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361 results for “derived response”
Image-derived indicators of phytoplankton community responses to Pseudo-nitzschia blooms
<p>Data associated with the manuscript "Image-derived indicators of phytoplankton community responses to <em>Pseudo-nitzschia</em> blooms" submitted to the journal <em>Harmful Algae</em>. There is an additional R script that calculates an interaction metric as described in the paper. </p>
Cross-reactive CD8+ T cell responses to tumor-associated antigens (TAAs) and homologous microbiota-derived antigens (MoAs)
<p><strong><span>Background: </span></strong><span>We have recently shown extensive sequence and conformational homology between tumor-associated antigens (TAAs) and antigens derived from microorganisms (MoAs). The present study aimed to assess the breadth of T-cell recognition specific to MoAs and the corresponding TAAs in healthy subjects (HS) and patients with cancer (CP).</span></p> <p><strong><span>Method: </span></strong><span>A library of >100 peptide-MHC (pMHC) combinations was used to generate DNA-barcode labelled multimers. Homologous peptides were selected from the Cancer Antigenic Peptide Database, as well as Bacteroidetes/Firmicutes-derived peptides. They were incubated with CD8+ T cells from the peripheral blood of HLA-A*02:01 healthy individuals (n=10) and cancer patients (n=16). T cell recognition was identified using tetramer-staining analysis. Cytotoxicity assay was performed using as target cells TAP-deficient T2 cells loaded with MoA or the paired TuA.</span></p> <p><strong><span>Results: </span></strong><span>A total of 66 unique pMHC recognized by CD8+ T cells across all groups were identified. Of these, 21 epitopes from microbiota were identified as novel immunological targets. Reactivity against selected TAAs was observed for both HS and CP. pMHC tetramer staining confirmed CD8+ T cell populations cross-reacting with CTA SSX2 and paired microbiota epitopes. Moreover, PBMCs activated with the MoA where shown to release IFNγ as well as to exert cytotoxic activity against cells presenting the paired TuA.</span></p> <p><strong><span>Conclusions: </span></strong><span>Several predicted microbiota-derived MoAs are recognized by T cells in HS and CP. Reactivity against TAAs was observed also in HS, primed by the homologous bacterial antigens. CD8+ T cells cross-reacting with MAGE-A1 and paired microbiota epitopes were identified in three subjects. Therefore, the microbiota can elicit an extensive repertoire of natural memory T cells to TAAs, possibly able to control tumor growth (“natural anti-cancer vaccination”). In addition, non-self MoAs can be included in preventive/therapeutic off-the-shelf cancer vaccines with more potent anti-tumor efficacy than those based on TAAs.</span></p>
Analysis of hMSC-derived chondrocytes in response to stimulation with SARS-CoV-2 spike proteins
<p>Previous studies have detected the presence of SARS-CoV-2 viral proteins in bronchial cartilage chondrocytes. We hypothesised that the leakage of viral proteins to local joint tissue was due to virus-induced endothelial dysfunction. Studies have also shown upregulation of endothelin-1 (ET-1), the most potent vasoconstrictor, in COVID patients. We are investigating the direct effect of SARS-CoV-2 spike protein (SP) and the host response to chondrocytes.</p> <p>Human mesenchymal stem cells (hMSCs)-differentiated chondrocytes were treated with either full-length SARS-CoV-2 spike protein (SP) only or a combination of spike protein, neutralising antibody to S1 and endothelin-1 (SAE) to mimic viral insult and host response respectively. RNA sequencing was performed to compared the change in transcriptome in control, SP, and SAE. All samples were processed in the same batch. Default quality control parameters were used.</p>
Figure 5.(a)Linear (y=0.45x + 57.74) dose-response relationship between plasma propranolol to % β- adrenergeric blockade derived from healthy study participants and translate into patients with angina pectoris. This image has been adapted from(Pine et al., 1975).-The Brain and Propranolol Pharmacokinetics in the Elderly
<p>Apharmacodynamic model,with parameters in the table below, may be used to visualize the<br> propranolol concentration-effect (β-blockade) relationship in patients suffering from angina pectoris.<br> These results have been adapted from the Pine et al article published in Circulation in 1975 which<br> identified a linear relationship plasma Propranolol (ng/mL) to an effect of % β-Adrenergic Blockade<br> in a single-oral dose of 40mg Propranolol in exercising individuals (Pine et al., 1975).</p>
Data for "Tropical Cyclone Supercell Response to the Coast using a Climatology of Radar-Derived Azimuthal Shear"
<p>This dataset contains a .csv file published alongside the article entitled "Tropical Cyclone Supercell Response to the Coast using a Climatology of Radar-Derived Azimuthal Shear" for consideration in <em>Geophysical Research Letters</em>.</p>
Dataset for "Analytic High-order Geometric Derivatives with Polarizable Embedding in a Response Function Framework"
<p>This dataset contains data for the article "Analytic High-order Geometric Derivatives with Polarizable Embedding in a Response Function Framework"</p>
A transposase-derived gene responsible for human brain development
<p><span>Vertebrate brain development is associated with prominent neuronal cell death and DNA breaks, but their causes and functions are not well understood. DNA transposable elements and transposase-derived genes could contribute to DNA breaks and somatic genome rearrangements, however their contributions to brain development are largely unknown. PiggyBac Transposable Element Derived 5 (PGBD5) is an evolutionarily conserved vertebrate DNA transposase-derived gene with retained nuclease activity in human cells. Here, we show that PGBD5 contributes to normal brain development in mice and humans, and its deficiency causes disorder of intellectual disability, movement, and seizures. In mice, Pgbd5 is required for the developmental induction of post-mitotic DNA breaks and recurrent somatic brain<em> </em>genome rearrangements. In the cerebral cortex, loss of Pgbd5 leads to aberrant differentiation and gene expression of distinct neuronal populations, including specific types of glutamatergic neurons, which can explain the features of PGBD5 deficiency in humans. Thus, PGBD5 is a transposase-derived gene required for brain development in mammals. </span></p>
Trellis Single-Cell Screening Reveals Stromal Regulation of Patient-Derived Organoid Drug Responses
<p>Patient-derived organoids (PDOs) can model personalized therapy responses, however current screening technologies cannot reveal drug response mechanisms or how tumor microenvironment cells alter therapeutic performance. To address this, we developed a highly-multiplexed mass cytometry platform to measure post translational modification (PTM) signaling, DNA-damage, cell-cycle activity, and apoptosis in >2,500 colorectal cancer (CRC) PDOs and cancer associated fibroblasts (CAFs) in response to clinical therapies at single-cell resolution. To compare patient- and microenvironment-specific drug responses in thousands of single-cell datasets, we developed <em>Trellis</em> — a highly-scalable, hierarchical tree-based treatment effect analysis method. Trellis single-cell screening revealed that on-target cell-cycle blockage and DNA-damage drug effects are common, even in chemorefractory PDOs. However, drug-induced apoptosis is rare, patient-specific, and aligns with cancer cell PTM signaling. We find that CAFs can regulate cancer cell plasticity — shifting proliferative stem cells to slow-cycling revival stem cells via YAP to protect cancer cells from chemotherapy.</p> <p> </p> <p>This repo contains the processed scRNA-seq Scanpy AnnData objects generated from the study. More information describing the data can be found at: https://github.com/TAPE-Lab/Ramos-et-al-Trellis</p>
Data from: Ocean acidification alters sperm responses to egg-derived chemicals in a broadcast spawning mussel
<p>The continued and unprecedented emissions of anthropogenic carbon dioxide (CO<sub>2</sub>) are causing progressive ocean acidification (OA). While deleterious effects of OA on biological systems are well documented in the growth of calcifying organisms, lesser studied impacts of OA include potential effects on gamete interactions that determine fertilisation, which are likely to influence the many marine species that spawn gametes externally. Here, we explore the effects of OA on the signalling mechanisms that enable sperm to track egg-derived chemicals (sperm chemotaxis). We focus on the mussel <i>Mytilus galloprovincialis</i>, where sperm chemotaxis enables eggs to selectively bias fertilisation in favour of genetically compatible males. Using a factorial experimental design, we test whether the experimental manipulation of seawater pH (comparing ambient conditions to predicted end-of-century scenarios) alters these patterns of differential sperm chemotaxis. While we find no evidence that patterns of male-female gametic compatibility are impacted by OA, we do find that individual males exhibit consistent variation in how their sperm perform in lowered pH levels. This finding of individual variability in the capacity of ejaculates to respond to chemoattractants under acidified conditions suggests that climate change will exert considerable pressure on male genotypes that can withstand an increasingly hostile fertilisation environment.</p>
Cartilage Responses to Inflammatory Stimuli and Adipose Stem/Stromal Cell-Derived Conditioned Medium: Results from an Ex Vivo Model
Open the record for dataset details and reuse information.
Data and statistical analysis for: Response to Elexacaftor/Tezacaftor/Ivacaftor in intestinal organoids derived from patients with cystic fibrosis
<p>Data and code to reproduce all statistical analyses and figure in the manuscript "Response to Elexacaftor/Tezacaftor/Ivacaftor in intestinal organoids derived from patients with cystic fibrosis".</p> <p>The dataset is stored in the file `area_data.csv`, the columns are:</p> <ul> <li>`well` The ID of the well within the plate the measurement was taken</li> <li>`time` time from start of measurement</li> <li>`area` area of the organoids</li> <li>`patient` Anonymized ID of the patient</li> <li>`date` Date when the experiment was performed (date and patient ID identify the plate)</li> <li>`filename` The filename in raw data (not published) this plate was stored in. (uniquely identifies a plate)</li> <li>`mix` Identifies one od two variants of plate layouts used</li> <li>`replicate` ID of technical replicate (two technical replicates were done for each condition on the same plate)</li> <li>`type` The main condition - one of "TEZ/IVA", "ELX/TEZ/IVA", "FskOnly" (Control, only forskolin)</li> <li>`fsk_concentration` concentration of forskolin (μM)</li> </ul> <p>The file "organoids.Rmd" reproduces the analyses, other files are supporting to let the main analysis run.</p> <p>The analysis is written in R markdown.</p> <p> </p>
Dose Response Oxidation of a Sweet-corn Derived Sugar (PhytoSpherix) During Exercise in Endurance Trained Athletes
ClinicalTrials.gov study NCT02909881. IPD Sharing: NO. Countries: 1. Publications: 1.
Patient-derived Organoids of Lung Cancer to Test Drug Response
ClinicalTrials.gov study NCT03979170. IPD Sharing: NO. Countries: 1. Publications: 1.
Immune Response of Individuals Vaccinated With Hypoallergenic Derivatives of the Major Birch Pollen Allergen, Bet v 1
ClinicalTrials.gov study NCT01353924. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Arterial Pressure Derived Dynamic Parameters to Detect Preload Responsiveness in Spontaneously Breathing Patients
ClinicalTrials.gov study NCT06480942. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Arterial Pressure Derived Dynamic Parameters to Detect Preload Responsiveness in Mechanically Ventilated Patients Under Spontaneous Mode
ClinicalTrials.gov study NCT06495489. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Brain Derived Neurotrophic Factor as a Predictor of Response to Treatment in Bipolar Depression and Mania: 16-weeks Follow-up With Quetiapine XR
ClinicalTrials.gov study NCT00879307. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Autologous Serum-derived EV for Venous Trophic Lesions Not Responsive to Conventional Treatments
ClinicalTrials.gov study NCT04652531. IPD Sharing: NO. Countries: 1. Publications: 3.
Randomized, Parallel Group, Placebo Control, Unicentric, Interventional Study to Assess the Effect of Expanded Human Allogeneic Adipose-derived Mesenchymal Adult Stem Cells on the Human Response to Li
ClinicalTrials.gov study NCT02328612. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Data from: Ocean acidification alters sperm responses to egg-derived chemicals in a broadcast spawning mussel
Open the record for dataset details and reuse information.
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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.