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3,684 results for “extract”
UPLC-QTOF data from a river sample extracted with various solid phase extraction phases - mz5 files with scans in centroid spectrum format
<p>This dataset has been acquired from a river sample (Marne River, France) collected as part of the Screenatm'eau project (Observatoire des Sciences de l’Univers - Enveloppes FLUides de la Ville à l’Exobiologie - OSU-EFLUVE, Université Paris-Est Créteil). The sample was processed by solid-phase extraction using multiple cartridges and phases, in triplicates (see the list of samples in the samplemetadata.csv file).</p> <p>Data was acquired with a SYNAPT HDMS QTOF (Waters) coupled with a Nano ACQUITY UPLC System (Waters), in ESI positive mode. Raw data was converted using Proteowizard MSConvert version 3.0.21288, using zlib compression, with the CWT peakpicking algorithm (snr=0, peakSpace=0) to transform profile to centroid data, and the zeroSamples option (removeExtra 1-). The chosen output formats were .mzML and .mz5.</p> <p>A list of markers was obtained after peak picking and alignment across all samples using the PatRoon R package with the OpenMS algorithm, and exported as a markertable.csv file. Each detected marker has m/z and retention time values (see the variablemetadata.csv file), and intensity values in all samples (markertable.csv).</p> <p>For file naming explanation and details about each SPE phase, see the readme.txt file.</p>
VAMDC extraction with identifier = 5ab8c38a-bdad-4c38-be72-40cbcf015797
<div>This is a dataset extracted from http://topbase.obspm.fr/12.07/vamdc/tap/ VAMDC node.</div><div>Query originating this dataset: query=select * where ( atomsymbol = 'li' ); </div><div> Data source version: 2017-01-30</div><div>Data format: XSAMS 12.07</div><div>Query uuid in VAMDC query store: 5ab8c38a-bdad-4c38-be72-40cbcf015797</div>
VAMDC extraction with identifier = b540b211-ea04-4092-8375-d55fd068f8c7
<div>This is a dataset extracted from http://topbase.obspm.fr/12.07/vamdc/tap/ VAMDC node.</div><div>Query originating this dataset: query=select * where ( IonCharge = '1' ) </div><div> Data source version: 2017-01-30</div><div>Data format: XSAMS 12.07</div><div>Query uuid in VAMDC query store: b540b211-ea04-4092-8375-d55fd068f8c7</div>
VAMDC extraction with identifier = 1ce2c1b9-f4dd-493c-ae3a-a36a9a32cde9
<div>This is a dataset extracted from http://vald.astro.uu.se/atoms-12.07/tap/ VAMDC node.</div><div>Query originating this dataset: query=select * where ( atomsymbol = 'h' ); </div><div> Data source version: 2018-04-04</div><div>Data format: XSAMS 12.07</div><div>Query uuid in VAMDC query store: 1ce2c1b9-f4dd-493c-ae3a-a36a9a32cde9</div>
VAMDC extraction with identifier = 60ccb3ad-4411-43d1-badd-5e09ee659f39
<div>This is a dataset extracted from http://stark-b.obspm.fr/12.07/vamdc/tap/ VAMDC node.</div><div>Query originating this dataset: query=select * where ( atomsymbol = 'mg' and ioncharge = 0 and radtranswavelength <= 5200 and radtranswavelength >= 5100 ); </div><div> Data source version: 2017-06-23</div><div>Data format: XSAMS 12.07</div><div>Query uuid in VAMDC query store: 60ccb3ad-4411-43d1-badd-5e09ee659f39</div>
VAMDC extraction with identifier = a9a38253-7788-496f-b12c-b5c44751535f
<div>This is a dataset extracted from http://tipbase.obspm.fr/12.07/vamdc/tap/ VAMDC node.</div><div>Query originating this dataset: query=select * where ( atomsymbol = 'fe' ); </div><div> Data source version: 2017-01-30</div><div>Data format: XSAMS 12.07</div><div>Query uuid in VAMDC query store: a9a38253-7788-496f-b12c-b5c44751535f</div>
VAMDC extraction with identifier = 0fd61e0e-2e5a-4c54-b5ab-c865271b0d87
<div>This is a dataset extracted from http://stark-b.obspm.fr/12.07/vamdc/tap/ VAMDC node.</div><div>Query originating this dataset: query=select * where ( atomsymbol = 'li' ); </div><div> Data source version: 2017-06-23</div><div>Data format: XSAMS 12.07</div><div>Query uuid in VAMDC query store: 0fd61e0e-2e5a-4c54-b5ab-c865271b0d87</div>
Human studies carried out with pomegranate-based products (juice and extract).
<p>Background</p> <p>The consumption of <a href="https://www.sciencedirect.com/topics/food-science/pomegranate">pomegranate</a> juices and extracts has long been linked to many health benefits beyond nutrition, described mainly by innumerable <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/preclinical-study">preclinical studies</a>. However, the European Food Safety Authority (EFSA) concluded in 2010 that a cause and effect relationship could not be established between the consumption of pomegranate-derived products and all the health claims presented. There are no additional EFSA opinions on health claims specifically addressed to pomegranate in the last decade.</p> <p>Scope and approach</p> <p>This review comprehensively compiles all human studies conducted on pomegranate. The aim is to discuss these studies critically to identify possible flaws and propose guidelines that might help establish a cause and effect relationship between pomegranate-derived product consumption and health.</p> <p>Key findings and conclusions</p> <p>To date, 86 human studies have evaluated the health benefits of pomegranate juices and extracts. The most promising, albeit scarce, evidence is related to blood pressure improvement. Less evidence deals with inflammation, cancer, cognitive function, physical activity, and <a href="https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/intestine-flora">gut microbiota</a> modulation (prebiotic effects). After a decade since EFSA's opinion, human evidence remains inconsistent, making it difficult to support most claimed health effects. The lack of effects and(or) data discrepancy might be attributable to design limitations, including insufficient product characterization and interindividual variability that influence pomegranate polyphenols' bioefficacy. New coordinated strategies between policy makers, research/academic institutions, and industry are needed to move forward. Therefore, this review presents a roadmap to conduct well-designed trials and cover existing gaps, which could establish a cause-effect relation between pomegranate consumption and health benefits beyond nutrition.</p>
Systematic Literature Mapping - Selected Articles Data Extraction
<p>- CSV with the raw data extracted from abstract + full-text review from the selected articles.</p> <p>- CSV with normalized data.</p> <p>- CSV with the normalized data after being a feature engineering step in which some columns have been deleted.</p> <p>- CSV with formal context to extract the concepts lattice.</p>
Text-fig.10. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. a–f: seeds extracted from seed-bearing capsule. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 1 cm. in Taimyria Gen. Nov., A New Genus Of Evolutionary Advanced Gymnosperms From Triassic Of The Taimyr Peninsula, Siberia, Russia
Text-fig.10. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. a–f: seeds extracted from seed-bearing capsule. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 1 cm.
Text-fig. 9. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. Structure of seed extracted from seed-bearing capsule. a: general morphology; b, c: detailed cellular structure. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 1 mm (a), 100 µm (b, c). in Taimyria Gen. Nov., A New Genus Of Evolutionary Advanced Gymnosperms From Triassic Of The Taimyr Peninsula, Siberia, Russia
Text-fig. 9. Taimyria triassica NAUGOLNYKH et MOGUTCHEVA gen. et sp. nov., holotype 4287/6. Structure of seed extracted from seed-bearing capsule. a: general morphology; b, c: detailed cellular structure. Locality: Tsvetkov Cape; Lower Triassic, Induan; Keshin Formation. Scale bar 1 mm (a), 100 µm (b, c).
Automatically Extracted SHACL Shapes for WikiData, DBpedia, YAGO-4, and LUBM & Associated Coverage Statistics
<p>The uploaded datasets contain <strong>automatically extracted </strong>SHACL shapes for the following datasets:</p> <ul> <li>WikiData (the truthy dump from September 2021 filtered by removing non-English strings) [1]</li> <li>DBpedia [2]</li> <li>YAGO-4 [3] </li> <li>LUBM (scale factor 500) [4]</li> </ul> <p>The validating shapes for these datasets are generated by a program that parses the corresponding RDF files (in `.nt` format). The extracted shapes encode various SHACL constraints, e.g., sh:minCount, sh:path, sh:class, sh:datatype etc. For each shape we encode coverage in terms of number of entities satisfying such shape, this information is encoded using the <a href="http://vocab.deri.ie/void#entities">void:entities</a> predicate. </p> <p>We have provided as executable Jar file the program we developed to extract these SHACL shapes.<br> More details about the datasets used to extract these shapes and <em>how to run the Jar</em> are available on our GitHub repository <a href="https://github.com/dkw-aau/qse">https://github.com/dkw-aau/qse</a>.</p> <p>Read more about our Quality Shapes Extraction (QSE) tool on our website <a href="https://relweb.cs.aau.dk/qse/">https://relweb.cs.aau.dk/qse/</a></p> <p>[1] Vrandečić, Denny, and Markus Krötzsch. "Wikidata: a free collaborative knowledgebase." Communications of the ACM 57.10 (2014): 78-85.</p> <p>[2] Auer, Sören, et al. "Dbpedia: A nucleus for a web of open data." The semantic web. Springer, Berlin, Heidelberg, 2007. 722-735.</p> <p>[3] Pellissier Tanon, Thomas, Gerhard Weikum, and Fabian Suchanek. "Yago 4: A reason-able knowledge base." European Semantic Web Conference. Springer, Cham, 2020.</p> <p>[4] Guo, Yuanbo, Zhengxiang Pan, and Jeff Heflin. "LUBM: A benchmark for OWL knowledge base systems." Journal of Web Semantics 3.2-3 (2005): 158-182.</p>
List of non-naturalized plant species present in France extracted from Pl@ntNet data (exotic ornamental and cultivated plants in particular).
<p>This dataset contains the list of plant species that have been observed on the French territory using the <a href="https://plantnet.org/">Pl@ntNet </a>application and that are NOT know as being either native or naturalized according to Kew's Plants of the World Online repository (<a href="https://powo.science.kew.org/">POWO</a>). Such species are typically exotic species managed by humans in anthropized environments such as guardens, houses or cultivated areas. This includes commercialized plants for various usage such as ornemental plants, eatable plants, phytotherapy, etc. The list contains 5,589 species, each associated with its scientific name and the number of valid Pl@ntNet observations of that species geo-localized in the metropolitan French territory. </p>
Assessing the Cytotoxicity of Phenolic and Terpene Fractions Extracted from Iraqi Prunus arabica on AMJ-13 and SK-GT-4 Human Cancer Cell Lines
<p>Breast and esophagus cancer are the most aggressive and prominent causes of death worldwide. In addition, these cancers showed resistance to current chemotherapy regimens with limited success rates and fatal outcomes. Recently many studies reported the significant cytotoxic effects of phenolic and terpene fractions extracted from various <em>Prunus</em> species against different cancer cell lines. This suggests the probability to be a candidate as an alternative or adjuvant to the current chemotherapeutic regimens. The study aimed to evaluate the cytotoxicity of phenolic and terpene fractions extracted from Iraqi <em>Prunus arabica</em> on breast (AMJ-13) and esophagus (SK-GT-4) cancer cell lines by using the MTT assay. Analysis using Chou-Talalay method performed to assess the synergistic effect between the extracted fractions and chemotherapeutic agent (docetaxel). Moreover, HPLC analysis has been conducted for the quantitative determination of different bioactive molecule of both phenolic and terpene fractions in the extract. According to the findings, the treatment modalities significantly decreased cancer cell viability of AMJ-13 and SK-GT-4 and had insignificant cytotoxicity on the normal cells (normal human fibroblast cell line) (all less than 50% cytotoxicity). Analyzing with Chou-Talalay showed a strong synergism with docetaxel on both cancer cell lines (higher cytotoxicity even in low concentrations) and failed to induce a cytotoxicity on the normal cells. Important flavonoid glycosides and terpenoids were detected by HPLC in the particularly ferulic acid, catechin, chlorogenic acid, B sitosterol, and campesterol. In conclusion, the extracted fractions selectively inhibited the proliferation of both cancer cell and showed minimal cytotoxicity on normal cells. Thus, the study suggested the possible natural source of selected fractions as breast and esophagus cancer drugs</p>
Extraction of clinical phenotypes for Alzheimer disease dementia from clinical notes using natural language processing
<p><strong>Objectives</strong></p> <p>There is much interest in utilizing clinical data for developing prediction models for Alzheimer disease (AD) risk, progression, and outcomes. Existing studies have mostly utilized curated research registries, image analysis, and structured Electronic Health Record (EHR) data. However, much critical information resides in relatively inaccessible unstructured clinical notes within the EHR.</p> <p><strong>Materials and Methods</strong></p> <p>We developed a natural language processing (NLP)-based pipeline to extract AD-related clinical phenotypes, documenting strategies for success and assessing the utility of mining unstructured clinical notes. We evaluated the pipeline against gold-standard manual annotations performed by two clinical dementia experts for AD-related clinical phenotypes including medical comorbidities, biomarkers, neurobehavioral test scores, behavioral indicators of cognitive decline, family history, and neuroimaging findings.</p> <p><strong>Results</strong></p> <p>Documentation rates for each phenotype varied in the structured versus unstructured EHR. Inter-annotator agreement was high (Cohen's kappa = 0.72–1) and positively correlated with the NLP-based phenotype extraction pipeline's performance (average F1-score = 0.65-0.99) for each phenotype.</p> <p><strong>Discussion</strong></p> <p>We developed an automated NLP-based pipeline to extract informative phenotypes that may improve the performance of eventual machine-learning predictive models for AD. In the process, we examined documentation practices for each phenotype relevant to the care of AD patients and identified factors for success.</p> <p><strong>Conclusion</strong></p> <p>Success of our NLP-based phenotype extraction pipeline depended on domain-specific knowledge and focus on a specific clinical domain instead of maximizing generalizability. </p>
Sound extracts from wild boars during their resting phase
<p>This folder contains tracks collected with animal-borne audiologgers deployed on wild boars.</p> <p>The tracks that were extracted from 40 minutes before to 5 minutes after a relocation was initiated are labelled as ‘relocation’. The tracks labelled as ‘control’ were extracted at the same time of day as the ‘relocation’ tracks, but on different dates, when relocations did not occur. We also make available an additional track, corresponding to a dog barking, with the wild boar not reacting to it. It was identified upon opportunistic listening of the dataset.</p>
Hot carrier extraction from 2D semiconductor photoelectrodes
<p>Hot carrier-based energy conversion systems could double the efficiency of conventional solar energy technology or drive photochemical reactions that would not be possible using fully thermalized, "cool" carriers, but current strategies require expensive multi-junction architectures. Using an unprecedented combination of photoelectrochemical and in situ transient absorption spectroscopy measurements, we demonstrate ultrafast (<50 fs) hot exciton and free carrier extraction under applied bias in a proof-of-concept photoelectrochemical solar cell made from earth-abundant and potentially inexpensive monolayer (ML) MoS<sub>2</sub>. Our approach facilitates ultrathin 7 Å charge transport distances over 1 cm<sup>2</sup> areas by intimately coupling ML-MoS<sub>2</sub> to an electron-selective solid contact and a hole-selective electrolyte contact. Our theoretical investigations of the spatial distribution of exciton states suggest greater electronic coupling between hot exciton states located on peripheral S atoms and neighboring contacts likely facilitates ultrafast charge transfer. Our work delineates future 2D semiconductor design strategies for practical implementation in ultrathin photovoltaic and solar fuels applications.</p>
ENPKG from 1,600 plant extracts
<p>These files constitute the Experimental Natural Products Knowledge Graph (ENPKG) generated from the LC-MS analysis and the anti-trypanosomatid screening of a 1,600 plant extracts dataset.</p>
Dataset from: Ultraviolet refractive index values of organic aerosol extracted from deciduous forestry, urban and marine environments
<p>The refractive index values of atmospheric aerosols are required to address the large uncertainties in the magnitude of atmospheric radiative forcing and measurements of the refractive index dispersion with wavelength of particulate matter sampled from the atmosphere are rare over ultraviolet wavelengths. An ultraviolet-optimized spectroscopic system illuminates optically-trapped single particles from a range of tropospheric environments to determine the particle’s optical properties. Aerosol from remote marine, polluted urban, and forestry environments is collected on quartz filters, and the organic fraction is extracted and nebulized to form micron-sized spherical particles. The radius and the real component of refractive index dispersion with wavelength of the optically trapped particles are determined to a precision of 0.001 µm and 0.002 respectively over a near-ultraviolet-visible wavelength range of 0.320–0.480 µm. Remote marine aerosol is observed to have the lowest refractive index (n=1.442 (λ=0.350 µm)), with above-canopy rural forestry aerosol (n=1.462–1.481 (λ=0.350 µm)) and polluted urban aerosol (n=1.444–1.485 (λ=0.350 µm)) showing similar refractive index dispersions with wavelength. In-canopy rural forestry aerosol is observed to have the highest refractive index value (n=1.508 (λ=0.350 µm)). The study presents the first single particle measurements of the dispersion of refractive index with wavelength of atmospheric aerosol samples below wavelengths of 0.350 µm. The Cauchy dispersion equation, commonly used to describe the visible refractive index variation of aerosol particles, is demonstrated to extend to ultraviolet wavelengths below 0.350 µm for the urban, forestry, and atmospheric aerosol water-insoluble extracts from these environments. A 1D radiative-transfer calculation of the difference in top-of-the-atmosphere albedo between atmospheric core-shell mineral aerosol with and without films of this material demonstrates the importance of organic films forming on mineral aerosol.</p> <p>The raw experimental spectra collected and analysed in this study are provided, as well as files for the calibrated wavelengths.</p>
Extracted ASCADv2 with labels
<p>Extracted dataset from the original ASCADv2 database (https://www.data.gouv.fr/fr/datasets/ascadv2/).</p> <p> </p> <p>The dataset is separated in three splits:</p> <p>- training with 200k traces</p> <p>- validation with 50k traces</p> <p>- attack with 50k traces</p> <p> </p> <p>For each trace, the extracted samples are : </p> <p>- samples from the masked inputs of the sboxes</p> <p>- samples from the input mask r_in</p> <p>- samples from the multiplicative mask r_m</p> <p>- labels for most intermediates</p> <p> </p> <p> </p>
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.