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321 results for “Drug response”
Pilot Study of an Implantable Microdevice for Evaluating Drug Responses in Situ in Prostate Cancer
ClinicalTrials.gov study NCT04399876. IPD Sharing: YES. Countries: 1. Publications: 1.
Filgotinib Versus Placebo in Adults With Active Rheumatoid Arthritis (RA) Who Have an Inadequate Response to Biologic Disease-modifying Anti-rheumatic Drug(s) (DMARDs) Treatment
ClinicalTrials.gov study NCT02873936. IPD Sharing: NO. Countries: 15. Publications: 7.
A Study of Subcutaneous (SC) Tocilizumab (RoActemra/Actemra) in Participants With Active Rheumatoid Arthritis (RA) and Inadequate Response to Disease-Modifying Anti-Rheumatic Drugs (DMARDs)
ClinicalTrials.gov study NCT02046616. IPD Sharing: Not stated. Countries: 4. Publications: 4.
A Study of Tocilizumab (RoActemra) in Tocilizumab-Naive Participants With Rheumatoid Arthritis and Inadequate Response to Non-Biologic Disease-Modifying Antirheumatic Drugs (DMARDs) and/or Biologic Th
ClinicalTrials.gov study NCT02001987. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Data from: Anthelmintic drugs modulate the acute phase immune response but not the microbiota in wild Song Sparrows
Open the record for dataset details and reuse information.
MOLI: multi-omics late integration with deep neural networks for drug response prediction
<p>Harmonized data used in "MOLI: multi-omics late integration with deep neural networks for drug response prediction", 2019, <em>Bioinformatics </em><a href="https://academic.oup.com/bioinformatics/article/35/14/i501/5529255">https://academic.oup.com/bioinformatics/article/35/14/i501/5529255</a>. <br> CNA.tar.gz contains CNA profiles with non-integer estimates of copy number, e.g. log-ratios. Please use binarized CNA profiles (CNA_binary.tar.gz) to replicate the results described in the paper. </p> <p><br> All raw data were obtained from open sources:<br> - https://www.cancerrxgene.org/<br> - ArrayExpress https://www.ebi.ac.uk/arrayexpress/<br> - Firehose Broad GDAC http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/<br> - Supplementary of Gao et al., 2015 https://www.nature.com/articles/nm.3954</p> <p>Gene symbols were mapped to Entrez Gene IDs. Data preprocessing is described in detail in supplementary materials. The code is available at <a href="https://github.com/hosseinshn/MOLI/tree/master/preprocessing_scr">https://github.com/hosseinshn/MOLI/tree/master/preprocessing_scr</a>.</p>
DNA mechanocapsules for programmable piconewton responsive drug delivery
<p>The mechanical dysregulation of cells is associated with a number of disease states, that spans from fibrosis to tumorigenesis. Hence, it is highly desirable to develop strategies to deliver drugs based on the "mechanical phenotype" of a cell. To achieve this goal, we outline and synthesize DNA mechanocapsules (DMC) comprised of DNA tetrahedrons that are force responsive. Modeling shows the trajectory of force-induced DMC rupture and predicts how applied force spatial position and orientation tunes the force-response threshold. DMCs functionalized with adhesion ligands mechanically denature <i>in vitro</i> as a result of cell receptor forces. DMCs are designed to encapsulate macromolecular cargos such as dextran and oligonucleotide drugs with minimal cargo leakage and high nuclease resistance. Force-induced release and uptake of DMC cargo is validated using flow cytometry. Finally, we demonstrate force-induced mRNA knockdown of HIF-1α in a manner that is dependent on the magnitude of cellular traction forces. These results show that DMCs can be effectively used to target biophysical phenotypes which may find useful applications in immunology and cancer biology. </p>
Dual-Responsive Nanoparticles for Smart Drug Delivery: a NIR light Sensitive and Redox- Reactive PEG-PCL based System
<p>This folder contains raw data for the paper titled "Dual-Responsive Nanoparticles for Smart Drug Delivery: A NIR Light-Sensitive and Redox-Reactive PEG–PCL-Based System" authored by Nancy Ferrentino, Taha Behroozi Kohlan, Shokoufeh Mehrtashfar, Anna Finne-Wistrand, and Daniela Pappalardo, published in Biomacromolecules journal. <a title="DOI URL" href="https://doi.org/10.1021/acs.biomac.4c00889">https://doi.org/10.1021/acs.biomac.4c00889</a></p>
Spatial Transcriptomics in Breast Cancer Reveals Tumour Microenvironment-Driven Drug Responses and Clonal Therapeutic Heterogeneity
<p>We acquired 10x Visium spatial transcriptomics (ST) data from 9 patients with invasive adenocarcinomas [1–5] to explore the role of the tumour microenvironment (TME) on intratumor heterogeneity (ITH) and drug response in breast cancer. By leveraging a new version of Beyondcell [6] (<a href="https://github.com/cnio-bu/beyondcell" target="_blank" rel="noopener">cnio-bu/beyondcell</a>), a tool for identifying tumour cell subpopulations with distinct drug response patterns, we predicted sensitivity to over 1,200 drugs while accounting for the spatial context and interaction between the tumour and TME compartments. Moreover, we also used Beyondcell to compute spot-wise functional enrichment scores and identify niche-specific biological functions.</p> <p>Here, you can find:</p> <p>In signatures folder:</p> <ul> <li><strong>SSc breast:</strong> Collection of gene signatures used to predict sensitivity to > 1,200 drugs derived from breast cancer cell lines.</li> <li><strong>Functional signatures:</strong> Collection of gene signatures used to compute enrichment in different biological pathways.</li> </ul> <p>In visium folder:</p> <ul> <li><strong>Visium objects:</strong> Processed ST Seurat objects with deconvoluted spots, SCTransform-normalised counts, and clonal composition predicted with SCEVAN [7]. These objects, together with the signatures, were used to compute the Beyondcell objects.</li> </ul> <p>In single-cell folder:</p> <ul> <li><strong>Single-cell objects:</strong> Raw and filtered merged single-cell RNA-seq (scRNA-seq) Seurat objects with unnormalised counts used as a reference for spot deconvolution.</li> </ul> <p>In beyondcell folder:</p> <ul> <li><strong>Beyondcell </strong><strong>sensitivity </strong><strong>objects</strong> with prediction scores for all drug response signatures in SSc breast.</li> <li><strong>Beyondcell functional objects </strong>with enrichment scores for all functional signatures.</li> </ul>
Design of Modular Autoproteolytic Gene Switches Responsive to Anti-Coronavirus Drug Candidates
<p>Data underlying the figures in the publication “Design of modular autoproteolytic gene switches responsive to anti-coronavirus drug candidates”, published in <em>Nat. Commun.</em>, <strong>2021</strong>, 12, 6786.</p> <p><a href="https://doi.org/10.1038/s41467-021-27072-3">https://doi.org/10.1038/s41467-021-27072-3</a></p> <p> </p> <p>Table of contents:</p> <p><strong>1. Supplementary Information.pdf</strong>: Document containing the Supplementary Tables 1-7 and the Supplementary Figures 1-10.</p> <p><strong>2. Dataset 1</strong>: Raw data points used to create the main and supplementary figures of the paper arranged in worksheets panel by panel.</p> <p> </p> <p>Data availability</p> <p>Sequence data of plasmids encoding PLpro-TAGS and Mpro-TAGS have been deposited in GenBank under accession codes OK425851, OK425852, and OK425853. Original plasmids are available upon request. All vector information is provided in Supplementary Table 4. Detailed statistical analysis is provided in Supplementary Table 7. Source data is provided in the Source data file. Source data are provided with this paper.</p>
Drug Response Phenotype Terms
<p>Data and code for "Leveraging a Pharmacogenomics Knowledge-base to Formulate a Drug Response Phenotype Terminology for Genomic Medicine" published in <em>Bioinformatics</em></p>
Perturbation response scanning of drug-target networks: Drug repurposing for multiple sclerosis
<p>This dataset contains molecular dynamics trajectories and corresponding input files used for simulations. The simulations were conducted using GROMACS and include detailed information about the simulated systems, such as the types of molecules, box dimensions, temperature, pressure, simulation time range, and time step.</p>
Clinical Dataset for the Paper 'Machine Learning Prediction of Treatment Response to Biological Disease-Modifying Antirheumatic Drugs in Rheumatoid Arthritis'
<p>This dataset accompanies the manuscript titled "Machine Learning Prediction of Treatment Response to Biological Disease-Modifying Antirheumatic Drugs in Rheumatoid Arthritis." It includes clinical data used for training and evaluating the machine learning models described in the paper. The dataset contains baseline clinical data of 154 RA patients who were treated with bDMARDs. The labels for remission, and effectiveness (remission and low disease activity) were applied after a 6-month follow-up based on EULAR criteria on DAS28ESR. The sustained effectiveness label indicates maintaining effectiveness within 6 months after initially achieving effectiveness.</p> <p><strong>Crossponder Authors:</strong></p> <ul> <li>Fatemeh Salehi (email: <a rel="noreferrer">fatemeh.salehihafshejni@fau.de</a>)</li> </ul>
A pH-responsive amphiphilic hydrogel based on pseudo-peptides and poly(ethylene glycol) for oral drug delivery
<p>The original data for the paper titled "A pH-responsive amphiphilic hydrogel based on pseudo-peptides and poly(ethylene glycol) for oral drug delivery"</p>
In Situ-Forming Gels Loaded with Stimuli-Responsive Gated Mesoporous Silica Nanoparticles for Local Sustained Drug Delivery
<p>A novel combination of in situ-forming hydrogels of hyaluronic acid with gated mesoporous materials was developed to design depots for local sustained release of chemotherapeutics. The depot consists of a hyaluronic-based gel loaded with redox-responsive mesoporous silica nanoparticles loaded with safranin O or doxorubicin and capped with polyethylene glycol chains containing a disulfide bond. The nanoparticles are able to deliver the payload in the presence of the reducing agent, glutathione (GSH), that promotes the cleavage of the disulfide bonds and the consequent pore opening and cargo delivery. Release studies and cellular assays demonstrated that the depot can successfully liberate the nanoparticles to the media and, subsequently, that the nanoparticles are internalized into the cells where the high concentration of GSH induces cargo delivery. When the nanoparticles were loaded with doxorubicin, a significant reduction in cell viability was observed. Our research opens the way to the development of new depots that enhance the local controlled release of chemotherapeutics by combining the tunable properties of hyaluronic gels with a wide range of gated materials.</p>
Nanocomposite formulation for a sustained release of free drug and drug-loaded responsive nanoparticles: an approach for a local therapy of glioblastoma multiforme
<p>Malignant gliomas are a type of primary brain tumour that originates in glial cells. Among them, glioblastoma multiforme (GBM) is the most common and the most aggressive brain tumour in adults, classified as grade IV by the World Health Organization. The standard care for GBM, known as the Stupp protocol includes surgical resection followed by oral chemotherapy with temozolomide (TMZ). This treatment option provides a median survival prognosis of only 16–18 months to patients mainly due to tumour recurrence. Therefore, enhanced treatment options are urgently needed for this disease. Here we show the development, characterization, and in vitro and in vivo evaluation of a new composite material for local therapy of GBM post-surgery. We developed responsive nanoparticles that were loaded with paclitaxel (PTX), and that showed penetration in 3D spheroids and cell internalization. These nanoparticles were found to be cytotoxic in 2D (U-87 cells) and 3D (U-87 spheroids) models of GBM. The incorporation of these nanoparticles into a hydrogel facilitates their sustained release in time. Moreover, the formulation of this hydrogel containing PTX-loaded responsive nanoparticles and free TMZ was able to delay tumour recurrence in vivo after resection surgery. Therefore, our formulation represents a promising approach to develop combined local therapies against GBM using injectable hydrogels containing nanoparticles.</p>
Investigation of the Faecal Loss of Vedolizumab and Its Role in Influencing Serum Drug Levels, Outcomes and Response in Ulcerative Colitis
ClinicalTrials.gov study NCT04006080. IPD Sharing: NO. Countries: 1. Publications: 8.
Community-led Responses for Elimination: Controlled Trial of Reactive Case Detection Versus Reactive Drug Administration
ClinicalTrials.gov study NCT02654912. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Individual Differences in the Response to Drugs
ClinicalTrials.gov study NCT02485158. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Association of Ex Vivo Drug Response (EVDR) and Clinical Outcome in Ovarian Cancer
ClinicalTrials.gov study NCT06068738. IPD Sharing: NO. Countries: 2. Publications: 1.
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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.
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DANDI Archive for NWB datasets
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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.