Find research datasets worth reusing

opencc-by-4.0May 2024View details →

FIGURE 4 in Cytogenetic profiles of two circumglobal snake mackerel species (Scombriformes: Gempylidae) from deep waters of the São Pedro and São Paulo Archipelago

FIGURE 4 | Karyotypes of Ruvettus pretiosus and Promethichthys prometheus showing the distribution of the Tol2 and Rex3 elements in the chromosomes under fluorescence in situ hybridization. Scale bar = 5 µm.

opencc-by-4.0Aug 2022View details →

Immune repertoire profiling reveals its clinical application potential and triggers for Neuromyelitis Optica Spectrum Disorders

This dataset, containing TCRbeta-chain sequcening data of Neuromyelitis Optica Spectrum Disorders patients and healthy, is the basis for the following publication:  "Immune repertoire profiling reveals its clinical application potential and triggers for Neuromyelitis Optica Spectrum Disorders".

opencc-by-4.0Aug 2024View details →

Analyses of metabolite profiling of Drosophila Parkinson's Disease model for identifying novel glial-based therapeutic targets

Analysis for genetic screening and metabolomics identify glial adenosine metabolism as a therapeutic target in Parkinson’s disease This project contains the analysis of metabolite abundance measurements obtained with four different liquid chromatography mass spectrometry methods of synuclein expressing or control or fly brains in a wilde type or Adk1 knockout background.   <div> <h2>Table of contents</h2> <a href="https://github.com/jravilap/Olsen_Analyses#table-of-contents"></a></div> <div> <h3>Prerequisites</h3> <a href="https://github.com/jravilap/Olsen_Analyses#prerequisites"></a></div> <ul> <li>R (version 4.3.1 or higher)</li> <li>RStudio (optional, but recommended)</li> </ul> <div> <h3>R Packages</h3> <a href="https://github.com/jravilap/Olsen_Analyses#r-packages"></a></div> The following R packages are required. You can install them using the commands below: <div> <pre>install.packages(c("readxl", "calibrate", "dplyr", "ggplot2"))</pre> <div> </div> </div> <div> <h3>Package versions</h3> <a href="https://github.com/jravilap/Olsen_Analyses#package-versions"></a></div> <ul> <li>ggplot2_3.5.1</li> <li>dplyr_1.1.4</li> <li>yaml_2.3.8</li> <li>calibrate_1.7.7</li> <li>readxl_1.4.3</li> </ul> <div> <h2>Project Structure</h2> <a href="https://github.com/jravilap/Olsen_Analyses#project-structure"></a></div> <ul> <li><code>code/</code>: Contains the R scripts for the analysis.</li> <li><code>data/</code>: Processed data files. <ul> <li><code>22_0322_alphaSyn_fly_pilot_Classes.xlsx</code>: metabolite profiling data</li> <li><code>dup_metabs_decision.csv</code>: Table defining which metabolites profiled in more than one method should be used.</li> </ul> </li> <li><code>results/</code>: Output files, including plots and tables.</li> <li><code>common_functions/</code>: Custom R functions used in the analysis.</li> <li><code>config.yml</code>: Configuration file for setting paths.</li> </ul>

opencc-by-4.0Sep 2024View details →

Data for device simulation in the article "Analysing the impact of the hole transport layer on the space charge distribution and hysteresis in perovskite solar cells using capacitance-voltage profiling"

This repository contains the data used to perform device simulation in the article "Analysing the impact of the hole transport layer on the space charge distribution and hysteresis in perovskite solar cells using capacitance-voltage profiling", submitted in September 2024 to the journal Sustainable Energy and Fuels. The authors of this data and the article are E. Regalado-Pérez, Evelyn B. Díaz-Cruz, and J. Villanueva-Cab  The scripts (.m) and input files (.csv) hosted here are based on the files created by the authors of the Driftfusion code, which can be found in the GitHub repository  "barnesgroupICL/Driftfusion" at https://github.com/barnesgroupICL/Driftfusion.

openmit-licenseSep 2024View details →

The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation

Additional files, Scripts and Data related to the manuscript Papadopoulos et al, The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation.  Additional file 1: contains supplemental figures and tables of the manuscript Additional file 2: contains the complete list of the 89 Ribo-Seq datasets (89 biological replicas). Papadopoulos_et_al_2024.tar.gz: contains the scripts, raw data, intermediate data and final (processed) data to reproduce the analyses, Figures, and Tables of the manuscript Papadopoulos et al, The ribosome profiling landscape of yeast reveals a high diversity in pervasive translation.  The archive contains 3 directories: *** input: contains the protocols, raw data, and the associated intermediate processed data that are used as inputs of the scripts that perform the subsequent analyses and generate the Figures and Tables *** scripts: all the scripts necessary to perform the analyses of the manuscript and generate the final data, Figures and Tables available in the ./output directory *** output: contains the final processed data including the final lists and tables resulting from MSMS analyses or RiboSeq analyses, the final Figures and Tables of the manuscript     as well as the 3 final tables that integrate the processed data from Ribo-Seq, MSMS, evolutionary analyses, sequence and structural analyses, final analyses on codon propensities. These 3 tables, beyond being necessary for the anlayses performed for this study can also be useful for users to realize their own analyses. All the data, Figures and Tables contained in this directory can be directly generated from the scripts available in the directory ./scripts and the data contained in the directory ./input. Please see the README in the different directories to reproduce everything.

opencc-by-4.0Sep 2024View details →

Discrete Flow Cytometry of Depth Profile Samples from TN413 (2023) Using a BD Influx Cell Sorter

The dataset consists of BD Influx-based analysis of phytoplankton populations from discrete flow cytometry data collected underway during the University of Washington School of Oceanography 2023 undergraduate senior thesis cruise (TN413) oceanographic research cruise from Hawaii to Fiji. The data consists of cell abundance, cell size (equivalent spherical diameter), carbon quota, and carbon biomass for heterotrophic bacteria, picophytoplankton populations, namely the cyanobacteria Prochlorococcus and Synechococcus, and small eukaryotic phytoplankton (<5 μm ESD). Time is in UTC format, latitude and longitude are in decimal degrees, and depth is in meters. Further information can be found here: https://github.com/fribalet/FCSplankton

opencc-by-4.0Sep 2024View details →

ERT and topographic profiles from the Sarpang terraces (Bhutan)

This dataset provides data used for Gautier et al. (2024) paper. See reference for details. Electrical Resistivity Tomography profiles at 1 m, 2 m and 5 m electrode spacing with Wenner-Schlumberger (ws) and Dipole-Dipole (dd) geometries. Topographic profiles P0 to P8 from staellite photogrammetry and post-processed to remove vegetation.

TROPOMI research ozone profile dataset in August 2022

This dataset contains ozone profile retrievals from TROPOMI (TROPOspheric Monitoring Instrument) backscattered ultraviolet measurements  during the Asian Summer Monsoon Chemical and Climate Impacts Project (ACCLIP) conducted over the Western Pacific in summer 2022. The data is stored in individual files for each date, with all variables described in the attribute field. This dataset has been used in Bak et al. (submitted) for an integrated analysis of ozone and carbon monoxide alongside ACCLIP field datasets and other satellite products. Details on Retrieval Methodology: <ol> <li>Inverse Method: Optimal estimation</li> <li>Radiative Transfer Model: PCA-VLIDORT v2.8</li> <li>A Priori Ozone: Tropopause-based ozone profile climatology</li> <li>Fitting Window: 310-335 nm in the TROPOMI UV3 channel</li> <li>Spatial Resolution: Cross-track pixels are binned to match the spatial resolution of the TROPOMI UV1 channel, with every 5 scan pixels coadded.</li> <li>Spatial coveragne : 50E-180E, 10S-70S</li> <li>Heritage: OMI PROFOZ ozone profile algorithm (Liu et al., 2010; Bak et al., 2024)</li> </ol>

Vertically pointing doppler radar profiles (24 GHz Metek MRR-2) at Concordia Station (Dome C, Antarctica), aggregated to 5min, monthly netCDF archive

Vertical profiles along the first three kilometres of atmosphere above the ground (from 300 to 3000 m AGL) of equivalent radar reflectivity factor (Ze), Doppler velocity (W) and Doppler spectral width (Sw) from a 24-GHz vertically pointing Micro Rain Radar MRR-2 by METEK GmbH positioned at Concordia Station (Dome C, Antarctica). Metadata available at <a href="https://antarcticdatacenter.cnr.it/geonetwork/srv/eng/catalog.search#/metadata/6dc25ff0-4c03-4ca8-af0d-cba06a411dc2" target="_blank" rel="noopener">https://antarcticdatacenter.cnr.it/geonetwork/srv/eng/catalog.search#/metadata/6dc25ff0-4c03-4ca8-af0d-cba06a411dc2</a>  -------------------------------------------------------------------- Example of netCDF file structure: <h2>File "DMC_MRR_MeK_201901_5min.nc"</h2> <pre> dimensions: range = 31; time = UNLIMITED; // (7736 currently) variables: float Ze(range=31, time=7736); :description = "Equivalent reflectivity factor relative to the most significant peak, dealiased, 5min non-logarithmic average. NaN means clear sky at the specified height."; :units = "dBZ"; :_ChunkSizes = 31U, 1U; // uint long time_UTC(time=7736); :description = "Measurement time. Timestamp indicates the end of the aggregation interval, e.g. 01-Mar-2020 00:05:00 represents the average of the variables between 01-Mar-2020 00:00:01 and 01-Mar-2020 00:05:00."; :time_zone = "UTC"; :units = "Seconds since 1970-01-01 00:00:00 (Unix time)."; :_ChunkSizes = 512U; // uint float W(range=31, time=7736); :description = "Mean Doppler Velocity of the most significant peak, dealiased, 5min average. Value not available in clear-sky conditions."; :units = "m s^-1"; :_ChunkSizes = 31U, 1U; // uint float height(range=31, time=7736); :description = "Height above instrument."; :units = "m"; :_ChunkSizes = 31U, 1U; // uint float spectralWidth(range=31, time=7736); :description = "Doppler Spectral Width of the most significant peak, dealiased, 5min average. Value not available in clear-sky conditions."; :units = "m s^-1"; :_ChunkSizes = 31U, 1U; // uint // global attributes: :title = "Micro rain radar data processed with IMProToo (Maahn, M. and Kollias, P., 2012), aggregated to 5min, monthly netCDF archive."; :comment = "IMProToo has been developed for improved snow measurements. Note that this data has been processed regardless of precipitation type."; :time_label = "Jan 2019"; :source = "Micro Rain Radar 2 (MRR-2), METEK GmbH, at DMC (Antarctica), frequency: 24 GHz, power: 50 mW, antenna diameter: 60 cm [https://metek.de/product/mrr-2/]"; :institution = "CNR-INO, Florence (IT)"; :contact_person = "Gianluca Di Natale, CNR-INO, Florence (IT), gianluca.dinatale@ino.cnr.it"; :location = "Concordia Station (Dome C, Antarctica, 75°06\'S, 123°21\'E, 3233 m a.s.l.)"; :author = "Giacomo Roversi, Ca\' Foscari University, Venice (IT) and CNR-ISAC, Rome (IT), g.roversi@isac.cnr.it"; :creation_date = "22-Oct-2024 17:32:24 UTC"; :coverage = "Monthly coverage (Jan 2019): 90.3226 %"; :time_resolution = "5 minutes"; :history = "Created with IMProToo v0.107 [https://github.com/maahn/IMProToo], aggregated to 5 minutes temporal resolution with an average of the 1-minute values if least 3 out of 5 are not NaN."; </pre>

Global cellular proteo-lipidomic profiling of diverse lysosomal storage disease mutants using nMOST

<div> <div> <div> <div> Lysosomal storage diseases (LSDs) comprise ~50 monogenic disorders marked by the buildup of cellular material in lysosomes, yet systematic global molecular phenotyping of proteins and lipids is lacking. We present a nanoflow-based multi-omic single-shot technology (nMOST) workflow that quantifies HeLa cell proteomes and lipidomes from over two dozen LSD mutants. Global cross-correlation analysis between lipids and proteins identified autophagy defects, notably the accumulation of ferritinophagy substrates and receptors, especially in NPC1-/- and NPC2-/- mutants, where lysosomes accumulate cholesterol. Autophagic and endocytic cargo delivery failures correlated with elevated lyso-phosphatidylcholine species and multi-lamellar structures visualized by cryo-electron tomography. Loss of mitochondrial cristae, MICOS-complex components, and OXPHOS components rich in iron-sulfur cluster proteins in NPC2-/- cells was largely alleviated when iron was provided through the transferrin system. This study reveals how lysosomal dysfunction affects mitochondrial homeostasis and underscores nMOST as a valuable discovery tool for identifying molecular phenotypes across LSDs. </div> </div> </div> </div>

Raw image files in Fig. S1E associated with "Endo-IP and Lyso-IP Toolkit for Endolysosomal Profiling of Human Induced Neurons"

This entry contains raw ND2 files shown in Fig. S1E associated with: https://doi.org/10.1101/2024.09.24.614704

Raw image files of uncropped western blots associated with "Endo-IP and Lyso-IP Toolkit for Endolysosomal Profiling of Human Induced Neurons"

This entry contains uncropped blots for Fig. 1C, S1C, S1D, 2I, and S3B for: https://doi.org/10.1101/2024.09.24.614704

opencc-by-4.0Nov 2024View details →

Vertical Microstructure Profiler (VMP-2000) data from Investigator cruise IN2018 V05

VMP-2000 CTD and microstructure data from IN2018_v05 measured temperature [C] salinity [PSU] pressure [Dbars] rate of dissipation of kinetic energy [W/kg] rate of dissipation of thermal variance [C^2/s]

Polysome profile glucose beta-cells

Polysome profile analysis of human pancreatic beta-cells exposure to glucose A human pancreatic beta cell line (betaH2) was exposed to glucose after starvation. Total RNA was collected for a bulk RNA-seq analysis. Three biological repeats were produced for each of the the low and high glucose conditions resulting in to 6 sequence (fastq) files. Three different mRNA-ribosomal fractions were selected from a sucrose gradient corresponding to single ribosomes (monosomes), light ribosomes (2-4) and heavy ribosomes (5 and more). Three biological repeats were produced for each fraction and for the two conditions (low and high glucose) resulting to 18 different (fastq) sequenced files. In total the study consists of 24 submitted fastq files, 6 corresponding to total RNA from two conditions (three replicates) and 18 corresponding to polysome profile, 3 fractions times two conditions times 3 replicates. All 24 *.fastq.gz files are available in the reads_PolysomeProfile_RNAseq_BetaCells.tar archive. In addition to the raw reads we provide the processed data: The raw counts table ( countsTOTALS_CodingGenes.tsv) and the Transcripts Per Million table (TPMs) (polysomeProfile_TPM_proteinCoding.csv) files of the data produced from the polysome profile and RNA-seq experiments described in the experimental design that can be found in: https://github.com/parisepigenetics/Translatome_Bcells_glucose

Normalized profile of industrial demand response

Normalized profile of industrial demand response based on an industrial facility in Austria in 2019

ASSESSMENT OF ADHERENCE TO NEW ORAL ANTICOAGULANTS IN ATRIAL FIBRILLATION PATIENTS WITHIN THE OUTPATIENT REGISTRY PROFILE. PROSPECTIVE OBSERVATIONAL STUDY (ANTEY study)

Rationale Prevention of stroke and thromboembolic complications in non-valvular atrial fibrillation is one of the most common indications for the use of all NOACs and warfarin in cardiology. The issue of regular intake of all OACs, i.e. the issue of adherence to anticoagulation therapy, is paramount for better treatment. The problem of assessment of different aspects of adherence to OACs in patients with atrial fibrillation within an outpatient registry is of current interest. Primary Study Objectives The aim of the present study is to assess adherence to therapy and factors associated with adherence in patients with CV disease complicated by non-valvular atrial fibrillation requiring OAC treatment within the outpatient registry PROFILE (prospective, observational study). <ol> <li>Data collection in patients with non-valvular atrial fibrillation requiring OAC treatment included in the registry</li> <li>Evaluation of actual patient adherence to OACs</li> </ol> Secondary Study Objective(s) <ol> <li>Evaluation of potential patient adherence to OACs</li> <li>Determination of most significant factors associated with adherence to OACs in patients with non-valvular AF</li> <li>Validation of new original questionnaire</li> <li>Evaluation of doctor’s adherence to OAC prescription according to Guidelines (ESC). Management of atrial fibrillation,2016)</li> </ol> Material and methods .The study included 201 patients with nonvalvular AF from the outpatient "PROFILE" registry, 118 (58,7%) males. The mean age was 71,1 ±8,7 years. The study protocol consisted of the inclusion visit (V0), 6-month follow-up visit (V1), and phone contact 1 year after V0 (follow-up, FU). In V0, all patients were prescribed one of the NOACs. At V1 doctors could recommend warfarin or another NOAC to patients, who have refused to take prescribed NOAC. Medical adherence was determined using the original questionnaire Inclusion Criteria (detailed) <ul> <li>Men and women above 18 years of age who were included in the "PROFILE" registry by the start of the observational study</li> <li>Presence of written informed consent to participate in the study, fill in the study questionnaires, and have personal data analyzed</li> <li>Presence of any form of non-valvular atrial fibrillation with CHA2DS2-VASc score of ≥1 or patients with CHA2DS2-VASc score = 0, who are already taking OAK</li> </ul> Exclusion Criteria Patients with high bleeding risk, including patients with: <ul> <li>Congenital or acquired bleeding disorders</li> <li>Uncontrolled resistant hypertension</li> <li>Exacerbation of gastric and duodenal ulcer</li> <li>Vascular retinopathy</li> <li>Recent history of intracranial or intracerebral hemorrhage</li> <li>Pathology of the brain and spinal cord vessels</li> <li>Recent history of the brain, spinal cord, or eye surgery</li> <li>History of bronchiectasis or pulmonary hemorrhage</li> <li>A CHA2DS2-VASc score of 0 (OACs are not indicated)</li> <li>Pregnancy, lactation</li> <li>Planned surgery</li> <li>Known hypersensitivity to ingredients of medications used in the study</li> </ul> Visit schedule Visit schedule Two visits at 6-month intervals are scheduled for each patient as part of routine clinical practice: Visit 0– visit at study entry: <ul> <li>receiving written informed consent to participate in research from patients</li> <li>inclusion in the program</li> <li>assessment of inclusion and exclusion criteria</li> <li>verification of non-valvular atrial fibrillation diagnosis (according to medical documentation, confirming the history of atrial fibrillation: ECG, Holter monitoring, etc..)</li> <li>collecting information on received medication therapy, including OACs</li> <li>physical examination of patients (measurements of blood pressure, heart rate, height, weight, waist circumference)</li> <li>questioning of patients to determine potential and actual adherence to OACs</li> <li>computation of points on the scale CHA2DS2-VASc and HAS-BLED to determine the indications for the appointment of the OACs and the identification of an increased risk of bleeding</li> <li>to determine the INR in patients who agreed to replace the use of warfarin with one of the NOACs</li> <li>prescription of OACs according to routine clinical practice and official labels for these medications</li> <li>instructing patients (according to the specifically designed scheme) to regularly take prescribed medications, be aware of precautionary measures when taking OACs, telling them about the pros and cons of treatment with OACs</li> </ul> Visit 1 – visit at 6 months after the Visit 0: <ul> <li>collecting information on patients’ compliance with doctor’s recommendations</li> <li>collecting information on patients’ actual medication therapy</li> <li>collecting information on the safety of treatment with OACs (in case the patient has been taking them), recording all adverse events that occurred during the study period</li> <li>measurements of blood pressure, heart rate as a part of routine clinical practice</li> <li>questioning of patients to determine potential and actual adherence to OACs</li> </ul> FU - follow-up calls to patients (one year) Phone contact to determine patient’s life status, possible (fatal and non-fatal complications of non-valvular atrial fibrillation) and fill (after receiving patient’s consent) the original questionnaire. Primary Outcome The proportion of complete, partial adherent and non-adherent patients according to the original questionnaire Secondary Outcomes <ul> <li>The proportion of potentially adherent patients (according to the original questionnaire)</li> <li>Identification of baseline characteristics associated with adherence</li> <li>The proportion of doctors prescribed OAC according to guidelines.</li> </ul> Safety Outcomes Adverse events and outcomes were recorded from the start of treatment with the OAC until the end of the observational study period. The doctor evaluated the severity of adverse events and outcomes if necessary took measures for their medical treatment according to current clinical practice.

Deep spatial profiling of human COVID-19 brains

Imaging mass cytometry data (txt files and folders containing single tiffs + cell masks) generated for the analysis of postmortem brains of COVID-19 patients and control groups (multiple sclerosis and patients who received ECMO therapy).

opencc-by-4.0Nov 2020View details →

Georeferenced Spanish Soil Profile Database (SODES)

The Georeferenced Spanish Soil Profile Database (SODES) contains soil information and data values for 1683 georereferenced soil profiles, compiled from an extensive bibliographic review. SODES allows the characterisation of the different peninsular Spanish soil types and is a suitable tool for assessments and decision making purposes dealing with different issues.

opencc-by-4.0Jul 2021View details →

The effect of the graded bilayer design on the strain depth profiles and microstructure of CuW nano-multilayers

In this document we share: -the XRD in-plane scans acquired on Cu/W multilayers at different incidence angle, -the in-situ stress curvature data acquired during multilayer growth, -the in plane d-spacing derived at different incidence angle, used for the simulation of the strain gradient.