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30 results for “actionable profiler”
Figure 5 in Anthropic action affects the cuticular chemical profile of social wasps
Figure 5. Ordering by Detrended Correspondence Analyses (Axes 1 and 2) based on the cuticular hydrocarbon profile of the samples of the 3 species whose colonies were nested in two types of environments. The points on Axis 1, between 0 and 50 on the left, represent compounds more characteristic of samples from more anthropized environments and between 100 and 150 on the right, from less anthropized environments.
Figure 4 in Anthropic action affects the cuticular chemical profile of social wasps
Figure 4. Similarity dendrogram based on the cuticular hydrocarbon profile of the samples of the 3 species whose colonies were nested in two types of environments. Pentagon: more anthropized areas. Star: less anthropized areas.
Figure 3 in Anthropic action affects the cuticular chemical profile of social wasps
Figure 3. Bar charts showing the relative abundance and number of compounds belonging to the different classes of cuticular hydrocarbons present in the samples of Polistes versicolor (A), Polybia paulista (B) and Polybia occidentalis (C) whose colonies were nesting in more anthropized environments (black box) and less anthropized (white box). LA = Linear Alkanes, BA = Branched Alkanes, AK = Alkenes, ALD = Alkadienes.
Figure 2 in Anthropic action affects the cuticular chemical profile of social wasps
Figure 2. Similarity dendrogram generated based on the percentages of different types of land use in the municipalities where the colonies of the 3 species of social wasps were sampled. Pentagon: more anthropized areas. Star: less anthropized areas. DDS1: Dourados point 1; DDS2: Dourados point 2; IVIN: Ivinhema; MN1: Mundo Novo point 1; MN2: Mundo Novo point 2; PP: Ponta Porã.
Figure 1 in Anthropic action affects the cuticular chemical profile of social wasps
Figure 1. Satellite image showing the places in the municipalities where the colonies of the 3 social wasp species were nesting and, the percentages (pie charts) of the different types of land use and occupation (adapted from the IBGE, 2013 definition). Number 1 and 2 indicates the two collection points in the same city.
Integrating QSAR models predicting acute contact toxicity and mode of action profiling in honey bees (A. mellifera): Data curation using open source databases, performance testing and validation
<p>This excel file (DOI: <a href="https://doi.org/10.5281/zenodo.3755675">https://doi.org/10.5281/zenodo.3755675</a>) provides the collection of raw data used for developing the first integrative Quantitative Structure-Activity Relationship (QSAR) model using EFSA's OpenFoodTox, US-EPA ECOTOX and Pesticide Properties DataBase i) to predict acute contact toxicity (LD<sub>50</sub>) and ii) to profile the Mode of Action (MoA) of pesticides active substances in honey bees (<em>Apis mellifera</em>)<em>. </em>Chemical identifiers (e.g. SMILES, CAS n., InChI) and acute contact toxicity data (LD<sub>50</sub>) on honey bees were used to develop and validate i) a two-category QSAR model (toxic/non-toxic; n=411) (sensitivity =0.93), specificity =0.85), balanced accuracy =0.90), Matthews correlation coefficient MCC=0.78), and ii) a regression-based model (n=113) (R2=0.74; MAE=0.52). Similarly, current study proposes the first MoA profiling for 113 pesticides active substances and the first harmonised MoA classification scheme for acute contact toxicity in honey bees, including LD<sub>50s</sub> data points from three different databases such as EFSA's OpenFoodTox, US-EPA ECOTOX and Pesticide Properties DataBase. Such classification allows to further define MoAs and the target site of Plant Protection Products (PPPs) active substances, thus enabling regulators and scientists to refine chemical grouping and toxicity extrapolations for single chemicals and component-based mixture risk assessment of multiple chemicals.</p> <p>The full data collection and analysis of QSAR models, toxicity data (LD<sub>50</sub>) and Mode of Action (Moa) data are described in Carnesecchi et al., 2020 (DOI: doi.org/10.1016/j.scitotenv.2020.139243).</p> <p>This work was supported by the European Food Safety Authority (EFSA) [contract number: OC/EFSA/SCER/2018/01 and NP/EFSA/AFSCO/2016/02 (Edoardo Carnesecchi)].</p>
Genomic profiling of NSCLC tumors with the TruSight Oncology 500 assay provides broad coverage of clinically actionable genomic alterations and detection of known and novel associations between genomic alterations, TMB, and PD-L1
<p>Wallen ZD, Ko H, Nesline MK, Tierno M, Roos A, Schnettler E, Husain H, Sathyan P, Caveney B, Eisenberg M, Severson EA, Ramkissoon SH. <strong>Genomic profiling of NSCLC tumors with the TruSight Oncology 500 assay provides broad coverage of clinically actionable genomic alterations and detection of known and novel associations between genomic.</strong> <em>Front Oncol.</em> 2024 Nov 5;14:1473327. doi: <a href="https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2024.1473327">10.3389/fonc.2024.1473327</a>.</p> <p><strong>ABSTRACT</strong></p> <p><strong>Introduction: </strong>Matching patients to an effective targeted therapy or immunotherapy is a challenge for <br>advanced and metastatic non-small cell lung cancer (NSCLC), especially when relying on assays that test one <br>marker at a time. Unlike traditional single marker tests, comprehensive genomic profiling (CGP) can <br>simultaneously assess NSCLC tumors for hundreds of genomic biomarkers and markers for immunotherapy <br>response, leading to quicker and more precise matches to therapeutics. <strong>Methods: </strong>In this study, we performed <br>CGP on 7,606 patients with advanced or metastatic NSCLC using the Illumina TruSight Oncology 500 (TSO <br>500) CGP assay to show its coverage and utility in detecting known and novel features of NSCLC. <strong>Results: </strong><br>Testing revealed distinct genomic profiles of lung adenocarcinoma and squamous cell carcinomas and <br>detected variants with a current targeted therapy or clinical trial in >72% of patient tumors. Known associations <br>between genomic alterations and immunotherapy markers were observed including significantly lower TMB <br>levels in tumors with therapy-associated alterations and significantly higher PD-L1 levels in tumors with ALK, <br>MET, BRAF, or ROS1 driver mutations. Co-occurrence analysis followed by network analysis with gene <br>module detection revealed known and novel co-occurrences between genomic alterations. Further, certain <br>modules of genes with co-occurring genomic alterations had dose-dependent relationships with histology and <br>increasing or decreasing levels of PD-L1 and TMB, suggesting a complex relationship between PD-L1, TMB, <br>and genomic alterations in these gene modules. <strong>Discussion:</strong> This study is the largest clinical study to date <br>utilizing the TSO 500. It provides an opportunity to further characterize the landscape of NSCLC using this <br>newer technology and show its clinical utility in detecting known and novel facets of NSCLC to inform treatment <br>decision-making.</p> <p><strong>DATA AVAILABILITY</strong></p> <p>The data and code presented in the study are deposited in this Zenodo repository, accession number <br>13137232 (<a href="https://zenodo.org/record/13137232">https://zenodo.org/record/13137232</a>). Raw sequencing data were derived from routine clinical testing of real-world patients and cannot be shared publicly. Further data inquiries can be directed to the corresponding <br>author. </p>
Safe cardiac action potential test (www.scaptest.com) : a database describing the in silico cardiac safety profile of drugs and their propensity to induce early afterdepolarization - Part II : description of 50 additional drugs
<p><span>This file describes the<em> in silico</em> cardiac safety profile of 50 additional drugs (in addition to the 150 drugs already described in the zenodo file 7541554) in order to complete the “scaptest” database.<span> </span>The aim of this database is to describe the <em>in silico</em> cardiac safety profile of drugss and their propensity to induce early afterdepolarization.<span> </span>This is based on the study of the effects of drugs on the non-failing human ventricular myocyte action potential (endo-, mid- and epicardial subtypes) reconstructed by computational simulation (O’Hara-Rudy dynamic algorithm) in order to identify cardiac action potential abnormalities such as high variations and/or occurrence of resting membrane potential, action potential amplitude, maximal rate of action potential rise, action potential duration, triangulation, early afterdepolarization, transmural dispersion of repolarization, reverse use dependence, qNet or minimal rate of action potential decrease at early afterdepolarization take-off voltage. These various parameters are useful in order to assume a more accurate predictability of pro-arrhythmic liabilities of new drug candidate in the cardiac safety pharmacology screening process, which is the aim of the comprehensive in vitro pro-arrhythmia assay (CiPA) initiative. The <em>in silico</em> cardiac safety profile of each drug is illustrated by a separate page describing the effects induced by each compound on these various parameters. The results are summarized regarding the expected pro-arrhythmia profile of the various compounds as described by the CredibleMeds classification evaluating their propensity to induce torsade de pointes.</span></p>
Safe cardiac action potential test (www.scaptest.com): a database describing the in silico cardiac safety profile of drugs and their propensity to induce early afterdepolarization
<p>The aim of the present database is to describe the <em>in silico</em> cardiac safety profile of drugs and their propensity to induce early afterdepolarization. This is based on the study of the effects of drugs on the non-failing human ventricular myocyte action potential (endo-, mid- and epicardial subtypes) reconstructed by computational simulation (O’Hara-Rudy dynamic algorithm) in order to identify cardiac action potential abnormalities such as high variations and/or occurrence of resting membrane potential, action potential amplitude, maximal rate of action potential rise, action potential duration, triangulation, early afterdepolarization, transmural dispersion of repolarization, reverse use dependence, qNet or minimal rate of action potential decrease at early afterdepolarization take-off voltage. These various parameters are useful in order to assume a more accurate predictability of pro-arrhythmic liabilities of new drug candidate in the cardiac safety pharmacology screening process, which is the aim of the comprehensive in vitro pro-arrhythmia assay (CiPA) initiative. The <em>in silico</em> cardiac safety profile of each drug (150 drugs described in this first version) is illustrated by a separate page describing the effects induced by each compound on these various parameters. The results are summarized regarding the expected pro-arrhythmia profile of the various compounds as described by the CredibleMeds classification evaluating their propensity to induce torsade de pointes.</p>
A Trial Investigating the Pharmacokinetic (Mode of Action in the Body) and Safety Profiles of NN1250 (Insulin Degludec) in Subjects With Various Degrees of Impaired Liver Function and in Subjects With
ClinicalTrials.gov study NCT00976326. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Identifying actionable targets through integrative analyses of GEM model and human prostate cancer profiling [Agilent]
GEO Series GSE61382. Mus musculus. 55 samples. Type: Genome variation profiling by array.
CIC-DUX4 chromatin profiling reveals new epigenetic dependencies and actionable therpaeutic targets in CIC-rearranged sarcomas [RNA-seq]
GEO Series GSE248116. Homo sapiens. 10 samples. Type: Expression profiling by high throughput sequencing.
Transcriptomics profiling of ccc_R08 for mechanism-of-action investigation with forward pharmacology
GEO Series GSE214515. Homo sapiens. 90 samples. Type: Expression profiling by high throughput sequencing.
Comparative analysis of transcriptome profiles reveals organ-dependent (Intestine and Tail) genomic and nongenomic actions of thyroid hormone in Xenopus tropicalis tadpoles
GEO Series GSE210456. Xenopus tropicalis. 24 samples. Type: Expression profiling by high throughput sequencing.
Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo
GEO Series GSE33671. Escherichia coli. 8 samples. Type: Expression profiling by high throughput sequencing.
Identifying actionable targets through integrative analyses of GEM model and human prostate cancer profiling (Illumina)
GEO Series GSE61379. Mus musculus. 24 samples. Type: Expression profiling by array.
Identifying actionable targets through integrative analyses of GEM model and human prostate cancer profiling
GEO Series GSE61383. Mus musculus. 79 samples. Type: Expression profiling by array; Genome variation profiling by array.
Genomic profiling of biliary tract cancer cell lines reveals molecular subtypes and actionable drug targets
GEO Series GSE138772. Homo sapiens. 20 samples. Type: Expression profiling by high throughput sequencing.
A single-cell RNA-seq survey of the action profile of general anaesthetics on the human prefrontal cortex cells
GEO Series GSE196239. Homo sapiens. 5 samples. Type: Expression profiling by high throughput sequencing.
Coupled Single Cell RNA Sequencing and TCR Profiling of T Cells in Large Granular Lymphocytosis to Infer Pathophysiology and Mechanism of Drug Action
GEO Series GSE168859. Homo sapiens. 64 samples. Type: Expression profiling by high throughput sequencing; Other.
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.