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3,684 results for “extract”
Heather nectar extracts reduce within-colony epidemics of the bumblebee parasite <em>Crithidia bombi</em>
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Custom script for feature extraction from Genbank files
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Using convolutional neural networks to efficiently extract immense phenological data from community science images
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Evaluation of DNA extracted from timber rattlesnake (Cotalus horridus) cloacal and blood swabs for microsatellite genotyping
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Monitoring the compaction of single DNA molecules in Xenopus egg extract in real time
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Marcell Experimental Forest peat core extraction chemical analysis data (DOC, Fe, Ca, Mg, K, P, Al)
This data set reports iron (Fe), dissolved organic carbon (DOC), calcium (Ca), magnesium (Mg), potassium (K), phosphorus (P), and aluminum (Al) measured in extractions of soil cores sampled from two boreal peatlands, the S1 and S2 bogs, in the Marcell Experimental Forest (MEF) in Itasca County, Minnesota. The soil cores were sampled on September 2, 2017. Elements were quantified in extractions with hydrochloric acid, sodium dithionite, sodium sulfate, and sodium dithionite plus hydrochloric acid to examine how iron influences carbon and nutrient cycling in peatlands. The S1 and S2 sites are research catchments instrumented for hydrologic monitoring. The S1 bog is also the location of the Spruce and Peatland Responses Under Changing Environments (SPRUCE) experiment. These data are used, analyzed, and reported in Curtinrich et al. (2021, Ecosystems).
Depth profiles of water column dissolved methane, density and biomass of zooplankton (specifically, Chaoborus spp.), and measurements of methane extracted from Chaoborus spp. during two sampling campaigns in 2016
Depth profiles of water column dissolved methane (CH4), density and biomass of zooplankton (specifically, Chaoborus spp.), and measurements of methane extracted from Chaoborus spp. were collected from Beaverdam Reservoir, Vinton, VA, USA during two, 24-hr intensive sampling campaigns in fall 2016 (3-4 August and 16-17 September). The sampling campaign was designed to test the hypothesis that Chaoborus spp. can transport CH4 from the hypolimnion to the epilimnion of lakes and reservoirs as they migrate to the surface waters from the benthos at night in search of zooplankton prey, and results of the project are published in Carey et al. 2018. During both sampling events, depth profiles of water column methane and Chaoborus spp. density were collected at noon, dusk, midnight, 2 a.m., dawn, and noon the following day at a 1 m resolution. In addition, during the September sampling event depth profiles were collected 1 hour prior to and after dusk. Methane gas was extracted from live Chaoborus individuals at every depth and time point immediately after collection via gentle centrifugation in distilled water following McGinnis et al. 2017. REFERENCES: Carey, C.C., R.P. McClure, J.P. Doubek, M.E. Lofton, N.K. Ward, and D. Scott. 2018. Chaoborus spp. transport CH4 from the sediments to the surface waters of a eutrophic reservoir, but their contribution to water column CH4 concentrations and diffusive efflux is minor. Environmental Science & Technology. 52:1165-1173. DOI 10.1021/acs.est.7b04384 McGinnis, D. F., Flury, S., Tang, K. W., Grossart, H.-P. 2017. Porewater methane transport within the gas vesicles of diurnally migrating Chaoborus spp.: an energetic advantage. Scientific Reports. 7(44478) DOI 10.1038/srep44478
Plant available NH4, NO3, and PO4 was determined at sites near ARC LTER Toolik acidic tundra and at a toposequence along the floodplain of the Sagavanirktuk River using 2 N KCL and weak HCL extracts, Arctic LTER 1987 to 2002
Plant available NH4, NO3, and PO4 was determined at sites near ARC LTER Toolik acidic tundra and at a toposequence along the floodplain of the Sagavanirktuk River using 2 N KCL and weak HCL extracts. This file complies data collected at different times from 1987 through 2001 and includes initial extracts taken for buried bag method of net nitrogen mineralization.
Extractable NH4-N and NO3-N (2 N KCl), PO4-P (0.025 N HCl) and pH (0.01 M CaCl2) were measured on soils from a transect along the Dalton road, Arctic LTER 1991.
Extractable NH4-N and NO3-N (2 N KCl), PO4-P (0.025 N HCl) and pH (0.01 M CaCl2) were measured on soils from a transect along the Dalton road. Sites are Gus Shaver flowering sites and Arctic LTER sites.
Extractable soil cations (K, Ca, Mg, Na) for intertussock O and B horizon soils on moist acidic and non-acidic tundra, Arctic LTER 1997.
Extractable soil cations (K, Ca, Mg, Na) for intertussock O and B horizon soils on moist acidic and non-acidic tundra.
Eight Mile Lake Research Watershed, Carbon in Permafrost Experimental Heating Research (CiPEHR): Off Plot Soil Incubation By Depth III - Soil Extracts 2013-2014
The Carbon in Permafrost Experimental Heating Research (CiPEHR) project addresses the following questions: 1) Does ecosystem warming cause a net release of C from the ecosystem to the atmosphere?, 2) Does the decomposition of old C, that comprises the bulk of the soil C pool, influence ecosystem C loss?, and 3) How do winter and summer warming alone, and in combination, affect ecosystem C exchange? We are answering these questions using a combination of field and laboratory experiments to measure ecosystem carbon balance and radiocarbon isotope ratios at a warming experiment located in an upland tundra field site near Healy, Alaska in the foothills of the Alaska Range. We investigated C and nitrogen (N) mineralization within the soil profile by incubating soil cores collected adjacent to (but not within) the CiPEHR site. These soil cores spanned the entire active layer and approximately 30 cm of permafrost. Soil cores were separated into 10 cm depth intervals and incubated for 241 days at 15 degC and field moisture was maintained with water additions. This dataset contains extractable pools of dissolved inorganic N (DIN, NH4 + NO3) and non-particulate organic carbon (NPOC). Measurements were made periodically throughout the incubation by destructively harvesting subsamples of soil and performing 2M KCl vacuum extractions.
Data for "A Dataset for Multi-lingual Epidemiological Event Extraction"
<p>This is the data for the LREC 2020 paper "<a href="https://zenodo.org/record/3693647">A Dataset for Multi-lingual Epidemiological Event Extraction</a>". If you use this resource, please cite the paper:</p> <pre><code>@inproceedings{mutuvi2020dataset, title = "A Dataset for Multi-lingual Epidemiological Event Extraction", author = {Mutuvi, Stephen and Doucet, Antoine, and Lejeune, Gaël and Odeo, Moses}, booktitle = "Proceedings of the Eighth International Conference on Language Resources and Evaluation ({LREC}'20)", year = "2020", location = "Marseille" }</code></pre> <p> </p> <p>This work has been supported by the European Union Horizon 2020 research and innovation programme under grants 825153 (Embeddia) and 770299 (NewsEye).</p>
Online Aerosol Chemical Characterization by Extractive Electrospray Ionization − Ultrahigh-Resolution Mass Spectrometry (EESI-Orbitrap)
<p>These datasets are the raw data presented in the presented work of "Online Aerosol Chemical Characterization by Extractive Electrospray Ionization − Ultrahigh-Resolution Mass Spectrometry (EESI-Orbitrap)" in <em>Environmental Science & Technology Journal</em>, doi:10.1021/acs.est.9b07090.</p> <p>Abstract: Current mass spectrometry techniques for the online measurement of organic aerosol (OA) composition are subjected to either thermal/ionization-induced artifacts or limited mass resolving power, hindering accurate molecular characterization. Here, we combined the soft ionization capability of extractive electrospray ionization (EESI) and the ultrahigh mass resolution of Orbitrap for real-time, near-molecular characterization of OAs. Detection limits as low as tens of ng m<sup>−3</sup> with linearity up to hundreds of μg m<sup>−3</sup> at 0.2 Hz time resolution were observed for single- and mixed-component calibrations. The performance of the EESI-Orbitrap system was further evaluated with laboratory-generated secondary OAs (SOAs) and filter extracts of ambient particulate matter. The high mass accuracy and resolution (140 000 at <em>m/z</em> 200) of the EESI-Orbitrap system enable unambiguous identification of the aerosol components’ molecular composition and allow a clear separation between adjacent peaks, which would be significantly overlapping if a medium-resolution (20 000) mass analyzer was used. Furthermore, the tandem mass spectrometry (MS<sup>2</sup>) capability provides valuable insights into the compound structure. For instance, the MS<sup>2</sup> analysis of ambient OA samples and lab-generated biogenic SOAs points to specific SOA precursors in ambient air among a range of possible isomers based on fingerprint fragment ions. Overall, this newly developed and characterized EESI-Orbitrap system will advance our understanding of the formation and evolution of atmospheric aerosols.</p> <p>Structure of the datasets: The raw data are separated into individual file of excel format for the figures. Simulation data from Figure 4 can be generated using the matlab code named <em>Figure4PeakSimulation.m.</em> </p>
Results "Anti-obesity effects of individual or combination treatment with Spirulina platensis and green coffee bean aqueous extracts in high-fat diet-induced obese rats"
<p><strong>Background</strong>: Obesity, a chronic disease, is associated with serious health risks, including premature mortality. This study aimed to investigate the anti-obesity effects of individual or combination treatment with <em>Spirulina platensis</em> and green coffee bean aqueous extracts in high-fat diet-induced (HFD) obese rats.</p> <p><strong>Methods</strong>: Rats were fed on HFD to induce obesity. Corn oil in the HFD accounted for 50.98 % of the calories. Fifty rats were divided into the following five groups (10 rats/group): control, HFD, HFD-<em>Spirulina</em>, HFD-coffee, HFD-<em>Spirulina</em> and coffee co-treatment groups. The serum levels of lipid, leptin, and insulin, as well as the hepatic mRNA levels of fatty acid synthase (FAS), peroxisome proliferator-activated receptor gamma coactivator-1 alpha (PGC-1α), and peroxisome proliferator-activated alpha receptor (PPARα) were estimated.</p> <p><strong>Results</strong>: The <em>Spirulina</em> and/or green coffee bean aqueous extracts decreased the final bodyweight and liver weight, and the serum levels of alanine aminotransferase, aspartate aminotransferase, and alkaline phosphatase. Additionally, the extracts decreased the serum levels of total cholesterol, triacylglycerol, low-density lipoprotein-cholesterol, leptin, and glucose, and enhanced the serum insulin level. Furthermore, the extracts enhanced the PGC-1α and PPARα mRNA levels and decreased the FAS mRNA levels.</p> <p><strong>Conclusion</strong>: The individual or combination treatment with <em>Spirulina</em> and green coffee bean extracts decreased obesity-induced hyperlipidemia. Thus, <em>Spirulina platensis</em> and green coffee can be potentially used to treat obesity.</p>
The zebra mussel (Dreissena polymorpha) as a model organism for ecotoxicological studies: a prior 1H NMR spectrum interpretation of a whole body extract for metabolism monitoring.
<p>NMR data of the zebra mussel <em>Dreissena polymorpha</em> whole body polar extract metabolome</p> <p>- 1D <sup>1</sup>H annotated spectrum - 600 MHz</p> <p>- 2D <sup>1</sup>H-<sup>1</sup>H JRES spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>1</sup>H COSY spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>1</sup>H TOCSY spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>13</sup>C HSQC spectrum - 600 MHz</p> <p>- 2D<sup>1</sup>H-<sup>13</sup>C HSQC spectrum - 800 MHz</p> <p>- 2D<sup>1</sup>H-<sup>31</sup>P HSQC spectrum - 800 MHz</p> <p>- <sup>1</sup>H annotated spectrum description tables (.xlsx)</p> <p>- Instructions for data visualization in Topspin</p>
TESTAR State Model extracted while executing MyThaiStar as web system under test
<p>TESTAR extracted State Model datasets with TESTAR tool using MyThaiStar web application as System Under Test (SUT). This State Models has been generated to be used as an example to be automatically generated and introduced locally in DECODER PKM, from H2020 DECODER Project.</p> <p>TESTAR tool is an open source tool (www.testar.org) for automated testing through graphical user interface (GUI) currently being developed by the Universitat Politecnica de Valencia and the Open University of the Netherlands.</p> <p>MyThaiStar (<a href="https://github.com/devonfw/my-thai-star">github.com/devonfw/my-thai-star</a>) is the reference application that Capgemini uses internally to promote best programming practices and the correct use of last technologies. It’s is developed with Devon Framework, the standard tool for development at the company.</p> <p>PKM is the Persistent Knowledge Monitor developed as main infrastructure from H2020 DECODER Project (www.decoder-project.eu) under grant agreement number 824231.</p> <p>As TESTAR explores automatically the SUT, it will use the Document Object Model (DOM) information extracted from MyThaiStar SUT, to generate and save a TESTAR State Model in the OrientDB graph database. This model contains information about the Widgets, States and Actions, that were found in the SUT.<br> <br> - MyThaiStar.json.gz: JSON file exported from OrientDB that contains a database with the TESTAR State Model. It can be imported into OrientDB using the TESTAR tool, to analyze and interact with the State Model.<br> <br> - ArtefactStateModel_MyThaiStar_2020.1_zpnffj5c3407972370_2020-06-15_12h14m24s: for DECODER project purposes, the knowledge extracted with TESTAR in the generation of the State Model has been summarized and referenced in an artifact JSON file to be adapted to PKM input requirements.</p>
Data from: Optimisation of biogenic synthesis of silver nanoparticles from flavonoid-rich Clinacanthus nutans leaf and stem aqueous extracts
<p>BACKGROUND: Silver nanoparticles (AgNPs) are widely used in food industries, biomedical, dentistry, catalysis, diagnostic biological probes, and sensors. The use of plant extract for AgNPs synthesis eliminates the process of maintaining cell culture and the process could be scaled up under a non-aseptic environment. The purpose of this study is to determine the classes of phytochemicals, to biosynthesise and characterise the AgNPs using Clinacanthus nutans leaf and stem extracts. In this study, AgNPs was synthesised from the aqueous extracts of C. nutans leaves and stems through a non-toxic, cost effective and eco-friendly method.</p> <p>RESULTS: The formation of AgNPs was confirmed by UV-Vis spectroscopy, and the size of AgNP-L (leaf) and AgNP-S (stem) were 114 and 129 nm, respectively. Transmission electron microscopy (TEM) analysis showed spherical nanoparticles with AgNP-L and AgNP-S ranging from 10-300 nm and 10-180 nm; with zeta potentials of AgNP-L and AgNP-S at -42.8 and -43.9 mV, respectively. XRD analysis matched the face-centred cubic structure of silver and was capped with bioactive compounds. FTIR analysis revealed the presence of few functional groups of phenolic and flavonoid compounds. These functional groups act as reducing agents in AgNPs synthesis.</p> <p>CONCLUSION: This result showed that the biogenically synthesised nanoparticles reduced silver ions to silver nanoparticles in aqueous condition and the AgNPs formed were stable and less toxic.</p>
Table S1: Data extraction table. A summary of the 166 candidate biomarkers that met the inclusion/exclusion criteria.
<p>Supplementary material to Translating Biomarkers of Cholangiocarcinoma for Theranosis: A Systematic Review. Version 2. </p>
Mass spectra of leaf extracts from maize
<p>Mass fingerprints of leaf extracts from B73 and Mo17 maize lines. Eleven biological replicates for each genotype were evaluated.</p>
Source code for models of floral initiation in pea and gene expression data extracted from published sources
<p>The dataset contains the source code for computational models of a gene network controlling transition to flowering in pea (<em>Pisum sativum</em>). The models were based on ordinary differential equations (ODE) or neural networks. It also includes data on the expression dynamics of genes involved in the network, which was used for model fitting. The expression data was extracted from the following papers: </p> <p>Hecht, V., Laurie, R. E., Schoor, K. Vander, Ridge, S., Knowles, C. L., Liew, L. C., Sussmilch, F. C., et al. (2011). The Pea GIGAS Gene Is a FLOWERING LOCUS T Homolog Necessary for Graft-Transmissible Specification of Flowering but Not for Responsiveness to Photoperiod. 23, 147–161. doi:10.1105/tpc.110.081042</p> <p>Sussmilch, F. C., Berbel, A., Hecht, V., Schoor, K. Vander, Ferrándiz, C., Madueño, F., et al. (2015). Pea VEGETATIVE2 Is an FD Homolog That Is Essential for Flowering and Compound In fl orescence Development. 27, 1046–1060. doi:10.1105/tpc.115.136150</p> <p>The source code of the DEEP software used for parameter optimization in the model fitting can be found in the Gitlab repository (https://gitlab.com/mackoel/deepmethod/-/tree/master).</p> <p>The files are the supplement to the following manuscript, submitted to Frontiers in Genetics:</p> <p>"Dynamical Modeling of the Core Gene Network Controlling Transition to Flowering in <em>Pisum sativum</em>" by Polina Pavlinova, Maria G. Samsonova, and Vitaly V. Gursky.</p> <p>All possible questions can be sent to: Polina Pavlinova (polina.pavlina1004@gmail.com), Vitaly Gursky (gursky@math.ioffe.ru).</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.