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3,684 results for “extract”
Raw data of sequencing results of our study: Bovine milk microbiota: Evaluation of different DNA extraction protocols in challenging samples
<p>Clean reads of the repeated milk samples with used Primer Pairs V1V2 and V3V4</p> <p>Raw data of sequencing results (amplicon single variants)</p>
FIGURE. Floral habit and structure of C. spongifolia. A. Type specimen in situ with open, spathe limb (apex is reflexed out of view), and green spathe tube (ca. 6 cm long). B. Adjacent plant with inflorescences and prophylls. C. Spadix showing from top: sterile appendix, staminate (male) zone, sterile interstice, and green pistillate (female) zone with tapered, conical form. D. Detail of female zone showing a few basal staminodes. E–G. Berries of the preserved type specimen. G. Dissected berry with orthotropous ovules (some outlined) attached by funicles to parietal placentae (arrows). H. Surface of male zone showing closely-packed synandria. I. Synandria separated to show fused anther sacs beneath apical pores (example in center has 8 pores, 8 anthers) J. Mature fruiting head, with single berry removed to show seed packing and 67 seeds extracted (scale bar units: 1 mm) (Bach Ma NP; type 2020; fruit and seeds 2018). Photos: NVD and PJM. in Colocasia spongifolia sp. nov. (Araceae) in southern China and central Vietnam
FIGURE. Floral habit and structure of C. spongifolia. A. Type specimen in situ with open, spathe limb (apex is reflexed out of view), and green spathe tube (ca. 6 cm long). B. Adjacent plant with inflorescences and prophylls. C. Spadix showing from top: sterile appendix, staminate (male) zone, sterile interstice, and green pistillate (female) zone with tapered, conical form. D. Detail of female zone showing a few basal staminodes. E–G. Berries of the preserved type specimen. G. Dissected berry with orthotropous ovules (some outlined) attached by funicles to parietal placentae (arrows). H. Surface of male zone showing closely-packed synandria. I. Synandria separated to show fused anther sacs beneath apical pores (example in center has 8 pores, 8 anthers) J. Mature fruiting head, with single berry removed to show seed packing and 67 seeds extracted (scale bar units: 1 mm) (Bach Ma NP; type 2020; fruit and seeds 2018). Photos: NVD and PJM.
Cotton-based nucleic acid extraction
<p><strong>Abstract</strong>: Nucleic acid amplification technique (NAAT)-assisted detection is the primary intervention for pathogen molecular diagnostics. However, NAATs such as quantitative real-time polymerase chain reaction (qPCR) require prior purification or extraction of target nucleic acid from the sample of interest since the latter often contains polymerase inhibitors. Similarly, genetic disease screening is also reliant on the successful extraction of pure patient genomic DNA from the clinical sample. However, such extraction techniques traditionally utilize spin-column techniques that in turn require centralized high-speed centrifuges. This hinders any potential deployment of qPCR- or PCR-like NAAT methods in resource-constrained settings. The development of instrument-free nucleic acid extraction methods, especially those utilizing readily available materials would be of great interest and benefit to NAAT-mediated molecular diagnosis workflows in resource-constrained settings. In this report, we screened medical-grade cotton, a readily available over-the-counter biomaterial to extract <em>E. coli</em> genomic DNA (gDNA) spiked in 30%, 45%, and 60% serum. The extraction was carried out in a completely instrument-free manner using cotton and a sterilized toothpick and was completed in 30 min (with using chaotropic salt) or 10 min (without using chaotropic salt). The quality of the extracted DNA was then probed using PCR followed by agarose gel analysis, qPCR, and sequencing. Our method demonstrated that the high-quality DNA extraction could be performed both with or without using a chaotropic salt, albeit with a difference in the quality of the extracted DNA</p>
datacleanr manuscript animated example: Extract Recipe
<p>Animated example (GIF) of datacleanr's capabilities showing the "Extract Recipe" Tab.</p> <p>The software <a href="https://github.com/the-Hull/datacleanr">datacleanr </a>is an R package for reproducible and interactive data processing.</p>
Bayesian evidence-driven likelihood selection for sky-averaged 21-cm signal extraction data
<p>Nested sampling posterior samples of different noise distributions with the following pattern:</p> <p>[Noise Model]_[Likelihood used]_[Noise parameter]_[Noise parameter value]</p> <p>The enhanced/ folders contain the more accurate posterior samples of the enhanced run of PolyChord.</p>
Data from: Shelf life and quality of tomato (Lycopersicon esculentum Mill.) fruits as affected by neem leaf extract dipping and beeswax coating
<p>The data was generated to investigate the effect of Beeswax (BW) coating and Neem leaf extract (NLE) dipping on the shelf life and quality of tomatoes (<em>Lycopersicon esculentum</em> Mill.) over a storage period of 36 days. A factorial combination of four levels of Neem plant extract (control, 15%, 20% and 25%) and four levels of beeswax coating (control, 3%, 6% and 9%) storage treatments with three replications were applied on fully matured green tomatoes in the study. The treatments were arranged in a randomized complete block design. The average storage room air temperature and relative humidity varied from 15.2 ºC to 20.4 ºC and 55.53% to 69.46% RH during 36 days of storage period at Haramaya University from February to April 2020. Data were recorded on 4, 8, 12, 16, 20, 24, 28, 32, and 36 days after storage. Data on physiological loss in weight, chemical compositions (total soluble solids, pH, titratable acidity, and ascorbic acid), decay (%), percentage marketability, and shelf life were assessed at an interval of four days during 36 days of storage period under ambient conditions.</p>
Deep Learning for Extracting Dispersion Curves (Dataset)
<p>The Dataset of Deep Learning for Extracting Dispersion Curves</p> <p>2021-01-06 | Surveys in Geophysics</p> <p>DOI: <a href="https://doi.org/10.1007/s10712-020-09615-3">10.1007/s10712-020-09615-3</a></p> <p>authors: Tianyu Dai; Jianghai Xia; Ling Ning; Chaoqiang Xi; Ya Liu; Huaixue Xing</p> <p>URL: <a href="https://doi.org/10.1007/s10712-020-09615-3">https://doi.org/10.1007/s10712-020-09615-3</a></p> <p> </p>
One million articles from five post socialist countries with extracted features: sentiment, basic emotions, LDA topics and presence of influential domestic politicians
<p>This is a replication data for my paper under blind review.<br> <br> This paper develops a new prediction model for media content presence on a website. It analyses a new corpus of one million articles from five countries: Poland, Russia, Belarus, Kazakhstan and Ukraine, in two languages, Polish and Russian. These articles were scraped daily from seventeen websites in 2017-2020 period. The research applies a wide range of natural language processing methods to automatically derive several properties of each article: its topic, sentiment, basic emotions, mentions of influential domestic politicians. The articles’ embeddings and their cosine similarity are used to calculate the news context, such as how an article differs from the daily issue main themes. These features are used to estimate a logistic regression assessing the likelihood that the same or slightly modified, as measured by cosine similarity, article will remain on the main web page the next day. The key, and somewhat unexpected result is that articles with negative sentiment polarity are less likely to be published for more than one day. This result holds for all countries analyzed. It means that the negative news bias documented in the literature is partly offset by their shorter life cycle.<br> <br> Data is in the Python pickle format. Should be read into Python using the pickle.load() function. Each element (row) is the data frames or list represents one news article. Each file has the same format. Loading a pickle file returns a list of four elements:<br> 1. A dummy variable equal to 1 when the article was published the next day, with the text being identical<br> 2. A dummy variable equal to 1 when the article was published the next day, but we allow for small text modifications (cosine similarity > 0.99)<br> 3. Dataframe with extracted features, described below.<br> 4. List with texts of articles in Polish or Russian<br> <br> Ad 3. The columns of the dataframe are as follows (we refer to row number i in description):<br> - pandas index (may appear once or twice in the datafame)<br> - maxcosine: maximum cosine similarity between art i and all articles published next day<br> - cosine_diff: cosine similarity between article i and the elementwise average of embeddings of all articles in the current issue. Measure how similar is the article i to the core narrative of the current issue<br> - cosine_std: std. dev. of cosine similarity measures between all pairs of articles in the current issue. Measures how focused or dispersed is the current issue news coverage<br> - thirteen LDA topic groups: politics, legislation and legal affairs (POL); economy, finance, various sectors of the economy (ECO); military, war, protests, crime, security threats (MIL); international affairs, specific issues concerning foreign countries (INT); technology (TECH); family issues, culture, sport, education (FAM); regional issues and housing (REG); health issues and the Covid-19 pandemic (HEA); media (MED); accidents (ACC); religion (REL); the Soviet Union (USSR); and articles for which no topic could be determined (MISC).<br> - rsent.c: relative sentiment that is dictionary based sentiment of articles i minus the average sentiment of the newspaper. This approach eliminates newspaper or country idiosyncratic sentiment factors. c stands for Covid, the sentiment lexicon was augmented with Covid related terms<br> - dip_*: Variable measuring if influential domestic politicians are mentioned in article i, * represent a country acronym. If N is equal to the number of occurrences of the names of influential domestic politicians in the article i, dip_* = 0 if N=0, dip_* = 1+ log(N) if N>0.<br> - three or four names of news portals from which the data was scraped.<br> - names of six basic emotions and the article i emotion scores calculated using zero-shot learning and the large version of the XLM (Conneau et al., 2019) model from the huggingface transformers library available at https://huggingface.co/vicgalle/xlm-roberta-large-xnli-anli<br> Names of the politicians used to calculate dip variables<br> Russia<br> "putin" "medvedev" "vaino" "shoigu" "bortnikov" "lavrov" "mishustin" "kirienko" "sechin"<br> Ukraine<br> "zelensky" "shmygal" "akhmetov" "avakov" "ermak" "poroshenko" "medvedchuk" "groisman"<br> Kazakhstan<br> "sagyntaev" "mamin" "tokayev" "nnazarbayev" "dnazarbayeva" "kulibayev" "masimov"<br> Belarus<br> "alukashenko" "vakulchik" "vlukashenko" "kobyakov" "makei" "myasnikovich" "rumas" "golovchenko"<br> Poland<br> "kaczynski" "duda" "morawiecki" "ziobro"<br> Data coverage<br> Country, news portal, numbr of articles<br> Russia iz.ru 43,782<br> Russia kommersant.ru 46,070<br> Russia novayagazeta.ru 29,357<br> Russia vedomosti.ru 27,797<br> Kazakhstan informburo.kz 29,375<br> Kazakhstan nur.kz 67,350<br> Kazakhstan tengrinews.kz 44,285<br> Kazakhstan zakon.kz 109,442<br> Belarus bdg.by 33,447<br> Belarus belgazeta.by 21,995<br> Belarus sb.by 83,685<br> Ukraine kp.ua 194,792<br> Ukraine segodnya.ua 45,835<br> Ukraine vesti.ua 90,559<br> Poland gazeta.pl 53,321<br> Poland rp.pl 49,587<br> Poland wpolityce.pl 76,625<br> <br> In the provided dataframes the number of observations is smaller, because the issues for which there was no next day issue, were removed.<br> <br> Data was scraped daily between 2017 or 2018 (depending on the country) and January 2021.</p>
Aesthetic Trends and Semantic Web Adoption of Media Outlets Identified through Automated Archival Data Extraction
<p>This dataset includes a variety of structured data gathered via various Web data extraction techniques which were employed in order to collect current and archival data from almost a thousand news websites that are popular in Greece, for the purpose of monitoring and recording their progress through time. The collected information, that took the form of a website’s source code and an impression of their homepage in different time instances of the last decade, has been used to identify trends concerning Semantic Web integration, DOM structure complexity, number of graphics, color usage and more. In total more than ten thousands impressions (including screenshots and source code) were analyzed which resulted to conclusions regarding the evolution of aesthetics and the adoption of new technologies.</p>
Preliminary study on the toxic effect of plant extracts against Philaenus spumarius L. (Hemiptera: Aphrophoridae)
<p>Data about: </p> <p>Figure 1 – Mean percentage (± SD) of mortality of <em>P. spumarius</em> adults recorded 1 h after treatment with different doses (0.25-2%) of Form A and with deltamethrin.</p> <p>Figure 2 - Lethal doses of different doses (0.25-2%) of Form A on <em>P. spumarius</em> at 1 h after treatment.</p> <p>Figure 3 – Mean percentage (± SD) of mortality of <em>P. spumarius</em> adults recorded 1 h after treatment with different doses (0.75-6%) of Form B and with deltamethrin.</p>
Dataset DOE of non-ionic aqueous micellar extraction of trypsin inhibitors and isoflavones from soybean meal
<p>Design of Experiments data from the work "Non-ionic aqueous micellar extraction of trypsin inhibitors and isoflavones from soybean meal: process optimization"</p>
DATASET -- IsiSPL : un processus automatisé pour faciliter l'ingénierie des LPL selon une stratégie d'adoption industrielle réactive ou extractive
<p>This archive contains the dataset that I have used to produce the experimentation describes in my Ph.D.</p>
Enhancing georeferenced biodiversity inventories: automated information extraction from literature records reveal the gaps
<p>Data and code supplement to our article revised submission to PeerJ.</p> <p> </p> <p>The file is compressed using standard zip. The uncompressed size is about 50 GB. There is a readme.md in the archive, which explains the structure of the contents.</p> <p> </p> <p>Abstract:</p> <p>We use natural language processing (NLP) to retrieve location data for cheilostome bryozoan species (text-mined occurrences [TMO]) in an automated procedure. We compare these results with data combined from two major public databases (DB): the Ocean Biogeographic Information System (OBIS), and the Global Biodiversity Information Facility (GBIF). Using DB and TMO data separately and in combination, we present latitudinal species richness curves using standard estimators (Chao2 and the Jackknife) and range-through approaches. Our combined DB and TMO species richness curves quantitatively document a bimodal global latitudinal diversity gradient for extant cheilostomes for the first time, with peaks in the temperate zones. 79% of the georeferenced species we retrieved from TMO (N = 1408) and DB (N = 4549) are non-overlapping. Despite clear indications that global location data compiled for cheilostomes should be improved with concerted effort, our study supports the view that many marine latitudinal species richness patterns deviate from the canonical latitudinal diversity gradient (LDG). Moreover, combining online biodiversity databases with automated information retrieval from the published literature is a promising avenue for expanding taxon-location datasets.</p>
ARCHI4MOM: Using Tracing Information to Extract the Architecture of Microservice-based Systems from Message-oriented Middleware
<p>The data published here are relevant for ESCA_2022 publication. </p>
FIGURE. Drosera hirtella: a, specimen Saint-Hilaire B1-1762bis (P00749158), with the designated lectotype highlighted; b, detail of the lectotype, showing the ascending scape and leaves with obovate lamina; c, detail of the individual to the left of the lectotype, representing the "western morphotype", with narrowly obovate lamina. Image extracted from A. de Saint-Hilaire virtual herbarium (2020). in A synopsis of the genus Drosera (Droseraceae) in Brazil
FIGURE. Drosera hirtella: a, specimen Saint-Hilaire B1-1762bis (P00749158), with the designated lectotype highlighted; b, detail of the lectotype, showing the ascending scape and leaves with obovate lamina; c, detail of the individual to the left of the lectotype, representing the "western morphotype", with narrowly obovate lamina. Image extracted from A. de Saint-Hilaire virtual herbarium (2020).
Causes and factors of cryogenic extraction biases on isotopes of xylem water
<p>Rehydration experiment on plant materials</p>
Fig. 2. Pairwise PCA plots for P. tricornutum endometabolome samples extracted 24 in Metabolic adaptation of diatoms to hypersalinity
Fig. 2. Pairwise PCA plots for P. tricornutum endometabolome samples extracted 24 (A, B) and 96 (C, D) hours after the salinity stress treatment. PCA plots of all data analyzed together (E, F). Panels A, C, and E show results from GC-MS. Panels B, D, and F result from the analysis of LC-MS data; the number of replicates analyzed is 5. (For interpretation of the colours in this figure legend, the reader is referred to the Web version of this article.)
Fig. 1. Pairwise PCA plots for T. pseudonana endometabolome samples extracted 24 in Metabolic adaptation of diatoms to hypersalinity
Fig. 1. Pairwise PCA plots for T. pseudonana endometabolome samples extracted 24 (A, B) and 96 (C, D) hours after salinity increase. PCA plots of all data analyzed together (E, F). Panels A, C, and E show results from GC-MS. Panels B, D, and F result from the analysis of LC-MS data; the number of replicates analyzed is 4–5 (see Experimental 5.13.). (For interpretation of the colours in this figure legend, the reader is referred to the Web version of this article.)
Fig. 3. Pairwise PCA plots for S. marinoi endometabolome samples extracted 24 in Metabolic adaptation of diatoms to hypersalinity
Fig. 3. Pairwise PCA plots for S. marinoi endometabolome samples extracted 24 (A, B) and 96 (C, D) hours after the salinity stress treatment. PCA plots of all data analyzed together (E, F). Panels A, C, and E show results from GC-MS. Panels B, D, and F result from the analysis of LC-MS data; the number of replicates analyzed is 4–5 (see Experimental 5.13.). (For interpretation of the colours in this figure legend, the reader is referred to the Web version of this article.)
Effect of Using Ethanol Extract of Artocarpus heterophyllus Leaves and Olea Europa Fruit Oil Combination on Facial Skin
<p>The volunteers were applied to the clay mask once a week and then were observed before and after application, as follows: moisture, skin oil, skin texture, collagen, wrinkle, pigment, and sensitivity using a skin analyzer (Skin Observed System).</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.