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3,684 results for “extract”
Data-Driven Extract Method Recommendations: A Study at ING: Appendix
<p>The appendix of our FSE 2021 industry track paper.</p>
Concordance between PCR-based extraction-free saliva and nasopharyngeal swabs for SARS-CoV-2 testing
<p><b>Introduction</b>: Saliva represents a less invasive alternative to nasopharyngeal swab (NPS) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. SalivaDirect is a nucleic acid extraction-free method for detecting SARS-CoV2 in saliva specimens. <span>Studies evaluating the concordance of gold standard NPS and newly developed SalivaDirect protocols are limited</span>. The aim of our study was to assess SalivaDirect as an alternative method for COVID-19 testing.</p> <p><b>Methods</b>: Matching NPS and saliva samples were analysed from a cohort of symptomatic (n=127) and asymptomatic (n=181) participants recruited from hospital and university settings respectively. RNA was extracted from NPS while saliva samples were subjected to the SalivaDirect protocol before RT-qPCR analysis. The presence of SARS-Cov-2 was assessed using <i>RdRP</i> and <i>N1</i> gene targets in NPS and saliva respectively.</p> <p><b>Results</b>: Overall we observed 94.3% sensitivity (95% CI 87.2-97.5%), and 95.9% specificity (95% CI 92.4-97.8%) in saliva when compared to matching NPS samples. Analysis of concordance demonstrated 95.5% accuracy overall for the saliva test relative to NPS, and a very high level of agreement (κ coefficient = 0.889, 95% CI 0.833–0.946) between the two sets of specimens. Fourteen of 308 samples were discordant, all from symptomatic patients. Ct values were >30 in 13/14 and >35 in 6/14 samples. No significant difference was found in the Ct values of matching NPS and saliva sample (<i>p</i>=0.860). A highly significant correlation (r = 0.475, <i>p</i><0.0001) was also found between the Ct values of the concordant positive saliva and NPS specimens.</p> <p><b>Conclusions</b>: Use of saliva processed according to the SalivaDirect protocol represents a valid method to detect SARS-CoV-2. Less invasive and accurate saliva screening is an attractive alternative to current testing methods based on NPS and would afford greater capacity to test asymptomatic populations especially in the context of frequent testing.</p>
Data extracted from Scopus database in BibTex format.
<p>Data extracted from Scopus database in BibTex format for publication in Healthcare.</p>
The dataset of 'The effects of 3% binahong (Anredera cordifolia) leaf extract gel on the alveolar bone healing in post-extraction tooth socket wound in Wistar rats (Rattus norvegicus)'
<p>Background: Binahong (<em>Anredera cordifolia</em> (Ten.) STEENIS) is a widely available herbal plant in Indonesia and has been intensely researched for its healing abilities due to its biological activities, but few studied its capability in accelerating hard tissue healing in post-extraction sockets. The purpose of this study was to analyze the effects of 3% binahong leaf extract gel on the alveolar bone healing in the post-extraction sockets in Wistar rats.</p> <p>Methods: In this study, 48 male Wistar rats were randomly allocated to twelve groups. After the extraction of the left mandibular incisor, sockets in Group I to IV were given 3% binahong leaf extract gel, group V to VIII were given base gel, and group IX to XII were given Gengigel® for 14 days. The residual socket volume (RSV) and fibroblast proliferation were observed on the 3rd, 7th, and 14th day post-extraction, while the osteoblast and osteocyte proliferation were observed on the 7th, 14th, and 28th day post-extraction. The RSV data were analyzed using repeated measures ANOVA and one-way ANOVA, while the histopathological data were analyzed using one-way ANOVA.</p> <p>Results: The results showed that the binahong group had the lowest RSV and the highest fibroblast proliferation compared to the other groups on the 7th day (p<0.05) and the highest osteoblast and osteocyte proliferation compared to the other groups on the 14th day (p<0.05).</p> <p>Conclusion: The experiment showed that 3% binahong leaf extract gel could enhance alveolar bone healing by increasing the proliferation of fibroblasts, osteoblasts, and osteocytes.</p>
Figure 3 in Successful identification of the final instar nymph of Quintilia carinata (Thunberg) (Hemiptera: Cicadidae) by DNA extraction from the exuvium
Figure 3. Ventral view of terminal segments of abdomen of female nymph.
Minerando Motivações para Aplicação de Extract Method: Um Estudo Preliminar
<p>Conjuntos de dados utilizados na pesquisa.</p>
Data extraction and synthesis table
<p>Table showing the data extraction and synthesis for a recent paper submission. </p>
Figure 5 from: Dadayan AS, Stepanyan LA, Sargsyan TH, Hovhannisyan AM, Dadayan SA (2021) Quantitative analysis of biologically active substances and the investigation of antioxidant and antimicrobial activities of some extracts of Osage orange fruits. Pharmacia 68(4): 731-739. https://doi.org/10.3897/pharmacia.68.e70180
Figure 5 Results of quantification and identification of flavonoids in ethanol extract of Osage Orange.
Figure 4 from: Dadayan AS, Stepanyan LA, Sargsyan TH, Hovhannisyan AM, Dadayan SA (2021) Quantitative analysis of biologically active substances and the investigation of antioxidant and antimicrobial activities of some extracts of Osage orange fruits. Pharmacia 68(4): 731-739. https://doi.org/10.3897/pharmacia.68.e70180
Figure 4 Results of quantification and identification of flavonoids in aqueous extract of Osage Orange.
Figure 10 from: Dadayan AS, Stepanyan LA, Sargsyan TH, Hovhannisyan AM, Dadayan SA (2021) Quantitative analysis of biologically active substances and the investigation of antioxidant and antimicrobial activities of some extracts of Osage orange fruits. Pharmacia 68(4): 731-739. https://doi.org/10.3897/pharmacia.68.e70180
Figure 10 Evaluation of the antimicrobial activity of Osage Orange extracts on strains of Bacillus subtilis 1820, E. Coli 5002, Serratia marcescens 5251 and Staphylococcus aureus ATCC-6538.
Figure 6 from: Dadayan AS, Stepanyan LA, Sargsyan TH, Hovhannisyan AM, Dadayan SA (2021) Quantitative analysis of biologically active substances and the investigation of antioxidant and antimicrobial activities of some extracts of Osage orange fruits. Pharmacia 68(4): 731-739. https://doi.org/10.3897/pharmacia.68.e70180
Figure 6 Results of quantification and identification of flavonoids in ethyl acetate extract of Osage Orange.
Assessment of animal diseases caused by bacteria resistant to antimicrobials: Swine - Appendix B: Excel file with all data extracted
<p>Information on all the full-text studies that were assessed, including the reason for exclusion for those that were excluded at the full-text screening and the data extracted from the included studies, can be consulted here. </p> <p>The extensive literature review was carried out by the University of Copenhagen under the contract OC/EFSA/ALPHA/2020/02 – LOT 1 (https://ted.europa.eu/udl?uri=TED:NOTICE:457654-2020:TEXT:EN:HTML)</p>
Assessment of animal diseases caused by bacteria resistant to antimicrobials: Poultry- Appendix B: Excel file with all data extracted
<p>Information on all the full-text studies that were assessed, including the reason for exclusion for those that were excluded at the full-text screening and the data extracted from the included studies, can be consulted here. </p> <p>The extensive literature review was carried out by the University of Copenhagen under the contract OC/EFSA/ALPHA/2020/02 – LOT 1 (https://ted.europa.eu/udl?uri=TED:NOTICE:457654-2020:TEXT:EN:HTML)</p>
Figure 1 from: Trifonova D, Gavrilova A, Dyakova G, Gavrilov G, Yotova M, Nikolov S (2021) Preliminary in vitro study of anti-oxidant activity and anti-diabetic potential of plant extracts from 4 herbal substances not traditionally used for treatment of diabetes mellitus. Pharmacia 68(4): 755-762. https://doi.org/10.3897/pharmacia.68.e72769
Figure 1 Relative enzyme activity of α-glucosidase by adding different concentration of (A) SKW and (B) acarbose IC50 values and relative enzyme activity were calculated for the samples which exhibited higher than 50% inhibition of α-glucosidase.
Figure 5 from: Bloom D, Thomer A, Vaidya G, Guralnick R, Russell L (2012) From documents to datasets: A MediaWiki-based method of annotating and extracting species observations in century-old field notebooks. ZooKeys 209: 235-253. https://doi.org/10.3897/zookeys.209.3247
Figure 5 - An example of how a location (Big Thompson Creek near Loveland), a date (Sunday, June 10, 1906), and a taxon (Cottonwood, genus Populus) are grouped from across multiple pages.
Figure 4 from: Bloom D, Thomer A, Vaidya G, Guralnick R, Russell L (2012) From documents to datasets: A MediaWiki-based method of annotating and extracting species observations in century-old field notebooks. ZooKeys 209: 235-253. https://doi.org/10.3897/zookeys.209.3247
Figure 4 - Editing a notebook page on Wikisource. This screenshot shows side-by-side transcription and wiki markup syntax.
Figure 2 from: Bloom D, Thomer A, Vaidya G, Guralnick R, Russell L (2012) From documents to datasets: A MediaWiki-based method of annotating and extracting species observations in century-old field notebooks. ZooKeys 209: 235-253. https://doi.org/10.3897/zookeys.209.3247
Figure 2 - Index page for Notebook #1. Each Index page corresponds to a multipage file. The Index page displays volume metadata and links to sections of the notebook, while also providing links out to each notebook page and color-coding to determine which pages have been already transcribed and proofed.
Figure 1 from: Bloom D, Thomer A, Vaidya G, Guralnick R, Russell L (2012) From documents to datasets: A MediaWiki-based method of annotating and extracting species observations in century-old field notebooks. ZooKeys 209: 235-253. https://doi.org/10.3897/zookeys.209.3247
Figure 1 - Web browser view of a scanned page of Henderson's journal displayed side-by-side with transcriptions and annotations using the MediaWiki Proofread Page extension.
Figure 3 from: Bloom D, Thomer A, Vaidya G, Guralnick R, Russell L (2012) From documents to datasets: A MediaWiki-based method of annotating and extracting species observations in century-old field notebooks. ZooKeys 209: 235-253. https://doi.org/10.3897/zookeys.209.3247
Figure 3 - Henderson's first sentence. "Boulder, Colo. July 28, 1905. Saw Say [sic] Phoebe and siskins, [American] Robins, [Northern] Flicker."
Figure 7 from: Giurginca A, Šustr V, Tajovský K, Giurginca M, Matei I (2015) Spectroscopic parameters of the cuticle and ethanol extracts of the fluorescent cave isopod Mesoniscus graniger (Isopoda, Oniscidea). In: Taiti S, Hornung E, Štrus J, Bouchon D (Eds) Trends in Terrestrial Isopod Biology. ZooKeys 515: 111–125. https://doi.org/10.3897/zookeys.515.9395
Figure 7 - FP spectra of the sample of solid phase of Mesoniscus graniger dragani (λex = 380 nm) (Int.- intensity of the peak).
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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.