Find research datasets worth reusing

opencc-by-4.0Nov 2021View details →

Probing Ion Channel Functional Architecture and Domain Recombination Compatibility by Massively Parallel Domain Insertion Profiling

Supplementary Data for a large insertional profiling study described in Coyote-Maestas et al. (2021) Nature Communications.

opencc-by-4.0Dec 2021View details →

Transcriptomic profiling of clobetasol propionate-induced immunosuppression in challenged zebrafish embryos

We have conducted an immune challenge experiment on 48h zebrafish embryos, which were previously treated with the immunosuppressive drug clobetasol propionate (CP). The embryos' immune system was challenged by injection of a mix of different pathogen associated molecular patterns (PAMPs). RNA sequencing was performed in order to detect altered molcular expression levels induced by CP, PAMPs and a combination of both. The data was published in <a href="https://doi.org/10.1016/j.ecoenv.2022.113346" target="_blank" rel="noopener">Essfeld et al. 2022</a>. The uploaded data archive (<a href="https://www.7-zip.org/">7-zip</a> compressed) consists of three major data types: 1. MultiQC reports from raw RNA-Seq read processing and QC (50bp SR) 2. Result tables from differential gene expression analysis (DGEA) with DESEq2 3. Result tables from Overrespresentation Analysis (ORA) with clusterProfiler Gene count normalization and DGEA was conducted with DESeq2 (<a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8">Love et al., 2014</a>, DOI 10.1186/s13059-014-0550-8) . Three biological replicates per condition, exposure treatments were compared with respect to the control group in a pairwise fashion, applying Wald’s t-test. P values were corrected for multiple testing with independent hypothesis weighting (IHW) (<a href="https://www.nature.com/articles/nmeth.3885">Ignatiadis et al., 2016</a>, DOI 10.1038/nmeth.3885 ) after Benjamini-Hochberg (BH). To improve the signal to statistical noise ratio, the obtained log2-fold change (lfc) values were shrunk with the apeglm method described by Zhu and colleagues (<a href="https://academic.oup.com/bioinformatics/article/35/12/2084/5159452?login=true">2019</a>, DOI 10.1093/bioinformatics/bty895 ) before DGEA result tables were subjected to ORA via clusterProfiler (<a href="https://www.liebertpub.com/doi/10.1089/omi.2011.0118">Yu et al., 2012</a>, DOI 10.1089/omi.2011.0118). The ArrayExpress accession number E-MTAB-11092, provides access to the raw and DESeq2 normalized gene count matrices upon which these analysis were performed. Genes were annotated through the biomaRt package (<a href="https://www.nature.com/articles/nprot.2009.97.pdf?origin=ppub">Durinck et al., 2009</a>, DOI 10.1038/nprot.2009.97 ) in R (<a href="https://www.r-project.org/">R Core Team 2021</a>).

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Immuno-proteomic profiling reveals aberrant immune cell regulation in the airways of individuals with ongoing post-COVID-19 respiratory disease

Some patients hospitalized with acute COVID-19 suffer respiratory symptoms that persist for many months. We delineated the immune-proteomic landscape in the airway and peripheral blood of healthy controls and post-COVID-19 patients 3 to 6 months after hospital discharge. Post-COVID-19 patients showed abnormal airway (but not plasma) proteomes, with elevated concentration of proteins associated with apoptosis, tissue repair and epithelial injury versus healthy individuals. Increased numbers of cytotoxic lymphocytes were observed in individuals with greater airway dysfunction, while increased B cell numbers and altered monocyte subsets were associated with more widespread lung abnormalities. 1 year follow-up of some post-COVID-19 patients indicated that these abnormalities resolved over time. In summary, COVID-19 causes a prolonged change to the airway immune landscape in those with persistent lung disease, with evidence of cell death and tissue repair linked to ongoing activation of cytotoxic T cells.

opencc-zeroJan 2022View details →

LEXIS Turbomachinary use case: T106 profile test case

The test case for T106 profile in a linear cascade. Cascade rigs are a way to test in a simple way various turbomachinery blades. Blades are cylindrical, which means equal 2D sections from hub to tip wall, and repeated tangentially according to the specified pitch. In this case, end walls are linear, not cylindrical and not tapered. The dataset contains an <ul> <li>excel file with  <ul> <li>description of the airfoil (x, y coordinates in [mm])</li> <li>geometric pitch /chord data, aspect ratio (parallel end walls)</li> <li>entry boundary conditions <ul> <li>total pressure</li> <li>total temperature</li> <li>flow angle</li> </ul> </li> <li>outlet boundary condition  <ul> <li>static pressure</li> </ul> </li> <li>Reynold number (120 000)</li> <li>Velocity at the exit (Mach = 0,59</li> </ul> </li> <li>OpenFOAM input files for <ul> <li>serial run (Allrun)</li> <li>parallel run (Allrun_parallel)</li> </ul> </li> <li>PDF file with the description of the case and obtained results</li> </ul>

LOAC in situ profiles of aerosol concentrations in la Reunion Island in 2015

Concentration profiles gave been obtained from balloon-borne observations. They are provided for 19 aerosol size classes (between 0.2 and ~50 µm) from the surface to the stratosphere. 2 flights are provided here: 19/05/2015 and 19/08/2015.

Dataset related to article "Plasma Lipid Profiling Contributes to Untangle the Complexity of Moyamoya Arteriopathy"

DATABASE REPORTING CLINICAL, NEURORADIOLOGICAL, DEMOGRAPHICAL AND BIOLOGICAL (“OMICS”)  ANONIMYZED DATA OF A SELECTED SUBGROUP OF PATIENTS AFFECTED BY MOYAMOYA ARTERIOPATHY

opencc-by-4.0Feb 2022View details →

Model-informed target product profiles of long-acting- injectables for use as seasonal malaria prevention: code and simulation data

This simulation data set and code reproduces the Figures and analysis of PLOS Global Public Health peer-reviewed article  Model-informed target product profiles of long-acting-injectables for use as seasonal malaria prevention Authors: Lydia Burgert1, 2, Theresa Reiker1, 2, Monica Golumbeanu1,2, Jörg J. Möhrle1, 2, 3, Melissa A. Penny*1, 2   1 Swiss Tropical and Public Health Institute, Basel, Switzerland 2 University of Basel, Basel, Switzerland 3 Medicines for Malaria Venture, Geneva, Switzerland *Corresponding author: <a href="mailto:melissa.penny@unibas.ch">melissa.penny@unibas.ch</a>

Dataset related to article "PLASMA LIPID PROFILING CONTRIBUTES TO UNTANGLE THE COMPLEXITY OF MOYAMOYA ARTERIOPATHY"

DATABASE REPORTING CLINICAL, NEURORADIOLOGICAL, DEMOGRAPHICAL AND BIOLOGICAL (“OMICS”)  ANONIMYZED DATA OF A SELECTED SUBGROUP OF PATIENTS AFFECTED BY MOYAMOYA ARTERIOPATHY

opencc-zeroFeb 2022View details →

dryad40/100

Datasets and code for manuscript: Age, breed, sex, and diet influence serum metabolite profiles of 2000 pet dogs

Physiology affects metabolism, but there is a lack of large-scale studies investigating the effects of different physiological factors on canine metabolism. We utilised generalised linear models to study how age, breed, sex, sterilisation status, size, diet type, and fasting time before blood sampling affect serum concentrations of 119 metabolite measurands in over 2000 pet dogs. This dataset contains input files and code for the analyses.

Dataset - Classification of abrupt changes along viewing profiles of scientific articles

This is the dataset used to run experiments described in "Classification of abrupt changes along viewing profiles of scientific articles" (more info in https://github.com/carolmb/viewing-profiles-of-scientific-articles). Data original from PlosOne papers views.

Raw Data for the article: Changes in the Transcriptome Profiles of Human Amnion-Derived Mesenchymal Stromal/Stem Cells Induced by Three-Dimensional Culture: A Potential Priming Strategy to Improve Their Properties

Mesenchymal stromal/stem cells (MSCs) are believed to function in vivo as a homeostatic tool that shows therapeutic properties for tissue repair/regeneration. Conventionally, these cells are expanded in two-dimensional (2D) cultures, and, in that case, MSCs undergo genotypic/phenotypic changes resulting in a loss of their therapeutic capabilities. Moreover, several clinical trials using MSCs have shown controversial results with moderate/insufficient therapeutic responses. Different priming methods were tested to improve MSC effects, and three-dimensional (3D) culturing techniques were also examined. MSC spheroids display increased therapeutic properties, and, in this context, it is crucial to understand molecular changes underlying spheroid generation. To address these limitations, we performed RNA-seq on human amnion-derived MSCs (hAMSCs) cultured in both 2D and 3D conditions and examined the transcriptome changes associated with hAMSC spheroid formation. We found a large number of 3D culture-sensitive genes and identified selected genes related to 3D hAMSC therapeutic effects. In particular, we observed that these genes can regulate proliferation/differentiation, as well as immunomodulatory and angiogenic processes. We validated RNA-seq results by qRT-PCR and methylome analysis and investigation of secreted factors. Overall, our results showed that hAMSC spheroid culture represents a promising approach to cell-based therapy that could significantly impact hAMSC application in the field of regenerative medicine.

Model profiles at satellite locations, 09 - 21 UTC, 7th September, 2017

Summary This dataset contains atmospheric profiles generated from an experimental run of the ECMWF integrated forecast system (IFS), interpolated to the observation locations and times of various satellite observations using the internal IFS observation operator (known as 'the GOM arrays'). The date and time range gives a snapshot of Hurricane Irma, 2017. Satellite observations Two satellite instruments are included: <ul> <li>The Global Precipitation Mission (GPM) Microwave Imager (GMI): The profile locations are at the centres of boxes of roughly 40 km by 40 km. These boxes are used for superobbing the data, combining a minimum 15 raw GMI observations. The process of superobbing is used at ECMWF for a number of reasons including to colocate the various channels of GMI level 1b data, which are at different locations. Note that the 40 km superobbing resolution used here is different from the operational ECMWF superobbing resolution for this data (which is 80 km).</li> <li>The Advanced Technology Microwave Sounder (ATMS) on the Suomi NPP satellite. All locations in the raw level 1B dataset are included (note that the 3 x 3 averaging that is normally applied at ECMWF was switched off)</li> </ul> The satellite observations themselves are not included in this dataset and must be obtained from the relevant data providers. The profiles are provided in a semi-random order and must be colocated to the relevant observations by the user. Model details IFS cycle 47r1 has been used; further information is at https://www.ecmwf.int/en/publications/ifs-documentation. The model profiles are generated from a run of the atmospheric forecast model that is initialised from the operational analysis at 00 UTC 7th September 2017. The profiles are hence based on a short forecast of 9 - 21 hours duration that is equivalent to the 'background forecast' in the data assimilation cycle. The model uses a horizontal resolution of T1279co (equivalent to 8 - 9 km) and 137 hybrid pressure levels in the vertical. Profiles represent slabs of atmosphere that are centred on the 'full' pressure levels and are bounded by 'half' pressure levels. Hence, half pressure level 1 is 0 hPa and half pressure at level 138 is the surface pressure.  The dataset contains most of the necessary inputs for driving a radiative transfer model to simulate satellite-observed radiances. One important input that is not included is the surface emissivity, which may be estimated using a physical model integrated into the radiative transfer model, or it may be obtained from an emissivity atlas (in the context of the IFS data assimilation is in some cases estimated with a dynamic emissivity retrieval, which is not supplied in this dataset). There are 6 hydrometeors represented by the IFS. The large-scale condensation scheme represents cloud water, cloud ice, rain and snow as prognostic variables. Relating to these are a sub-grid cloud fraction which applies to cloud water and ice, and a precipitation fraction that applies to the large-scale rain and snow. Additionally, the mass flux convection scheme represents rain and snow generated by convection. The sub-grid fraction occupied by convection is not given in the file, since it is assumed to be a constant 0.05. The convection scheme does not represent convective cloud (e.g. non-precipitating particles) but it does represent the convective anvils via detrainment into the large-scale condensation scheme (hence convective anvils are represented in the large-scale cloud ice). Rain and snow were originally obtained as fluxes and converted to mixing ratios using assumptions of fall-speed and particle size distribution, as is standard within the all-sky satellite data processing at ECMWF. All mixing ratios [kg kg-1] are given relative to the moist atmosphere. The profile times are those of a model timestep close in time to when the observation was made. The model timestep is 7.5 minutes, but only every fourth timestep is available to the IFS observation operator, meaning that profile times are quantised at 0, 30 60 minutes (and so on) through the forecast range. Essentially, there should be no more than a 15 minute time mismatch between the validity time of the profile and the satellite observation time. Licensing and copyright <ul> <li>Copyright statement: Copyright "© 2022 European Centre for Medium-Range Weather Forecasts (ECMWF)".</li> <li>Source: www.ecmwf.int</li> <li>Licence Statement: This data is published under a Creative Commons Attribution 4.0 International (CC BY 4.0). https://creativecommons.org/licenses/by/4.0/</li> <li>Disclaimer: ECMWF does not accept any liability whatsoever for any error or omission in the data, their availability, or for any loss or damage arising from their use.</li> <li>Where applicable, when redistributing the data, give an indication if the material has been modified and an indication of previous modifications.</li> <li>Full ECMWF licence terms are given at https://apps.ecmwf.int/datasets/licences/general/ </li> </ul>

Water Droplet Evaporation Profiles Calculated Using SADKAT Model

Evaporation profiles of pure water droplets calculated using SADKAT model. Initial size: 25 µm Temperature range: 278.15 - 343.15 K RH range:  0 - 100 % Particle motion is ignored (gravity = 0 m^2/s) in these calculations. Evaporation profiles are saved individually as comma separated .txt files. Data is also saved as .npy files, containing lists of evaporation profiles. These may be accessed using Python 3 with the Numpy and Pandas libraries.

opencc-by-4.0Dec 2020View details →

Host and pathogen gene expression profiles in Necrotizing Soft Tissue Infections

Data underlying the article Analysis of host-pathogen gene association networks reveals patient-specific response to streptococcal and poly-microbial necrotizing soft tissue infections Sanjeevan Jahagirdar1, Lorna Morris2, Nirupama Benis3, Oddvar Oppegaard4, Mattias Svenson5, Ole Hyldegaard6, Steinar Skrede4,7, Anna Norrby-Teglund5, INFECT Study group, Vitor A. P. Martins dos Santos1,2, Edoardo Saccenti1* Contains Data described in 4.3.2 Sample Selection and in Figure 6: INFECT_DualRNASeq_norm_counts_Human.txt  Normalised counts from Kallisto mapping to GRCh38 (release 91) for 81 NSTI patients INFECT_DualRNASeq_relative_abundance_Bacteria.txt Relative abundance for all species from HumanN2 mapping for 81 NSTI patients BStrep_filtered_D1 - INFECT_DualRNASeq_relative_abundance_Bacteria.txt filtered for samples classified as Streptococcal from Thänert et al (2019) taken on the day of admission (day 1). BPoly_filtered_D1 - INFECT_DualRNASeq_relative_abundance_Bacteria.txt filtered for samples classified as polymicrobial from Thänert et al (2019) taken on the day of admission (day 1). HStrep_filtered_D1 - INFECT_DualRNASeq_norm_counts_Human.txt filtered for samples classified as Streptococcal from Thänert et al (2019) taken on the day of admission (day 1). HPoly_filtered_D1 - INFECT_DualRNASeq_norm_counts_Human.txt filtered for samples classified as polymicrobial from Thänert et al (2019) taken on the day of admission (day 1).

Electron concentration profiles calculated using different plasma chemical models during solar X-ray flares

The files contain electron concentration Ne profiles during solar X-ray flares that occurred on 24-25 October 2013 and 9-11 June 2014. The altitude range is 50-90 km. Values of electron concentration were calculated using four-, five- and eight-component models of the ionospheric D-region. Results are obtained on four VLF paths: from European transmitters ICV, FTA, GQD, DHO to Mikhnevo geophysical observatory (55°N 38°E). The data is presented as MATLAB files. Each .mat file contains data and variable "description" with data's structure information.

opencc-zeroApr 2022View details →

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Gene expression plasticity, genetic variation and fatty acid remodelling in divergent populations of a tropical bivalve species: lipid profiles

Ocean warming challenges marine organisms' resilience, especially for species experiencing temperatures close to their upper thermal limits. A potential increase in thermal tolerance might significantly reduce the risk of population decline, which is intrinsically linked to variability in local habitat temperatures. Our goal was to assess the plastic and genetic potential of response to elevated temperatures in a tropical bivalve model, Pinctada margaritifera. We benefit from two ecotypes for which local environmental conditions are characterized by either large diurnal variations in the tide-pools (Marquesas archipelago) or lower mean temperature with stable to moderate seasonal variations (Gambier archipelago). We explored the physiological basis of individual responses to elevated temperature, genetic divergence as well as plasticity and acclimation by combining lipidomic and transcriptomic approaches. We show that P. margaritifera has certain capacities to adjust to long-term elevated temperatures that was thus far largely underestimated. Genetic variation across populations overlaps with gene expression and involves the mitochondrial respiration machinery, a central physiological process that contributes to species thermal sensitivity and their distribution ranges. Our results present evidence for acclimation potential in P. margaritifera and urge for longer term studies to assess populations resilience in face of climate change.

opencc-zeroMay 2019View details →

IODP Expedition 372A Laser height profile (section half)

Height profile data were measured on the Section Half Multisensor Logger (SHMSL) by a rangefinding laser and recorded in uncorrected height units in millimeters in CSV files.

opencc-zeroAug 2019View details →

IODP Expedition 374 Laser height profile (section half)

Height profile data were measured on the Section Half Multisensor Logger (SHMSL) by a rangefinding laser and recorded in uncorrected height units in millimeters in CSV files.

opencc-by-4.0May 2022View details →

Supporting dataset for: "Plasma essential amino acid concentration and profile are associated with performance of lactating dairy cows as revealed through meta-analysis and hierarchical clustering"

This dataset was used in the meta-analysis and hierarchical clustering published in "Plasma essential amino acid concentration and profile are associated with performance of lactating dairy cows as revealed through meta-analysis and hierarchical clustering" in the Journal of Dairy Science. We searched Web of Science and Google Scholar databases through March 2020 with the terms “plasma EAA,” “milk urea” or “blood urea,” and “dairy” or lactating dairy”. To be included in our study, the papers must have met the following selection criteria: (1) been published in English in a peer-reviewed journal; (2) reported dietary ingredients on a DM basis and at minimum dietary CP concentration; (3) used treatments based on diet changes (e.g., no infusion trials were included); (4) reported DMI, lactation performance, and milk components yield; (5) reported all individual [EAA]p (excluding Trp); and (6) reported blood urea-N or plasma urea-N. Infusion studies were excluded to avoid possible effects of method of EAA supply (e.g., infusion vs. feeding) and to narrow the scope of application. The final dataset included 22 studies and 96 dietary treatments. For a more complete description of the methods, please refer to the published paper.

Trajectories and driving profiles for hybrid h2 multiple units.

Identifier: DOI Creator: German Aerospace Center, Institute of Vehicle Concepts nameType: Organizantional Title: Trajectories and driving profiles for hybrid h2 multiple units. Publisher: Deutsches Zentrum für Luft- und Raumfahrt e.V. (DLR), Institut für Fahrzeugkonzepte. Publication Year: 2022 ResourceType: Simulated Trajectories Subject: This data set comprises driving profiles and simulated trajectories for bi-mode fuel cell hydrogen multiple units. Date: 2022-02-10 Description: This data set comprises driving profiles and simulated trajectories for bi-mode fuel cell hydrogen multiple units. Methodology is described in relatedItem. FundingReference: FCH2Rail; Fuel Cell Hybrid Power Pack for Rail Applications; Grant Agreement Number: 101006633 RelatedItem: "D1.1 - Report on line and use case based requirements" of the FCH2Rail project. This dataset comprises following files: characteristic_traction_curve.csv Resembles the maximum force applicable by the electric engine at a given velocity to accelerate the train. Velocity is given in kilometer per hour [km/h], traction_force is given in newton [N]. characteristic_maximal_electrical_breaking_curve.csv Resembles the maximum force applicable by the electric engine at a given velocity to decelerate the train. Velocity is given in kilometer per hour [km/h], max_elec_braking_force is given in newton [N]. characteristic_maximal_mechanical_breaking_curve.csv Resembles the maximum force applicable by the mechanical brake at a given velocity to decelerate the train. Velocity is given in kilometer per hour [km/h], max_mech_braking_force is given in newton [N]. electrifications.csv Electrifications are derived from open street map (OSM). pkm resembles distances from start in kilometers. Electrification: 1 = electrified, 0 = not electrified. maxspeeds.csv pkm resembles distances from start in kilometers. Maxspeeds are derived from Open Street Map data. Data gaps are manually corrected with infrastructure maps from Adif. Maxspeeds in km/h. slopes.csv pkm resembles distances from start in kilometers. Slopes in permille are derived from JAXA ALOS 0.1 X 0.1 DEM. Underlying method is described in the public deliverable "D1.1 - Report on line and use case based requirements" of the FCH2Rail project. timetable.csv pkm resembles distances from start in kilometers. station_name represents common name of railway stations where the train stops. standing_time [s] resembles the standing time within the station in seconds. driving_time [s] resembles driving time to the next station in seconds. vehicle.csv Contains the descriptive values for the vehicle. Vehicle resembles the name of the train to which the corresponding  values are assigned. Static_mass is specified in kilogram [kg], rotating_mass is specified in kilogram [kg]. Davis coefficient davis_a is specified in newton [N], davis_b is specified in newton per kilometers per hour [N/(km/h)] & davis_c is specified in newton per squared kilometers per hour [N/(km/h)^2].   simulated_trajectory.csv Underlying simulation method, with which simulated trajectory is obtained is described in the public deliverable "D1.1 - Report on line and use case based requirements" of the FCH2Rail project. Traveltime is specified in seconds, starts with zero. Traveled distance is specified in meters [m]. Velocity is specified in meters per second [m/s].  Power at the wheel is specified in watt [W].