trapping, clean-up, and in-situ tryptic digestion, our workflow is compatible with both qualitative and quantitative MS-based proteomic analysis.  The workflow includes collection of endogenous peptides for peptidomic analysis of BALF, if desired, as well as amenability to offline semi-preparative or microscale fractionation of peptide mixtures prior to LC-MS/MS analysis, for increased depth of analysis.  We show the effectiveness of this workflow on BALF samples from COPD patients.  Overall, our workflow should allow MS-based proteomics to be applied to a wide variety of studies focused on BALF clinical samples.       Note:  Due to the nature of some of the files, file wendt005_ostr0103_18260_20210831_BALF_FAIMS_MS2_TMT16.msf, wendt005_ostr0103_18976_20230202_quantReport.msf, cmsptc_higgi022_18988_20230203_18976DW_EnF_hcdlT_1R.raw, cmsptc_higgi022_18988_20230203_18976DW_EnF_hcdlT_2R.raw, cmsptc_higgi022_18988_20230203_18976DW_EnF_hcdlT_3R.raw and cmsptc_higgi022_18988_20230203_18976DW_Eclipse_noFAIMS_quantReport.msf were zipped into compressed folders before uploading.

opencc-by-4.0Jul 2022View details →

Simulated genomes from manuscript "On the Genes, Genealogies and Geographies of Quebec"

Tree sequences of simulated whole genomes of 1.4M present day individuals with at least four grandparents linked to the BALSAC French-Canadian pedigree. Although the tree sequences have been censored to remove personal identifying information, we have included temporal (decade) and spatial (latitude and longitude) information for the 1.4M samples and their ~2M genealogically recoded genetic ancestors.

opencc-by-4.0Mar 2023View details →

Raw and analyzed data for manuscript "Atmospheric non-thermal plasma reduction of natively oxidized iron surfaces"

Raw and analyzed data for manuscript "Atmospheric non-thermal plasma reduction of natively oxidized iron surfaces"

opencc-by-4.0Mar 2023View details →

Supporting data for the manuscript "Protein quality assessment with graph convolution guided by a loss function designed for high quality decoys"

This dataset provides the predictions of the protein quality assessment method Q_epsilon with respect to CASP13 and CASP14, as well as a snapshot of the github repository providing the code for the method. The format of the file is as follows:  The first column represents the target and decoy names in the format  <target name>_<decoy name>.  The second column is the true GDTTS, and the third column represents the predicted GDTTS by Q_epsilon.

opencc-by-4.0Mar 2023View details →

Supplementary data for the manuscript entitled "Evolution of the convective boundary layer in a WRF simulation nested down to 100 m resolution during a cloud-free case of LAFE 2017 and comparison to observations" (JGR Atmospheres)

This dataset contains additional material to reproduce the simulation and some of the figures of the manuscipt entitled "Evolution of the convective boundary layer in a WRF simulation nested down to 100 m resolution during a cloud-free case of LAFE 2017 and comparison to observations" in the Journal of Geophysical Reasseach - Atmospheres.