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3,684 results for “extract”
Extraction of Crossref datadump for benchmarking purpose
<p>Extracted form a datadump provided <a href="https://www.crossref.org/blog/2022-public-data-file-of-more-than-134-million-metadata-records-now-available/">here</a>. The file contains several JSON files limiting to benchmark tools that have to process huge dataset in JSON format.</p>
A novel technique to simulate and characterize a yarn's mechanical behavior based on a geometrical fiber model extracted from micro-CT imaging: geometry and simulation data
<p>This dataset contains the original µCT scan data, the scripts and intermediate results for the generation of the geometrical fiber model, as well as the structural simulation files and their experimental validation data described in the paper <a href="https://journals.sagepub.com/doi/10.1177/00405175221137009">"A novel technique to simulate and characterize a yarn's mechanical behavior based on a geometrical fiber model extracted from micro-CT imaging"</a>, published in Textile Research Journal.</p>
SSP2017 - Experiment Data - Towards Extracting Realistic User Behavior Models
<p>This package contains the monitoring data, the ideal behavior models, computed clustering results for behavior models based on the monitoring data, and the interpretation of the analysis results. We processed these data with the following two tooling sources:</p> <p>Experiment setup: https://doi.org/10.5281/zenodo.883069</p> <p>Analysis software: https://doi.org/10.5281/zenodo.883061</p>
Soft tissue changes in extraction versus non-extraction treatment with fixed orthodontic appliances: a systematic review and meta-analysis
<p>Export of the dataset used in Stata to conduct all meta-analyses reported in the published paper.</p>
EuroparlExtract - Directional Parallel Corpora Extracted from the European Parliament Proceedings Parallel Corpus
<p>This dataset contains directional parallel corpora extracted from the European Parliament Proceedings Corpus (Europarl) v7 created by Philipp Koehn (see http://www.statmt.org/europarl/). For the extraction, the EuroparlExtract corpus processing toolkit by Michael Ustszewski (2017) was used. EuroparlExtract is freely available under the MIT License (see https://github.com/mustaszewski/europarl-extract).</p>
EuroparlExtract - Comparable Corpora Extracted from the European Parliament Proceedings Parallel Corpus
<p>This dataset contains comparable translational corpora extracted from the European Parliament Proceedings Corpus (Europarl) v7 created by Philipp Koehn (see http://www.statmt.org/europarl/). For the extraction, the EuroparlExtract corpus processing toolkit by Michael Ustszewski (2017) was used. Europarl Extract is freely available under the MIT License (see https://github.com/mustaszewski/europarl-extract).</p>
Enhanced Kinase Dictionaries associated with KinDER: A Biocuration Tool for Extracting Kinase Knowledge from Biomedical Literature
<p>This zip file contains Kinase dictionaries used for annotating documents with KinDER described in the following paper: </p> <p>Dopp, Daniel, Adam Morrone, and Indika Kahanda. "KinDER: A Biocuration Tool for Extracting Kinase Knowledge from Biomedical Literature." <em>Proceedings of the BioCreative VI Workshop</em>. 2017.</p>
Hop Flower Supercritical Carbon Dioxide Extracts Coupled with Carriers with Solubilizing Properties—Antioxidant Activity and Neuroprotective Potential
<p>Article, Dataset for article</p> <p> </p> <h1>Hop Flower Supercritical Carbon Dioxide Extracts Coupled with Carriers with Solubilizing Properties—Antioxidant Activity and Neuroprotective Potential</h1> <p> </p> <h2>Abstract</h2> <div><span>Lupuli flos</span> shows many biological activities like antioxidant potential, extended by a targeted effect on selected enzymes, the expression of which is characteristic for neurodegenerative changes within the nervous system. <span>Lupuli flos</span> extracts (LFE) were prepared by supercritical carbon dioxide (scCO<sub>2</sub>) extraction with various pressure and temperature parameters. The antioxidant, chelating activity, and inhibition of acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and tyrosinase by extracts were studied. The extracts containing ethanol were used as references. The most beneficial neuroprotective effects were shown by the extract obtained under 5000 PSI and 50 °C. The neuroprotective effect of active compounds is limited by poor solubility; therefore, carriers with solubilizing properties were used for scCO<sub>2</sub> extracts, combined with post-scCO<sub>2</sub> ethanol extract. Hydroxypropyl-β-cyclodextrin (HP-β-CD) in combination with magnesium aluminometasilicate (Neusilin US2) in the ratio 1:0.5 improved dissolution profiles to the greatest extent, while the apparent permeability coefficients of these compounds determined using the parallel artificial membrane permeability assay in the gastrointestinal (PAMPA GIT) model were increased the most by only HP-β-CD.</div> <div> <div> <div>Keywords: </div> <a href="https://www.mdpi.com/search?q=neuroprotection">neuroprotection</a>; <a href="https://www.mdpi.com/search?q=hop+strobile">hop strobile</a>; <a href="https://www.mdpi.com/search?q=inhibition+of+enzymes">inhibition of enzymes</a>; <a href="https://www.mdpi.com/search?q=xanthohumol">xanthohumol</a></div> </div>
Extracted data for meta-analysis: Distal versus proximal radial access in coronary angiography
<p>Data base underlying quantitative meta-analysis in the manuscript titled "Distal versus proximal radial access in coronary angiography: A meta-analysis" by Lueg, Schulze, Stöhr, & Leistner.</p> <p>Data allows meta-analysis of primary endpoint (RAO), secondary endpoints, meta-regression for moderator analysis, and publication bias analysis.</p>
Determining Antioxidant Activity of Cannabis Leaves Extracts from Different Varieties—Unveiling Nature's Treasure Trove
<p>Article, Dataset for article</p> <p> </p> <h1>Determining Antioxidant Activity of Cannabis Leaves Extracts from Different Varieties—Unveiling Nature’s Treasure Trove</h1> <p> </p> <h2>Abstract</h2> <div>Cannabis leaves contain a diverse range of antioxidants, including cannabinoids, flavonoids, and phenolic compounds, which offer significant health benefits. Utilising cannabis leaves as a source of antioxidants presents a cost-effective approach because they are typically discarded during the cultivation of cannabis plants for their seeds or fibres. Therefore, this presented study aimed to assess the antioxidant activity of the leaves of selected hemp cultivars, such as Białobrzeska, Tygra, and Henola, based on the results obtained with the 2,2′-Azino-bis(3-ethylbenzthiazoline-6-sulfonic acid, ferric reducing antioxidant power, cupric reducing antioxidant capacity, and 2,2-Diphenyl-1-picrylhydrazyl assays. The cannabinoid profile was analysed for the antioxidant activity to the contents of cannabidiol (CBD), cannabigerol (CBG), Δ<sup>9</sup>-tetrahydrocannabinol (Δ<sup>9</sup>-THC), and cannabichromene (CBC), determined based on chromatographic assays. The following variables were tested: the impact of various extractants (methanol, ethanol, and isopropanol), and their mixtures (50:50, <span>v/v</span>, as well as extraction methods (maceration and ultra-sound-assisted extraction) significant in obtaining hemp extracts characterised by different cannabinoid profiles. The results revealed that the selection of extractant and extraction conditions significantly influenced the active compounds’ extraction efficiency and antioxidant activity. Among the tested conditions, ultrasound-assisted extraction using methanol yielded the highest cannabinoid profile: CBD = 184.51 ± 5.61; CBG = 6.10 ± 0.21; Δ9-THC = 0.51 ± 0.01; and CBC = 0.71 ± 0.01 μg/g antioxidant potential in Białobrzeska leaf extracts.</div> <div> <div> <div>Keywords: </div> <a href="https://www.mdpi.com/search?q=Cannabis+sativa"><span>Cannabis sativa</span></a>; <a href="https://www.mdpi.com/search?q=antioxidant">antioxidant</a>; <a href="https://www.mdpi.com/search?q=cannabidiol">cannabidiol</a>; <a href="https://www.mdpi.com/search?q=cannabigerol">cannabigerol</a>; <a href="https://www.mdpi.com/search?q=oxidative+stress">oxidative stress</a></div> </div>
The Antioxidant and Neuroprotective Potential of Leaves and Inflorescences Extracts of Selected Hemp Varieties Obtained with scCO2
<p>Article, Dataset for the article</p> <p> </p> <h2>Abstract</h2> <div><span>Cannabis sativa</span>, a versatile plant with numerous varieties, holds promising potential for a wide range of biological activity. As raw materials for research, we chose leaves and inflorescences of hemp varieties such as Białobrzeskie, Henola, and Tygra, which are cultivated mainly for their fibers or seeds. The choice of extraction is a key step in obtaining the selected compositions of active compounds from plant material. Bearing in mind the lipophilic nature of cannabinoids, we performed supercritical carbon dioxide (scCO<sub>2</sub>) extraction at 50 °C under 2000 (a) and 6000 PSI (b). The cannabinoid contents were determined with the use of the HPLC-DAD method. The antioxidant capabilities were assessed through a series of procedures, including the DPPH, ABTS, CUPRAC, and FRAP methods. The capacity to inhibit enzymes that play a role in the progression of neurodegenerative diseases, such as acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and tyrosinase was also studied. The dominant cannabinoids in the extracts were cannabidiol (CBD) and cannabidiolic acid (CBDA). The highest concentration of eight cannabinoids was detected in the Tygra inflorescences extract (b). The most notable antioxidant properties were provided by the Tygra inflorescences extract (b). Nonetheless, it was the Henola inflorescences extract (b) that demonstrated the most efficient inhibition of AChE and BChE, and tyrosinase was inhibited the most significantly by the Białobrzeskie inflorescences extract (b). Multidimensional comparative analysis enrolled all assays and revealed that the Henola inflorescences extract (b) showed the most substantial neuroprotective potential.</div> <div> <div> <div>Keywords: </div> <a href="https://www.mdpi.com/search?q=Cannabis+sativa"><span>Cannabis sativa</span></a>; <a href="https://www.mdpi.com/search?q=antioxidant">antioxidant</a>; <a href="https://www.mdpi.com/search?q=neuroprotection">neuroprotection</a></div> </div>
Data set for the figures in the manuscript "Real-Time Identification of Aerosol-Phase Carboxylic Acid Production Using Extractive Electrospray Ionization Mass Spectrometry"
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Data for: Environmental DNA storage and extraction method affects detectability for multiple aquatic invasive species
<p>Environmental DNA (eDNA) refers to genetic material released by organisms into their surrounding environment. Collecting and identifying eDNA has gained popularity for monitoring and surveillance of aquatic invasive species. Invasive species management is most successful when an invasion is identified early while population size is likely to be low, highlighting the importance of eDNA detection sensitivity. Various factors influence DNA yield recovered from environmental samples. Environmental DNA storage and extraction methods, for example, can be adjusted to maximize DNA yield, thereby improving detectability. In this study, we compared the performance of two eDNA storage and extraction methods in detecting three common aquatic invasive species (<em>Bythotrephes longimanus</em>, <em>Dreissena polymorpha</em>, and <em>Faxonius rusticus</em>) across five natural ecosystems of Minnesota, United States. One method involved storing filters in 95% ethanol (EtOH) and extracting DNA using a DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany), whereas the other method used cetyl trimethylammonium bromide (CTAB) for storage and a phenol–chloroform–isoamyl (PCI) procedure for DNA extraction. We also investigated the effect of DNA extract volume (1 μL relative to 3 μL) in qPCR reactions on eDNA detections for the commercial kit method. The CTAB‐PCI method yielded significantly more positive detections, across all three species, compared to the EtOH‐Qiagen method. Moreover, we found that using 1 μL of DNA extract in qPCR reactions was equally effective as using 3 μL. To improve detections of aquatic invasive species, we recommend that researchers store eDNA sample filters in CTAB or a similar lysis buffer such as Longmire's solution and extract with PCI when feasible, but note that lower extract volumes might be used without negative effect when either increasing technical replicates or repurposing samples for the detection of multiple species.</p>
Improving the recovery for dissolved eDNA State: A comparative analysis of isopropanol precipitation, magnetic bead extraction, and centrifugal dialysis
<p>Environmental DNA consists of multiple states including but not limited to membrane-bound, adsorbed, and dissolved states. Because of their chemical and physical properties, each of these states may have different degradation and transport potential. Essential to the study of eDNA states is being able to isolate them from an environmental sample. Here we focus on improving the DNA recovery of the dissolved state of eDNA from water. We compared three recovery methods, namely isopropanol precipitation, magnetic bead extraction, and centrifugal dialysis. We evaluated the effectiveness of these methods based on the measured DNA recovery of two different species' DNA of different sizes. DNA recovery was assessed with qPCR. We also checked for the effect of inhibitor removal, and lastly estimated the cost of reagents and consumables (not labor). The DNA recovery varied among extraction methods, with isopropanol precipitation yielding the highest recovery (52.47 ± 19.69%), followed by centrifugal dialysis (12.58 ± 7.15%) and magnetic bead extraction (9.92 ± 3.89%). However, isopropanol precipitation's efficacy was influenced by humic acid concentration in the water matrix. The presence of humic acids significantly affected isopropanol precipitation, with higher humic acid concentrations leading to increased DNA recovery. This suggests that humic acids act as co-precipitators during isopropanol precipitation. We observed that longer DNA fragments (chicken) had lower recovery compared to shorter fragments (salmon) across all extraction methods. Magnetic bead extraction effectively removed inhibitors, while centrifugal dialysis and isopropanol extraction required an additional inhibitor removal step. Isopropanol, magnetic bead extraction, and centrifugal dialysis methods have estimated costs of 7.74, 8.53, and 23.62 USD in 2023 respectively. Overall, isopropanol precipitation was the least expensive and most effective with the highest measured recoveries, but it was dependent on humic acid concentration in the environmental sample.</p>
Extracted synthesis conditions for Nb:TiO2 films from scientific papers
<p>The csv file contains the dataset for synthesis conditions for Nb doped TiO2 films extracted from scientific papers using a knowledge graph.</p>
Figure S1 Surgical extraction of supernumerary teeth under sedation and analgesia, and a periapical radiograph 2 weeks later.
<p>Figure S1 Surgical extraction of supernumerary teeth under sedation and analgesia, and a periapical radiograph 2 weeks later.</p>
Green Extraction of depsidones and depsides from H. physodes using Natural Deep Eutectic Solvents
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NED data for the paper Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts
<p>This data repository contains NED data from the paper, <em><a href="https://arxiv.org/abs/2309.01812">Into the Single Cell Multiverse: an End-to-End Dataset for Procedural Knowledge Extraction in Biomedical Texts.</a></em></p> <p>Additional data for the NER classification task can be found here: <a href="../records/10050681">zenodo</a></p> <p> </p> <p> </p>
Data from: Minimally destructive hDNA extraction method for retrospective genetics of pinned historical Lepidoptera specimens
<p>The millions of specimens stored in entomological collections provide a unique opportunity to study historical insect diversity. Current technologies allow to sequence entire genomes of historical specimens and estimate past genetic diversity of present-day endangered species, advancing our understanding of anthropogenic impact on genetic diversity and enabling the implementation of conservation strategies. A limiting challenge is the extraction of historical DNA (hDNA) of adequate quality for sequencing platforms. We tested four hDNA extraction protocols on five body parts of pinned false heath fritillary butterflies, <em>Melitaea diamina</em>, aiming to minimise specimen damage, preserve their scientific value to the collections, and maximise DNA quality and yield for whole-genome re-sequencing. We developed a very effective approach that successfully recovers hDNA appropriate for short-read sequencing from a single leg of pinned specimens using silica-based DNA extraction columns and an extraction buffer that includes SDS, Tris, Proteinase K, EDTA, NaCl, PTB, and DTT. We observed substantial variation in the ratio of nuclear to mitochondrial DNA in extractions from different tissues, indicating that optimal tissue choice depends on project aims and anticipated downstream analyses. We found that sufficient DNA for whole genome re-sequencing can reliably be extracted from a single leg, opening the possibility to monitor changes in genetic diversity maintaining the scientific value of specimens while supporting current and future conservation strategies.</p>
Supporting material for von Fromm et al (2024) Moisture and soil depth govern relationships between soil organic carbon and oxalate-extractable metals at the global scale
<p>This file contains the supporting material for von Fromm et al (2024) Moisture and soil depth govern relationships between soil organic carbon and oxalate-extractable metals at the global scale (<em>submitted</em>). </p> <p>For more details see the corresponding manuscript (once it is published) and the github repository (https://github.com/SophievF/Global_Mox_analysis/tree/main). </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.