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3,684 results for “extract”
Figure 1 from: Nykyforuk A, Fira L, Lykhatskyi P, Pyda V (2020) Experimental research of garden spinach extract as a potential anabolic medicinal product. Pharmacia 67(4): 277-282. https://doi.org/10.3897/pharmacia.67.e56880
Figure 1 The content of TBA-active products in serum, liver and muscles of rats during starvation and after the use of DESL and KO, %. Note: * – probable changes (p ≤ 0.05) between the indicators of animals of all groups before starvation and after 7 days of starvation; # – probable changes (p ≤ 0.05) between the indicators of animals of control pathology and animals that received the experimental extract and the reference drug.
Peptide base for titanium functionalization (Automated extraction)
<p>This dataset has peptide sequence that is used in titanium functionalization.</p>
Figure 6 from: Budniak L, Vasenda M, Marchyshyn S, Kurylo K (2020) Determination of the optimum extraction regime of reducing compounds and flavonoids of Primula denticulata Smith leaves by a dispersion analysis. Pharmacia 67(4): 373-378. https://doi.org/10.3897/pharmacia.67.e54170
Figure 6 Effect of the extraction method on the extraction of reducing compounds from Рrimula denticulata Smith leaves.
Figure 2 from: Budniak L, Vasenda M, Marchyshyn S, Kurylo K (2020) Determination of the optimum extraction regime of reducing compounds and flavonoids of Primula denticulata Smith leaves by a dispersion analysis. Pharmacia 67(4): 373-378. https://doi.org/10.3897/pharmacia.67.e54170
Figure 2 Influence of the extractant nature on the extraction of reducing compounds from Рrimula denticulata Smith leaves.
Figure 1 from: Budniak L, Vasenda M, Marchyshyn S, Kurylo K (2020) Determination of the optimum extraction regime of reducing compounds and flavonoids of Primula denticulata Smith leaves by a dispersion analysis. Pharmacia 67(4): 373-378. https://doi.org/10.3897/pharmacia.67.e54170
Figure 1 Influence of extractant nature on the extraction of flavonoids from Рrimula denticulata Smith leaves.
Figure 5 from: Budniak L, Vasenda M, Marchyshyn S, Kurylo K (2020) Determination of the optimum extraction regime of reducing compounds and flavonoids of Primula denticulata Smith leaves by a dispersion analysis. Pharmacia 67(4): 373-378. https://doi.org/10.3897/pharmacia.67.e54170
Figure 5 Effect of the extraction method on the extraction of flavonoids from Рrimula denticulata Smith leaves.
Figure 4 from: Budniak L, Vasenda M, Marchyshyn S, Kurylo K (2020) Determination of the optimum extraction regime of reducing compounds and flavonoids of Primula denticulata Smith leaves by a dispersion analysis. Pharmacia 67(4): 373-378. https://doi.org/10.3897/pharmacia.67.e54170
Figure 4 Influence of the ratio of raw materials to extractant on the extraction of reducing compounds from the Рrimula denticulata Smith leaves.
Figure 3 from: Budniak L, Vasenda M, Marchyshyn S, Kurylo K (2020) Determination of the optimum extraction regime of reducing compounds and flavonoids of Primula denticulata Smith leaves by a dispersion analysis. Pharmacia 67(4): 373-378. https://doi.org/10.3897/pharmacia.67.e54170
Figure 3 Influence of the ratio of the raw materials to extractant on the flavonoids extraction from the Рrimula denticulata Smith leaves.
Work Data Extraction and Recommendations
<p>Work Data Extraction and Recommendations</p>
Codes used to extract coeliac disease, type I diabetes, rotavirus vaccination and DTP vaccination from CPRD Aurum
<p>Codes used in medcode and prodcode fields of CPRD Aurum data</p>
Extended Cookbook Data Extraction and Recommendations
<p>Extended Cookbook Data Extraction and Recommendations</p>
Figure 1 from: Voynova M, Shkondrov A, Krasteva I, Kondeva-Burdina M (2021) In vitro effects of synthetic muscimol and an extract from Amanita muscaria on human recombinant MAOB enzyme. Pharmacia 68(1): 147-150. https://doi.org/10.3897/pharmacia.68.e60705
Figure 1 Effects of muscimol (M) (at different concentrations) and selegiline (S) on hMAOB activity; * P < 0.05; ** P < 0.01; *** P < 0.001 vs control (pure hMAOB).
Figure 2 from: Voynova M, Shkondrov A, Krasteva I, Kondeva-Burdina M (2021) In vitro effects of synthetic muscimol and an extract from Amanita muscaria on human recombinant MAOB enzyme. Pharmacia 68(1): 147-150. https://doi.org/10.3897/pharmacia.68.e60705
Figure 2 Effects of Amanita muscaria extract (at different concentrations muscimol) and Selegiline (S) on hMAOB activity. ** P < 0.01 vs control (pure hMAOB).
Data from: Optimizing techniques to capture and extract environmental DNA for detection and quantification of fish
Few studies have examined capture and extraction methods for environmental DNA (eDNA) to identify techniques optimal for detection and quantification. In this study, precipitation, centrifugation and filtration eDNA capture methods and six commercially available DNA extraction kits were evaluated for their ability to detect and quantify common carp (Cyprinus carpio) mitochondrial DNA using quantitative PCR in a series of laboratory experiments. Filtration methods yielded the most carp eDNA, and a glass fibre (GF) filter performed better than a similar pore size polycarbonate (PC) filter. Smaller pore sized filters had higher regression slopes of biomass to eDNA, indicating that they were potentially more sensitive to changes in biomass. Comparison of DNA extraction kits showed that the MP Biomedicals FastDNA SPIN Kit yielded the most carp eDNA and was the most sensitive for detection purposes, despite minor inhibition. The MoBio PowerSoil DNA Isolation Kit had the lowest coefficient of variation in extraction efficiency between lake and well water and had no detectable inhibition, making it most suitable for comparisons across aquatic environments. Of the methods tested, we recommend using a 1.5 μm GF filter, followed by extraction with the MP Biomedicals FastDNA SPIN Kit for detection. For quantification of eDNA, filtration through a 0.2–0.6 μm pore size PC filter, followed by extraction with MoBio PowerSoil DNA Isolation Kit was optimal. These results are broadly applicable for laboratory studies on carps and potentially other cyprinids. The recommendations can also be used to inform choice of methodology for field studies.
Data from: Toward synthesizing our knowledge of morphology: using ontologies and machine reasoning to extract presence/absence evolutionary phenotypes across studies
The reality of larger and larger molecular databases and the need to integrate data scalably have presented a major challenge for the use of phenotypic data. Morphology is currently primarily described in discrete publications, entrenched in noncomputer readable text, and requires enormous investments of time and resources to integrate across large numbers of taxa and studies. Here we present a new methodology, using ontology-based reasoning systems working with the Phenoscape Knowledgebase (KB; kb.phenoscape.org), to automatically integrate large amounts of evolutionary character state descriptions into a synthetic character matrix of neomorphic (presence/absence) data. Using the KB, which includes more than 55 studies of sarcopterygian taxa, we generated a synthetic supermatrix of 639 variable characters scored for 1051 taxa, resulting in over 145,000 populated cells. Of these characters, over 76% were made variable through the addition of inferred presence/absence states derived by machine reasoning over the formal semantics of the source ontologies. Inferred data reduced the missing data in the variable character-subset from 98.5% to 78.2%. Machine reasoning also enables the isolation of conflicts in the data, that is, cells where both presence and absence are indicated; reports regarding conflicting data provenance can be generated automatically. Further, reasoning enables quantification and new visualizations of the data, here for example, allowing identification of character space that has been undersampled across the fin-to-limb transition. The approach and methods demonstrated here to compute synthetic presence/absence supermatrices are applicable to any taxonomic and phenotypic slice across the tree of life, providing the data are semantically annotated. Because such data can also be linked to model organism genetics through computational scoring of phenotypic similarity, they open a rich set of future research questions into phenotype-to-genome relationships.
Data from: DNA extraction method affects the detection of a fungal pathogen in formalin-fixed specimens using qPCR
Museum collections provide indispensable repositories for obtaining information about the historical presence of disease in wildlife populations. The pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has played a significant role in global amphibian declines, and examining preserved specimens for Bd can improve our understanding of its emergence and spread. Quantitative PCR (qPCR) enables Bd detection with minimal disturbance to amphibian skin and is significantly more sensitive to detecting Bd than histology; therefore, developing effective qPCR methodologies for detecting Bd DNA in formalin-fixed specimens can provide an efficient and effective approach to examining historical Bd emergence and prevalence. Techniques for detecting Bd in museum specimens have not been evaluated for their effectiveness in control specimens that mimic the conditions of animals most likely to be encountered in museums, including those with low pathogen loads. We used American bullfrogs (Lithobates catesbeianus) of known infection status to evaluate the success of qPCR to detect Bd in formalin-fixed specimens after three years of ethanol storage. Our objectives were to compare the most commonly used DNA extraction method for Bd (PrepMan, PM) to Macherey-Nagel DNA FFPE (MN), test optimizations for Bd detection with PM, and provide recommendations for maximizing Bd detection. We found that successful detection is relatively high (80–90%) when Bd loads before formalin fixation are high, regardless of the extraction method used; however, at lower infection levels, detection probabilities were significantly reduced. The MN DNA extraction method increased Bd detection by as much as 50% at moderate infection levels. Our results indicate that, for animals characterized by lower pathogen loads (i.e., those most commonly encountered in museum collections), current methods may underestimate the proportion of Bd-infected amphibians. Those extracting DNA from archived museum specimens should ensure that the techniques they are using are known to provide high-quality throughput DNA for later analysis.
Data from: More than skin and bones: comparing extraction methods and alternative sources of DNA from avian museum specimens
Next-generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol-chloroform and silica column) to three different sources of DNA (toe pad, skin punch, and bone) from ten historical avian museum specimens. We show that a modified phenol-chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol-chloroform protocol, likely a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol-chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.
Data from: Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data
In vivo calcium imaging through microendoscopic lenses enables imaging of previously inaccessible neuronal populations deep within the brains of freely moving animals. However, it is computationally challenging to extract single-neuronal activity from microendoscopic data, because of the very large background fluctuations and high spatial overlaps intrinsic to this recording modality. Here, we describe a new constrained matrix factorization approach to accurately separate the background and then demix and denoise the neuronal signals of interest. We compared the proposed method against previous independent components analysis and constrained nonnegative matrix factorization approaches. On both simulated and experimental data recorded from mice, our method substantially improved the quality of extracted cellular signals and detected more well-isolated neural signals, especially in noisy data regimes. These advances can in turn significantly enhance the statistical power of downstream analyses, and ultimately improve scientific conclusions derived from microendoscopic data.
Data from: Photocatalytic activity of graphene oxide–TiO2 thin films sensitized by natural dyes extracted from Bactris guineensis
This study synthesized and characterized composites of graphene oxide and TiO2 (GO-TiO2). GO-TiO2 thin films were deposited using the Doctor Blade technique. Subsequently, the thin films were sensitized with a natural dye extracted from a Colombian source (Bactris guineensis). Thermogravimetric analysis, X-ray diffraction, Raman spectroscopy, scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and diffuse reflectance measurements were used for physicochemical characterization. All the samples were polycrystalline in nature, and the diffraction signals corresponded to the TiO2 anatase crystalline phase. Raman spectroscopy and FT-IR verified the synthesis of composite thin films, and the SEM analysis confirmed the TiO2 films morphological modification after the process of GO incorporation and sensitization. XPS results suggested a possibility of appearance of Titanium (III) through the formation of oxygen vacancies (Ov). Furthermore, the optical results indicated that the presence of the natural sensitizer and GO improved the optical properties of TiO2 in the visible range. Finally, the photocatalytic degradation of Methylene Blue (MB) was studied under visible irradiation in aqueous solution, and pseudo-first order model was used to obtain kinetic information about photocatalytic degradation. These results indicated that the presence of GO has an important synergistic effect in conjunction with the natural sensitizer, reaching a photocatalytic yield of 33%.
Data from: Preservation-induced morphological change in salamanders and failed DNA extraction from a decades-old museum specimen: implications for Plethodon ainsworthi
<p>Natural history collections are important data repositories, but different chemical treatments of specimens can influence morphological measurements and DNA extraction, complicating taxonomic and conservation decisions dependent upon these data. One such example is the Bay Springs Salamander (<i>Plethodon ainsworthi</i>), the only United States amphibian categorized as Extinct by the IUCN.<i> </i>Recent research has proposed that <i>P. ainsworthi </i>is an invalid taxon, arguing that the 55-year-old type specimens' morphological distinctiveness from syntopic <i>P. mississippi</i> is a preservation artifact. To address this controversy, we tested for morphological changes across five experimental treatments in proxy <i>P. shermani</i> specimens, and we re-examined the datasets used to support the invalidity of <i>P. ainsworthi</i>. We also tested recently developed DNA extraction techniques on the putatively formalin-fixed <i>P. ainsworthi</i> holotype. We used Bayesian models to demonstrate that preservation method can differentially bias morphological measurements, with most methods causing lower estimates of mass and modestly higher estimates of snout-vent-length:head width ratio. These results are broadly consistent with previous studies of other vertebrates, but inconsistent with the hypothesis that <i>P. ainsworthi </i>type specimens are actually poorly preserved <i>P. mississippi</i>. Attempts to extract DNA from the <i>P. ainsworthi</i> holotype unfortunately proved unsuccessful, preventing conclusive resolution of its status and emphasizing the limitations of promising new methods. Nonetheless, we tentatively recommend continued recognition of <i>P. ainsworthi</i> as a valid but possibly extinct taxon. More generally, we invite all authors who study preserved specimens to recognize and report how certain chemical treatments might impact their results.</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.