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3,684 results for “extract”
Assessment of real-time PCR for Helicobacter pylori DNA detection in stool with co-infection of intestinal parasites: a comparative study of DNA extraction methods
<p>Background</p> <p>Many studies reported high prevalence of <em>H. pylori</em> infection among patients co-infected with intestinal parasites. Molecular approach for the DNA detection of those microbes in stool have been proposed. However there are a few reports that evaluated the effect of bead-beating in relation to the <em>H. pylori</em> outcome. Therefore, we developed and evaluated two TaqMan-based real-time PCR (rt-PCR) qualitative assays for the detection of <em>ureC</em> (<em>glmM</em>) and <em>cagA</em> of <em>Helicobacter pylori</em> on DNA extracted by three procedures.</p> <p>Results</p> <p>The two PCRs were analysed on 100 stool samples from patients who were screened for intestinal parasites. Three DNA extraction procedures were used: 1) automation with bead beating, 2) automation without bead beating and 3) hand column. The specificity of the new assays was confirmed by sequencing the PCR products and by the lack of cross-reactivity with other bacteria or pathogens DNA. Rt-PCR assays showed a detection limit of 10^4 bacteria/200 mg stool. The <em>ureC</em>_PCR with bead beating process was compared to conventional stool antigen test (SAT), with 94.12 and 93.75% of respectively sensitivity and specificity. However, the discordant samples were confirmed by DNA sequencing suggesting a potential higher sensitivity and specificity of PCR.</p> <p>Conclusions</p> <p>Our findings showed that the automation with bead-beating –suggested procedure for intestinal parasitic infections- can reach highly sensitive results in <em>H. pylori</em> detection on stool compared also with SAT. Thus, this work can provide new insights into the practice of a clinical microbiology laboratory in order to optimize detection of gastro-intestinal infections. Further studies are needed to better define the clinical value of this technique.</p>
Separation, Preconcentration, and Determination of Lead, Cadmium and Iron Using Cloud Point Extraction with FAAS
<p>The concentration of heavy metals in drinking water is a significant standard for water quality evaluation and water pipeline corrosion detection. This research aimed to develop a new method based on cloud point extraction (CPE) for the separation, preconcentration and detection of lead, cadmium, and iron with flame atomic absorption spectrometry (FAAS) when the concentration of metallic trace elements in the sample was lower than the limits of detection (LOD). The experimental LODs for Pb, Cd and Fe, determined based on significant sensitivity change and break in the slope of the standard curve, were 0.01, 0.01, and 0.3 ppm, respectively. With joint utilization of both 2,6-diamino-4-phenyl-1,3,5-triazine (DPT) and 3-amino-7-dimethylamino-2-methylphenazine (Neutral Red, NR) as chelating agents, and using Triton X-114 as surfactant, those metallic elements could be effectively enriched in water samples. The preconcentration procedure was optimized by varying the experimental factors such as temperature, equilibrium time, pH, and the concentration of the chelates and surfactant. With the optimization, this method allowed the determination of these three trace elements with a 20-times reduced LOD and yielded substantial recoveries of 99.8, 97.3 and 99.3% for Pb, Cd and Fe, respectively.</p>
Col d'Olen, soil chemistry (extractable N-NO3) 2008-2019
<p>Dataset provides information about soil temperature, soil C and N dynamics at different sites in the alpine tundra, along an elevational gradient from 2500 to 2900 m asl during the period 2005-2018. The soil was sampled in triplicate in each the sites and the N-NO3 concentration is measured in soil K2SO4 extracts. The ongoing studies aimed at investigating how the meteorological variables affect the biogeochemistry of seasonally snow covered areas, with a special focus on the effect of the snow cover duration on soil and water C and N dynamics during the growing season.</p>
Dendropanax morbifera leaf extracts improved alcohol liver injury in association with changes in the gut microbiota of rats
<p>Supplementary information for <em>Dendropanax morbifera</em> leaf extracts improved alcohol liver injury in association with changes in the gut microbiota of rats</p> <p>Figure S1. Animal experiment design</p> <p>Table S1. Total polyphenol and total flavonoid contents of <em>Dendropanax morbifer</em> leaf and stem extracts.</p> <p>Table S2. Antioxidant activity of the <em>Dendropanax morbifer </em>leaf and stem extracts.</p> <p>Figure S2. HPLC chromatogram of <em>Dendropanax morbifer</em> leaf and stem extracts.</p> <p>Table S3. Body weight change and liver-body weight ratio of <em>Dendropanax morbifer </em>leaf ethanol and D.W extracts in alcohol-fed rats.</p> <p>Figure S3. Comparison of microbiota according to the concentrations of DML extracts. Numbers indicate the concentrations of DML treatments.</p> <p>Figure S4. Comparison of microbiota before DML extract treatment.</p> <p>Table S4. Analysis of molecular variances (AMOVA)</p> <p>Figure S5. Comparison of the taxonomic composition.</p>
Modeling ultrasound extraction of phenolic compounds from grape pomace
<p>The provided data include measurements of antioxidant activity, total phenolic content, concentrations of individual phenols and individual anthocyanins of grape pomace extracts for initial (DoE1) and final (DoE2) ultrasound method optimization.</p>
The effect of piezocision vs no piezocision on maxillary extraction space closure: a split-mouth, randomized controlled clinical trial.
<p>This is a “2-arm-parallel”, split-mouth trial with the aim to investigate the effects of piezocision compared to no piezocision on maxillary canine distalization and to evaluate patients’ perceptions on the surgical procedure.</p>
Data from: Extraction and separation of active ingredients in Schisandra chinensis (Turcz.) Baill and the study of their antifungal effects
Schisandra chinensis extracts (SEs) have traditionally been used as an oriental medicine for the treatment of various human diseases, however, their further application in the biocontrol of plant disease remains poorly understood. This study was conducted to develop eco-friendly botanical pesticides from extracts of S. chinensis and assess whether they could play a key role in plant disease defense. Concentrated active fractions (SE-I, SE-II, and SE-III) were obtained from S. chinensis via specific extraction and separation. Then, lignan-like substances, such as Schisanhenol B, were detected via High-Performance Liquid Chromatography-ElectroSpray Ionization-Mass Spectrometry (HPLC-ESI-MS) analyses of the active fractions. Moreover, the results from biological tests on colony growth inhibition and spore germination indicated that SE-I, SE-II, and SE-III could inhibit hyphal growth and spore generation of three important plant pathogenic fungi (Monilinia fructicola, Fusarium oxysporum, and Botryosphaeria dothidea). The study of the mechanisms of resistant fungi revealed that the oxidation resistance system, including reactive oxygen species (ROS), malondialdehyde (MDA), catalase (CAT), and superoxide dismutase (SOD), was activated. The expression of genes related to defense, such as pathogenesis-related protein (PR4), α-farnesene synthase (AFS), polyphenol oxidase (PPO), and phenylalanine ammonia lyase (PAL) were shown to be up-regulated after treatment with SEs, which suggested an increase in apple immunity and that fruits were induced to effectively defend against the infection of pathogenic fungi (B. dothidea). This study revealed that SEs and their lignans represent promising resources for the development of safe, effective, and multi-targeted agents against pathogenic fungi.
Scheme 1 from: Voynikov Y, Gevrenova R, Zheleva-Dimitrova D, Balabanova V, Nikolova I, Marinov L, Benbassat I, Momekov G (2023) UHPLC-Orbitrap screening of oleraindoles in hydromethanolic extracts of Portulaca oleracea. Pharmacia 70(4): 1521-1527. https://doi.org/10.3897/pharmacia.70.e113577
Scheme 1 Scheme 1. Common scaffold of an oleraindole.
Figure 2 from: Abdullah RK, Issa RA, Abu-Samak M, Mohammad BA, Abbas MA, Awwad SH (2024) Nephroprotective effects of Equisetum ramosissimum L. extract in streptozotocin-induced diabetic rats. Pharmacia 71: 1-11. https://doi.org/10.3897/pharmacia.71.e113659
Figure 2 Chromatogram of E. ramosissimum ethanol extract.
Figure 1 from: Abdullah RK, Issa RA, Abu-Samak M, Mohammad BA, Abbas MA, Awwad SH (2024) Nephroprotective effects of Equisetum ramosissimum L. extract in streptozotocin-induced diabetic rats. Pharmacia 71: 1-11. https://doi.org/10.3897/pharmacia.71.e113659
Figure 1 Chromatogram of E. ramosissimum methanol extract.
Figure 3 from: Warsi W, Jaswir I, Ahmed QU, Mahfudh N, bin Mohd. Nawi MS, Rohman A, Khatib A (2024) Morphological, teratogenic and behavioral evaluations of Gelidium spinosum methanol extract on zebrafish embryos. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e109918
Figure 3 The effect of various dosages of GsME on zebrafish embryos heart rate
Figure 1 from: Warsi W, Jaswir I, Ahmed QU, Mahfudh N, bin Mohd. Nawi MS, Rohman A, Khatib A (2024) Morphological, teratogenic and behavioral evaluations of Gelidium spinosum methanol extract on zebrafish embryos. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e109918
Figure 1 Effect of GsME on mortality rate (%) at 1, 2, 3 and 4 dpf, n = 20.
Figure 5 from: Warsi W, Jaswir I, Ahmed QU, Mahfudh N, bin Mohd. Nawi MS, Rohman A, Khatib A (2024) Morphological, teratogenic and behavioral evaluations of Gelidium spinosum methanol extract on zebrafish embryos. Pharmacia 71: 1-10. https://doi.org/10.3897/pharmacia.71.e109918
Figure 5 GC-MS analysis of phytoconstituents in GsME.
Figure 1 from: Andri Deswati D, Anggadiredja K, Nuryanti Garmana A (2024) Potent antioxidant activity of black grass jelly (Mesona palustris BL) leaf extract and fractions. Pharmacia 71: 1-5. https://doi.org/10.3897/pharmacia.71.e117435
Figure 1 HPLC Spectrogram of black grass jelly extract.
Data from: Towards a Methodology for Technoscientific Objects Extraction (Short Paper)
<p>This dataset includes data adopted in the paper "Towards a Methodology for Technoscientific Objects Extraction (Short Paper)". </p> <p>The file "articles_urls_2022.txt.zip" is an archive containing a txt file; each line of the txt file is an article URL. </p> <p>The libraries adopted to process the articles are reported in the paper or in the paper references. </p>
• Bibliographic search on global warming effects and extracted metadata (pH, salinity, oxygen, temperatures, diseases observed in field/ in vitro/ in vivo, clinical signs, pathology, morbidity/mortality);
<p><a><span>B ibliographic search on global warming effects and extracted metadata </span></a><span><span><a href="#_msocom_1" name="_msoanchor_1">[MOU1]</a><span> </span></span></span><span>(pH, salinity, oxygen, temperatures, diseases observed in field/ <em>in</em> <em>vitro</em>/ <em>in</em> <em>vivo</em>, clinical signs, pathology, morbidity/mortality);</span><span></span></p>
Oil extraction report from Chlamydomonas reinhardtii engineered to produce ketocarotenoids
<p>Report of oil extraction efficiency on <em>Chlamydomonas reinhardtii</em> strain engineered to produce ketocarotenoids and astaxanthin.</p> <p> </p> <p><strong>Oil report on lab scale:</strong></p> <p>Oil extraction was performed as described in Perozeni et al. Plant Biotechnology Journal 2020, starting from different volumes of saturated culture (300, 600, 900, and 1800 ml). The cells were pelleted and dissolved in 25 ml of sunflower oil. The extraction was thus performed on wet biomass. After centrifugation, the oil extract was diluted in oil and the absorption spectrum was used to determine the ketocarotenoid concentration as described in Perozeni et al. Plant Biotechnology Journal 2020.</p> <p> </p> <p>The spectra recorded are in the sheet “Raw”. In the sheets “Quantification” there are the results of the ketocarotenoids quantification and the extraction efficiency. In the sheet "summary" the overall results in terms of starting material, final oil volume, ketocarotenoid concentration and extraction efficiency are presented.</p> <p>Samples:</p> <p>1x: extraction starting from 300ml of C. reinhardtii EN1 strain saturated culture, oil extract diluted 1:10 before measuring the absorption spectrum.</p> <p>2x: extraction starting from 600ml of C. reinhardtii EN1 strain saturated culture, oil extract diluted 1:100 before measuring the absorption spectrum.</p> <p>3x: extraction starting from 900ml of C. reinhardtii EN1 strain saturated culture, oil extract diluted 1:100 before measuring the absorption spectrum.</p> <p>6x: extraction starting from 1800ml of C. reinhardtii EN1 strain saturated culture, oil extract diluted 1:1000 before measuring the absorption spectrum.</p> <p>6x 3<sup>rd</sup> cycle: extraction starting from 5400ml of C. reinhardtii EN1 strain saturated culture in three extraction steps recycling in each step the oil used for extraction to increase ketocarotenoid concentration, oil extract diluted 1:1000 before measuring the absorption spectrum.</p> <p>6x 4<sup>th</sup> cycle: extraction starting from 7200ml of C. reinhardtii EN1 strain saturated culture in three extraction steps recycling in each step the oil used for extraction to increase ketocarotenoid concentration, oil extract diluted 1:1000 before measuring the absorption spectrum.</p> <p>6x 5<sup>th</sup> cycle: extraction starting from 9000ml of C. reinhardtii EN1 strain saturated culture in three extraction steps recycling in each step the oil used for extraction to increase ketocarotenoid concentration, oil extract diluted 1:1000 before measuring the absorption spectrum.</p> <p>6x 6<sup>th</sup> cycle: extraction starting from 10800ml of C. reinhardtii EN1 strain saturated culture in three extraction steps recycling in each step the oil used for extraction to increase ketocarotenoid concentration, oil extract diluted 1:1000 before measuring the absorption spectrum.</p> <p> </p> <p> </p> <p><strong>Oil extraction report on large scale:</strong></p> <p>Oil extraction was performed according to the procedure developed for lab scale starting from 200 gr of total dry biomass (corresponding to a volume of 250L of a saturated cell culture). The overall biomass was extracted in three independent extractions (Extraction 1, 2, and 3), recycling the oil extract for up to 4th cycle, keeping the same ratio of oil/biomass adopted in the lab scale experiment. In the case of Extraction 1 the extraction was performed on wet biomass, while Extraction 2 and 3 were performed on dry biomass. After Extractions 1 and 2, the final pellet obtained was further extracted in oil (samples “ 2nd extraction 1” and “2nd extraction 2”). The spectra recorded are in the sheet “Raw”. In the sheet “Quantification” there are the results of the ketocarotenoids quantification considering the dilution (in oil) applied to the oil extracts. </p> <p>In the sheet “extraction eff." the finalresults in terms of starting material, final oil volume, ketocarotenoid concentration and extraction efficiency are presented. The overall extraction efficiency obtained considering all the extraction performed and the total oil extracts obtained is also reported </p> <p> </p>
Figure 2 from: Sadaqa E, Utami RA, Mudhakir D (2024) In vitro cytotoxic and genotoxic effects of Phyllanthus niruri extract loaded chitosan nanoparticles in TM4 cells and their influence on spermatogenesis. Pharmacia 71: 1-14. https://doi.org/10.3897/pharmacia.71.e112138
Figure 2 FTIR spectra of A.PN extract; B. chitosan; C.STPP; D.PNNP.
Evaluating the utility of the Threshold of Toxicological Concern (TTC) and its exclusions in the biocompatibility assessment of extractable chemical substances from medical devices
<p>Data supporting manuscript Patlewicz G, Nelms M, Rua D. Evaluating the utility of the Threshold of Toxicological Concern (TTC) and its exclusions in the biocompatibility assessment of extractable chemical substances from medical devices. Computational Toxicology, 2022, in press <a href="https://doi.org/10.1016/j.comtox.2022.100246" rel="nofollow">https://doi.org/10.1016/j.comtox.2022.100246</a></p>
Figure 4 from: Peleshok K, Bondar B, Kryskiw L, Kucher T, Poliak O, Logoyda L (2021) Non-extractive spectrophotometric determination of valsartan in pure form and in pharmaceutical products by ion-pair complex formation with bromophenol blue and methyl red. Pharmacia 68(4): 851-858. https://doi.org/10.3897/pharmacia.68.e73559
Figure 4 Absorption spectra of BPB and valsartan with BPB in different solvents.
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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.