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990 results for “quantification”
Quantification and qualification of in-flight fragmentation of bombs from low-viscosity magma
<p>The dataset contains both automatic and manual image analyses of four videos: from (i) fountaining and (ii) spattering activities at the 2021 Tajogaite eruption of Cumbre Vieja volcano, La Palma, Canary Islands, Spain; from the 2021 Mount Etna eruption (iii) fountaining activity, Sicily, Italy); and from Strombolian activity (iv) in 2023 at Stromboli, Aeolian Islands, Italy.</p> <p>This dataset consists of one MATLAB file and 15 CSV files. Fourteen CSV files are named according to the case studies (e.g., T. fountaining, T. spattering, E. fountaining, S. Strombolian), the acquisition mode (Manual or Automatic), the data type (e.g., Collision, Fragmenting, Non-Fragmenting, Total), and specific case details. Notably, the "T.spattering_Manual_Collision" files are split into two categories (e.g., coarser, finer) based on bomb size classification of the colliding-pairs. Additionally, the "E. fountaining_Manual_Collision / Fragmentation" dataset is divided into two regions of interest (ROI1 and ROI2) to reflect separate analyzed areas described in the manuscript. The 15th CSV file, “FragmentingModes_All.csv”, aggregates bomb counts by fragmenting mode across all case studies and corresponds to Figure 3 in the manuscript.</p> <p>Automated analyses were performed on five different frames: four used for measuring bomb velocity and size (saved in the MATLAB file “Fourframes.mat”), and a fifth frame used for measuring bombs velocity, size, and circularity (saved in the CSV files). The MATLAB file contains four matrices, named according to the case studies (e.g., T. fountaining, T. spattering, E. fountaining, S. Strombolian). Each matrix is composed of two columns: the first for velocity and the second for bomb size. The fifth frame’s data is saved in four separate CSV files for each case study, named as “namecasestudies_Auto_Total.csv”, where “namecasestudies” changes to reflect the specific case studies analyzed. Each CSV includes three columns: velocity, bomb size, and bomb circularity respectively.</p> <p>Manual data collected in .csv files include the velocity, size and circularity and additional parameters such as: area, position, major axis and minor axis. In the “Fragmenting” files additional fields detail the fragmenting mode, the number of pyroclasts generated, and the fragmentation direction (upward, transitional, or downward). In the “Collision” files an additional field includes the number of pyroclasts produced.</p> <p>The dataset is graphically represented in the manuscript, particularly in Figures 4,5, 6, and 7. </p>
Dataset for "On the quantification of thermodynamic phases of raining clouds: insights from multi-year CloudSat and ground-based radar observations over Longmen, Southern China"
Open the record for dataset details and reuse information.
Uncertainty quantification of a thrombosis model considering the clotting assay PFA-100Ⓡ
<p>Scripts and datasets that were used to obtain figures 4B, 6, 7, 8, 9, 10, and 11.</p>
Quantification of faecal glucocorticoid metabolites as a measure of stress in the rock hyrax (Procavia capensis) living in an urban green space
<p>Despite the abundance of rock hyrax (<i>Procavia capensis</i>) within South Africa's urban areas, there is not much information available about the effect of anthropogenic activities on rock hyrax wellbeing. To determine the potential impact of anthropogenic disturbance on adrenocortical activity, we conducted an ACTH challenge to identify a suitable enzyme-immunoassay (EIA) for measuring faecal glucocorticoid metabolite (fGCM) concentrations in the rock hyrax. This study identified an 11β-hydroxyaetiocholanolone EIA as the most suitable assay in this regard. The fGCM levels measured, indicate the physiological stress response in different rock hyrax populations, living in an area with varying degrees of anthropogenic activity (low, medium, high) within the National Botanical Garden of Pretoria, South Africa. The species' habituation to human numbers <span>(weekly mean number of people</span>) was examined by determining individual flight initiation distance (FID). Seasonally, there were overall higher fGCM concentrations in late spring compared to winter. The fGCM concentrations, although not significantly different but possibly biologically relevant, in the section with the lowest anthropogenic disturbance were ~10% higher compared to those in the section with medium disturbance, and ~20% higher compared to those in the section with the highest disturbance. Animal FID did not differ significantly between seasons but they did differ significantly between sections, and decreased in accordance with fGCM concentrations. The non-invasive approach established in this study provides a foundation for assessing rock hyrax wellbeing, and can help better understand how anthropogenic presence is perceived as a stressor in this species.</p>
Dataset supporting the book chapter entitled "Ratiometric Fluorescent Safranin-O staining allows the quantification of lignin contents in muro" and published in "Histochemistry of Single Molecules"
<p>This dataset aims to test the algorithms presented in the book chapter entitled</p> <p><strong>“Ratiometric Fluorescent Safranin-O staining allows the quantification of lignin contents <em>in muro</em>” </strong></p> <p>and published in “Histochemistry of Single Molecules”</p> <p><strong>Are available:</strong></p> <p>-The algorithm, provided has an ImageJ macro ("safranine_ratio_segmentation")</p> <p>- A representative image for testing (“safranine wt-60x.nd2”)</p>
Non-intrusive semi-analytical uncertainty quantification using Bayesian quadrature with application to CFD simulations
<p>The data contained in the uploaded '.zip' file is for some of the plots in the paper ‘Duan Y*, Eaton MD, Bluck MJ, 2021, Non-intrusive semi-analytical uncertainty quantification using Bayesian quadrature with application to CFD simulations, International Journal of Heat and Fluid Flow.’ (accepted)</p>
Supplementary files for "Fast and sensitive quantification of AccQ-Tag derivatized amino acids and biogenic amines by UHPLC-UV from complex biological samples"
<p>Supplementary files for "Fast and sensitive quantification of AccQ-Tag derivatized amino acids and biogenic amines by UHPLC-MS from complex biological samples"</p>
Quantifications of FCHo2 interaction with in vitro and in cellulo systems
<p>Clathrin-mediated endocytosis (CME) is a central trafficking pathway in eukaryotic cells regulated by phosphoinositides. The plasma membrane phosphatidylinositol-4,5-bisphosphate (PI(4,5)P<sub>2</sub>) plays an instrumental role in driving CME initiation. The F-BAR domain only protein 1 and 2 complex (FCHo1/2) is among the early proteins that reach the plasma membrane, but the exact mechanisms triggering its recruitment remain elusive. Here, we show the molecular dynamics of FCHo2 self-assembly on membranes by combining minimal reconstituted <i>in vitro</i> and cellular systems. Our results indicate that PI(4,5)P<sub>2</sub> domains assist FCHo2 docking at specific membrane regions, where it self-assembles into ring-like shape protein patches. We show that the binding of FCHo2 on cellular membranes promotes PI(4,5)P<sub>2</sub> clustering at the boundary of cargo receptors and that this accumulation enhances clathrin assembly. Thus, our results provide a mechanistic framework that could explain the recruitment of early PI(4,5)P<sub>2</sub>-interacting proteins at endocytic sites.</p>
Absolute measurement of cellular activities using photochromic single-fluorophore biosensors and intermittent quantification: data and code example
<p>Minimal code example, raw and derived data for the publication on 'Absolute measurement of cellular activities using photochromic single-fluorophore biosensors and intermittent quantification'.</p>
Establishment of a fecal DNA quantification technique for rare and cryptic diet constituents in small mammals - raw data
<p class="MsoNormal"><span>DNA-based approaches have highly improved the applicability of dietary studies aimed at investigating ecological processes. These studies have provided direct insights into, otherwise difficult to measure, interactions between species and trophic levels, food web structure and ecosystem functioning. However, despite these advances, DNA-based methods have been struggling to accurately quantify the whole breadth of diet constituents because of methodological biases, such as amplification bias and digestive processes. This study is, to our knowledge, the first diet study that used droplet digital PCR to quantify diet constituents. We manipulated the diet of wild caught wood mice (<em>Apodemus sylvaticus</em>) by feeding them with a known amount of small vegetable seeds (onion and carrot) and quantified the DNA traces of these diet constituents in fecal samples. The sensitivity of the technique combined with the control on the experimental design allowed mitigation of methodological bias. We were able to accurately determine DNA concentrations of small vegetable seeds in the diet of wood mice. Quantification of target DNA demonstrated significant differences in DNA content when one vs. five seeds were consumed. <a name="_Hlk96526385"></a>These differences remained significant when the age, sex, and other diet constituents of the mice were altered. Different DNA markers, targeting different parts of the chloroplast, influenced onion DNA detectability. However, all onion and carrot markers showed higher DNA content for higher seed numbers. Overall, the sensitive DNA based approach developed in this study allows for minimally-invasive quantification of small diet constituents in feces, which would otherwise be undetectable with traditional methods.</span></p>
TPM quantification (StringTie) of long-read isoforms in TCGA breast tumors and GTEx
<p>StringTie was applied to quantify the expression of long-read isoforms sequenced in TCGA and GTEx samples.</p> <p>Inputs:</p> <ul> <li>RNA-seq samples (bam files) from breast cancer samples from TCGA (tumors) and GTEx tissues (healthy controls).</li> <li>GTF: full-length isoforms sequenced using PacBio long-read sequencing in breast tumors. See <a href="https://www.science.org/doi/10.1126/sciadv.abg6711">A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer</a>.</li> </ul> <p>Output: tab-delimited files with TPM values for isoforms parsed from StringTie results.</p> <p>More details: <a href="https://www.science.org/doi/10.1126/sciadv.abg6711">A comprehensive long-read isoform analysis platform and sequencing resource for breast cancer</a></p> <p> </p> <p> </p> <p> </p> <p> </p>
[Suplemental Materials] Accuracy of bird identifications in citizen science data: a quantification of errors using photographic records
<p><strong>Supporting Information</strong></p> <p><strong>Appendix S1</strong>. The full dataset used in this study with a reproducible R code to perform data quality and network analyses. </p> <p><strong>Appendix S2</strong>. All species ranking of identification accuracy of photo reports submitted to eBird in Argentina. The ranking is first ordered by the minimum value found for either precision and recall scores, and second by the number of samples analyzed for each species. Species that were tagged as difficult to identify are indicated as ‘TRUE’ in column D named ‘hard_to_id’.</p> <p><strong>Appendix S3</strong>. High-resolution network (Html file).</p>
Accuracy of bird identifications in citizen science data: a quantification of errors using photographic records [R code]
<p><strong>Appendix S1</strong>. The full dataset used in this study with a reproducible R code to perform data quality and network analyses. R code archived to Zenodo for publication. </p>
Uncertainty quantification in cerebral circulation simulations focusing on the collateral flow: Surrogate model approach with machine learning
<p>Data and code underlying the findings reported in the paper titled "Uncertainty quantification in cerebral circulation simulations focusing on the collateral flow: Surrogate model approach with machine learning."</p>
Statistics and quantification dataset of Haspin and its related proteins analysis in mouse spermatocytes
<p><span>Chromosome segregation requires that centromeres properly attach to spindle microtubules. This essential step regulates the accuracy of cell division and therefore must be precisely regulated. One of the main centromeric regulatory signaling pathways is the Haspin-H3T3ph-</span><span>chromosomal passenger complex (</span><span>CPC) cascade, which is responsible for the recruitment of the</span><span> CPC to the centromeres</span><span>. In mitosis, Haspin kinase phosphorylates histone H3 at threonine 3 (H3T3ph), an essential epigenetic mark that recruits the CPC, whose catalytic component is Aurora B kinase. However, the centromeric Haspin-H3T3ph-CPC pathway remains largely uncharacterized in mammalian male meiosis. We have analyzed Haspin functions by either its chemical inhibition in cultured spermatocytes using LDN-192960, or the ablation of <em>Haspin</em> gene in <em>Haspin-/-</em>. Our studies suggest that Haspin kinase activity is required for proper chromosome congression during both meiotic divisions and for the recruitment of Aurora B and kinesin MCAK to meiotic centromeres. However, the absence of H3T3ph histone mark does not alter Borealin and SGO2 centromeric localization. These results add new and relevant information regarding the regulation of the Haspin-H3T3ph-CPC pathway and centromere function during meiosis. </span></p>
Spatial patterns and quantification of lacustrine groundwater discharge determined based on 222Rn
<p>Shape of water pixels calculated by Modified Normalized Difference Water Index algorithm based on Landsat8 images</p>
Spatial patterns and quantification of lacustrine groundwater discharge determined based on 222Rn
<p>The field parameter [temperature (T), electrical conductivity (EC), pH, dissolved oxygen (DO), redox potential (Eh) and 222Rn concentration] were listed here. </p>
Spatial patterns and quantification of lacustrine groundwater discharge determined based on 222Rn
<p>The 132 bathymetric data from the lake while lake samples were taken on board. We created a bathymetric contour map in ArcGIS 10.2 using the natural neighborhood method to reflect the overall bathymetry of the lake through 116 randomly selected bathymetric data. The size of the Landsat 8 image was used as the basic unit (30*30 m) to divide the lake into 30*30 m areas and read data from 16 other bathymetric points that were not involved in the production of the bathymetric map.</p>
Spatial patterns and quantification of lacustrine groundwater discharge determined based on 222Rn
<p>Wind speed data were collected from the Shishou weather station monitored by the China Meteorological Network (http://data.cma.cn/dataService/cdcindex/datacode/A.0012.0001/show_value/normal.html).</p>
A Rapid and Simple UHPLC-MS/MS Method for Quantification of Plasma Globotriaosylsphingosine (lyso-Gb3)
<p>Fabry disease (FD) is a rare X-linked lysosomal storage disorder caused by α-galactosidase A gene (GLA) mutations, resulting in loss of activity of the lysosomal hydrolase, α-galactosidase A (α-Gal A). As a result, the main glycosphingolipid substrates, globotriaosylceramide (Gb3) and globotriaosylsphingosine (lyso-Gb3), accumulate in plasma, urine, and tissues. Here, we propose a simple, fast, and sensitive method for plasma quantification of lyso-Gb3, the most promising secondary screening target for FD. Assisted protein precipitation with methanol using Phree cartridges was performed as sample pre-treatment and plasma concentrations were measured using UHPLC-MS/MS operating in MRM positive electrospray ionization. Method validation provided excellent results for the whole calibration range (0.25–100 ng/mL). Intra-assay and inter-assay accuracy and precision (CV%) were calculated as <10%. The method was successfully applied to 55 plasma samples obtained from 34 patients with FD, 5 individuals carrying non-relevant polymorphisms of the GLA gene, and 16 healthy controls. Plasma lyso-Gb3 concentrations were larger in both male and female FD groups compared to healthy subjects (<em>p </em>< 0.001). Normal levels of plasma lyso-Gb3 were observed for patients carrying non-relevant mutations of the GLA gene compared to the control group (<em>p </em>= 0.141). Dropping the lower limit of quantification (LLOQ) to 0.25 ng/mL allowed us to set the optimal plasma lyso-Gb3 cut-off value between FD patients and healthy controls at 0.6 ng/mL, with a sensitivity of 97.1%, specificity of 100%, and accuracy of 0.998 expressed by the area under the ROC curve (C.I. 0.992 to 1.000, <em>p</em>-value < 0.001). Based on the results obtained, this method can be a reliable tool for early phenotypic assignment, assessing diagnoses in patients with borderline GalA activity, and confirming non-relevant mutations of the GLA gene.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.