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7,518 results for “screenings”
Screening conditions for electron microscopy of full-length huntingtin protein samples
<p>Huntingtin structure-function open lab notebook project</p>
Huntingtin +/- DNA oligo cryo and negative stain grid set up and screening
<p>Huntingtin structure-function open lab notebook project. </p>
Crystal Structures of SARS-CoV-2 main protease with screening fragments and COVID Moonshot compounds from the XChem facility at Diamond Light Source
<p>Bulk repositiory of structures of SARS-CoV-2 main protease in complex with fragment molecules from inital XChem screen and designed COVID Moonshot inhibtor compounds. Each structure has a PDB ID, coordinate file, structure factor file, ligand restraint (cif) and PANDDA event maps (as appropriate).</p><p>2023-10-26 - updated to include <strong>all </strong>initial fragment screening hits alongside follow up compounds</p>
Suspect and Nontarget Screening Reveal the Underestimated Risks of Antibiotic Transformation Products in Wastewater Treatment Plant Effluents
<p>This repository is supplementary to the manuscript "Suspect and Nontarget Screening Reveal the Underestimated Risks of Antibiotic Transformation Products in Wastewater Treatment Plant Effluents" (DOI: 10.1021/acs.est.3c05008). This repository contains scripts of TPs collection and QSRR model as well the generated data set.</p><p>We compiled a suspect list of antibiotics containing 663 compounds. Corresponding suspect TPs were collected in silico with BioTransformer 3.0 and through a library search from PubChem data, which were both performed in batch mode using the patRoon 2.0 package. After merging results and removing duplicates, 88,823 TPs remained for suspect screening. Quantitative-structure retention relationship (QSRR) models were developed for the suspect antibiotics and TPs using target compounds to predict their retention times with the Retip package.</p>
Complete Data HGS vs Blood glc Regulation (Handgrip strength as a screening tool for diabetes in resource-constrained settings)
<p><strong>Abstract</strong></p><p><strong>Background Information: </strong>Diabetes mellitus is an escalating global health concern, especially in low and middle-income countries. Handgrip strength (HGS), a measure of muscle strength, emerges as a potential non-invasive and affordable screening tool for diabetes, particularly in areas with limited healthcare access.</p><p><strong>Objective: </strong>To investigate the relationship between handgrip strength and blood glucose regulation in non-diabetic young adults and to provide valuable insights into the potential of handgrip strength as a preventive and affordable approach to managing diabetes.</p><p><strong>Methods: </strong>A cross-sectional study included 59 University of Ilorin students aged 18-21 in Nigeria. Handgrip strength was measured with a dynamometer, and its links to blood glucose markers (fasting blood glucose, 2-hour post-prandial glucose, and HbA1c) were explored using multiple regression models.</p><p><strong>Results: </strong>Findings revealed significant associations between HGS and glucose regulation markers, particularly FBS, among males. The relationship was evident in females only after adjusting for body mass index (BMI). Furthermore, a notable connection between HGS and 2-hour post-prandial glucose levels was observed in females but not males. However, no significant associations were found between HGS and serum insulin levels across genders.</p><p> </p>
Cystic Fibrosis Diagnosis in Newborns with Machine Learning]{Newborn Cystic Fibrosis Diagnosis Made Accurate and Efficient with Machine Learning to Reduce False Positives in IRT-Trypsinogen Immunoreactive Screening Program
<p>Datasets to training models in this article and generator code.</p>
Replication package of article "Screening Articles for Systematic Reviews with ChatGPT"
<ul><li>/experiments - Full experimental data</li><li>/prompts - Full prompts of the six experiments</li><li>/results - Results: data and plots<ul><li>rq1.xlsx - Data related to RQ1</li><li>rq2.xlsx - Data related to RQ2</li><li>significance.xlsx - Results of Spearman's rank test</li></ul></li><li>/topics-and-exclusion-criteria - Topics and exclusion criteria of the five datasets</li></ul>
Computer-Aided Drug Design (CADD): To Screen Potential Antibiotics Against Klebsiella Pneumoniae Beta-Lactamase Enzyme
Open the record for dataset details and reuse information.
COLSCREEN: 16S-sequencing of fecal microbiota from a population-based CRC screening program
<p><span>The research cohort (COLSCREEN study) was recruited among individuals that participated during 2016-2020 in the ongoing population-based CRC screening program overseen by the Catalan Institute of Oncology in L’Hospitalet del Llobregat, Barcelona, Spain. This program invites men and women between the ages of 50 and 69 to partake in the immunochemical fecal occult blood test (FIT). In the event of a positive FIT result (≥ 20 μg Hb/g feces), the participants are then recommended to undergo colonoscopy. Participants of the COLSCREEN study (N=997) were invited to participate after receiving a positive FIT result. Since CRC diagnosis is rare in screening, this cohort includes patients diagnosed clinically from the CRC Functional Unit (N=45). Furthermore, a subset of participants with a negative FIT is also included (N=140). All of them underwent a colonoscopy and participants were categorized based on the risk stratification proposal by Castells et al. after careful review of the colonoscopy and histopathology reports. All participants who agreed to take part of the COLSCREEN study provided written informed consent and donated a fecal and blood sample at recruitment (samples obtained before colonoscopy) and answered an epidemiological questionnaire. Clinically diagnosed CRC patients usually underwent a colonoscopy before recruitment, and the fecal samples were obtained prior surgery. In the present study, we excluded those participants that reported having used antibiotics or probiotics one month before sampling. </span></p>
A massive proteogenomic screen identifies thousands of novel human protein coding sequences
<p>Accurate annotation of genes in the human genome is fundamental for biomedical research and genomic data interpretation. The Ensembl, RefSeq, and GENCODE consortiums continuously update the human genome annotations based on new computational and experimental evidence, and new proteins were identified constantly. The Genotype-Tissue Expression (GTEx) project has generated more than 15,000 RNA sequencing dataset from multiple-tissues of more than 800 donors which allows to model almost all transcripts and proteins in the human genome. Using proteins translated from the GTEx transcript model, more than 21 million in-silico trypsin-digested peptides were generated. To identify high-confidence novel proteins with proteomic support, we screened more than 2,000 proteomic projects in the PRIDE database and selected more than 50,000 mass spectrometry (MS) runs from 923 projects. These MS data were used to validate the predicted novel peptides. With a stringent standard, we identified almost 20,000 novel peptides. </p> <p>This dataset include files used in the the above analysis. More details can be found in the GitHub page (https://github.com/ATPs/human_novo_protein_2022). </p>
Chinese Painted Screen
Source: Objaverse 1.0 / Sketchfab
Replication package for: Labor Market Screening and the Design of Social Insurance: An Equilibrium Analysis of the Labor Market for the Disabled
<p>This is a replication package for "Labor Market Screening and the Design of Social Insurance: An Equilibrium Analysis of the Labor Market for the Disabled." It contains all the necessary codes and data to replicate empirical and quantitative findings in the paper.</p>
SLR AI Ethics - Screening records (Phase 1 & 2)
<p>These two spreadsheets detail the rigorous screening carried out by the four members of the research team during phase 1 and phase 2. </p>
Carbon sources screening assay
<p><span>The FACS optimized GFPmut3 </span><sup><span>69</span></sup><span> was fused to promoter of interest and cloned into a plasmid pSC101. <a name="_Hlk156916219"></a><span>For the first screening, </span>overnight cultures of the strain carrying the screening system were diluted 200X in MOPS Rich <span>(Teknova EZ rich defined medium) supplemented with carbenicillin for plasmid maintenance. </span><span>The phenotype Microarray (Biolog) plates PM1 and PM2B (carbon sources), and PM3B, for a total of 198 molecules including 7 nucleosides and 6 nucleotides were used for molecules screening. Each well was filled with 100 µl of inoculated media and mixed by pipetting. Media were transferred to 96 well dark-bottom plates (Thermo Scientific). GFP fluorescence was followed on the Tecan Infinite 200 PRO (Life Science) at 37°C for 8 hours. Fluorescence induction by the substrate was calculated using the ratio </span>fluorescence (t8h-t0h) over growth (t8h-t0h OD<sub>600nm</sub>).</span></p> <p><span>For flow cytometry quantification, </span><span>overnight cultures in MH of strain carrying the screening system were diluted 200X in rich MOPS <span>(Teknova EZ rich defined medium), or MH supplemented with carbenicillin for plasmid maintenance<span> and grown overnight, and the molecule tested at 0.5% (except uracil: 0.1%, limit of solubility). Fluorescence was read on 5 µl of overnight cultures diluted in 200 µl of PBS with the B1 laser. </span></span></span></p>
Identification of Potential IL4I1 Inhibitors through Structure-Based Virtual Screening and Molecular Dynamics Simulations, Molecular dynamics trajectory file
<p>Dataset for molecular dynamics simulations of the article: Identification of Potential IL4I1 Inhibitors through Structure-Based Virtual Screening and Molecular Dynamics Simulations.</p> <p><a href="../api/records/10473570/draft/files/First_600ns_MD.rar/content" target="_blank" rel="noopener noreferrer">First_600ns_MD.rar</a> contains the 600ns molecular dynamics simulation trajectory file of IL4I1-FAD-CIT complex using desmond.</p> <p><a href="../api/records/10473570/draft/files/Second_500ns_MD_ZL35_F963.rar/content" target="_blank" rel="noopener">Second_500ns_MD_ZL35_F963.rar </a>contains the 500ns molecular dynamics simulation trajectory file of IL4I1-FAD-ZL35 complex, which initial conformation of this part of dynamics simulation was obtained by docking the conformation of the 963rd frame from the first dynamics simulation with ZL35 through induced fit.</p> <p>script.rar include scripts and calculation methods for free energy landscape, RMSD matrix, and thermol MM/GBSA.</p>
Galaxy Training Network - Screening assembled genomes for contamination using NCBI FCS
<p>This is a toy dataset generated from an assembled yeast genome (Saccharomyces cerevisiae; GCA_000146045.2) with contaminants added from human, Pseudomonas aeruginosa, and Illumina PCR primers.</p>
Expectations and basic knowledge in ultrasound screening among pregnant women: A questionnaire survey
<h3>Objective</h3> <p>This study aimed to evaluate the disparity of the expectations and basic knowledge of prenatal ultrasound (US) screening among pregnant women and make a comparison with the current scientific knowledge and national recommendations. We hypothesize that sociodemographic factors, including age, education, and professional occupation, may be associated with different levels of knowledge.</p> <h3>Methods</h3> <p>This was a cross-sectional study performed in 2021 of 336 women aged 18 to 46 years in a maternity facility in a tertiary hospital in Portugal. The main outcome measures were questionnaire data from questions divided into four categories (sociodemographic, expectations, knowledge, and final considerations/suggestions). The data were grouped according to the sociodemographic factors (age, educational level, and professional occupation) and analyzed and compared as a function of the social groups as well as overall tendencies.</p> <h3>Results</h3> <p>Our data confirmed a significant discrepancy between the expectations and general knowledge of pregnant women regarding prenatal US when compared with the current scientific knowledge. Importantly, we found that both depended greatly on sociodemographic factors, particularly educational level. This reiterated the importance of conducting effective dissemination actions of current scientific knowledge, focusing on the main objectives of US screening as well as the limitations of the existing technology.</p> <h3>Conclusion</h3> <p>This study will help in defining strategies for future dissemination actions aiming to improve current practice and lead to a higher synchrony of expectations towards US between couples and practitioners.</p>
Supporting Information for Cholinergic Selectivity of FDA-approved and Metabolite Compounds Examined with Molecular Docking-based Virtual Screening
<p><span>Typical docking configurations, detailed docking and visualization results for representative ligands and proteins. </span></p>
CRISPuRe-seq: pooled screening of barcoded ribonucleoprotein reporters reveals regulation of RNA polymerase III transcription by the Integrated Stress Response via mTOR
<p>NAR_Data_Package.zip contains the data required for generating figures, including original gel images for western blots and a step-by-step protocol for CRISPuRe-seq.</p> <p>SupplementaryData.xlsx contains all of the Supplemental Data directly referred to in the manuscript.</p> <p>Plasmid maps.zip contains plasmid maps for constructs used in the manuscript in genbank format.</p> <p>Scripts.zip contains the scripts used for screen processing with a text file explaining their usage.</p> <p>Look_Up_Table.zip contains the look-up-table for decoding barcode and sgRNA pairings.</p>
Code for "On the interplay of electronic and lattice screening on exciton binding in two-dimensional lead halide perovskites"
<p>The code and Adobe Illustrator file used to generate the figures for "On the interplay of electronic and lattice screening on exciton binding in two-dimensional lead halide perovskites" is provided. The renormalized exciton binding energies are stored in arrays in the Python script, and the P(r)'s are stored in the "bta" and "pea" folders. The source code for the path integral Monte Carlo calculations is provided in Github. </p>
ScienceDex guides
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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.