Rapid and Efficient Isolation of High-Quality Small RNAs from Recalcitrant Plant Species Rich in Polyphenols and Polysaccharides

PubMed Central

Pu, Jinji; Guo, Jianrong; Fan, Zaifeng

2014-01-01

Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are important regulators of plant development and gene expression. The acquisition of high-quality small RNAs is the first step in the study of its expression and function analysis, yet the extraction method of small RNAs in recalcitrant plant tissues with various secondary metabolites is not well established, especially for tropical and subtropical plant species rich in polysaccharides and polyphenols. Here, we developed a simple and efficient method for high quality small RNAs extraction from recalcitrant plant species. Prior to RNA isolation, a precursory step with a CTAB-PVPP buffer system could efficiently remove compounds and secondary metabolites interfering with RNAs from homogenized lysates. Then, total RNAs were extracted by Trizol reagents followed by a differential precipitation of high-molecular-weight (HMW) RNAs using polyethylene glycol (PEG) 8000. Finally, small RNAs could be easily recovered from supernatant by ethanol precipitation without extra elimination steps. The isolated small RNAs from papaya showed high quality through a clear background on gel and a distinct northern blotting signal with miR159a probe, compared with other published protocols. Additionally, the small RNAs extracted from papaya were successfully used for validation of both predicted miRNAs and the putative conserved tasiARFs. Furthermore, the extraction method described here was also tested with several other subtropical and tropical plant tissues. The purity of the isolated small RNAs was sufficient for such applications as end-point stem-loop RT-PCR and northern blotting analysis, respectively. The simple and feasible extraction method reported here is expected to have excellent potential for isolation of small RNAs from recalcitrant plant tissues rich in polyphenols and polysaccharides. PMID:24787387

Comparison of lignin extraction processes: Economic and environmental assessment.

PubMed

Carvajal, Juan C; Gómez, Álvaro; Cardona, Carlos A

2016-08-01

This paper presents the technical-economic and environmental assessment of four lignin extraction processes from two different raw materials (sugarcane bagasse and rice husks). The processes are divided into two categories, the first processes evaluates lignin extraction with prior acid hydrolysis step, while in the second case the extraction processes are evaluated standalone for a total analysis of 16 scenarios. Profitability indicators as the net present value (NPV) and environmental indicators as the potential environmental impact (PEI) are used through a process engineering approach to understand and select the best lignin extraction process. The results show that both economically and environmentally process with sulfites and soda from rice husk presents the best results; however the quality of lignin obtained with sulfites is not suitable for high value-added products. Then, the soda is an interesting option for the extraction of lignin if high quality lignin is required for high value-added products at low costs. Copyright © 2016 Elsevier Ltd. All rights reserved.

Polyphenolic content, antiradical activity, stability and microbiological quality of elderberry (Sambucus nigra L.) extracts.

PubMed

Pliszka, Barbara

2017-01-01

The pharmaceutical and food industries expect detailed knowledge on the physicochemical properties of elderberry fruit extracts, their stability and microbiological quality, as well as the polyphenol content in elderberry cultivars. The characteristics of the extracts might be additionally modified by citric acid, which improves the stability of anthocyanins and protects processed fruits and syrups from pathogenic microorganisms. The choice of the method with citric acid was a consequence of the physicochemical charac teristics of elderberry pigments, which are not stable under the effect of light in alcoholic solutions. The aim of study was to analyze the properties of elderberry fruit extracts regarding polyphenol content and antiradical activity, as well as their stability and microbiological quality. The plant material consisted of fruit from four cultivars (Alleso, Korsor, Sampo, Samyl) of black elderberry (Sambucus nigra L.). The following were determined in fruit extracts: polyphe- nolic content (HPLC), antiradical activity (ABTS and DPPH) and stability and microbiological quality. The HPLC analysis of polyphenols demonstrated that the extracts from fruits collected from cv. Samyl had the highest 3-sambubioside cyanidin content and those from cv. Korsor contained the highest quantity of 3-glucoside cyanidin. The extracts from cv. Sampo fruit had a dominant 3-sambubioside-5-gluco- side cyanidin and 3,5-diglucoside cyanidin content. The highest quercetin (5.92 mg 100 mg-1 of extract) and caffeic acid (1.21 mg 100 mg-1 of extract) content was found in fruit extracts from cv. Alleso. The cultivars Samyl and Korsor had a higher level of anthocyanins and higher antiradical activity (ABTS) in fruit extracts than cv. Alleso and Sampo. The antiradical activity (DPPH) of fruit extracts from elderberry cultivars as- sessed in this research was similar. The degradation index for all fruit extracts was similar (DI = 1.035). The microbiological species detected in extracts were classified as moulds (Penicillum sp., Aspergillus sp.) and yeasts (Rhodotorula sp., Torulopsis sp., Trichosporon sp., Saccharomyces sp.). The research findings may support the selection of certain cultivars for industrial applications. The high stability of anthocyanins and low level of microbiological impurities in elderberry extracts ensure the high quality of such a raw material in food and pharmaceutical processing.

High performance thin layer chromatography fingerprinting, phytochemical and physico-chemical studies of anti-diabetic herbal extracts

PubMed Central

Itankar, Prakash R.; Sawant, Dattatray B.; Tauqeer, Mohd.; Charde, Sonal S.

2015-01-01

Introduction: Herbal medicines have gained increasing popularity in the last few decades, and this global resurgence of herbal medicines increases their commercial value. However, this increasing demand has resulted in a decline in their quality, primarily due to a lack of adequate regulations pertaining to herbal medicines. Aim: To develop an optimized methodology for the standardization of herbal raw materials. Materials and Methods: The present study has been designed to examine each of the five herbal anti-diabetic drugs, Gymnema sylvester R. Br., Pterocarpus marsupium Roxburgh., Enicostema littorale Blume., Syzygium cumini (L.) Skeels. and Emblica officinalis Gaertn. The in-house extracts and marketed extracts were evaluated using physicochemical parameters, preliminary phytochemical screening, quantification of polyphenols (Folin–Ciocalteu colorimetric method) and high performance thin layer chromatography (HPTLC) fingerprint profiling with reference to marker compounds in plant extracts. Results: All the plants mainly contain polyphenolic compounds and are quantified in the range of 3.6–21.72% w/w. E. officinalis contain the highest and E. littorale contain the lowest content of polyphenol among plant extracts analyzed. HPTLC fingerprinting showed that the in-house extracts were of better quality than marketed extracts. Conclusion: The results obtained from the study could be utilized for setting limits for the reference phytoconstituents (biomarker) for the quality control and quality assurance of these anti-diabetic drugs. PMID:27011722

Long-term purification efficiency of a wetland constructed to treat runoff from peat extraction.

PubMed

Karjalainen, Satu M; Heikkinen, Kaisa; Ihme, Raimo; Kløve, Bjørn

2016-01-01

Peat extraction increases the phosphorus, nitrogen, organic matter, suspended solids, and iron concentrations in runoff, resulting in negative effects on downstream water bodies. Wetlands are commonly used as natural cost-effective solutions to mitigate these negative effects. This study analyzed changes in the quality of runoff water from peat extraction areas and the long-term efficiency of constructed wetlands. The results indicate that the quality of runoff water changed after the initial drainage and during peat extraction. Nitrogen leached at high concentrations in the early stages of peat extraction following drainage, whereas the leaching of iron and phosphorus increased after peat extraction from deeper layers. Comparison of water quality and impurities retained immediately after treatment wetland construction and 14 years later showed that the treatment wetland remained functional, with good retention capacity, over a long period.

Comparison of reduced sugar high quality chocolates sweetened with stevioside and crude stevia 'green' extract.

PubMed

Torri, Luisa; Frati, Alessandra; Ninfali, Paolino; Mantegna, Stefano; Cravotto, Giancarlo; Morini, Gabriella

2017-06-01

The demand for zero and reduced-sugar food products containing cocoa is expanding continuously. The present study was designed to evaluate the feasibility of producing high-quality chocolate sweetened with a crude extract of Stevia rebaudiana (Bertoni) prepared by a green microwave-assisted water-steam extraction procedure. Seven approximately isosweet chocolate formulations were developed, mixing cocoa paste, sucrose, commercial stevioside, crude green extract and maltitol in different proportions. All samples were analyzed for the determination of polyphenol and flavonoid content, antioxidant activity, and sensory acceptability. The use of a crude stevia extract allowed low-sugar, high-quality chocolates to be obtained that were also acceptable by consumers and had a significant increased antioxidant activity. Moreover, consumers' segmentation revealed a cluster of consumers showing the same overall liking for the sample with 50% sucrose replaced by the stevia crude extract as that obtained with the commercial stevioside and the control sample (without sucrose replacement). The results provide information that can contribute to promoting the development of sweet food products, with advantages in terms of an improved nutritional value (reduced sugar content and increased antioxidant activity) and a reduced impact of the production process on the environment. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Qualitative and quantitative assessment of single fingerprints in forensic DNA analysis.

PubMed

Ostojic, Lana; Klempner, Stacey A; Patel, Rosni A; Mitchell, Adele A; Axler-DiPerte, Grace L; Wurmbach, Elisa

2014-11-01

Fingerprints and touched items are important sources of DNA for STR profiling, since this evidence can be recovered in a wide variety of criminal offenses. However, there are some fundamental difficulties in working with these samples, including variability in quantity and quality of extracted DNA. In this study, we collected and analyzed over 700 fingerprints. We compared a commercially available extraction protocol (Zygem) to two methods developed in our laboratory, a simple one-tube protocol and a high sensitivity protocol (HighSens) that includes additional steps to concentrate and purify the DNA. The amplification protocols tested were AmpFLSTR® Identifiler® using either 28 or 31 amplification cycles, and Identifiler® Plus using 32 amplification cycles. We found that the HighSens and Zygem extraction methods were significantly better in their DNA yields than the one-tube method. Identifiler® Plus increased the quality of the STR profiles for the one-tube extraction significantly. However, this effect could not be verified for the other extraction methods. Furthermore, microscopic analysis of single fingerprints revealed that some individuals tended to shed more material than others onto glass slides. However, a dense deposition of skin flakes did not strongly correlate with a high quality STR profile. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Quality of reporting and risk of bias in therapeutic otolaryngology publications.

PubMed

Kaper, N M; Swart, K M A; Grolman, W; Van Der Heijden, G J M G

2018-01-01

High-quality trials have the potential to influence clinical practice. Ten otolaryngology journals with the highest 2011 impact factors were selected and publications from 2010 were extracted. From all medical journals, the 20 highest impact factor journals were selected, and publications related to otolaryngology for 2010 and 2011 were extracted. For all publications, the reporting quality and risk of bias were assessed. The impact factor was 1.8-2.8 for otolaryngology journals and 6.0-101.8 for medical journals. Of 1500 otolaryngology journal articles, 262 were therapeutic studies; 94 had a high reporting quality and 5 a low risk of bias. Of 10 967 medical journal articles, 76 were therapeutic studies; 57 had a high reporting quality and 8 a low risk of bias. Reporting quality was high for 45 per cent of otolaryngology-related publications and 9 per cent met quality standards. General journals had higher impact factors than otolaryngology journals. Reporting quality was higher and risk of bias lower in general journals than in otolaryngology journals. Nevertheless, 76 per cent of articles in high impact factor journals carried a high risk of bias. Better reported and designed studies are the goal, with less risk of bias, especially in otolaryngology journals.

Using Computer-Extracted Data from Electronic Health Records to Measure the Quality of Adolescent Well-Care

PubMed Central

Gardner, William; Morton, Suzanne; Byron, Sepheen C; Tinoco, Aldo; Canan, Benjamin D; Leonhart, Karen; Kong, Vivian; Scholle, Sarah Hudson

2014-01-01

Objective To determine whether quality measures based on computer-extracted EHR data can reproduce findings based on data manually extracted by reviewers. Data Sources We studied 12 measures of care indicated for adolescent well-care visits for 597 patients in three pediatric health systems. Study Design Observational study. Data Collection/Extraction Methods Manual reviewers collected quality data from the EHR. Site personnel programmed their EHR systems to extract the same data from structured fields in the EHR according to national health IT standards. Principal Findings Overall performance measured via computer-extracted data was 21.9 percent, compared with 53.2 percent for manual data. Agreement measures were high for immunizations. Otherwise, agreement between computer extraction and manual review was modest (Kappa = 0.36) because computer-extracted data frequently missed care events (sensitivity = 39.5 percent). Measure validity varied by health care domain and setting. A limitation of our findings is that we studied only three domains and three sites. Conclusions The accuracy of computer-extracted EHR quality reporting depends on the use of structured data fields, with the highest agreement found for measures and in the setting that had the greatest concentration of structured fields. We need to improve documentation of care, data extraction, and adaptation of EHR systems to practice workflow. PMID:24471935

Oriented modulation for watermarking in direct binary search halftone images.

PubMed

Guo, Jing-Ming; Su, Chang-Cheng; Liu, Yun-Fu; Lee, Hua; Lee, Jiann-Der

2012-09-01

In this paper, a halftoning-based watermarking method is presented. This method enables high pixel-depth watermark embedding, while maintaining high image quality. This technique is capable of embedding watermarks with pixel depths up to 3 bits without causing prominent degradation to the image quality. To achieve high image quality, the parallel oriented high-efficient direct binary search (DBS) halftoning is selected to be integrated with the proposed orientation modulation (OM) method. The OM method utilizes different halftone texture orientations to carry different watermark data. In the decoder, the least-mean-square-trained filters are applied for feature extraction from watermarked images in the frequency domain, and the naïve Bayes classifier is used to analyze the extracted features and ultimately to decode the watermark data. Experimental results show that the DBS-based OM encoding method maintains a high degree of image quality and realizes the processing efficiency and robustness to be adapted in printing applications.

Effective Subcritical Butane Extraction of Bifenthrin Residue in Black Tea.

PubMed

Zhang, Yating; Gu, Lingbiao; Wang, Fei; Kong, Lingjun; Qin, Guangyong

2017-03-30

As a natural and healthy beverage, tea is widely enjoyed; however, the pesticide residues in tea leaves affect the quality and food safety. To develop a highly selective and efficient method for the facile removal of pesticide residues, the subcritical butane extraction (SBE) technique was employed, and three variables involving temperature, time and extraction cycles were studied. The optimum SBE conditions were found to be as follows: extraction temperature 45 °C, extraction time 30 min, number of extraction cycles 1, and in such a condition that the extraction efficiency reached as high as 92%. Further, the catechins, theanine, caffeine and aroma components, which determine the quality of the tea, fluctuated after SBE treatment. Compared with the uncrushed leaves, pesticide residues can more easily be removed from crushed leaves, and the practical extraction efficiency was 97%. These results indicate that SBE is a useful method to efficiently remove the bifenthrin, and as appearance is not relevant in the production process, tea leaves should first be crushed and then extracted in order that residual pesticides are thoroughly removed.

A Bayesian framework for extracting human gait using strong prior knowledge.

PubMed

Zhou, Ziheng; Prügel-Bennett, Adam; Damper, Robert I

2006-11-01

Extracting full-body motion of walking people from monocular video sequences in complex, real-world environments is an important and difficult problem, going beyond simple tracking, whose satisfactory solution demands an appropriate balance between use of prior knowledge and learning from data. We propose a consistent Bayesian framework for introducing strong prior knowledge into a system for extracting human gait. In this work, the strong prior is built from a simple articulated model having both time-invariant (static) and time-variant (dynamic) parameters. The model is easily modified to cater to situations such as walkers wearing clothing that obscures the limbs. The statistics of the parameters are learned from high-quality (indoor laboratory) data and the Bayesian framework then allows us to "bootstrap" to accurate gait extraction on the noisy images typical of cluttered, outdoor scenes. To achieve automatic fitting, we use a hidden Markov model to detect the phases of images in a walking cycle. We demonstrate our approach on silhouettes extracted from fronto-parallel ("sideways on") sequences of walkers under both high-quality indoor and noisy outdoor conditions. As well as high-quality data with synthetic noise and occlusions added, we also test walkers with rucksacks, skirts, and trench coats. Results are quantified in terms of chamfer distance and average pixel error between automatically extracted body points and corresponding hand-labeled points. No one part of the system is novel in itself, but the overall framework makes it feasible to extract gait from very much poorer quality image sequences than hitherto. This is confirmed by comparing person identification by gait using our method and a well-established baseline recognition algorithm.

Efficient method of protein extraction from Theobroma cacao L. roots for two-dimensional gel electrophoresis and mass spectrometry analyses.

PubMed

Bertolde, F Z; Almeida, A-A F; Silva, F A C; Oliveira, T M; Pirovani, C P

2014-07-04

Theobroma cacao is a woody and recalcitrant plant with a very high level of interfering compounds. Standard protocols for protein extraction were proposed for various types of samples, but the presence of interfering compounds in many samples prevented the isolation of proteins suitable for two-dimensional gel electrophoresis (2-DE). An efficient method to extract root proteins for 2-DE was established to overcome these problems. The main features of this protocol are: i) precipitation with trichloroacetic acid/acetone overnight to prepare the acetone dry powder (ADP), ii) several additional steps of sonication in the ADP preparation and extractions with dense sodium dodecyl sulfate and phenol, and iii) adding two stages of phenol extractions. Proteins were extracted from roots using this new protocol (Method B) and a protocol described in the literature for T. cacao leaves and meristems (Method A). Using these methods, we obtained a protein yield of about 0.7 and 2.5 mg per 1.0 g lyophilized root, and a total of 60 and 400 spots could be separated, respectively. Through Method B, it was possible to isolate high-quality protein and a high yield of roots from T. cacao for high-quality 2-DE gels. To demonstrate the quality of the extracted proteins from roots of T. cacao using Method B, several protein spots were cut from the 2-DE gels, analyzed by tandem mass spectrometry, and identified. Method B was further tested on Citrus roots, with a protein yield of about 2.7 mg per 1.0 g lyophilized root and 800 detected spots.

Magnetic field extraction of trap-based electron beams using a high-permeability grid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hurst, N. C.; Danielson, J. R.; Surko, C. M., E-mail: csurko@physics.ucsd.edu

2015-07-15

A method to form high quality electrostatically guided lepton beams is explored. Test electron beams are extracted from tailored plasmas confined in a Penning-Malmberg trap. The particles are then extracted from the confining axial magnetic field by passing them through a high magnetic permeability grid with radial tines (a so-called “magnetic spider”). An Einzel lens is used to focus and analyze the beam properties. Numerical simulations are used to model non-adiabatic effects due to the spider, and the predictions are compared with the experimental results. Improvements in beam quality are discussed relative to the use of a hole in amore » high permeability shield (i.e., in lieu of the spider), and areas for further improvement are described.« less

Optimization of subculture and DNA extraction steps within the whole genome sequencing workflow for source tracking of Salmonella enterica and Listeria monocytogenes.

PubMed

Gimonet, Johan; Portmann, Anne-Catherine; Fournier, Coralie; Baert, Leen

2018-06-16

This work shows that an incubation time reduced to 4-5 h to prepare a culture for DNA extraction followed by an automated DNA extraction can shorten the hands-on time, the turnaround time by 30% and increase the throughput while maintaining the WGS quality assessed by high quality Single Nucleotide Polymorphism analysis. Copyright © 2018. Published by Elsevier B.V.

A Modified Protocol for High-Quality RNA Extraction from Oleoresin-Producing Adult Pines.

PubMed

de Lima, Júlio César; Füller, Thanise Nogueira; de Costa, Fernanda; Rodrigues-Corrêa, Kelly C S; Fett-Neto, Arthur G

2016-01-01

RNA extraction resulting in good yields and quality is a fundamental step for the analyses of transcriptomes through high-throughput sequencing technologies, microarray, and also northern blots, RT-PCR, and RTqPCR. Even though many specific protocols designed for plants with high content of secondary metabolites have been developed, these are often expensive, time consuming, and not suitable for a wide range of tissues. Here we present a modification of the method previously described using the commercially available Concert™ Plant RNA Reagent (Invitrogen) buffer for field-grown adult pine trees with high oleoresin content.

Quality evaluation of extracted ion chromatograms and chromatographic peaks in liquid chromatography/mass spectrometry-based metabolomics data

PubMed Central

2014-01-01

Background Extracted ion chromatogram (EIC) extraction and chromatographic peak detection are two important processing procedures in liquid chromatography/mass spectrometry (LC/MS)-based metabolomics data analysis. Most commonly, the LC/MS technique employs electrospray ionization as the ionization method. The EICs from LC/MS data are often noisy and contain high background signals. Furthermore, the chromatographic peak quality varies with respect to its location in the chromatogram and most peaks have zigzag shapes. Therefore, there is a critical need to develop effective metrics for quality evaluation of EICs and chromatographic peaks in LC/MS based metabolomics data analysis. Results We investigated a comprehensive set of potential quality evaluation metrics for extracted EICs and detected chromatographic peaks. Specifically, for EIC quality evaluation, we analyzed the mass chromatographic quality index (MCQ index) and propose a novel quality evaluation metric, the EIC-related global zigzag index, which is based on an EIC's first order derivatives. For chromatographic peak quality evaluation, we analyzed and compared six metrics: sharpness, Gaussian similarity, signal-to-noise ratio, peak significance level, triangle peak area similarity ratio and the local peak-related local zigzag index. Conclusions Although the MCQ index is suited for selecting and aligning analyte components, it cannot fairly evaluate EICs with high background signals or those containing only a single peak. Our proposed EIC related global zigzag index is robust enough to evaluate EIC qualities in both scenarios. Of the six peak quality evaluation metrics, the sharpness, peak significance level, and zigzag index outperform the others due to the zigzag nature of LC/MS chromatographic peaks. Furthermore, using several peak quality metrics in combination is more efficient than individual metrics in peak quality evaluation. PMID:25350128

Quality evaluation of extracted ion chromatograms and chromatographic peaks in liquid chromatography/mass spectrometry-based metabolomics data.

PubMed

Zhang, Wenchao; Zhao, Patrick X

2014-01-01

Extracted ion chromatogram (EIC) extraction and chromatographic peak detection are two important processing procedures in liquid chromatography/mass spectrometry (LC/MS)-based metabolomics data analysis. Most commonly, the LC/MS technique employs electrospray ionization as the ionization method. The EICs from LC/MS data are often noisy and contain high background signals. Furthermore, the chromatographic peak quality varies with respect to its location in the chromatogram and most peaks have zigzag shapes. Therefore, there is a critical need to develop effective metrics for quality evaluation of EICs and chromatographic peaks in LC/MS based metabolomics data analysis. We investigated a comprehensive set of potential quality evaluation metrics for extracted EICs and detected chromatographic peaks. Specifically, for EIC quality evaluation, we analyzed the mass chromatographic quality index (MCQ index) and propose a novel quality evaluation metric, the EIC-related global zigzag index, which is based on an EIC's first order derivatives. For chromatographic peak quality evaluation, we analyzed and compared six metrics: sharpness, Gaussian similarity, signal-to-noise ratio, peak significance level, triangle peak area similarity ratio and the local peak-related local zigzag index. Although the MCQ index is suited for selecting and aligning analyte components, it cannot fairly evaluate EICs with high background signals or those containing only a single peak. Our proposed EIC related global zigzag index is robust enough to evaluate EIC qualities in both scenarios. Of the six peak quality evaluation metrics, the sharpness, peak significance level, and zigzag index outperform the others due to the zigzag nature of LC/MS chromatographic peaks. Furthermore, using several peak quality metrics in combination is more efficient than individual metrics in peak quality evaluation.

Extraction of High Quality DNA from Seized Moroccan Cannabis Resin (Hashish)

PubMed Central

El Alaoui, Moulay Abdelaziz; Melloul, Marouane; Alaoui Amine, Sanaâ; Stambouli, Hamid; El Bouri, Aziz; Soulaymani, Abdelmajid; El Fahime, Elmostafa

2013-01-01

The extraction and purification of nucleic acids is the first step in most molecular biology analysis techniques. The objective of this work is to obtain highly purified nucleic acids derived from Cannabis sativa resin seizure in order to conduct a DNA typing method for the individualization of cannabis resin samples. To obtain highly purified nucleic acids from cannabis resin (Hashish) free from contaminants that cause inhibition of PCR reaction, we have tested two protocols: the CTAB protocol of Wagner and a CTAB protocol described by Somma (2004) adapted for difficult matrix. We obtained high quality genomic DNA from 8 cannabis resin seizures using the adapted protocol. DNA extracted by the Wagner CTAB protocol failed to give polymerase chain reaction (PCR) amplification of tetrahydrocannabinolic acid (THCA) synthase coding gene. However, the extracted DNA by the second protocol permits amplification of THCA synthase coding gene using different sets of primers as assessed by PCR. We describe here for the first time the possibility of DNA extraction from (Hashish) resin derived from Cannabis sativa. This allows the use of DNA molecular tests under special forensic circumstances. PMID:24124454

Evaluation of different pulverisation methods for RNA extraction in squash fruit: lyophilisation, cryogenic mill and mortar grinding.

PubMed

Román, Belén; González-Verdejo, Clara I; Peña, Francisco; Nadal, Salvador; Gómez, Pedro

2012-01-01

Quality and integrity of RNA are critical for transcription studies in plant molecular biology. In squash fruit and other high water content crops, the grinding of tissue with mortar and pestle in liquid nitrogen fails to produce a homogeneous and fine powered sample desirable to ensure a good penetration of the extraction reagent. To develop an improved pulverisation method to facilitate the homogenisation process of squash fruit tissue prior to RNA extraction without reducing quality and yield of the extracted RNA. Three methods of pulverisation, each followed by the same extraction protocol, were compared. The first approach consisted of the lyophilisation of the sample in order to remove the excess of water before grinding, the second one used a cryogenic mill and the control one a mortar grinding of frozen tissue. The quality of the isolated RNA was tested by carrying out a quantitative real time downstream amplification. In the three situations considered, mean values for A(260) /A(280) indicated minimal interference by proteins and RNA quality indicator (RQI) values were considered appropriate for quantitative real-time polymerase chain reaction (qRT-PCR) amplification. Successful qRT-PCR amplifications were obtained with cDNA isolated with the three protocols. Both apparatus can improve and facilitate the grinding step in the RNA extraction process in zucchini, resulting in isolated RNA of high quality and integrity as revealed by qRT-PCR downstream application. This is apparently the first time that a cryogenic mill has been used to prepare fruit samples for RNA extraction, thereby improving the sampling strategy because the fine powder obtained represents a homogeneous mix of the organ tissue. Copyright © 2012 John Wiley & Sons, Ltd.

Impact of industrial hammer mill rotor speed on extraction efficiency and quality of extra virgin olive oil.

PubMed

Polari, Juan J; Garcí-Aguirre, David; Olmo-García, Lucía; Carrasco-Pancorbo, Alegría; Wang, Selina C

2018-03-01

Crushing is a key step during olive oil extraction. Among commercial crushers, the hammer mill is the most widely used due to its robustness and high throughput. In the present work, the impact of hammer mill rotor speed on extraction yield and overall quality of super-high-density Arbosana olive oils were assessed in an industrial facility. Our results show that increasing the rotor speed from 2400rpm to 3600rpm led to a rise in oil yield of 1.2%, while conserving quality parameters. Sensory analysis showed more pungency with increased rotation speed, while others attributes were unaffected. Volatile compounds showed little variation with the differences in crusher speed; however, total phenols content, two relevant secoiridoids, and triterpenoids levels increased with rotor speed. Hammer mill rotor speed is a processing variable that can be tuned to increase the extraction efficiency and modulate the chemical composition of extra virgin olive oil. Copyright © 2017 Elsevier Ltd. All rights reserved.

A method for extracting high-quality total RNA from plant rich in polysaccharides and polyphenols using Dendrobium huoshanense

PubMed Central

Yu, Nianjun; Zhang, Wei; Xing, Lihua; Xie, Dongmei; Peng, Daiyin

2018-01-01

Acquiring high quality RNA is the basis of plant molecular biology research, plant genetics and other physiological investigations. At present, a large number of nucleotide isolation methods have been exploited or modified, such as commercial kits, CTAB, SDS methods and so on. Due to the nature of different plants, extraction methods vary. Moreover, efficiency of certain approach cannot be guaranteed due to composition of different plants and extracting high quality RNA from plants rich in polysaccharides and polyphenols are often difficult. The physical and chemical properties of polysaccharides which are similar to nucleic acids and other secondary metabolites will be coprecipitated with RNA irreversibly. Therefore, how to remove polysaccharides and other secondary metabolites during RNA extraction is the primary challenge. Dendrobium huoshanense is an Orchidaceae perennial herb that is rich in polysaccharides and other secondary metabolites. By using D. huoshanense as the subject, we improved the method originated from CHAN and made it suitable for plants containing high amount of polysaccharides and polyphenols. The extracted total RNA was clear and non-dispersive, with good integrity and no obvious contamination with DNA and other impurities. And it was also evaluated by gel electrophoresis, nucleic acid quantitative detector and PCR assessment. Thus, as a simple approach, it is suitable and efficient in RNA isolation for plants rich in polysaccharides and polyphenols. PMID:29715304

Changes during storage of quality parameters and in vitro antioxidant activity of extra virgin monovarietal oils obtained with two extraction technologies.

PubMed

Fadda, C; Del Caro, A; Sanguinetti, A M; Urgeghe, P P; Vacca, V; Arca, P P; Piga, A

2012-10-01

Extraction technology has a great effect on quality of olive oils. This paper studied 18 months of storage of two Sardinian extra virgin monovarietal oils obtained with a traditional and with a low oxidative stress technology. Oil samples were subjected to the following chemical analyses: acidity, peroxide value, ultraviolet light absorption K₂₃₂ and K₂₇₀, carotenoids, chlorophylls, tocopherols and total polyphenols. The antioxidant capacity of oils, polyphenol extract and oil extract (remaining after polyphenol extraction) was also determined as radical scavenging activity. The results show that both extraction technologies resulted in minor changes in legal and quality indices during storage, due surely to the high quality of the oils as well as to the very good storage conditions used. Oils obtained with the low oxidative stress technology showed lower peroxide value and acidity and resulted in up to 103% higher total polyphenol content as well as increased radical-scavenging activity, with respect to oils obtained with the traditional technology. Copyright © 2012 Elsevier Ltd. All rights reserved.

Identifying well-formed biomedical phrases in MEDLINE® text.

PubMed

Kim, Won; Yeganova, Lana; Comeau, Donald C; Wilbur, W John

2012-12-01

In the modern world people frequently interact with retrieval systems to satisfy their information needs. Humanly understandable well-formed phrases represent a crucial interface between humans and the web, and the ability to index and search with such phrases is beneficial for human-web interactions. In this paper we consider the problem of identifying humanly understandable, well formed, and high quality biomedical phrases in MEDLINE documents. The main approaches used previously for detecting such phrases are syntactic, statistical, and a hybrid approach combining these two. In this paper we propose a supervised learning approach for identifying high quality phrases. First we obtain a set of known well-formed useful phrases from an existing source and label these phrases as positive. We then extract from MEDLINE a large set of multiword strings that do not contain stop words or punctuation. We believe this unlabeled set contains many well-formed phrases. Our goal is to identify these additional high quality phrases. We examine various feature combinations and several machine learning strategies designed to solve this problem. A proper choice of machine learning methods and features identifies in the large collection strings that are likely to be high quality phrases. We evaluate our approach by making human judgments on multiword strings extracted from MEDLINE using our methods. We find that over 85% of such extracted phrase candidates are humanly judged to be of high quality. Published by Elsevier Inc.

An assessment of the efficiency of fungal DNA extraction methods for maximizing the detection of medically important fungi using PCR.

PubMed

Karakousis, A; Tan, L; Ellis, D; Alexiou, H; Wormald, P J

2006-04-01

To date, no single reported DNA extraction method is suitable for the efficient extraction of DNA from all fungal species. The efficiency of extraction is of particular importance in PCR-based medical diagnostic applications where the quantity of fungus in a tissue biopsy may be limited. We subjected 16 medically relevant fungi to physical, chemical and enzymatic cell wall disruption methods which constitutes the first step in extracting DNA. Examination by light microscopy showed that grinding with mortar and pestle was the most efficient means of disrupting the rigid fungal cell walls of hyphae and conidia. We then trialled several published DNA isolation protocols to ascertain the most efficient method of extraction. Optimal extraction was achieved by incorporating a lyticase and proteinase K enzymatic digestion step and adapting a DNA extraction procedure from a commercial kit (MO BIO) to generate high yields of high quality DNA from all 16 species. DNA quality was confirmed by the successful PCR amplification of the conserved region of the fungal 18S small-subunit rRNA multicopy gene.

Improved extraction of avocado oil by application of sono-physical processes.

PubMed

Martínez-Padilla, Laura Patricia; Franke, Lisa; Xu, Xin-Qing; Juliano, Pablo

2018-01-01

Ultrasound treatment is known to increase the oil extractability in olive and palm oil processes. This work examined the effect of ultrasound conditioning of avocado puree on oil extractability and quality, at low (18+40kHz) and high (2MHz) frequencies, at litre-scale. Other ultrasound parameters evaluated included high frequency effect (0.4, 0.6, and 2MHz; 5min; 90kJ/kg) and sonication time (2.5-10min at 2MHz), without malaxation. Finally, a megasonic post-malaxation intervention was assessed at selected malaxation times (15, 30, and 60min). Both low and high frequency ultrasound treatments of the non-malaxed avocado puree improved extractability by 15-24% additional oil recovery, with the highest extractability achieved after 2MHz treatments, depending on the fruit maturity and oil content. There was no preferential improvement on oil extractability observed across high frequencies, even though extractability increased with sonication time. Ultrasound treatment also showed a positive effect after puree malaxation. Oils obtained from sonicated purees showed peroxide and free fatty acid values below the industrial specification levels and an increase in total phenolic compounds after 2MHz treatment. High frequency ultrasound conditioning of avocado puree can enhance oil separation and potentially decrease the malaxation time in industrial processes without impacting on oil quality. Copyright © 2017 Elsevier B.V. All rights reserved.

Citrus juice extraction systems: effect on chemical composition and antioxidant activity of clementine juice.

PubMed

Álvarez, Rafael; Carvalho, Catarina P; Sierra, Jelver; Lara, Oscar; Cardona, David; Londoño-Londoño, Julian

2012-01-25

Clementines are especially appreciated for their delicious flavor, and recent years have seen a great increase in the consumption of clementine juice. In previous decades, antioxidant compounds have received particular attention because of widely demonstrated beneficial health effects. In this work, the organoleptic, volatile flavor, and antioxidant quality of clementine juice were studied with regard to the influence on them by different juice extraction systems: plug inside fruit and rotating cylinders. The results showed that juice extracted by the former method presented higher yields and hesperidin content, which was related to higher antioxidant activity, demonstrated by ORAC and LDL assays. The organoleptic quality was not affected by the processing technique, whereas there were significant differences in the chemical flavor profile. There are important differences in chemical and functional quality between juice extraction techniques, which must be taken into account when employing processing systems to produce high-quality products.

Nonstarch polysaccharides in wheat flour wire-cut cookie making.

PubMed

Guttieri, Mary J; Souza, Edward J; Sneller, Clay

2008-11-26

Nonstarch polysaccharides in wheat flour have significant capacity to affect the processing quality of wheat flour dough and the finished quality of wheat flour products. Most research has focused on the effects of arabinoxylans (AX) in bread making. This study found that water-extractable AX and arabinogalactan peptides can predict variation in pastry wheat quality as captured by the wire-cut cookie model system. The sum of water-extractable AX plus arabinogalactan was highly predictive of cookie spread factor. The combination of cookie spread factor and the ratio of water-extractable arabinose to xylose predicted peak force of the three-point bend test of cookie texture.

An Efficient Method for Genomic DNA Extraction from Different Molluscs Species

PubMed Central

Pereira, Jorge C.; Chaves, Raquel; Bastos, Estela; Leitão, Alexandra; Guedes-Pinto, Henrique

2011-01-01

The selection of a DNA extraction method is a critical step when subsequent analysis depends on the DNA quality and quantity. Unlike mammals, for which several capable DNA extraction methods have been developed, for molluscs the availability of optimized genomic DNA extraction protocols is clearly insufficient. Several aspects such as animal physiology, the type (e.g., adductor muscle or gills) or quantity of tissue, can explain the lack of efficiency (quality and yield) in molluscs genomic DNA extraction procedure. In an attempt to overcome these aspects, this work describes an efficient method for molluscs genomic DNA extraction that was tested in several species from different orders: Veneridae, Ostreidae, Anomiidae, Cardiidae (Bivalvia) and Muricidae (Gastropoda), with different weight sample tissues. The isolated DNA was of high molecular weight with high yield and purity, even with reduced quantities of tissue. Moreover, the genomic DNA isolated, demonstrated to be suitable for several downstream molecular techniques, such as PCR sequencing among others. PMID:22174651

DNA extraction for streamlined metagenomics of diverse environmental samples.

PubMed

Marotz, Clarisse; Amir, Amnon; Humphrey, Greg; Gaffney, James; Gogul, Grant; Knight, Rob

2017-06-01

A major bottleneck for metagenomic sequencing is rapid and efficient DNA extraction. Here, we compare the extraction efficiencies of three magnetic bead-based platforms (KingFisher, epMotion, and Tecan) to a standardized column-based extraction platform across a variety of sample types, including feces, oral, skin, soil, and water. Replicate sample plates were extracted and prepared for 16S rRNA gene amplicon sequencing in parallel to assess extraction bias and DNA quality. The data demonstrate that any effect of extraction method on sequencing results was small compared with the variability across samples; however, the KingFisher platform produced the largest number of high-quality reads in the shortest amount of time. Based on these results, we have identified an extraction pipeline that dramatically reduces sample processing time without sacrificing bacterial taxonomic or abundance information.

Quality Characteristics of Wholemeal Flour and Bread from Durum Wheat (Triticum turgidum L subsp. durum Desf.) after Field Treatment with Plant Water Extracts.

PubMed

Carrubba, Alessandra; Comparato, Andrea; Labruzzo, Andrea; Muccilli, Serena; Giannone, Virgilio; Spina, Alfio

2016-09-01

The use of selected plant water extracts to control pests and weeds is gaining growing attention in organic and sustainable agriculture, but the effects that such extracts may exert on the quality aspects of durum wheat are still unexplored. In 2014, 5 plant water extracts (Artemisia arborescens, Euphorbia characias, Rhus coriaria, Thymus vulgaris, Lantana camara) were prepared and distributed on durum wheat cv Valbelice to evaluate their potential herbicidal effects. After crop harvesting, the major physicochemical and technological parameters of wholemeal flours obtained from each treatment were measured and compared with those from chemical weeding and untreated controls. A baking test was also performed to evaluate the breadmaking quality. In wholemeal flours obtained after the treatment with plant extracts protein and dry gluten content were higher than in control and chemical weeding. Wholemeal flours obtained after chemical weeding reached the highest Mixograph parameters, and that from durum wheat treated with R. coriaria extract demonstrated a very high α-amylase activity. We concluded that the treatments with plant water extracts may influence many quality traits of durum wheat. This occurrence must be taken into account in overall decisions concerning the use of plant extracts in pest and weed management practice. © 2016 Institute of Food Technologists®

Comparative analysis of protocols for DNA extraction from soybean caterpillars.

PubMed

Palma, J; Valmorbida, I; da Costa, I F D; Guedes, J V C

2016-04-07

Genomic DNA extraction is crucial for molecular research, including diagnostic and genome characterization of different organisms. The aim of this study was to comparatively analyze protocols of DNA extraction based on cell lysis by sarcosyl, cetyltrimethylammonium bromide, and sodium dodecyl sulfate, and to determine the most efficient method applicable to soybean caterpillars. DNA was extracted from specimens of Chrysodeixis includens and Spodoptera eridania using the aforementioned three methods. DNA quantification was performed using spectrophotometry and high molecular weight DNA ladders. The purity of the extracted DNA was determined by calculating the A260/A280 ratio. Cost and time for each DNA extraction method were estimated and analyzed statistically. The amount of DNA extracted by these three methods was sufficient for PCR amplification. The sarcosyl method yielded DNA of higher purity, because it generated a clearer pellet without viscosity, and yielded high quality amplification products of the COI gene I. The sarcosyl method showed lower cost per extraction and did not differ from the other methods with respect to preparation times. Cell lysis by sarcosyl represents the best method for DNA extraction in terms of yield, quality, and cost effectiveness.

Technical aspects on production of fluid extract from Brosimum gaudichaudii Trécul roots

PubMed Central

Martins, Frederico Severino; Pascoa, Henrique; de Paula, José Realino; da Conceição, Edemilson Cardoso

2015-01-01

Instruction: Despite the increased use of Brosimum gaudichaudii roots as raw material on medicine to treatment of vitiligo, there are not studies that showing the impact of unit operations on the quality and standardized of the extract of B. gaudichaudii. The quality of the herbal extract is essential to ensure the safety and efficacy of pharmaceutical product. Due the medical and commercial importance, this study aimed to evaluate the impact of the extraction method (ultrasound or percolation) on the quality of herbal extract and optimize the extraction of psoralen and 8-methoxypsoralen (8-MOP) from B. gaudichaudii. Materials and Methods: The extraction recovery was evaluate by high-performance liquid chromatography (C8 reverse phase column and acetonitrile: Water 45:55 and flow rate 0.6 mL/min). The extraction was performed by ultrasound-assisted extraction (UEA) or percolation using a Box-Behnken design. Results: From both chemical markers (psoralen and bergapten), the optimal conditions for the UEA were an extraction time of 25 min, the mean particle size of 100 μm, and an ethanol: Water ratio of 55:45 (v/v). Conclusion: The extraction by percolation revealed that ethanol 55% was more efficient than ethanol 80% to extract psoralen and bergapten. PMID:25709236

Assessing the Quality and Potential Efficacy of Commercial Extracts of Rhodiola rosea L. by Analyzing the Salidroside and Rosavin Content and the Electrophysiological Activity in Hippocampal Long-Term Potentiation, a Synaptic Model of Memory.

PubMed

Dimpfel, Wilfried; Schombert, Leonie; Panossian, Alexander G

2018-01-01

Rhodiola rosea L. roots and rhizome extracts are active ingredients in adaptogenic herbal medicinal products (HMP) and dietary supplements for temporary relief of symptoms of stress, such as fatigue and weakness. R. rosea extract has a stimulating effect on the CNS, suggesting potential benefits on cognitive functions, memory, learning, and attention. The reproducible efficacy and quality of preparations of the underground parts of R. rosea depend on the highly variable content of the active markers, salidroside and rosavin, which affect the quality of HMP and dietary supplements. However, it is not clear which analytical markers are important for assessing the efficacy of R. rosea preparations intended for use in aging-induced mild cognitive disorders, such as attenuated memory, attention, and learning. Furthermore, the activity of various commercial R. rosea extracts has not been correlated with their content. Here, the biological activities of salidroside, rosavin, and seven commercial extracts of underground parts of R. rosea were assessed using a synaptic model of memory: long-term potentiation (LTP) of synaptic transmission in hippocampus slices. A high degree of variation in the content of all active markers was observed. One extract from China lacked rosavin, and there was even variation in the extracts from the Altai geographic region. In vitro , rosavin, salidroside and all tested R. rosea extracts potentiated electric stimulation of an intra-hippocampal electric circuit, which resulted in higher responses of the pyramidal cells in isolated hippocampus slices. Rosavin was more active at higher concentrations than salidroside; while, salidroside was more effective at lower concentrations. The highest content of both active markers was found in the extracts that were active at the lowest concentrations tested; while, some extracts contained some other compounds that presumably reduced the efficacy due to antagonistic interactions. Standardized content of active markers is necessary for the quality control of herbal preparations containing R. rosea extracts, but insufficient for assessment of their potential efficacy. Additional bioassays are needed to assure the reproducible pharmacological activity of R. rosea extracts; therefore, the LTP of synaptic transmission in hippocampus slices may serve as a validation tool for the quality control of R. rosea extracts.

A novel approach to rapidly explore analytical markers for quality control of Radix Salviae Miltiorrhizae extract granules by robust principal component analysis with ultra-high performance liquid chromatography-ultraviolet-quadrupole time-of-flight mass spectrometry.

PubMed

Song, Jing-Zheng; Li, Song-Lin; Zhou, Yan; Qiao, Chun-Feng; Chen, Shi-Lin; Xu, Hong-Xi

2010-11-02

In a well-controlled experiment, outliers discriminated by robust principal component analysis (RPCA) represent contents in samples which are of particular quality distinguishable from the rest of the others, therefore chemical constituents in a natural product causing discrimination between outliers and the majority of samples could be considered as analytical markers for quality control. Based on this strategy, a novel approach for rapidly exploring characteristic analytical markers was proposed for the quality control of extract granules of Radix Salviae Miltiorrhizae (EGRSM). In this study, large sizes of samples were analyzed via high-throughput ultra-high performance liquid chromatography-ultraviolet-quadrupole time-of-flight mass spectrometry (UHPLC-UV-Q-Tof MS). RPCA was first performed on the three groups of samples: RSM (the raw material), the in-house prepared aqueous extract of Radix Salviae Miltiorrhizae (AERSM) and commercial product of EGRSM, to determine the variation of specific constituents between raw material and the final products as well as the effect of manufacturing process on the overall quality. Then RPCA was performed on the commercial products of EGRSM to explore the applicability of identified characteristic markers for the quality control of EGRSM. Candidate markers were extracted by RPCA, and their molecular formulae were determined by high resolution electrospray ionization-mass spectrometric (ESI-MS) analysis. The suitability of identified markers was then evaluated by determining the relationship between quantities of the identified markers with their antioxidant activities biologically, and further confirmed in a variety of samples. In conclusion, the combination of RPCA with UHPLC-UV-Q-Tof MS is a reliable means to identify chemical markers for evaluating quality of herbal medicines. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion-exchange treatments.

PubMed

Desai, Chirayu; Madamwar, Datta

2007-03-01

PCR inhibitor-free metagenomic DNA of high quality and high yield was extracted from highly polluted sediments using a simple remediation strategy of adsorption and ion-exchange chromatography. Extraction procedure was optimized with series of steps, which involved gentle mechanical lysis, treatment with powdered activated charcoal (PAC) and ion-exchange chromatography with amberlite resin. Quality of the extracted DNA for molecular diversity analysis was tested by amplifying bacterial 16S rDNA (16S rRNA gene) with eubacterial specific universal primers (8f and 1492r), cloning of the amplified 16S rDNA and ARDRA (amplified rDNA restriction analysis) of the 16S rDNA clones. The presence of discrete differences in ARDRA banding profiles provided evidence for expediency of the DNA extraction protocol in molecular diversity studies. A comparison of the optimized protocol with commercial Ultraclean Soil DNA isolation kit suggested that method described in this report would be more efficient in removing metallic and organic inhibitors, from polluted sediment samples.

Extractions of High Quality RNA from the Seeds of Jerusalem Artichoke and Other Plant Species with High Levels of Starch and Lipid.

PubMed

Mornkham, Tanupat; Wangsomnuk, Preeya Puangsomlee; Fu, Yong-Bi; Wangsomnuk, Pinich; Jogloy, Sanun; Patanothai, Aran

2013-04-29

Jerusalem artichoke (Helianthus tuberosus L.) is an important tuber crop. However, Jerusalem artichoke seeds contain high levels of starch and lipid, making the extraction of high-quality RNA extremely difficult and the gene expression analysis challenging. This study was aimed to improve existing methods for extracting total RNA from Jerusalem artichoke dry seeds and to assess the applicability of the improved method in other plant species. Five RNA extraction methods were evaluated on Jerusalem artichoke seeds and two were modified. One modified method with the significant improvement was applied to assay seeds of diverse Jerusalem artichoke accessions, sunflower, rice, maize, peanut and marigold. The effectiveness of the improved method to extract total RNA from seeds was assessed using qPCR analysis of four selected genes. The improved method of Ma and Yang (2011) yielded a maximum RNA solubility and removed most interfering substances. The improved protocol generated 29 to 41 µg RNA/30 mg fresh weight. An A260/A280 ratio of 1.79 to 2.22 showed their RNA purity. Extracted RNA was effective for downstream applications such as first-stranded cDNA synthesis, cDNA cloning and qPCR. The improved method was also effective to extract total RNA from seeds of sunflower, rice, maize and peanut that are rich in polyphenols, lipids and polysaccharides.

Short Communication An efficient method for simultaneous extraction of high-quality RNA and DNA from various plant tissues.

PubMed

Oliveira, R R; Viana, A J C; Reátegui, A C E; Vincentz, M G A

2015-12-29

Determination of gene expression is an important tool to study biological processes and relies on the quality of the extracted RNA. Changes in gene expression profiles may be directly related to mutations in regulatory DNA sequences or alterations in DNA cytosine methylation, which is an epigenetic mark. Correlation of gene expression with DNA sequence or epigenetic mark polymorphism is often desirable; for this, a robust protocol to isolate high-quality RNA and DNA simultaneously from the same sample is required. Although commercial kits and protocols are available, they are mainly optimized for animal tissues and, in general, restricted to RNA or DNA extraction, not both. In the present study, we describe an efficient and accessible method to extract both RNA and DNA simultaneously from the same sample of various plant tissues, using small amounts of starting material. The protocol was efficient in the extraction of high-quality nucleic acids from several Arabidopsis thaliana tissues (e.g., leaf, inflorescence stem, flower, fruit, cotyledon, seedlings, root, and embryo) and from other tissues of non-model plants, such as Avicennia schaueriana (Acanthaceae), Theobroma cacao (Malvaceae), Paspalum notatum (Poaceae), and Sorghum bicolor (Poaceae). The obtained nucleic acids were used as templates for downstream analyses, such as mRNA sequencing, quantitative real time-polymerase chain reaction, bisulfite treatment, and others; the results were comparable to those obtained with commercial kits. We believe that this protocol could be applied to a broad range of plant species, help avoid technical and sampling biases, and facilitate several RNA- and DNA-dependent analyses.

Effects of different biomass drying and lipid extraction methods on algal lipid yield, fatty acid profile, and biodiesel quality.

PubMed

Hussain, Javid; Liu, Yan; Lopes, Wilson A; Druzian, Janice I; Souza, Carolina O; Carvalho, Gilson C; Nascimento, Iracema A; Liao, Wei

2015-03-01

Three lipid extraction methods of hexane Soxhlet (Sox-Hex), Halim (HIP), and Bligh and Dyer (BD) were applied on freeze-dried (FD) and oven-dried (OD) Chlorella vulgaris biomass to evaluate their effects on lipid yield, fatty acid profile, and algal biodiesel quality. Among these three methods, HIP was the preferred one for C. vulgaris lipid recovery considering both extraction efficiency and solvent toxicity. It had the highest lipid yields of 20.0 and 22.0% on FD and OD biomass, respectively, with corresponding neutral lipid yields of 14.8 and 12.7%. The lipid profiling analysis showed that palmitic, oleic, linoleic, and α-linolenic acids were the major fatty acids in the algal lipids, and there were no significant differences on the amount of these acids between different drying and extraction methods. Correlative models applied to the fatty acid profiles concluded that high contents of palmitic and oleic acids in algal lipids contributed to balancing the ratio of saturated and unsaturated fatty acids and led to a high-quality algal biodiesel.

High-throughput immunomagnetic scavenging technique for quantitative analysis of live VX nerve agent in water, hamburger, and soil matrixes.

PubMed

Knaack, Jennifer S; Zhou, Yingtao; Abney, Carter W; Prezioso, Samantha M; Magnuson, Matthew; Evans, Ronald; Jakubowski, Edward M; Hardy, Katelyn; Johnson, Rudolph C

2012-11-20

We have developed a novel immunomagnetic scavenging technique for extracting cholinesterase inhibitors from aqueous matrixes using biological targeting and antibody-based extraction. The technique was characterized using the organophosphorus nerve agent VX. The limit of detection for VX in high-performance liquid chromatography (HPLC)-grade water, defined as the lowest calibrator concentration, was 25 pg/mL in a small, 500 μL sample. The method was characterized over the course of 22 sample sets containing calibrators, blanks, and quality control samples. Method precision, expressed as the mean relative standard deviation, was less than 9.2% for all calibrators. Quality control sample accuracy was 102% and 100% of the mean for VX spiked into HPLC-grade water at concentrations of 2.0 and 0.25 ng/mL, respectively. This method successfully was applied to aqueous extracts from soil, hamburger, and finished tap water spiked with VX. Recovery was 65%, 81%, and 100% from these matrixes, respectively. Biologically based extractions of organophosphorus compounds represent a new technique for sample extraction that provides an increase in extraction specificity and sensitivity.

Improving iris recognition performance using segmentation, quality enhancement, match score fusion, and indexing.

PubMed

Vatsa, Mayank; Singh, Richa; Noore, Afzel

2008-08-01

This paper proposes algorithms for iris segmentation, quality enhancement, match score fusion, and indexing to improve both the accuracy and the speed of iris recognition. A curve evolution approach is proposed to effectively segment a nonideal iris image using the modified Mumford-Shah functional. Different enhancement algorithms are concurrently applied on the segmented iris image to produce multiple enhanced versions of the iris image. A support-vector-machine-based learning algorithm selects locally enhanced regions from each globally enhanced image and combines these good-quality regions to create a single high-quality iris image. Two distinct features are extracted from the high-quality iris image. The global textural feature is extracted using the 1-D log polar Gabor transform, and the local topological feature is extracted using Euler numbers. An intelligent fusion algorithm combines the textural and topological matching scores to further improve the iris recognition performance and reduce the false rejection rate, whereas an indexing algorithm enables fast and accurate iris identification. The verification and identification performance of the proposed algorithms is validated and compared with other algorithms using the CASIA Version 3, ICE 2005, and UBIRIS iris databases.

Semiautomated Device for Batch Extraction of Metabolites from Tissue Samples

PubMed Central

2012-01-01

Metabolomics has become a mainstream analytical strategy for investigating metabolism. The quality of data derived from these studies is proportional to the consistency of the sample preparation. Although considerable research has been devoted to finding optimal extraction protocols, most of the established methods require extensive sample handling. Manual sample preparation can be highly effective in the hands of skilled technicians, but an automated tool for purifying metabolites from complex biological tissues would be of obvious utility to the field. Here, we introduce the semiautomated metabolite batch extraction device (SAMBED), a new tool designed to simplify metabolomics sample preparation. We discuss SAMBED’s design and show that SAMBED-based extractions are of comparable quality to extracts produced through traditional methods (13% mean coefficient of variation from SAMBED versus 16% from manual extractions). Moreover, we show that aqueous SAMBED-based methods can be completed in less than a quarter of the time required for manual extractions. PMID:22292466

Extracting DNA from 'jaws': high yield and quality from archived tiger shark (Galeocerdo cuvier) skeletal material.

PubMed

Nielsen, E E; Morgan, J A T; Maher, S L; Edson, J; Gauthier, M; Pepperell, J; Holmes, B J; Bennett, M B; Ovenden, J R

2017-05-01

Archived specimens are highly valuable sources of DNA for retrospective genetic/genomic analysis. However, often limited effort has been made to evaluate and optimize extraction methods, which may be crucial for downstream applications. Here, we assessed and optimized the usefulness of abundant archived skeletal material from sharks as a source of DNA for temporal genomic studies. Six different methods for DNA extraction, encompassing two different commercial kits and three different protocols, were applied to material, so-called bio-swarf, from contemporary and archived jaws and vertebrae of tiger sharks (Galeocerdo cuvier). Protocols were compared for DNA yield and quality using a qPCR approach. For jaw swarf, all methods provided relatively high DNA yield and quality, while large differences in yield between protocols were observed for vertebrae. Similar results were obtained from samples of white shark (Carcharodon carcharias). Application of the optimized methods to 38 museum and private angler trophy specimens dating back to 1912 yielded sufficient DNA for downstream genomic analysis for 68% of the samples. No clear relationships between age of samples, DNA quality and quantity were observed, likely reflecting different preparation and storage methods for the trophies. Trial sequencing of DNA capture genomic libraries using 20 000 baits revealed that a significant proportion of captured sequences were derived from tiger sharks. This study demonstrates that archived shark jaws and vertebrae are potential high-yield sources of DNA for genomic-scale analysis. It also highlights that even for similar tissue types, a careful evaluation of extraction protocols can vastly improve DNA yield. © 2016 John Wiley & Sons Ltd.

Toxic reagents and expensive equipment: are they really necessary for the extraction of good quality fungal DNA?

PubMed

Rodrigues, P; Venâncio, A; Lima, N

2018-01-01

The aim of this work was to evaluate a fungal DNA extraction procedure with the lowest inputs in terms of time as well as of expensive and toxic chemicals, but able to consistently produce genomic DNA of good quality for PCR purposes. Two types of fungal biological material were tested - mycelium and conidia - combined with two protocols for DNA extraction using Sodium Dodecyl Sulphate (SDS) and Cetyl Trimethyl Ammonium Bromide as extraction buffers and glass beads for mechanical disruption of cell walls. Our results showed that conidia and SDS buffer was the combination that lead to the best DNA quality and yield, with the lowest variation between samples. This study clearly demonstrates that it is possible to obtain high yield and pure DNA from pigmented conidia without the use of strong cell disrupting procedures and of toxic reagents. There are numerous methods for DNA extraction from fungi. Some rely on expensive commercial kits and/or equipments, unavailable for many laboratories, or make use of toxic chemicals such as chloroform, phenol and mercaptoethanol. This study clearly demonstrates that it is possible to obtain high yields of pure DNA from pigmented conidia without the use of strong and expensive cell disrupting procedures and of toxic reagents. The method herein described is simultaneously inexpensive and adequate to DNA extraction from several different types of fungi. © 2017 The Society for Applied Microbiology.

Sample preservation, transport and processing strategies for honeybee RNA extraction: Influence on RNA yield, quality, target quantification and data normalization.

PubMed

Forsgren, Eva; Locke, Barbara; Semberg, Emilia; Laugen, Ane T; Miranda, Joachim R de

2017-08-01

Viral infections in managed honey bees are numerous, and most of them are caused by viruses with an RNA genome. Since RNA degrades rapidly, appropriate sample management and RNA extraction methods are imperative to get high quality RNA for downstream assays. This study evaluated the effect of various sampling-transport scenarios (combinations of temperature, RNA stabilizers, and duration) of transport on six RNA quality parameters; yield, purity, integrity, cDNA synthesis efficiency, target detection and quantification. The use of water and extraction buffer were also compared for a primary bee tissue homogenate prior to RNA extraction. The strategy least affected by time was preservation of samples at -80°C. All other regimens turned out to be poor alternatives unless the samples were frozen or processed within 24h. Chemical stabilizers have the greatest impact on RNA quality and adding an extra homogenization step (a QIAshredder™ homogenizer) to the extraction protocol significantly improves the RNA yield and chemical purity. This study confirms that RIN values (RNA Integrity Number), should be used cautiously with bee RNA. Using water for the primary homogenate has no negative effect on RNA quality as long as this step is no longer than 15min. Copyright © 2017 Elsevier B.V. All rights reserved.

Fruit wastes fermentation for phenolic antioxidants production and their application in manufacture of edible coatings and films.

PubMed

Martinez-Avila, G C G; Aguilera, A F; Saucedo, S; Rojas, R; Rodriguez, R; Aguilar, C N

2014-01-01

Agro-industrial by-products are important sources of potent bioactive phenolic compounds. These compounds are of extreme relevance for food and pharmacological industries due to their great variety of biological activities. Fermentation represents an environmentally clean technology for production and extraction of these bioactive compounds, providing high quality and high activity extracts, which can be incorporated in foods using coatings/films wax-based in order to avoid alterations in their quality. In this document is presented an overview about importance and benefits of solid-state fermentation, pointing out this bioprocess as an alternative technology for use agro-industrial by-products as substrates to produce valuable secondary metabolites and their applications as food quality conservatives.

Methods of analysis by the U.S. Geological Survey National Water Quality Laboratory; determination of pesticides in water by Carbopak-B solid-phase extraction and high-preformance liquid chromatography

USGS Publications Warehouse

Werner, Stephen L.; Burkhardt, Mark R.; DeRusseau, Sabrina N.

1996-01-01

In accordance with the needs of the National Water-Quality Assessment Program (NAWQA), the U.S. Geological Survey has developed and implemented a graphitized carbon-based solid-phase extraction and high-performance liquid chromatographic analytical method. The method is used to determine 41 pesticides and pesticide metabolites that are not readily amenable to gas chromatography or other high-temperature analytical techniques. Pesticides are extracted from filtered environmental water samples using a 0.5-gram graphitized carbon-based solid-phase cartridge, eluted from the cartridge into two analytical fractions, and analyzed using high-performance liquid chromatography with photodiode-array detection. The upper concentration limit is 1.6 micrograms per liter (=B5g/L) for most compounds. Single-operator method detection limits in organic-free water samples ranged from 0.006 to 0.032 =B5g/L= Recoveries in organic-free water samples ranged from 37 to 88 percent. Recoveries in ground- and surface-water samples ranged from 29 to 94 percent. An optional on-site extraction procedure allows for samples to be collected and processed at remote sites where it is difficult to ship samples to the laboratory within the recommended pre-extraction holding time of 7 days.

Methods for the guideline-based development of quality indicators--a systematic review

PubMed Central

2012-01-01

Background Quality indicators (QIs) are used in many healthcare settings to measure, compare, and improve quality of care. For the efficient development of high-quality QIs, rigorous, approved, and evidence-based development methods are needed. Clinical practice guidelines are a suitable source to derive QIs from, but no gold standard for guideline-based QI development exists. This review aims to identify, describe, and compare methodological approaches to guideline-based QI development. Methods We systematically searched medical literature databases (Medline, EMBASE, and CINAHL) and grey literature. Two researchers selected publications reporting methodological approaches to guideline-based QI development. In order to describe and compare methodological approaches used in these publications, we extracted detailed information on common steps of guideline-based QI development (topic selection, guideline selection, extraction of recommendations, QI selection, practice test, and implementation) to predesigned extraction tables. Results From 8,697 hits in the database search and several grey literature documents, we selected 48 relevant references. The studies were of heterogeneous type and quality. We found no randomized controlled trial or other studies comparing the ability of different methodological approaches to guideline-based development to generate high-quality QIs. The relevant publications featured a wide variety of methodological approaches to guideline-based QI development, especially regarding guideline selection and extraction of recommendations. Only a few studies reported patient involvement. Conclusions Further research is needed to determine which elements of the methodological approaches identified, described, and compared in this review are best suited to constitute a gold standard for guideline-based QI development. For this research, we provide a comprehensive groundwork. PMID:22436067

High-quality and small-capacity e-learning video featuring lecturer-superimposing PC screen images

NASA Astrophysics Data System (ADS)

Nomura, Yoshihiko; Murakami, Michinobu; Sakamoto, Ryota; Sugiura, Tokuhiro; Matsui, Hirokazu; Kato, Norihiko

2006-10-01

Information processing and communication technology are progressing quickly, and are prevailing throughout various technological fields. Therefore, the development of such technology should respond to the needs for improvement of quality in the e-learning education system. The authors propose a new video-image compression processing system that ingeniously employs the features of the lecturing scene. While dynamic lecturing scene is shot by a digital video camera, screen images are electronically stored by a PC screen image capturing software in relatively long period at a practical class. Then, a lecturer and a lecture stick are extracted from the digital video images by pattern recognition techniques, and the extracted images are superimposed on the appropriate PC screen images by off-line processing. Thus, we have succeeded to create a high-quality and small-capacity (HQ/SC) video-on-demand educational content featuring the advantages: the high quality of image sharpness, the small electronic file capacity, and the realistic lecturer motion.

Optimisation of DNA extraction from the crustacean Daphnia

PubMed Central

Athanasio, Camila Gonçalves; Chipman, James K.; Viant, Mark R.

2016-01-01

Daphnia are key model organisms for mechanistic studies of phenotypic plasticity, adaptation and microevolution, which have led to an increasing demand for genomics resources. A key step in any genomics analysis, such as high-throughput sequencing, is the availability of sufficient and high quality DNA. Although commercial kits exist to extract genomic DNA from several species, preparation of high quality DNA from Daphnia spp. and other chitinous species can be challenging. Here, we optimise methods for tissue homogenisation, DNA extraction and quantification customised for different downstream analyses (e.g., LC-MS/MS, Hiseq, mate pair sequencing or Nanopore). We demonstrate that if Daphnia magna are homogenised as whole animals (including the carapace), absorbance-based DNA quantification methods significantly over-estimate the amount of DNA, resulting in using insufficient starting material for experiments, such as preparation of sequencing libraries. This is attributed to the high refractive index of chitin in Daphnia’s carapace at 260 nm. Therefore, unless the carapace is removed by overnight proteinase digestion, the extracted DNA should be quantified with fluorescence-based methods. However, overnight proteinase digestion will result in partial fragmentation of DNA therefore the prepared DNA is not suitable for downstream methods that require high molecular weight DNA, such as PacBio, mate pair sequencing and Nanopore. In conclusion, we found that the MasterPure DNA purification kit, coupled with grinding of frozen tissue, is the best method for extraction of high molecular weight DNA as long as the extracted DNA is quantified with fluorescence-based methods. This method generated high yield and high molecular weight DNA (3.10 ± 0.63 ng/µg dry mass, fragments >60 kb), free of organic contaminants (phenol, chloroform) and is suitable for large number of downstream analyses. PMID:27190714

High quality methylome-wide investigations through next-generation sequencing of DNA from a single archived dry blood spot

PubMed Central

Aberg, Karolina A.; Xie, Lin Y.; Nerella, Srilaxmi; Copeland, William E.; Costello, E. Jane; van den Oord, Edwin J.C.G.

2013-01-01

The potential importance of DNA methylation in the etiology of complex diseases has led to interest in the development of methylome-wide association studies (MWAS) aimed at interrogating all methylation sites in the human genome. When using blood as biomaterial for a MWAS the DNA is typically extracted directly from fresh or frozen whole blood that was collected via venous puncture. However, DNA extracted from dry blood spots may also be an alternative starting material. In the present study, we apply a methyl-CpG binding domain (MBD) protein enrichment-based technique in combination with next generation sequencing (MBD-seq) to assess the methylation status of the ~27 million CpGs in the human autosomal reference genome. We investigate eight methylomes using DNA from blood spots. This data are compared with 1,500 methylomes previously assayed with the same MBD-seq approach using DNA from whole blood. When investigating the sequence quality and the enrichment profile across biological features, we find that DNA extracted from blood spots gives comparable results with DNA extracted from whole blood. Only if the amount of starting material is ≤ 0.5µg DNA we observe a slight decrease in the assay performance. In conclusion, we show that high quality methylome-wide investigations using MBD-seq can be conducted in DNA extracted from archived dry blood spots without sacrificing quality and without bias in enrichment profile as long as the amount of starting material is sufficient. In general, the amount of DNA extracted from a single blood spot is sufficient for methylome-wide investigations with the MBD-seq approach. PMID:23644822

High quality methylome-wide investigations through next-generation sequencing of DNA from a single archived dry blood spot.

PubMed

Aberg, Karolina A; Xie, Lin Y; Nerella, Srilaxmi; Copeland, William E; Costello, E Jane; van den Oord, Edwin J C G

2013-05-01

The potential importance of DNA methylation in the etiology of complex diseases has led to interest in the development of methylome-wide association studies (MWAS) aimed at interrogating all methylation sites in the human genome. When using blood as biomaterial for a MWAS the DNA is typically extracted directly from fresh or frozen whole blood that was collected via venous puncture. However, DNA extracted from dry blood spots may also be an alternative starting material. In the present study, we apply a methyl-CpG binding domain (MBD) protein enrichment-based technique in combination with next generation sequencing (MBD-seq) to assess the methylation status of the ~27 million CpGs in the human autosomal reference genome. We investigate eight methylomes using DNA from blood spots. This data are compared with 1,500 methylomes previously assayed with the same MBD-seq approach using DNA from whole blood. When investigating the sequence quality and the enrichment profile across biological features, we find that DNA extracted from blood spots gives comparable results with DNA extracted from whole blood. Only if the amount of starting material is ≤ 0.5µg DNA we observe a slight decrease in the assay performance. In conclusion, we show that high quality methylome-wide investigations using MBD-seq can be conducted in DNA extracted from archived dry blood spots without sacrificing quality and without bias in enrichment profile as long as the amount of starting material is sufficient. In general, the amount of DNA extracted from a single blood spot is sufficient for methylome-wide investigations with the MBD-seq approach.

A modified protocol for RNA extraction from different peach tissues suitable for gene isolation and real-time PCR analysis.

PubMed

Tong, Zhaoguo; Qu, Shenchun; Zhang, Jiyu; Wang, Fei; Tao, Jianmin; Gao, Zhihong; Zhang, Zhen

2012-03-01

RNA extraction is the first step in the study of gene isolation and expression. However, it is difficult to extract high quantity and quality RNA from tissues containing large quantities of polysaccharides and polyphenols. Peach (Prunus persica), in addition to containing high levels of polysaccharides and polyphenols, is a challenging starting material for RNA isolation using a single method because of different amounts of those substances in diverse tissues. Based on three reported methods, we developed a modified RNA isolation protocol to solve this problem, leading to high quality and quantity of total RNA from peach mesocarp tissues of fruits which were sampled from all developmental stages and different storage periods, as well as from other tissues including flowers, leaves, stems, and roots. With our modified method, 28-650 μg of total RNA was routinely obtained from per gram of fresh material, gave at least a 1.16-fold improvement by compared with those isolated by other seven methods. The RNA extracts were successfully used in downstream applications such as RT-PCR, RACE, and real-time PCR.

No-reference image quality assessment based on natural scene statistics and gradient magnitude similarity

NASA Astrophysics Data System (ADS)

Jia, Huizhen; Sun, Quansen; Ji, Zexuan; Wang, Tonghan; Chen, Qiang

2014-11-01

The goal of no-reference/blind image quality assessment (NR-IQA) is to devise a perceptual model that can accurately predict the quality of a distorted image as human opinions, in which feature extraction is an important issue. However, the features used in the state-of-the-art "general purpose" NR-IQA algorithms are usually natural scene statistics (NSS) based or are perceptually relevant; therefore, the performance of these models is limited. To further improve the performance of NR-IQA, we propose a general purpose NR-IQA algorithm which combines NSS-based features with perceptually relevant features. The new method extracts features in both the spatial and gradient domains. In the spatial domain, we extract the point-wise statistics for single pixel values which are characterized by a generalized Gaussian distribution model to form the underlying features. In the gradient domain, statistical features based on neighboring gradient magnitude similarity are extracted. Then a mapping is learned to predict quality scores using a support vector regression. The experimental results on the benchmark image databases demonstrate that the proposed algorithm correlates highly with human judgments of quality and leads to significant performance improvements over state-of-the-art methods.

Fingerprint chromatogram analysis of extracts from the leaves of Tripterygium wilfordii Hook. F. by high performance liquid chromatography.

PubMed

Li, Ke; Wang, Shudong

2005-05-01

A simple and reliable high performance liquid chromatographic (HPLC) method has been developed and validated for the study of fingerprint chromatograms of extracts from the leaves of Tripterygium wilfordii Hook. F. (TWHF) and for controlling the quality of the herb. HPLC separation of the extracts was performed on a Lichrospher RP-18 column and detected by ultraviolet absorbance at 210 nm. The column temperature was maintained at 35 degrees C. A mobile phase composed of acetonitrile:H2O in the ratio of 39:61 (v/v) was found to be most suitable for this separation at a flow rate of 0.8 mL/min with isocratic elution. Under the chromatographic conditions described, the peak profile of the 10 components collected within 35 min made up the fingerprint of the extracts from leaves of TWHF with universal features. The fingerprint chromatograms had a good stability, precision, and reproducibility. The similarity of the extracts from leaves of TWHF collected in summer and winter was studied with triptolide as a reference peak. The method is suitable for differentiation of extracts from the leaves of TWHF, and can be used as a quality control method for this herb.

High-quality and -quantity DNA extraction from frozen archival blood clots for genotyping of single-nucleotide polymorphisms.

PubMed

Bank, Steffen; Nexø, Bjørn Andersen; Andersen, Vibeke; Vogel, Ulla; Andersen, Paal Skytt

2013-06-01

The recovery of biological samples for genetic epidemiological studies can be cumbersome. Blood clots are routinely collected for serological examinations. However, the extraction of DNA from blood clots can be difficult and often results in low yields. The aim was to compare the efficiency of commercial purification kits for extracting DNA from long-term frozen clotted blood. Serum tubes with clotted blood were stored at -20°C for 1 to 2.5 years before DNA extraction. DNA was extracted from 10 blood clot samples using PureGene (Qiagen) with and without glycogen, the QIAamp DNA Micro kit (Qiagen), and the Nucleospin 96 Blood kit (Macherey-Nagel). Furthermore, blood clots from 1055 inflammatory bowel disease patients were purified using the Maxwell 16 Blood purification kit (Promega). The DNA was extracted according to the manufacturers` instructions and real-time PCR and the A(260)/A(280) ratio were used to evaluate the quality of the extracted DNA. The highest DNA yield was obtained by the Maxwell 16 Blood purification kit (Promega) with a median of 4.90 μg (range 0.8-25 μg) pr 300 μL total blood. PureGene with glycogen (Qiagen) had the second highest yield with a median of 0.65 μg (range 0.5-2.6 μg) pr 300 μL total blood. The yield obtained by the different commercial kits varied considerably. Our work demonstrates that high-quality and -quantity DNA can be extracted with the Maxwell 16 Blood purification kit (Promega) from cryopreserved blood clots, even after prolonged storage. The recovered DNA served as a reliable PCR template for single-nucleotide polymorphism assays.

Chemopreventive effects of free and bound phenolics associated to steep waters (nejayote) obtained after nixtamalization of different maize types.

PubMed

Rojas-García, Carlos; García-Lara, Silverio; Serna-Saldivar, Sergio O; Gutiérrez-Uribe, Janet A

2012-03-01

Free and bound phenolics extracts from nejayote solids were obtained after optimally lime-cooking blue, normal white, red, normal yellow, high-carotenoid and quality protein maize types. The extraction yield ranged from 4.47 to 10.05%. Bound phenolics extracts had higher content of total phenolics, antioxidant activity and ferulic acid compared to the free phenolics extracts. In general, free phenolics extracts were less cytotoxic than the bound phenolics counterparts. Bound phenolics extracts had higher induction of quinone reductase (QR) and particularly the normal yellow nejayote exerted the highest chemopreventive index tested in Hepa1c1c7 cells. When tested for monofunctional phase 2 induction capacity in BPrc1 cells, the bound phenolics extracts of blue, normal white and quality protein nejayotes were better inducers than the normal yellow counterpart. Particularly, the free phenolics extract of the white maize nejayote induced BPrc1 cells QR and exerted a higher chemopreventive index compared to the bound phenolics extract. Therefore, the nejayote of the normal white maize was the best source of monofunctional phase 2 enzyme inducers.

Thue-Morse nanostructures for tunable light extraction in the visible region

NASA Astrophysics Data System (ADS)

Rippa, M.; Castagna, R.; Marino, A.; Tkachenko, V.; Palermo, G.; Pane, A.; Umeton, C.; Tabiryan, N.; Petti, L.

2018-05-01

Controlling light propagation at the nanoscale is a fascinating opportunity offered by modern photonics, more than a challenge to face off. This study is aimed at investigating a particular kind of nanocomposite and reconfigurable optical metamaterials that can be exploited for the realization of a new class of switchable photonic devices, representing a breakthrough with respect to the state of the art. Existing photonic devices exhibit, in general, a drawback in the absence of tunability; this work aims to the design and characterization of metamaterials exploiting reconfigurable media, like LCs, which enable realization of a tunable, high quality, photonic quasi-crystal based switchable mode selector. It turned out that, starting from an unpolarized white light source, through a light extraction mechanism based on the diffraction of light, the high quality structure, combined with a uniformly aligned Photo-responsive Liquid Crystal (PLC), is able to give rise to an extremely narrow (FWHM ≈5 nm) and linearly polarized single mode peak of the extracted light intensity. Moreover, we have shown that the spectral properties (switching) of the samples can be finely controlled by using both an external applied voltage and a suitable pump light source with a maximum increase of 45% of the extracted light. Finally, both Scanning Electron Microscopy (SEM) and Far Field Diffraction (FFD) analysis have shown the high quality morphology of the realized structure.

A new strategy for accelerated extraction of target compounds using molecularly imprinted polymer particles embedded in a paper-based disk.

PubMed

Zarejousheghani, Mashaalah; Schrader, Steffi; Möder, Monika; Schmidt, Matthias; Borsdorf, Helko

2018-03-01

In this study, a general simple and inexpensive method is introduced for the preparation of a paper-based selective disk-type solid phase extraction (SPE) technique, appropriate for fast and high throughput monitoring of target compounds. An ion exchange molecularly imprinted polymer (MIP) was synthesized for the extraction and analysis of acesulfame, an anthropogenic water quality marker. Acesulfame imprinting was used as an example for demonstrating the benefits of a nanosized, swellable MIP extraction sorbents integrated in an on-site compatible concept for water quality monitoring. Compared with an 8 mL standard SPE cartridge, the paper-based MIP disk (47 mm ø) format allowed (1) high sample flow rates up to 30 mL•min -1 without losing extraction efficiency (2) extracting sample volumes up to 500 mL in much shorter times than with standard SPE, (3) the reuse of the disks (up to 3 times more than SPE cartridge) due to high robustness and an efficient post-cleaning, and (4) reducing the sampling time from 100 minutes (using the standard SPE format) to about 2 minutes with the MIP paper disk for 50 mL water sample. Different parameters like cellulose fiber/polymer ratios, sample volume, sample flow-rate, washing, and elution conditions were evaluated and optimized. Using developed extraction technique with high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS-MS) analysis, a new protocol was established that provides detection and quantification limits of 0.015 μg•L -1 and 0.05 μg•L -1 , respectively. The developed paper disks were used in-field for the selective extraction of target compounds and transferred to the laboratory for further analysis. Copyright © 2017 John Wiley & Sons, Ltd.

Optimized DNA extraction from neonatal dried blood spots: application in methylome profiling

PubMed Central

2014-01-01

Background Neonatal dried blood spots (DBS) represent an inexpensive method for long-term biobanking worldwide and are considered gold mines for research for several human diseases, including those of metabolic, infectious, genetic and epigenetic origin. However, the utility of DBS is restricted by the limited amount and quality of extractable biomolecules (including DNA), especially for genome wide profiling. Degradation of DNA in DBS often occurs during storage and extraction. Moreover, amplifying small quantities of DNA often leads to a bias in subsequent data, particularly in methylome profiles. Thus it is important to develop methodologies that maximize both the yield and quality of DNA from DBS for downstream analyses. Results Using combinations of in-house-derived and modified commercial extraction kits, we developed a robust and efficient protocol, compatible with methylome studies, many of which require stringent bisulfite conversion steps. Several parameters were tested in a step-wise manner, including blood extraction, cell lysis, protein digestion, and DNA precipitation, purification and elution. DNA quality was assessed based on spectrophotometric measurements, DNA detectability by PCR, and DNA integrity by gel electrophoresis and bioanalyzer analyses. Genome scale Infinium HumanMethylation450 and locus-specific pyrosequencing data generated using the refined DBS extraction protocol were of high quality, reproducible and consistent. Conclusions This study may prove useful to meet the increased demand for research on prenatal, particularly epigenetic, origins of human diseases and for newborn screening programs, all of which are often based on DNA extracted from DBS. PMID:24980254

Ginkgo Biloba extract for angina pectoris: a systematic review.

PubMed

Sun, Tian; Wang, Xian; Xu, Hao

2015-07-01

To evaluate the efficacy and safety of Ginkgo Biloba extract for patients with angina pectoris according to the available evidence. Electronic databases were searched for all of the randomized controlled trials (RCTs) of angina pectoris treatments with Ginkgo Biloba extract, either alone or combined with routine Western medicine (RWM), and controlled by untreated, placebo, Chinese patent medicine, or RWM treatment. The RCTs were retrieved from the following electronic databases: PubMed/MEDLINE, ProQuest Health and Medical Complete, Springer, Elsevier, and ProQuest Dissertations and Theses, Wanfang Data, China National Knowledge Infrastructure (CNKI), VIP database, China Biology Medicine (CBM), Chinese Medical Citation Index (CMCI), from the earliest database records to December 2012. No language restriction was applied. Study selection, data extraction, quality assessment, and data analyses were conducted according to the Cochrane standards. RevMan 5.1.0 provided by Cochrane Collaboration The data were analysed by using. A total of 23 RCTs (involving 2,529 patients) were included and the methodological quality was evaluated as generally low. Ginkgo Biloba extract with RWM was more effective in angina relief and electrocardiogram improvement than RWM alone. Reported adverse events included epigastric discomfort, nausea, gastrointestinal reaction, and bitter taste. Ginkgo Biloba extract may have beneficial effects on patients with angina pectoris, although the low quality of existing trials makes it difficult to draw a satisfactory conclusion. More rigorous, high quality clinical trials are needed to provide conclusive evidence.

Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities.

PubMed

Oldham, Athenia L; Drilling, Heather S; Stamps, Blake W; Stevenson, Bradley S; Duncan, Kathleen E

2012-11-20

The analysis of microbial assemblages in industrial, marine, and medical systems can inform decisions regarding quality control or mitigation. Modern molecular approaches to detect, characterize, and quantify microorganisms provide rapid and thorough measures unbiased by the need for cultivation. The requirement of timely extraction of high quality nucleic acids for molecular analysis is faced with specific challenges when used to study the influence of microorganisms on oil production. Production facilities are often ill equipped for nucleic acid extraction techniques, making the preservation and transportation of samples off-site a priority. As a potential solution, the possibility of extracting nucleic acids on-site using automated platforms was tested. The performance of two such platforms, the Fujifilm QuickGene-Mini80™ and Promega Maxwell®16 was compared to a widely used manual extraction kit, MOBIO PowerBiofilm™ DNA Isolation Kit, in terms of ease of operation, DNA quality, and microbial community composition. Three pipeline biofilm samples were chosen for these comparisons; two contained crude oil and corrosion products and the third transported seawater. Overall, the two more automated extraction platforms produced higher DNA yields than the manual approach. DNA quality was evaluated for amplification by quantitative PCR (qPCR) and end-point PCR to generate 454 pyrosequencing libraries for 16S rRNA microbial community analysis. Microbial community structure, as assessed by DGGE analysis and pyrosequencing, was comparable among the three extraction methods. Therefore, the use of automated extraction platforms should enhance the feasibility of rapidly evaluating microbial biofouling at remote locations or those with limited resources.

Automated DNA extraction platforms offer solutions to challenges of assessing microbial biofouling in oil production facilities

PubMed Central

2012-01-01

The analysis of microbial assemblages in industrial, marine, and medical systems can inform decisions regarding quality control or mitigation. Modern molecular approaches to detect, characterize, and quantify microorganisms provide rapid and thorough measures unbiased by the need for cultivation. The requirement of timely extraction of high quality nucleic acids for molecular analysis is faced with specific challenges when used to study the influence of microorganisms on oil production. Production facilities are often ill equipped for nucleic acid extraction techniques, making the preservation and transportation of samples off-site a priority. As a potential solution, the possibility of extracting nucleic acids on-site using automated platforms was tested. The performance of two such platforms, the Fujifilm QuickGene-Mini80™ and Promega Maxwell®16 was compared to a widely used manual extraction kit, MOBIO PowerBiofilm™ DNA Isolation Kit, in terms of ease of operation, DNA quality, and microbial community composition. Three pipeline biofilm samples were chosen for these comparisons; two contained crude oil and corrosion products and the third transported seawater. Overall, the two more automated extraction platforms produced higher DNA yields than the manual approach. DNA quality was evaluated for amplification by quantitative PCR (qPCR) and end-point PCR to generate 454 pyrosequencing libraries for 16S rRNA microbial community analysis. Microbial community structure, as assessed by DGGE analysis and pyrosequencing, was comparable among the three extraction methods. Therefore, the use of automated extraction platforms should enhance the feasibility of rapidly evaluating microbial biofouling at remote locations or those with limited resources. PMID:23168231

Impact of extractables from rubber closures on protein stability under heat stress.

PubMed

Richter, Carolin; Lipperheide, Cornelia; Lipke, Uwe; Lamprecht, Alf

2018-06-09

Commercially available, uncoated elastomeric closures were examined in regard to a potential contribution of extracted compounds from the rubber stoppers to protein aggregation under worst-case conditions. All rubber stoppers were confirmed to comply with Ph. Eur. quality requirements. Extraction with 2-propanol under reflux-conditions for 3 h led to closure-specific extraction profiles of the tested samples. One type of rubber stopper exhibited a considerably greater number and higher content of extractables. Four extracted compounds were identified as trialkyl benzene-1, 2, 4-tricarboxylates (trivial name: trimellitates), a substance class which is increasingly established as an alternative to phthalates. A highly concentrated aqueous solution of total extractables from this rubber stopper facilitated the formation of soluble and non-soluble high-molecular aggregates when incubated with model biopharmaceuticals (recombinant human immunoglobulin G (IgG) and recombinant erythropoietin (EPO)) under stress conditions (IgG: 60-64°C for 130 min, EPO: 55°C for 8 days). Furthermore, it was shown that the surfactant concentration (polysorbate 20, 0.1 m/v % vs. 1.0 m/v %) decisively influenced the formation of high-molecular aggregates. In case of EPO, the 10 fold increased concentration of surfactant was sufficient to prevent the aggregate formation completely. This study suggests the necessity of revisiting the current test system of Ph. Eur. monograph 3.2.9 for appropriate rubber stopper quality evaluation. Copyright © 2018. Published by Elsevier B.V.

High density FTA plates serve as efficient long-term sample storage for HLA genotyping.

PubMed

Lange, V; Arndt, K; Schwarzelt, C; Boehme, I; Giani, A S; Schmidt, A H; Ehninger, G; Wassmuth, R

2014-02-01

Storage of dried blood spots (DBS) on high-density FTA(®) plates could constitute an appealing alternative to frozen storage. However, it remains controversial whether DBS are suitable for high-resolution sequencing of human leukocyte antigen (HLA) alleles. Therefore, we extracted DNA from DBS that had been stored for up to 4 years, using six different methods. We identified those extraction methods that recovered sufficient high-quality DNA for reliable high-resolution HLA sequencing. Further, we confirmed that frozen whole blood samples that had been stored for several years can be transferred to filter paper without compromising HLA genotyping upon extraction. Concluding, DNA derived from high-density FTA(®) plates is suitable for high-resolution HLA sequencing, provided that appropriate extraction protocols are employed. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

[A study on the method of DNA extraction from unbuffered formalin-fixed and paraffin-embedded samples].

PubMed

Tian, Zi-Qiang; Liu, Jun-Feng; Zhang, Shao-Wei; Li, Bao-Qing; Wang, Fu-Shun; Zhang, Yue-Feng

2004-03-01

Unbuffered formalin is widely used to fix resected specimens in China. The DNA in unbuffered formalin-fixed and paraffin-embedded tissues is usually degraded seriously, so the extraction of DNA from these samples is difficult. This study was conducted to seek an optimal method to extract DNA from these samples. Fifteen blocks of esophageal carcinoma resected in Fourth Hospital of Hebei Medical University in 2000 were selected. The cells were lyzed by proteinase K digestion or heating under different pH values, then DNA was extracted by phenol:chloroform. After that, four parameters (deparaffined by xylene or histolene; digested for 48 h or 72 h at 37 degrees C or 56 degrees C; extracted by salting-out or phenol:chloroform) were optimized according to the principle of cross design. At last, the quality of obtained DNA was analyzed with electrophoresis and PCR amplification. The quality and quantity of DNA obtained by proteinase K digestion (the average yield is 17.88 microg) were better than that of heating under different pH (7-12)(P< 0.05). The quality and quantity of DNA digested at 56 degrees C were better than that at 37 degrees C, and similarly, digestion for 72 hours was better than that for 48 hours. The methods of deparaffin and extraction had no obvious influence on the quality and quantity of DNA. By means of NaCl salting-out after proteinase K digestion, more reliable quality of DNA can be obtained from unbuffered formalin-fixed and paraffin-embedded samples. Furthermore,digestion for three days at 56 degrees C is more likely to obtain DNA with high quality and quantity.

Automatic evidence quality prediction to support evidence-based decision making.

PubMed

Sarker, Abeed; Mollá, Diego; Paris, Cécile

2015-06-01

Evidence-based medicine practice requires practitioners to obtain the best available medical evidence, and appraise the quality of the evidence when making clinical decisions. Primarily due to the plethora of electronically available data from the medical literature, the manual appraisal of the quality of evidence is a time-consuming process. We present a fully automatic approach for predicting the quality of medical evidence in order to aid practitioners at point-of-care. Our approach extracts relevant information from medical article abstracts and utilises data from a specialised corpus to apply supervised machine learning for the prediction of the quality grades. Following an in-depth analysis of the usefulness of features (e.g., publication types of articles), they are extracted from the text via rule-based approaches and from the meta-data associated with the articles, and then applied in the supervised classification model. We propose the use of a highly scalable and portable approach using a sequence of high precision classifiers, and introduce a simple evaluation metric called average error distance (AED) that simplifies the comparison of systems. We also perform elaborate human evaluations to compare the performance of our system against human judgments. We test and evaluate our approaches on a publicly available, specialised, annotated corpus containing 1132 evidence-based recommendations. Our rule-based approach performs exceptionally well at the automatic extraction of publication types of articles, with F-scores of up to 0.99 for high-quality publication types. For evidence quality classification, our approach obtains an accuracy of 63.84% and an AED of 0.271. The human evaluations show that the performance of our system, in terms of AED and accuracy, is comparable to the performance of humans on the same data. The experiments suggest that our structured text classification framework achieves evaluation results comparable to those of human performance. Our overall classification approach and evaluation technique are also highly portable and can be used for various evidence grading scales. Copyright © 2015 Elsevier B.V. All rights reserved.

[Validation of Differential Extraction Kit in forensic sexual assault cases].

PubMed

Wu, Dan; Cao, Yu; Xu, Yan; He, Bai-Fang; Bi, Gang; Zhou, Huai-Gu

2009-12-01

To evaluate the validity of Differential Extraction Kit in isolating spermatozoa and epithelial cell DNA from mixture samples. Selective lysis of spermatid and epithelial cells combined with paramagnetic particle method were applied to extract the DNA from the mock samples under controlled conditions and forensic case samples, and template DNA were analyzed by STR genotype method. This Differential Extraction Kit is efficient to obtain high quality spermatid and epithelial cell DNA from the mixture samples with different proportion of sperm to epithelial cell. The Differential Extraction Kit can be applied in DNA extraction for mixed stain from forensic sexual assault samples.

An optimized high quality male DNA extraction from spermatophores in open thelycum shrimp species.

PubMed

Planella, Laia; Heras, Sandra; Vera, Manuel; García-Marín, José-Luis; Roldán, María Inés

2017-09-01

The crucial step of most of the current genetic studies is the extraction of DNA of sufficient quantity and quality. Several genomic DNA isolation methods have been described to successfully obtain male DNA from shrimp species. However, all current protocols require invasive handling methods with males for DNA isolation. Using Aristeus antennatus as a model we tested a reliable non-invasive differential DNA extraction method to male DNA isolation from spermatophores attached to female thelycum. The present protocol provides high quality and quantity DNA for polymerase chain reaction amplification and male genotyping. This new approach could be useful to experimental shrimp culture to select sires with relevant genetic patterns for selective breeding programs. More importantly, it can be applied to identify the mating pairs and male structure in wild populations of species as A. antennatus, where males are often difficult to capture. Our method could be also valuable for biological studies on other spermatophore-using species, such as myriapods, arachnids and insects. © 2016 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and John Wiley & Sons Australia, Ltd.

Impact of water extractable arabinoxylan from rye bran on the frozen steamed bread dough quality.

PubMed

Wang, Pei; Tao, Han; Jin, Zhengyu; Xu, Xueming

2016-06-01

Impact of water extractable arabinoxylan from rye bran on frozen steamed bread dough quality was investigated in terms of the bread characteristics, ice crystallization, yeast activity as well as the gluten molecular weight distribution and glutenin macropolymer content in the present study. Results showed that water extractable arabinoxylan significantly improved bread characteristics during the 60-day frozen storage. Less water was crystallized in the water extractable arabinoxylan dough during storage, which could explain the alleviated yeast activity loss. For all the frozen dough samples, more soluble high molecular weight (Mw ≈ 91,000-688,000) and low molecular weight (Mw ≈ 91,000-16,000) proteins were derived from glutenin macropolymer depolymerization. Nevertheless, water extractable arabinoxylan dough developed higher glutenin macropolymer content with lowered level of soluble low molecular weight proteins throughout the storage. This study suggested water extractable arabinoxylan from rye bran had great potential to be served as an effective frozen steamed bread dough improver. Copyright © 2016 Elsevier Ltd. All rights reserved.

Normalization and standardization of electronic health records for high-throughput phenotyping: the SHARPn consortium

PubMed Central

Pathak, Jyotishman; Bailey, Kent R; Beebe, Calvin E; Bethard, Steven; Carrell, David S; Chen, Pei J; Dligach, Dmitriy; Endle, Cory M; Hart, Lacey A; Haug, Peter J; Huff, Stanley M; Kaggal, Vinod C; Li, Dingcheng; Liu, Hongfang; Marchant, Kyle; Masanz, James; Miller, Timothy; Oniki, Thomas A; Palmer, Martha; Peterson, Kevin J; Rea, Susan; Savova, Guergana K; Stancl, Craig R; Sohn, Sunghwan; Solbrig, Harold R; Suesse, Dale B; Tao, Cui; Taylor, David P; Westberg, Les; Wu, Stephen; Zhuo, Ning; Chute, Christopher G

2013-01-01

Research objective To develop scalable informatics infrastructure for normalization of both structured and unstructured electronic health record (EHR) data into a unified, concept-based model for high-throughput phenotype extraction. Materials and methods Software tools and applications were developed to extract information from EHRs. Representative and convenience samples of both structured and unstructured data from two EHR systems—Mayo Clinic and Intermountain Healthcare—were used for development and validation. Extracted information was standardized and normalized to meaningful use (MU) conformant terminology and value set standards using Clinical Element Models (CEMs). These resources were used to demonstrate semi-automatic execution of MU clinical-quality measures modeled using the Quality Data Model (QDM) and an open-source rules engine. Results Using CEMs and open-source natural language processing and terminology services engines—namely, Apache clinical Text Analysis and Knowledge Extraction System (cTAKES) and Common Terminology Services (CTS2)—we developed a data-normalization platform that ensures data security, end-to-end connectivity, and reliable data flow within and across institutions. We demonstrated the applicability of this platform by executing a QDM-based MU quality measure that determines the percentage of patients between 18 and 75 years with diabetes whose most recent low-density lipoprotein cholesterol test result during the measurement year was <100 mg/dL on a randomly selected cohort of 273 Mayo Clinic patients. The platform identified 21 and 18 patients for the denominator and numerator of the quality measure, respectively. Validation results indicate that all identified patients meet the QDM-based criteria. Conclusions End-to-end automated systems for extracting clinical information from diverse EHR systems require extensive use of standardized vocabularies and terminologies, as well as robust information models for storing, discovering, and processing that information. This study demonstrates the application of modular and open-source resources for enabling secondary use of EHR data through normalization into standards-based, comparable, and consistent format for high-throughput phenotyping to identify patient cohorts. PMID:24190931

Criteria to Extract High-Quality Protein Data Bank Subsets for Structure Users.

PubMed

Carugo, Oliviero; Djinović-Carugo, Kristina

2016-01-01

It is often necessary to build subsets of the Protein Data Bank to extract structural trends and average values. For this purpose it is mandatory that the subsets are non-redundant and of high quality. The first problem can be solved relatively easily at the sequence level or at the structural level. The second, on the contrary, needs special attention. It is not sufficient, in fact, to consider the crystallographic resolution and other feature must be taken into account: the absence of strings of residues from the electron density maps and from the files deposited in the Protein Data Bank; the B-factor values; the appropriate validation of the structural models; the quality of the electron density maps, which is not uniform; and the temperature of the diffraction experiments. More stringent criteria produce smaller subsets, which can be enlarged with more tolerant selection criteria. The incessant growth of the Protein Data Bank and especially of the number of high-resolution structures is allowing the use of more stringent selection criteria, with a consequent improvement of the quality of the subsets of the Protein Data Bank.

Extraction of Oleic Acid from Moroccan Olive Mill Wastewater

PubMed Central

Elkacmi, Reda; Kamil, Noureddine; Bennajah, Mounir; Kitane, Said

2016-01-01

The production of olive oil in Morocco has recently grown considerably for its economic and nutritional importance favored by the country's climate. After the extraction of olive oil by pressing or centrifuging, the obtained liquid contains oil and vegetation water which is subsequently separated by decanting or centrifugation. Despite its treatment throughout the extraction process, this olive mill wastewater, OMW, still contains a very important oily residue, always regarded as a rejection. The separated oil from OMW can not be intended for food because of its high acidity of 3.397% which exceeds the international standard for human consumption defined by the standard of the Codex Alimentarius, proving its poor quality. This work gives value addition to what would normally be regarded as waste by the extraction of oleic acid as a high value product, using the technique of inclusion with urea for the elimination of saturated and unsaturated fatty acids through four successive crystallizations at 4°C and 20°C to have a final phase with oleic acid purity of 95.49%, as a biodegradable soap and a high quality glycerin will be produced by the reaction of saponification and transesterification. PMID:26933663

Extraction of Oleic Acid from Moroccan Olive Mill Wastewater.

PubMed

Elkacmi, Reda; Kamil, Noureddine; Bennajah, Mounir; Kitane, Said

2016-01-01

The production of olive oil in Morocco has recently grown considerably for its economic and nutritional importance favored by the country's climate. After the extraction of olive oil by pressing or centrifuging, the obtained liquid contains oil and vegetation water which is subsequently separated by decanting or centrifugation. Despite its treatment throughout the extraction process, this olive mill wastewater, OMW, still contains a very important oily residue, always regarded as a rejection. The separated oil from OMW can not be intended for food because of its high acidity of 3.397% which exceeds the international standard for human consumption defined by the standard of the Codex Alimentarius, proving its poor quality. This work gives value addition to what would normally be regarded as waste by the extraction of oleic acid as a high value product, using the technique of inclusion with urea for the elimination of saturated and unsaturated fatty acids through four successive crystallizations at 4°C and 20°C to have a final phase with oleic acid purity of 95.49%, as a biodegradable soap and a high quality glycerin will be produced by the reaction of saponification and transesterification.

RNA isolation from mammalian cells using porous polymer monoliths: an approach for high-throughput automation.

PubMed

Chatterjee, Anirban; Mirer, Paul L; Zaldivar Santamaria, Elvira; Klapperich, Catherine; Sharon, Andre; Sauer-Budge, Alexis F

2010-06-01

The life science and healthcare communities have been redefining the importance of ribonucleic acid (RNA) through the study of small molecule RNA (in RNAi/siRNA technologies), micro RNA (in cancer research and stem cell research), and mRNA (gene expression analysis for biologic drug targets). Research in this field increasingly requires efficient and high-throughput isolation techniques for RNA. Currently, several commercial kits are available for isolating RNA from cells. Although the quality and quantity of RNA yielded from these kits is sufficiently good for many purposes, limitations exist in terms of extraction efficiency from small cell populations and the ability to automate the extraction process. Traditionally, automating a process decreases the cost and personnel time while simultaneously increasing the throughput and reproducibility. As the RNA field matures, new methods for automating its extraction, especially from low cell numbers and in high throughput, are needed to achieve these improvements. The technology presented in this article is a step toward this goal. The method is based on a solid-phase extraction technology using a porous polymer monolith (PPM). A novel cell lysis approach and a larger binding surface throughout the PPM extraction column ensure a high yield from small starting samples, increasing sensitivity and reducing indirect costs in cell culture and sample storage. The method ensures a fast and simple procedure for RNA isolation from eukaryotic cells, with a high yield both in terms of quality and quantity. The technique is amenable to automation and streamlined workflow integration, with possible miniaturization of the sample handling process making it suitable for high-throughput applications.

Characterization and Potential Environmental Risks of Leachate from Shredded Rubber Mulches

PubMed Central

Kanematsu, Masakazu; Hayashi, Ai; Denison, Michael S.; Young, Thomas M.

2009-01-01

In order to determine whether shredded rubber mulches (RM) posed water quality risks when used in stormwater best management practices (BMPs) such as bioretention basins, batch leaching tests were conducted to identify and quantify constituents in leachates from RM such as metal ions, nutrients, total organic carbon (TOC), and aryl hydrocarbon receptor (AhR) activity (determined by the chemically activated luciferase gene expression (CALUX) bioassay) at varied temperature and initial pH values. The results indicate that aqueous extracts of RM contain high concentrations of zinc (Zn) compared with wood mulches (WM), and its concentration increased at lower pH and higher temperature. Although methanol extracts of RM displayed high AhR activity, none of the aqueous extracts of RM had significant activity. Hence, while unknown constituents that have significant AhR activity are present in RM, they appear to be not measurably extracted by water under environmental conditions relevant for stormwater (5 < pH < 9, 10 < T < 40°C). Our results suggests that organic constituents in water extracts of RM which have AhR activity may not be of significant concern while leaching of Zn from RM appears to be a potentially larger water quality issue for RM. PMID:19450864

The effect of filler addition and oven temperature to the antioxidant quality in the drying of Physalis angulata fruit extract obtained by subcritical water extraction

NASA Astrophysics Data System (ADS)

Susanti, R. F.; Christianto, G.

2016-01-01

Physalis angulata or ceplukan is medicinal herb, which grows naturally in Indonesia. It has been used in traditional medicine to treat several diseases. It is also reported to have antimycobacterial, antileukemic, antipyretic. In this research, Pysalis angulata fruit was investigated for its antioxidant capacity. In order to avoid the toxic organic solvent commonly used in conventional extraction, subcritical water extraction method was used. During drying, filler which is inert was added to the extract. It can absorb water and change the oily and sticky form of extract to powder form. The effects of filler types, concentrations and drying temperatures were investigated to the antioxidant quality covering total phenol, flavonoid and antioxidant activity. The results showed that total phenol, flavonoid and antioxidant activity were improved by addition of filler because the drying time was shorter compared to extract without filler. Filler absorbs water and protects extract from exposure to heat during drying. The combination between high temperature and shorter drying time are beneficial to protect the antioxidant in extract. The type of fillers investigation showed that aerosil gave better performance compared to Microcrystalline Celullose (MCC).

Frequency of data extraction errors and methods to increase data extraction quality: a methodological review.

PubMed

Mathes, Tim; Klaßen, Pauline; Pieper, Dawid

2017-11-28

Our objective was to assess the frequency of data extraction errors and its potential impact on results in systematic reviews. Furthermore, we evaluated the effect of different extraction methods, reviewer characteristics and reviewer training on error rates and results. We performed a systematic review of methodological literature in PubMed, Cochrane methodological registry, and by manual searches (12/2016). Studies were selected by two reviewers independently. Data were extracted in standardized tables by one reviewer and verified by a second. The analysis included six studies; four studies on extraction error frequency, one study comparing different reviewer extraction methods and two studies comparing different reviewer characteristics. We did not find a study on reviewer training. There was a high rate of extraction errors (up to 50%). Errors often had an influence on effect estimates. Different data extraction methods and reviewer characteristics had moderate effect on extraction error rates and effect estimates. The evidence base for established standards of data extraction seems weak despite the high prevalence of extraction errors. More comparative studies are needed to get deeper insights into the influence of different extraction methods.

Design and Measurement of a Digital Phase Locked BWO for Accurately Extracting the Quality Factors in a Biconcave Resonator System

NASA Astrophysics Data System (ADS)

Gao, Yuanci; Charles, Jones R.; Yu, Guofen; Jyotsna, Dutta M.

2012-03-01

A long loop phase locked backward-wave oscillator (BWO) for a high quality factor resonator system operating at D-band frequencies (130-170GHz) was described, the phase noise of the phased locked BWO was analyzed and measured at typical frequencies. When it used with a high quality factor open resonator for measuring the quality factor of simple harmonic resonators based on the magnitude transfer characteristic, this system has proven to be capable of accurate measuring the quality factor as high as 0.8 million with an uncertainty of less than 1.3% (Lorentzian fitting) at typical frequencies in the range of 130GHz-170GHz.

PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.

PubMed

Fernandez-Ricaud, Luciano; Kourtchenko, Olga; Zackrisson, Martin; Warringer, Jonas; Blomberg, Anders

2016-06-23

Phenomics is a field in functional genomics that records variation in organismal phenotypes in the genetic, epigenetic or environmental context at a massive scale. For microbes, the key phenotype is the growth in population size because it contains information that is directly linked to fitness. Due to technical innovations and extensive automation our capacity to record complex and dynamic microbial growth data is rapidly outpacing our capacity to dissect and visualize this data and extract the fitness components it contains, hampering progress in all fields of microbiology. To automate visualization, analysis and exploration of complex and highly resolved microbial growth data as well as standardized extraction of the fitness components it contains, we developed the software PRECOG (PREsentation and Characterization Of Growth-data). PRECOG allows the user to quality control, interact with and evaluate microbial growth data with ease, speed and accuracy, also in cases of non-standard growth dynamics. Quality indices filter high- from low-quality growth experiments, reducing false positives. The pre-processing filters in PRECOG are computationally inexpensive and yet functionally comparable to more complex neural network procedures. We provide examples where data calibration, project design and feature extraction methodologies have a clear impact on the estimated growth traits, emphasising the need for proper standardization in data analysis. PRECOG is a tool that streamlines growth data pre-processing, phenotypic trait extraction, visualization, distribution and the creation of vast and informative phenomics databases.

Fiber-laser frequency combs for the generation of tunable single-frequency laser lines, mm- and THz-waves and sinc-shaped Nyquist pulses

NASA Astrophysics Data System (ADS)

Schneider, Thomas

2015-03-01

High-quality frequency comb sources like femtosecond-lasers have revolutionized the metrology of fundamental physical constants. The generated comb consists of frequency lines with an equidistant separation over a bandwidth of several THz. This bandwidth can be broadened further to a super-continuum of more than an octave through propagation in nonlinear media. The frequency separation between the lines is defined by the repetition rate and the width of each comb line can be below 1 Hz, even without external stabilization. By extracting just one of these lines, an ultra-narrow linewidth, tunable laser line for applications in communications and spectroscopy can be generated. If two lines are extracted, the superposition of these lines in an appropriate photo-mixer produces high-quality millimeter- and THz-waves. The extraction of several lines can be used for the creation of almost-ideally sinc-shaped Nyquist pulses, which enable optical communications with the maximum-possible baud rate. Especially combs generated by low-cost, small-footprint fs-fiber lasers are very promising. However due to the resonator length, the comb frequencies have a typical separation of 80 - 100 MHz, far too narrow for the selection of single tones with standard optical filters. Here the extraction of single lines of an fs-fiber laser by polarization pulling assisted stimulated Brillouin scattering is presented. The application of these extracted lines as ultra-narrow, stable and tunable laser lines, for the generation of very high-quality mm and THz-waves with an ultra-narrow linewidth and phase noise and for the generation of sinc-shaped Nyquist pulses with arbitrary bandwidth and repetition rate is discussed.

Optimising the Encapsulation of an Aqueous Bitter Melon Extract by Spray-Drying

PubMed Central

Tan, Sing Pei; Kha, Tuyen Chan; Parks, Sophie; Stathopoulos, Costas; Roach, Paul D.

2015-01-01

Our aim was to optimise the encapsulation of an aqueous bitter melon extract by spray-drying with maltodextrin (MD) and gum Arabic (GA). The response surface methodology models accurately predicted the process yield and retentions of bioactive concentrations and activity (R2 > 0.87). The optimal formulation was predicted and validated as 35% (w/w) stock solution (MD:GA, 1:1) and a ratio of 1.5:1 g/g of the extract to the stock solution. The spray-dried powder had a high process yield (66.2% ± 9.4%) and high retention (>79.5% ± 8.4%) and the quality of the powder was high. Therefore, the bitter melon extract was well encapsulated into a powder using MD/GA and spray-drying. PMID:28231214

Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format

PubMed Central

2011-01-01

The increasing popularity of systems-based approaches to plant research has resulted in a demand for high throughput (HTP) methods to be developed. RNA extraction from multiple samples in an experiment is a significant bottleneck in performing systems-level genomic studies. Therefore we have established a high throughput method of RNA extraction from Arabidopsis thaliana to facilitate gene expression studies in this widely used plant model. We present optimised manual and automated protocols for the extraction of total RNA from 9-day-old Arabidopsis seedlings in a 96 well plate format using silica membrane-based methodology. Consistent and reproducible yields of high quality RNA are isolated averaging 8.9 μg total RNA per sample (~20 mg plant tissue). The purified RNA is suitable for subsequent qPCR analysis of the expression of over 500 genes in triplicate from each sample. Using the automated procedure, 192 samples (2 × 96 well plates) can easily be fully processed (samples homogenised, RNA purified and quantified) in less than half a day. Additionally we demonstrate that plant samples can be stored in RNAlater at -20°C (but not 4°C) for 10 months prior to extraction with no significant effect on RNA yield or quality. Additionally, disrupted samples can be stored in the lysis buffer at -20°C for at least 6 months prior to completion of the extraction procedure providing a flexible sampling and storage scheme to facilitate complex time series experiments. PMID:22136293

Protocol: high throughput silica-based purification of RNA from Arabidopsis seedlings in a 96-well format.

PubMed

Salvo-Chirnside, Eliane; Kane, Steven; Kerr, Lorraine E

2011-12-02

The increasing popularity of systems-based approaches to plant research has resulted in a demand for high throughput (HTP) methods to be developed. RNA extraction from multiple samples in an experiment is a significant bottleneck in performing systems-level genomic studies. Therefore we have established a high throughput method of RNA extraction from Arabidopsis thaliana to facilitate gene expression studies in this widely used plant model. We present optimised manual and automated protocols for the extraction of total RNA from 9-day-old Arabidopsis seedlings in a 96 well plate format using silica membrane-based methodology. Consistent and reproducible yields of high quality RNA are isolated averaging 8.9 μg total RNA per sample (~20 mg plant tissue). The purified RNA is suitable for subsequent qPCR analysis of the expression of over 500 genes in triplicate from each sample. Using the automated procedure, 192 samples (2 × 96 well plates) can easily be fully processed (samples homogenised, RNA purified and quantified) in less than half a day. Additionally we demonstrate that plant samples can be stored in RNAlater at -20°C (but not 4°C) for 10 months prior to extraction with no significant effect on RNA yield or quality. Additionally, disrupted samples can be stored in the lysis buffer at -20°C for at least 6 months prior to completion of the extraction procedure providing a flexible sampling and storage scheme to facilitate complex time series experiments.

Effect of drying and co-matrix addition on the yield and quality of supercritical CO₂ extracted pumpkin (Cucurbita moschata Duch.) oil.

PubMed

Durante, Miriana; Lenucci, Marcello S; D'Amico, Leone; Piro, Gabriella; Mita, Giovanni

2014-04-01

In this work a process for obtaining high vitamin E and carotenoid yields by supercritical carbon dioxide (SC-CO₂) extraction from pumpkin (Cucurbita moschata Duch.) is described. The results show that the use of a vacuum oven-dried [residual moisture (∼8%)] and milled (70 mesh sieve) pumpkin flesh matrix increased SC-CO₂ extraction yields of total vitamin E and carotenoids of ∼12.0- and ∼8.5-fold, respectively, with respect to the use of a freeze-dried and milled flesh matrix. The addition of milled (35 mesh) pumpkin seeds as co-matrix (1:1, w/w) allowed a further ∼1.6-fold increase in carotenoid yield, besides to a valuable enrichment of the extracted oil in vitamin E (274 mg/100 g oil) and polyunsaturated fatty acids. These findings encourage further studies in order to scale up the process for possible industrial production of high quality bioactive ingredients from pumpkin useful in functional food or cosmeceutical formulation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Landsat surface reflectance quality assurance extraction (version 1.7)

USGS Publications Warehouse

Jones, J.W.; Starbuck, M.J.; Jenkerson, Calli B.

2013-01-01

The U.S. Geological Survey (USGS) Land Remote Sensing Program is developing an operational capability to produce Climate Data Records (CDRs) and Essential Climate Variables (ECVs) from the Landsat Archive to support a wide variety of science and resource management activities from regional to global scale. The USGS Earth Resources Observation and Science (EROS) Center is charged with prototyping systems and software to generate these high-level data products. Various USGS Geographic Science Centers are charged with particular ECV algorithm development and (or) selection as well as the evaluation and application demonstration of various USGS CDRs and ECVs. Because it is a foundation for many other ECVs, the first CDR in development is the Landsat Surface Reflectance Product (LSRP). The LSRP incorporates data quality information in a bit-packed structure that is not readily accessible without postprocessing services performed by the user. This document describes two general methods of LSRP quality-data extraction for use in image processing systems. Helpful hints for the installation and use of software originally developed for manipulation of Hierarchical Data Format (HDF) produced through the National Aeronautics and Space Administration (NASA) Earth Observing System are first provided for users who wish to extract quality data into separate HDF files. Next, steps follow to incorporate these extracted data into an image processing system. Finally, an alternative example is illustrated in which the data are extracted within a particular image processing system.

A quality score for coronary artery tree extraction results

NASA Astrophysics Data System (ADS)

Cao, Qing; Broersen, Alexander; Kitslaar, Pieter H.; Lelieveldt, Boudewijn P. F.; Dijkstra, Jouke

2018-02-01

Coronary artery trees (CATs) are often extracted to aid the fully automatic analysis of coronary artery disease on coronary computed tomography angiography (CCTA) images. Automatically extracted CATs often miss some arteries or include wrong extractions which require manual corrections before performing successive steps. For analyzing a large number of datasets, a manual quality check of the extraction results is time-consuming. This paper presents a method to automatically calculate quality scores for extracted CATs in terms of clinical significance of the extracted arteries and the completeness of the extracted CAT. Both right dominant (RD) and left dominant (LD) anatomical statistical models are generated and exploited in developing the quality score. To automatically determine which model should be used, a dominance type detection method is also designed. Experiments are performed on the automatically extracted and manually refined CATs from 42 datasets to evaluate the proposed quality score. In 39 (92.9%) cases, the proposed method is able to measure the quality of the manually refined CATs with higher scores than the automatically extracted CATs. In a 100-point scale system, the average scores for automatically and manually refined CATs are 82.0 (+/-15.8) and 88.9 (+/-5.4) respectively. The proposed quality score will assist the automatic processing of the CAT extractions for large cohorts which contain both RD and LD cases. To the best of our knowledge, this is the first time that a general quality score for an extracted CAT is presented.

[Contribution to the phytochemical study of polyphenols in ten hydroalcoholic extracts of Chamomile floss].

PubMed

Cioancă, Oana; Hăncianu, Monica; Spac, A; Miron, Anca; Stănescu, Ursula

2009-01-01

Continuing a series of studies that intend to evaluate the pharmaceutical quality of 10 commercial samples of chamomile, we tried to investigate the chemical composition of the hydroalcoholic extracts obtained in our laboratory, starting from this raw material. The qualitative and semiquantitative analysis of the extracts was done by HPLC means. All extractive solutions have a high content in ferulic acid, whereas the caffeic acid level is the lowest. Regarding the flavonoids, there are many quantitative differences between the samples: one extract lacking the rutoside and two of them having low apigenin-7-glucoside contents.

Optimization of conditions for isolation of high quality chitin from shrimp processing raw byproducts using response surface methodology and its characterization.

PubMed

Nidheesh, T; Suresh, P V

2015-06-01

Chitin is one of the most abundant bioactive biopolymer on earth. It is commercially extracted from seafood processing crustacean shell byproducts by harsh thermochemical treatments. The extraction conditions, the source and pretreatment of raw material significantly affect its quality and bioactivity. In this investigation response surface methodology (RSM) has been applied to optimize and evaluate the interaction of variables for extraction of high quality chitin from shrimp processing raw byproducts. Variables such as, concentration of HCl (%, v/v) 4.5 (for wet) and 4.9 (for dry), reaction time 3 h, solid liquid ratio of HCl (w/v) 1:5.5 (for wet) and 1:7.9 (for dry) with two treatments achieved >98 % demineralization of shrimp byproduct. Variables such as, concentration of NaOH 3.6 % (w/v), reaction time 2.5 h, temperature 69.0 ± 1 °C, solid liquid ratio of NaOH 7.4 (w/v) and two treatments accomplished >98 % deproteinization of demineralized byproducts. Significant (p ≤ 0.05-0.001) interactive effects were observed between different variables. Chitin obtained in these conditions had residual content (%, w/w) of ash <0.4 and protein <0.8 and the degree of N-acetylation was >93 % with purity of >98 %. In conclusion, the optimized conditions by RSM can be applied for large scale preparation of high quality chitin from raw shrimp byproduct.

Isolation of high quality RNA from cereal seeds containing high levels of starch.

PubMed

Wang, Guifeng; Wang, Gang; Zhang, Xiaowei; Wang, Fang; Song, Rentao

2012-01-01

Cereals are an important source of food, feed and fuel with a rapidly increasing global demand. However, cereal seeds contain high levels of starch and polysaccharides, making the isolation of high quality RNA extremely difficult. To develop a novel method for extracting high quality total RNA from various starch- and polysaccharides-rich cereal seeds, such as maize, rice, sorghum and wheat. We developed a modified sodium dodecyl sulphate (SDS)/TRIzol method. The combined use of a Tris buffer (pH 9.0) and SDS before TRIzol extraction effectively resolved the problem of seed homogenate solidification in such a buffer. A high concentration of SDS was used separately, not only to promote cell lysis but also to effectively dissolve seed sample containing high levels of starch. Moreover, acid phenol saturated with 0.1  M citrate buffer (pH 4.3) was used to separate RNA from DNAs, proteins and high levels of starch. This rapid protocol was compared with other RNA isolation methods preferentially used for plants rich in polysaccharides and secondary metabolites. Gel electrophoresis analysis indicated that the extracted total RNA had good integrity without apparent DNA contamination. Furthermore, an A₂₆₀/₂₈₀ ratio of approximately 2.0, an A₂₆₀/₂₃₀ ratio of more than 2.0 and RIN values of more than 8.6 indicated that the isolated RNA was of high purity. The isolated RNA was suitable for subsequent molecular manipulations, such as reverse-transcription polymerase chain reaction (PCR), rapid amplification of cDNA ends (RACE) and real-time PCR. The study has described an easy, efficient and highly reproducible method for RNA isolation from various cereal seeds. Copyright © 2011 John Wiley & Sons, Ltd.

The Metaproteome of "Park Grass" soil - a reference for EU soil science

NASA Astrophysics Data System (ADS)

Quinn, Gerry; Dudley, Ed; Doerr, Stefan; Matthews, Peter; Halen, Ingrid; Walley, Richard; Ashton, Rhys; Delmont, Tom; Francis, Lewis; Gazze, Salvatore Andrea; Van Keulen, Geertje

2016-04-01

Soil metaproteomics, the systemic extraction and identification of proteins from a soil, is key to understanding the biological and physical processes that occur within the soil at a molecular level. Until recently, direct extraction of proteins from complex soils have yielded only dozens of protein identifications due to interfering substances, such as humic acids and clay, which co-extract and/or strongly adsorb protein, often causing problems in downstream processing, e.g. mass spectrometry. Furthermore, the current most successful, direct, proteomic extraction protocol favours larger molecular weight and/or heat-stable proteins due to its extraction protocol. We have now developed a novel, faster, direct soil protein extraction protocol which also addressed the problem of interfering substances, while only requiring less than 1 gram of material per extraction. We extracted protein from the 'Genomic Observatory' Park Grass at Rothamsted Research (UK), an ideally suited geographic site as it is the longest (>150 years) continually studied experiment on ungrazed permanent grassland in the world, for which a rich history of environmental/ecological data has been collected, including high quality publically available metagenome DNA sequences. Using this improved methodology, in conjunction with the creation of high quality, curated metagenomic sequence databases, we have been able to significantly improve protein identifications from one soil due to extracting a similar number of proteins that were >90% different when compared to the best current direct protocol. This optimised metaproteomics protocol has now enabled identification of thousands of proteins from one soil, leading therefore to a deeper insight of soil system processes at the molecular scale.

[Studies on preparative technology and quantitative determination for extracts of total saponin in roof of Panax japonicus].

PubMed

He, Yu-min; Lu, Ke-ming; Yuan, Ding; Zhang, Chang-cheng

2008-11-01

To explore the optimum extraction and purification condition of the total saponins in the root of Panax japonicus (RPJ), and establish its quality control methods. Designed L16 (4(5)) orthogonal test with the extraction rate of total saponins as index, to determine the rational extraction process, and the techniques of water-saturated n-butanol extraction and acetone precipitation were applied to purify the alcohol extract of RPJ. Total saponins were detected by spectrophotometry and its triterpenoidal sapogenin oleanolic acid detected by HPLC. The optimum conditions of total saponins from RPJ was as follows: the material was pulverized, dipped in 60% ethanol aqueous solution as extract solvent at 10 times of volume, and refluxed 3 times for 3 h each time. Extractant of water-saturated n-butanol with extraction times of 3 and precipitant of acetone with precipitation amount of 4-5 times were included in the purification process, which would obtain the quality products. The content of total saponins could reach to 83.48%, and oleanolic acid to 38.30%. The optimized preparative technology is stable, convenient and practical. The extract rate of RPJ was high and steady with this technology, which provided new evidence for industrializing production of the plant and developing new drug.

Isolation and purification of RNA from tissues rich in polyphenols, polysaccharides, and pigments of annatto (Bixa orellana L.).

PubMed

Rodrigues, Simone M; Soares, Virgínia L F; de Oliveira, Tahise M; Gesteira, Abelmon S; Otoni, Wagner C; Costa, Marcio G C

2007-11-01

The tropical plant Bixa orellana L. (annatto) produces an array of natural products, including the pigment bixin used in the food and cosmetics industries. In order to understand the biochemical and molecular basis of the biosynthesis of these natural products, a reliable method for isolating high yields of high-quality RNA is required. Here we described a successful and reproducible method for isolation and purification of high-quantity and high-quality RNA from different tissues of annatto. This protocol overcomes the usual problems associated with large amounts of polyphenols, polysaccharides, pigments, and other secondary metabolites that are not easily removed by conventional extraction procedures. Furthermore, the proposed protocol can be easily carried out in any laboratory and it could also be extended to isolate RNA from other plant species showing similar abundance of compounds that interfere with RNA extractions. The yield and quality of the RNA were monitored by spectrophotometric analysis, separation on agarose gel, Reverse Transcription-Polymerase Chain Reaction (RT-PCR), and construction of a cDNA library.

Supercritical fluid extraction of peach (Prunus persica) almond oil: process yield and extract composition.

PubMed

Mezzomo, Natália; Mileo, Bruna R; Friedrich, Maria T; Martínez, Julian; Ferreira, Sandra R S

2010-07-01

Peach kernels are industrial residues from the peach processing, contain oil with important therapeutic properties and attractive nutritional aspects because of the high concentration of oleic and linoleic acids. The extraction method used to obtain natural compounds from raw matter is critical for product quality definition. Thus, the aim of this work was to compare peach almond extraction yields obtained by different procedures: soxhlet extractions (Sox) with different solvents; hydrodistillation (HD); ethanolic maceration (Mac) followed by fractionation with various solvents, and supercritical fluid extraction (SFE) at 30, 40 and 50 degrees C and at 100, 200 and 300bar, performed with pure CO(2) and with a co-solvent. The extracts were evaluated with respect to fatty acid composition (FAC), fractionated chemical profile (FCP) and total phenolic content (TPC). The Sox total yields were generally higher than those obtained by SFE. The crossover pressure for SFE was between 260 and 280bar. The FAC results show oleic and linoleic acids as main components, especially for Sox and SFE extracts. The FCP for samples obtained by Sox and Mac indicated the presence of benzaldehyde and benzyl alcohol, components responsible for almond flavor and with important industrial uses, whereas the SFE extracts present a high content of a possible flavonoid. The higher TPC values were obtained by Sox and Mac with ethanol. In general, the maximum pressure in SFE produced the highest yield, TPC and oleic acid content. The use of ethanol at 5% as co-solvent in SFE did not result in a significant effect on any evaluated parameter. The production of peach almond oil through all techniques is substantially adequate and SFE presented advantages, with respect to the quality of the extracts due to the high oleic acid content, as presented by some Sox samples. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

A comparison of sorptive extraction techniques coupled to a new quantitative, sensitive, high throughput GC-MS/MS method for methoxypyrazine analysis in wine.

PubMed

Hjelmeland, Anna K; Wylie, Philip L; Ebeler, Susan E

2016-02-01

Methoxypyrazines are volatile compounds found in plants, microbes, and insects that have potent vegetal and earthy aromas. With sensory detection thresholds in the low ng L(-1) range, modest concentrations of these compounds can profoundly impact the aroma quality of foods and beverages, and high levels can lead to consumer rejection. The wine industry routinely analyzes the most prevalent methoxypyrazine, 2-isobutyl-3-methoxypyrazine (IBMP), to aid in harvest decisions, since concentrations decrease during berry ripening. In addition to IBMP, three other methoxypyrazines IPMP (2-isopropyl-3-methoxypyrazine), SBMP (2-sec-butyl-3-methoxypyrazine), and EMP (2-ethyl-3-methoxypyrazine) have been identified in grapes and/or wine and can impact aroma quality. Despite their routine analysis in the wine industry (mostly IBMP), accurate methoxypyrazine quantitation is hindered by two major challenges: sensitivity and resolution. With extremely low sensory detection thresholds (~8-15 ng L(-1) in wine for IBMP), highly sensitive analytical methods to quantify methoxypyrazines at trace levels are necessary. Here we were able to achieve resolution of IBMP as well as IPMP, EMP, and SBMP from co-eluting compounds using one-dimensional chromatography coupled to positive chemical ionization tandem mass spectrometry. Three extraction techniques HS-SPME (headspace-solid phase microextraction), SBSE (stirbar sorptive extraction), and HSSE (headspace sorptive extraction) were validated and compared. A 30 min extraction time was used for HS-SPME and SBSE extraction techniques, while 120 min was necessary to achieve sufficient sensitivity for HSSE extractions. All extraction methods have limits of quantitation (LOQ) at or below 1 ng L(-1) for all four methoxypyrazines analyzed, i.e., LOQ's at or below reported sensory detection limits in wine. The method is high throughput, with resolution of all compounds possible with a relatively rapid 27 min GC oven program. Copyright © 2015 Elsevier B.V. All rights reserved.

DNA extraction from formalin-fixed, paraffin-embedded tissues: protein digestion as a limiting step for retrieval of high-quality DNA.

PubMed

Díaz-Cano, S J; Brady, S P

1997-12-01

Several DNA extraction methods have been used for formalin-fixed, paraffin-embedded tissues, with variable results being reported regarding the suitability of DNA obtained from such sources to serve as template in polymerase chain reaction (PCR)-based genetic analyses. We present a method routinely used for archival material in our laboratory that reliably yields DNA of sufficient quality for PCR studies. This method is based on extended proteinase K digestion (250 micrograms/ml in an EDTA-free calcium-containing buffer supplemented with mussel glycogen) followed by phenol-chloroform extraction. Agarose gel electrophoresis of both digestion buffer aliquots and PCR amplification of the beta-globin gene tested the suitability of the retrieved DNA for PCR amplification.

Preparation of RNA from bacteria infected with bacteriophages: a case study from the marine unicellular Synechococcus sp. WH7803 infected by phage S-PM2.

PubMed

Shan, Jinyu; Clokie, Martha

2009-01-01

Bacteriophages manipulate bacterial gene expression in order to express their own genes or influence bacterial metabolism. Gene expression can be studied using real-time PCR or microarrays. Either technique requires the prior isolation of high quality RNA uncontaminated by the presence of genomic DNA. We outline the considerations necessary when working with bacteriophage infected bacterial cells. We also give an example of a protocol for extraction and quantification of high quality RNA from infected bacterial cells, using the marine cyanobacterium WH7803 and the phage S-PM2 as a case study. This protocol can be modified to extract RNA from the host/bacteriophage of interest.

A rapid and efficient SDS-based RNA isolation protocol from different tissues of coffee.

PubMed

Huded, Arun Kumar C; Jingade, Pavankumar; Mishra, Manoj Kumar

2018-03-01

Isolation of high-quality RNA from coffee is challenging because of high level of polysaccharides, polyphenols and other secondary metabolites. In the present study, a rapid and efficient RNA extraction protocol from different tissues of coffee was optimized. Sufficiently high quality and quantity (225.6-454.8 µg/g) of RNA was obtained by using the optimized protocol. The presence of two distinct bands of 28S rRNA and 18S rRNA in agarose gel proved the intactness of the RNA samples. The average spectrophotometric values of the isolated RNA ranged from 1.96 to 2.02 ( A 260/280 ) and 1.95 to 2.14 ( A 260/230 ), indicating the high quality of RNA devoid of polyphenols, polysaccharides and protein contamination. In the optimized protocol, addition of PVPP to the extraction buffer and a brief incubation of samples at 65 °C and subsequent purification with potassium acetate resulted in good-quality RNA isolation. The suitability of RNA for downstream processing was confirmed by PCR amplification with cytochrome c oxidase gene-specific primers. The amplification of a single 392 bp fragment using cDNA and 1.5 kb fragment using genomic DNA samples confirmed the absence of DNA contamination. The present protocol is rapid and yielded good quality and quantity of RNA suitable for functional genomics studies.

DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms.

PubMed

Panova, Marina; Aronsson, Henrik; Cameron, R Andrew; Dahl, Peter; Godhe, Anna; Lind, Ulrika; Ortega-Martinez, Olga; Pereyra, Ricardo; Tesson, Sylvie V M; Wrange, Anna-Lisa; Blomberg, Anders; Johannesson, Kerstin

2016-01-01

The marine environment harbors a large proportion of the total biodiversity on this planet, including the majority of the earths' different phyla and classes. Studying the genomes of marine organisms can bring interesting insights into genome evolution. Today, almost all marine organismal groups are understudied with respect to their genomes. One potential reason is that extraction of high-quality DNA in sufficient amounts is challenging for many marine species. This is due to high polysaccharide content, polyphenols and other secondary metabolites that will inhibit downstream DNA library preparations. Consequently, protocols developed for vertebrates and plants do not always perform well for invertebrates and algae. In addition, many marine species have large population sizes and, as a consequence, highly variable genomes. Thus, to facilitate the sequence read assembly process during genome sequencing, it is desirable to obtain enough DNA from a single individual, which is a challenge in many species of invertebrates and algae. Here, we present DNA extraction protocols for seven marine species (four invertebrates, two algae, and a marine yeast), optimized to provide sufficient DNA quality and yield for de novo genome sequencing projects.

Image segmentation-based robust feature extraction for color image watermarking

NASA Astrophysics Data System (ADS)

Li, Mianjie; Deng, Zeyu; Yuan, Xiaochen

2018-04-01

This paper proposes a local digital image watermarking method based on Robust Feature Extraction. The segmentation is achieved by Simple Linear Iterative Clustering (SLIC) based on which an Image Segmentation-based Robust Feature Extraction (ISRFE) method is proposed for feature extraction. Our method can adaptively extract feature regions from the blocks segmented by SLIC. This novel method can extract the most robust feature region in every segmented image. Each feature region is decomposed into low-frequency domain and high-frequency domain by Discrete Cosine Transform (DCT). Watermark images are then embedded into the coefficients in the low-frequency domain. The Distortion-Compensated Dither Modulation (DC-DM) algorithm is chosen as the quantization method for embedding. The experimental results indicate that the method has good performance under various attacks. Furthermore, the proposed method can obtain a trade-off between high robustness and good image quality.

Fatty acids from high rate algal pond's microalgal biomass and osmotic stress effects.

PubMed

Drira, Neila; Dhouibi, Nedra; Hammami, Saoussen; Piras, Alessandra; Rosa, Antonella; Porcedda, Silvia; Dhaouadi, Hatem

2017-11-01

The extraction of oil from a wild microalgae biomass collected from a domestic wastewater treatment facility's high rate algal pond (HRAP) was investigated. An experiment plan was used to determine the most efficient extraction method, the optimal temperature, time and solvent system based on total lipids yield. Microwave-assisted extraction was the most efficient method whether in n-hexane or in a mixture of chloroform/methanol compared to Soxhlet, homogenization, and ultrasounds assisted extractions. This same wild biomass was cultivated in a photobioreactor (PBR) and the effect of osmotic stress was studied. The lipids extraction yield after 3days of stress increased by more than four folds without any significant loss of biomass, however, the quality of extracted total lipids in terms of saturated, monounsaturated and polyunsaturated fatty acids was not affected by salinity change in the culture medium. Copyright © 2017 Elsevier Ltd. All rights reserved.

A simple protocol for protein extraction of recalcitrant fruit tissues suitable for 2-DE and MS analysis.

PubMed

Song, Jun; Braun, Gordon; Bevis, Eric; Doncaster, Kristen

2006-08-01

Fruit tissues are considered recalcitrant plant tissue for proteomic analysis. Three phenol-free protein extraction procedures for 2-DE were compared and evaluated on apple fruit proteins. Incorporation of hot SDS buffer, extraction with TCA/acetone precipitation was found to be the most effective protocol. The results from SDS-PAGE and 2-DE analysis showed high quality proteins. More than 500 apple polypeptides were separated on a small scale 2-DE gel. The successful protocol was further tested on banana fruit, in which 504 and 386 proteins were detected in peel and flesh tissues, respectively. To demonstrate the quality of the extracted proteins, several protein spots from apple and banana peels were cut from 2-DE gels, analyzed by MS and have been tentatively identified. The protocol described in this study is a simple procedure which could be routinely used in proteomic studies of many types of recalcitrant fruit tissues.

RNA extraction from various recalcitrant plant tissues with a cethyltrimethylammonium bromide-containing buffer followed by an acid guanidium thiocyanate-phenol-chloroform treatment.

PubMed

Suzuki, Yuji; Mae, Tadahiko; Makino, Amane

2008-07-01

High-quality total RNA was extracted using a cethyltrimethylammonium bromide-containing buffer followed by an acid guanidium thiocyanate-phenol-chloroform treatment from recalcitrant plant tissues such as tree leaves (pine, Norway spruce, ginkgo, Japanese cedar, rose), flowers (rose, Lotus japonicus) and storage tissues (seeds of Lotus japonicus and rice, sweet potato tuber, banana fruit). This protocol greatly reduced the time required for RNA extraction.

Efficient isolation method for high-quality genomic DNA from cicada exuviae.

PubMed

Nguyen, Hoa Quynh; Kim, Ye Inn; Borzée, Amaël; Jang, Yikweon

2017-10-01

In recent years, animal ethics issues have led researchers to explore nondestructive methods to access materials for genetic studies. Cicada exuviae are among those materials because they are cast skins that individuals left after molt and are easily collected. In this study, we aim to identify the most efficient extraction method to obtain high quantity and quality of DNA from cicada exuviae. We compared relative DNA yield and purity of six extraction protocols, including both manual protocols and available commercial kits, extracting from four different exoskeleton parts. Furthermore, amplification and sequencing of genomic DNA were evaluated in terms of availability of sequencing sequence at the expected genomic size. Both the choice of protocol and exuvia part significantly affected DNA yield and purity. Only samples that were extracted using the PowerSoil DNA Isolation kit generated gel bands of expected size as well as successful sequencing results. The failed attempts to extract DNA using other protocols could be partially explained by a low DNA yield from cicada exuviae and partly by contamination with humic acids that exist in the soil where cicada nymphs reside before emergence, as shown by spectroscopic measurements. Genomic DNA extracted from cicada exuviae could provide valuable information for species identification, allowing the investigation of genetic diversity across consecutive broods, or spatiotemporal variation among various populations. Consequently, we hope to provide a simple method to acquire pure genomic DNA applicable for multiple research purposes.

Hard clam extracts induce atypical apoptosis in human gastric cancer cells

PubMed Central

Song, Eing-Ju; Chan, Michael W.Y.; Shin, Jyh-Wei; Chen, Che-Chun

2017-01-01

Hard clams (HCs) are a nutritionally high-quality and popular seafood, and are established to be a potent antitumor food. The aim of the present study was to determine whether HC extracts induce apoptosis in the human gastric cancer cell line, AGS. In contrast with previously reported methods of extraction, crude extracts of HC were obtained by freezing and thawing and by a method free of hot water or organic solvents. The composition, quality and properties of the HC extracts were demonstrated to be stable since the extracts that were evaluated by capillary electrophoresis and HPLC analysis at different timepoints were similar. HC extracts also have an inhibitory effect against the survival of AGS cells. Treatment with HC extracts induced a marked sub-G1 DNA peak and reduced the expression of the anti-apoptotic genes BIRC5 and KPNA2. However, hallmarks of classical apoptosis such as DNA fragmentation and apoptotic body formation were not observed, indicating atypical apoptosis. Furthermore, it was revealed that HC extracts interrupted cell cycle progression in AGS cells through altered expression of six cell cycle-associated genes: CDC20, KPNA2, BIRC5, ANAPC2, CDKN1A and RB1. The present findings suggest that HC may contribute to a novel future anticancer agent. PMID:28810604

Enhancing Food Processing by Pulsed and High Voltage Electric Fields: Principles and Applications.

PubMed

Wang, Qijun; Li, Yifei; Sun, Da-Wen; Zhu, Zhiwei

2018-02-02

Improvements in living standards result in a growing demand for food with high quality attributes including freshness, nutrition and safety. However, current industrial processing methods rely on traditional thermal and chemical methods, such as sterilization and solvent extraction, which could induce negative effects on food quality and safety. The electric fields (EFs) involving pulsed electric fields (PEFs) and high voltage electric fields (HVEFs) have been studied and developed for assisting and enhancing various food processes. In this review, the principles and applications of pulsed and high voltage electric fields are described in details for a range of food processes, including microbial inactivation, component extraction, and winemaking, thawing and drying, freezing and enzymatic inactivation. Moreover, the advantages and limitations of electric field related technologies are discussed to foresee future developments in the food industry. This review demonstrates that electric field technology has a great potential to enhance food processing by supplementing or replacing the conventional methods employed in different food manufacturing processes. Successful industrial applications of electric field treatments have been achieved in some areas such as microbial inactivation and extraction. However, investigations of HVEFs are still in an early stage and translating the technology into industrial applications need further research efforts.

Enhancement of Lipid Extraction from Marine Microalga, Scenedesmus Associated with High-Pressure Homogenization Process

PubMed Central

Cho, Seok-Cheol; Choi, Woon-Yong; Oh, Sung-Ho; Lee, Choon-Geun; Seo, Yong-Chang; Kim, Ji-Seon; Song, Chi-Ho; Kim, Ga-Vin; Lee, Shin-Young; Kang, Do-Hyung; Lee, Hyeon-Yong

2012-01-01

Marine microalga, Scenedesmus sp., which is known to be suitable for biodiesel production because of its high lipid content, was subjected to the conventional Folch method of lipid extraction combined with high-pressure homogenization pretreatment process at 1200 psi and 35°C. Algal lipid yield was about 24.9% through this process, whereas only 19.8% lipid can be obtained by following a conventional lipid extraction procedure using the solvent, chloroform : methanol (2 : 1, v/v). Present approach requires 30 min process time and a moderate working temperature of 35°C as compared to the conventional extraction method which usually requires >5 hrs and 65°C temperature. It was found that this combined extraction process followed second-order reaction kinetics, which means most of the cellular lipids were extracted during initial periods of extraction, mostly within 30 min. In contrast, during the conventional extraction process, the cellular lipids were slowly and continuously extracted for >5 hrs by following first-order kinetics. Confocal and scanning electron microscopy revealed altered texture of algal biomass pretreated with high-pressure homogenization. These results clearly demonstrate that the Folch method coupled with high-pressure homogenization pretreatment can easily destruct the rigid cell walls of microalgae and release the intact lipids, with minimized extraction time and temperature, both of which are essential for maintaining good quality of the lipids for biodiesel production. PMID:22969270

Assessment of visual landscape quality using IKONOS imagery.

PubMed

Ozkan, Ulas Yunus

2014-07-01

The assessment of visual landscape quality is of importance to the management of urban woodlands. Satellite remote sensing may be used for this purpose as a substitute for traditional survey techniques that are both labour-intensive and time-consuming. This study examines the association between the quality of the perceived visual landscape in urban woodlands and texture measures extracted from IKONOS satellite data, which features 4-m spatial resolution and four spectral bands. The study was conducted in the woodlands of Istanbul (the most important element of urban mosaic) lying along both shores of the Bosporus Strait. The visual quality assessment applied in this study is based on the perceptual approach and was performed via a survey of expressed preferences. For this purpose, representative photographs of real scenery were used to elicit observers' preferences. A slide show comprising 33 images was presented to a group of 153 volunteers (all undergraduate students), and they were asked to rate the visual quality of each on a 10-point scale (1 for very low visual quality, 10 for very high). Average visual quality scores were calculated for landscape. Texture measures were acquired using the two methods: pixel-based and object-based. Pixel-based texture measures were extracted from the first principle component (PC1) image. Object-based texture measures were extracted by using the original four bands. The association between image texture measures and perceived visual landscape quality was tested via Pearson's correlation coefficient. The analysis found a strong linear association between image texture measures and visual quality. The highest correlation coefficient was calculated between standard deviation of gray levels (SDGL) (one of the pixel-based texture measures) and visual quality (r = 0.82, P < 0.05). The results showed that perceived visual quality of urban woodland landscapes can be estimated by using texture measures extracted from satellite data in combination with appropriate modelling techniques.

Simultaneous production of bio-ethanol and bleached pulp from red algae.

PubMed

Yoon, Min Ho; Lee, Yoon Woo; Lee, Chun Han; Seo, Yung Bum

2012-12-01

The red algae, Gelidium corneum, was used to produce bleached pulp for papermaking and ethanol. Aqueous extracts obtained at 100-140 °C were subjected to saccharification, purification, fermentation, and distillation to produce ethanol. The solid remnants were bleached with chlorine dioxide and peroxide to make pulp. In the extraction process, sulfuric acid and sodium thiosulfate were added to increase the extract yield and to improve de-polymerization of the extracts, as well as to generate high-quality pulp. An extraction process incorporating 5% sodium thiosulfate by dry weight of the algae provided optimal production conditions for the production of both strong pulp and a high ethanol yield. These results suggest that it might be possible to utilize algae instead of trees and starch for pulp and ethanol production, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

Robotic solid phase extraction and high performance liquid chromatographic analysis of ranitidine in serum or plasma.

PubMed

Lloyd, T L; Perschy, T B; Gooding, A E; Tomlinson, J J

1992-01-01

A fully automated assay for the analysis of ranitidine in serum and plasma, with and without an internal standard, was validated. It utilizes robotic solid phase extraction with on-line high performance liquid chromatographic (HPLC) analysis. The ruggedness of the assay was demonstrated over a three-year period. A Zymark Py Technology II robotic system was used for serial processing from initial aspiration of samples from original collection containers, to final direct injection onto the on-line HPLC system. Automated serial processing with on-line analysis provided uniform sample history and increased productivity by freeing the chemist to analyse data and perform other tasks. The solid phase extraction efficiency was 94% throughout the assay range of 10-250 ng/mL. The coefficients of variation for within- and between-day quality control samples ranged from 1 to 6% and 1 to 5%, respectively. Mean accuracy for between-day standards and quality control results ranged from 97 to 102% of the respective theoretical concentrations.

Composition and protein quality of Lupinus mutabilis.

PubMed

Schoeneberger, H; Gross, R; Cremer, H D; Elmadfa, I

1982-01-01

The chemical composition and the protein quality of three samples of Lupinus mutabilis (a raw, semi-sweet variety; cooked, water-extracted seeds; and alcohol-extracted oil cake) were studied. The protein content varied from 47.7% dry weight (raw seeds) to 65.3% (oil-cake). Compared to the FAO reference pattern sulfur- containing amino acids are first limiting. The water-extracted sample contained 26.9% oil and the polyunsaturated/saturated fatty acid ratio of 30 seed samples was 5.3. Alkaloid content of raw seed was high (3.3%), but could be reduced or nearly eliminated by water-and-alcohol extraction or plant breeding. Other anti-nutritive substances were present only in trace quantities. Protein quality measured as protein efficiency ratio (PER) gave low values for the non-supplemented lupin proteins (1.34 semi-sweet variety; 1.53 water-extracted seeds; 1.19 oil-cake; 3.09 casein), but the PER's were improved by the addition of 0.2% DL-methionine to the diets (3.05, 2.69, 2,81, respectively). Raw as well as processed lupin protein showed an excellent apparent digestibility (80.0-85.8%, casein 87.1%). Studies of net protein utilization (NPU) and biological value (BV) confirmed the importance of methionine supplementation, The true digestibility of 92% was equivalent to that of casein.

Selection of process parameters for producing high quality defatted sesame flour at pilot scale.

PubMed

Manikantan, M R; Sharma, Rajiv; Yadav, D N; Gupta, R K

2015-03-01

The present work was undertaken to study the effect of pearling duration, soaking time, steaming duration and drying temperature on the quality of sesame seeds and mechanically extracted partially defatted sesame cake. On the basis of quality attributes i.e. high protein, low crude fibre, low residual oil and low oxalic acid, the optimum process parameters were selected. The combination of 20 min of pearling duration, 15 min of soaking, 15 min of steaming at 100 kPa pressure and drying at 50 °C yielded high quality partially defatted protein rich sesame flour as compared to untreated defatted sesame flour. The developed high quality partially defatted protein rich sesame flour may be used in various food applications as a vital ingredient to increase the nutritional significance of the prepared foodstuffs.

In vitro antioxidant and in vivo photoprotective effect of pistachio (Pistacia vera L., variety Bronte) seed and skin extracts.

PubMed

Martorana, Maria; Arcoraci, Teresita; Rizza, Luisa; Cristani, Mariateresa; Bonina, Francesco Paolo; Saija, Antonina; Trombetta, Domenico; Tomaino, Antonio

2013-03-01

Pistachio (Pistacia vera L.) nuts are a rich source of phenolic compounds, known for their high antioxidant activity, and contained not only in the seeds but also in the skin. A pistachio cultivar of high quality is typical of Bronte, Sicily, Italy. The purpose of our study was to investigate the chemical composition and antioxidant properties of two polyphenol-rich extracts from skins (TP) and decorticated seeds (SP) of Bronte pistachios, and to verify the potential use of these extracts for topical photoprotective products. Chemical analysis showed that the TP and SP extracts contain high levels of phenolic compounds, but the TP extract is about ten times richer in phenols than the SP extract, being anthocyanins the most abundant compounds found in the TP extract. Both these extracts, and especially the TP extract, possess good radical scavenger/antioxidant properties, as shown in a series of in vitro assays carried out using homogenous and non-homogenous chemical environment. Furthermore both the TP extract and, although at a lower degree, the SP extract reduce, when topically applied, UV-B-induced skin erythema in human volunteers. These findings suggest that extracts from Bronte TP and SP could be successfully employed as photoprotective ingredients in topical cosmetic and pharmaceutical formulations. Copyright © 2013 Elsevier B.V. All rights reserved.

Isolation of high quality and polysaccharide-free DNA from leaves of Dimorphandra mollis (Leguminosae), a tree from the Brazilian Cerrado.

PubMed

Souza, H A V; Muller, L A C; Brandão, R L; Lovato, M B

2012-03-22

Dimorphandra mollis (Leguminosae), known as faveiro and fava d'anta, is a tree that is widely distributed throughout the Brazilian Cerrado (a savanna-like biome). This species is economically valuable and has been extensively exploited because its fruits contain the flavonoid rutin, which is used to produce medications for human circulatory diseases. Knowledge about its genetic diversity is needed to guide decisions about the conservation and rational use of this species in order to maintain its diversity. DNA extraction is an essential step for obtaining good results in a molecular analysis. However, DNA isolation from plants is usually compromised by excessive contamination by secondary metabolites. DNA extraction of D. mollis, mainly from mature leaves, results in a highly viscous mass that is difficult to handle and use in techniques that require pure DNA. We tested four protocols for plant DNA extraction that can be used to minimize problems such as contamination by polysaccharides, which is more pronounced in material from mature leaves. The protocol that produced the best DNA quality initially utilizes a sorbitol buffer to remove mucilaginous polysaccharides. The macerated leaf material is washed with this buffer until there is no visible mucilage in the sample. This protocol is adequate for DNA extraction both from young and mature leaves, and could be useful not only for D. mollis but also for other species that have high levels of polysaccharide contamination during the extraction process.

A two-step electrodialysis method for DNA purification from polluted metallic environmental samples.

PubMed

Rodríguez-Mejía, José Luis; Martínez-Anaya, Claudia; Folch-Mallol, Jorge Luis; Dantán-González, Edgar

2008-08-01

Extracting DNA from samples of polluted environments using standard methods often results in low yields of poor-quality material unsuited to subsequent manipulation and analysis by molecular biological techniques. Here, we report a novel two-step electrodialysis-based method for the extraction of DNA from environmental samples. This technique permits the rapid and efficient isolation of high-quality DNA based on its acidic nature, and without the requirement for phenol-chloroform-isoamyl alcohol cleanup and ethanol precipitation steps. Subsequent PCR, endonuclease restriction, and cloning reactions were successfully performed utilizing DNA obtained by electrodialysis, whereas some or all of these techniques failed using DNA extracted with two alternative methods. We also show that his technique is applicable to purify DNA from a range of polluted and nonpolluted samples.

Microstructure, microbial profile and quality characteristics of high-pressure-treated chicken nuggets.

PubMed

Devatkal, Suresh; Anurag, Rahul; Jaganath, Bindu; Rao, Srinivasa

2015-10-01

High-pressure processing (300 MPa for 5 min) as a non-thermal post-processing intervention was employed to improve the shelf life and qualities of cooked refrigerated chicken nuggets. Pomegranate peel extract (1%) was also used as a source of natural antioxidant and antimicrobial in chicken nuggets. Microstructure, microbial profile, instrumental colour, texture profile and lipid oxidation were evaluated. High-pressure treatment and pomegranate peel extract did not influence significantly the colour and textural properties of cooked chicken nuggets. Thiobarbituric acid reactive substance values significantly (p < 0.05) increased in pressure-treated nuggets. Microstructural studies revealed shrinkage in the structure and loosening of the dense network of meat emulsion due to high-pressure treatment. Pressure treatment resulted in a reduction of 2-3.0 log10 cfu/g in total plate count and Enterobacteriaceae count. Molecular characterization studies revealed that Enterobacter amnigenus and Enterobacter sp. in control and Bacillus licheniformis, Enterococcus gallinarum and Acinetobacter baumannii in high-pressure-treated chicken nuggets were the major spoilage bacteria. © The Author(s) 2014.

Comparative mass spectrometry & nuclear magnetic resonance metabolomic approaches for nutraceuticals quality control analysis: a brief review.

PubMed

Farag, Mohamed A

2014-01-01

The number of botanical dietary supplements in the market has recently increased primarily due to increased health awareness. Standardization and quality control of the constituents of these plant extracts is an important topic, particularly when such ingredients are used long term as dietary supplements, or in cases where higher doses are marketed as drugs. The development of fast, comprehensive, and effective untargeted analytical methods for plant extracts is of high interest. Nuclear magnetic resonance spectroscopy and mass spectrometry are the most informative tools, each of which enables high-throughput and global analysis of hundreds of metabolites in a single step. Although only one of the two techniques is utilized in the majority of plant metabolomics applications, there is a growing interest in combining the data from both platforms to effectively unravel the complexity of plant samples. The application of combined MS and NMR in the quality control of nutraceuticals forms the major part of this review. Finally I will look at the future developments and perspectives of these two technologies for the quality control of herbal materials.

Comparative evaluation of total RNA extraction methods in Theobroma cacao using shoot apical meristems.

PubMed

Silva, D V; Branco, S M J; Holanda, I S A; Royaert, S; Motamayor, J C; Marelli, J P; Corrêa, R X

2016-03-04

Theobroma cacao is a species of great economic importance with its beans used for chocolate production. The tree has been a target of various molecular studies. It contains many polyphenols, which complicate the extraction of nucleic acids with the extraction protocols requiring a large amount of plant material. These issues, therefore, necessitate the optimization of the protocols. The aim of the present study was to evaluate different methods for extraction of total RNA from shoot apical meristems of T. cacao 'CCN 51' and to assess the influence of storage conditions for the meristems on the extraction. The study also aimed to identify the most efficient protocol for RNA extraction using a small amount of plant material. Four different protocols were evaluated for RNA extraction using one shoot apical meristem per sample. Among these protocols, one that was more efficient was then tested to extract RNA using four different numbers of shoot apical meristems, subjected to three different storage conditions. The best protocol was tested for cDNA amplification using reverse transcription-polymerase chain reaction; the cDNA quality was determined to be satisfactory for molecular analyses. The study revealed that with the best RNA extraction protocol, one shoot apical meristem was sufficient for extraction of high-quality total RNA. The results obtained might enable advances in genetic analyses and molecular studies using reduced amount of plant material.

Optimization of Supercritical Carbon Dioxide Extraction of Eucommia ulmoides Seed Oil and Quality Evaluation of the Oil.

PubMed

Zhang, Zhen-Shan; Liu, Yu-Lan; Che, Li-Ming

2018-03-01

Supercritical carbon dioxide extraction (SC-CO 2 ) technology was used to extract oil from Eucommia ulmoides seed. The optimum conditions and significant parameters in SC-CO 2 were obtained using response surface methodology (RSM). The qualities of the extracted oil were evaluated by physicochemical properties, fatty acid composition, vitamin E composition. It was found that the optimum extraction parameters were at pressure of 37 MPa, temperature of 40°C, extraction time of 125 min and CO 2 flow rate of 2.6 SL/min. Pressure, temperature and time were identified as significant parameter effecting on extraction yield. The importance of evaluated parameters decreased in the order of pressure > extraction time > temperature > CO 2 flow rate. GC analysis indicated that E. ulmoides seed oil contained about 61% of linolenic acid and its fatty acid composition was similar with that of flaxseed oil and perilla oil. The content and composition of vitamin E was determined using HPLC. The E. ulmoides seed oil was rich in vitamin E (190.72 mg/100 g), the predominant vitamin E isomers were γ- tocopherol and δ- tocopherol, which accounted for 70.87% and 24.81% of the total vitamin E, respectively. The high yield and good physicochemical properties of extracted oil support the notion that SC-CO 2 technology is an effective technique for extracting oil from E. ulmoides seed.

Thermomyces lanuginosus STm: a source of thermostable hydrolytic enzymes for novel application in extraction of high-quality natural rubber from Taraxacum kok-saghyz (rubber dandelion)

USDA-ARS?s Scientific Manuscript database

Hydrolytic enzymes from a newly isolated strain of the thermophilic fungus Thermomyces lanuginosus were used to extract rubber from Taraxacum kok-saghyz commonly known as rubber (or Russian or Kazak(h)) dandelion. The fungus was isolated from garden soil and identified as Thermomyces lanuginosus STm...

Optimized manual and automated recovery of amplifiable DNA from tissues preserved in buffered formalin and alcohol-based fixative.

PubMed

Duval, Kristin; Aubin, Rémy A; Elliott, James; Gorn-Hondermann, Ivan; Birnboim, H Chaim; Jonker, Derek; Fourney, Ron M; Frégeau, Chantal J

2010-02-01

Archival tissue preserved in fixative constitutes an invaluable resource for histological examination, molecular diagnostic procedures and for DNA typing analysis in forensic investigations. However, available material is often limited in size and quantity. Moreover, recovery of DNA is often severely compromised by the presence of covalent DNA-protein cross-links generated by formalin, the most prevalent fixative. We describe the evaluation of buffer formulations, sample lysis regimens and DNA recovery strategies and define optimized manual and automated procedures for the extraction of high quality DNA suitable for molecular diagnostics and genotyping. Using a 3-step enzymatic digestion protocol carried out in the absence of dithiothreitol, we demonstrate that DNA can be efficiently released from cells or tissues preserved in buffered formalin or the alcohol-based fixative GenoFix. This preparatory procedure can then be integrated to traditional phenol/chloroform extraction, a modified manual DNA IQ or automated DNA IQ/Te-Shake-based extraction in order to recover DNA for downstream applications. Quantitative recovery of high quality DNA was best achieved from specimens archived in GenoFix and extracted using magnetic bead capture.

Quality and stability of edible oils enriched with hydrophilic antioxidants from the olive tree: the role of enrichment extracts and lipid composition.

PubMed

Sánchez de Medina, Verónica; Priego-Capote, Feliciano; Jiménez-Ot, Carlos; Luque de Castro, María Dolores

2011-11-09

Phenolic extracts from olive tree leaves and olive pomace were used to enrich refined oils (namely, maize, soy, high-oleic sunflower, sunflower, olive, and rapeseed oils) at two concentration levels (200 and 400 μg/mL, expressed as gallic acid). The concentration of characteristic olive phenols in these extracts together with the lipidic composition of the oils to be enriched influenced the mass transfer of the target antioxidants, which conferred additional stability and quality parameters to the oils as a result. In general, all of the oils experienced either a noticeable or dramatic improvement of their quality-stability parameters (e.g., peroxide index and Rancimat) as compared with their nonenriched counterparts. The enriched oils were also compared with extra virgin olive oil with a natural content in phenols of 400 μg/mL. The healthy properties of these phenols and the scarce or nil prices of the raw materials used can convert oils in supplemented foods or even nutraceuticals.

Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method

PubMed Central

Elekwachi, Chijioke O.; Wang, Zuo; Wu, Xiaofeng; Rabee, Alaa; Forster, Robert J.

2017-01-01

Advances in high throughput, next generation sequencing technologies have allowed an in-depth examination of biological environments and phenomena, and are particularly useful for culture-independent microbial community studies. Recently the use of RNA for metatranscriptomic studies has been used to elucidate the role of active microbes in the environment. Extraction of RNA of appropriate quality is critical in these experiments and TRIzol reagent is often used for maintaining stability of RNA molecules during extraction. However, for studies using rumen content there is no consensus on (1) the amount of rumen digesta to use or (2) the amount of TRIzol reagent to be used in RNA extraction procedures. This study evaluated the effect of using various quantities of ground rumen digesta and of TRIzol reagent on the yield and quality of extracted RNA. It also investigated the possibility of using lower masses of solid-phase rumen digesta and lower amounts of TRIzol reagent than is used currently, for extraction of RNA for metatranscriptomic studies. We found that high quality RNA could be isolated from 2 g of ground rumen digesta sample, whilst using 0.6 g of ground matter for RNA extraction and using 3 mL (a 5:1 TRIzol : extraction mass ratio) of TRIzol reagent. This represents a significant savings in the cost of RNA isolation. These lower masses and volumes were then applied in the RNA-Seq analysis of solid-phase rumen samples obtained from 6 Angus X Hereford beef heifers which had been fed a high forage diet (comprised of barley straw in a forage-to-concentrate ratio of 70:30) for 102 days. A bioinformatics analysis pipeline was developed in-house that generated relative abundance values of archaea, protozoa, fungi and bacteria in the rumen and also allowed the extraction of individual rRNA variable regions that could be analyzed in downstream molecular ecology programs. The average relative abundances of rRNA transcripts of archaea, bacteria, protozoa and fungi in our samples were 1.4 ± 0.06, 44.16 ± 1.55, 35.38 ± 1.64, and 16.37 ± 0.65% respectively. This represents the first study to define the relative active contributions of these populations to the rumen ecosystem and is especially important in defining the role of the anaerobic fungi and protozoa. PMID:28983291

Total rRNA-Seq Analysis Gives Insight into Bacterial, Fungal, Protozoal and Archaeal Communities in the Rumen Using an Optimized RNA Isolation Method.

PubMed

Elekwachi, Chijioke O; Wang, Zuo; Wu, Xiaofeng; Rabee, Alaa; Forster, Robert J

2017-01-01

Advances in high throughput, next generation sequencing technologies have allowed an in-depth examination of biological environments and phenomena, and are particularly useful for culture-independent microbial community studies. Recently the use of RNA for metatranscriptomic studies has been used to elucidate the role of active microbes in the environment. Extraction of RNA of appropriate quality is critical in these experiments and TRIzol reagent is often used for maintaining stability of RNA molecules during extraction. However, for studies using rumen content there is no consensus on (1) the amount of rumen digesta to use or (2) the amount of TRIzol reagent to be used in RNA extraction procedures. This study evaluated the effect of using various quantities of ground rumen digesta and of TRIzol reagent on the yield and quality of extracted RNA. It also investigated the possibility of using lower masses of solid-phase rumen digesta and lower amounts of TRIzol reagent than is used currently, for extraction of RNA for metatranscriptomic studies. We found that high quality RNA could be isolated from 2 g of ground rumen digesta sample, whilst using 0.6 g of ground matter for RNA extraction and using 3 mL (a 5:1 TRIzol : extraction mass ratio) of TRIzol reagent. This represents a significant savings in the cost of RNA isolation. These lower masses and volumes were then applied in the RNA-Seq analysis of solid-phase rumen samples obtained from 6 Angus X Hereford beef heifers which had been fed a high forage diet (comprised of barley straw in a forage-to-concentrate ratio of 70:30) for 102 days. A bioinformatics analysis pipeline was developed in-house that generated relative abundance values of archaea, protozoa, fungi and bacteria in the rumen and also allowed the extraction of individual rRNA variable regions that could be analyzed in downstream molecular ecology programs. The average relative abundances of rRNA transcripts of archaea, bacteria, protozoa and fungi in our samples were 1.4 ± 0.06, 44.16 ± 1.55, 35.38 ± 1.64, and 16.37 ± 0.65% respectively. This represents the first study to define the relative active contributions of these populations to the rumen ecosystem and is especially important in defining the role of the anaerobic fungi and protozoa.

High-quality RNA extraction from the sea urchin Paracentrotus lividus embryos

PubMed Central

Ruocco, Nadia; Costantini, Susan; Zupo, Valerio; Romano, Giovanna; Ianora, Adrianna; Fontana, Angelo; Costantini, Maria

2017-01-01

The sea urchin Paracentrotus lividus (Lamarck, 1816) is a keystone herbivore in the Mediterranean Sea due to its ability to transform macroalgal-dominated communities into barren areas characterized by increased cover of bare substrates and encrusting coralline algae, reduced biodiversity and altered ecosystem functions. P. lividus is also an excellent animal model for toxicology, physiology and biology investigations having been used for more than a century as a model for embryological studies with synchronously developing embryos which are easy to manipulate and analyze for morphological aberrations. Despite its importance for the scientific community, the complete genome is still not fully annotated. To date, only a few molecular tools are available and a few Next Generation Sequencing (NGS) studies have been performed. Here we aimed at setting-up an RNA extraction method to obtain high quality and sufficient quantity of RNA for NGS from P. lividus embryos at the pluteus stage. We compared five different RNA extraction protocols from four different pools of plutei (500, 1000, 2500 and 5000 embryos): TRIzol®, and four widely-used Silica Membrane kits, GenElute™ Mammalian Total RNA Miniprep Kit, RNAqueous® Micro Kit, RNeasy® Micro Kit and Aurum™ Total RNA Mini Kit. The quantity of RNA isolated was evaluated using NanoDrop. The quality, considering the purity, was measured as A260/A280 and A260/230 ratios. The integrity was measured by RNA Integrity Number (RIN). Our results demonstrated that the most efficient procedures were GenElute, RNeasy and Aurum, producing a sufficient quantity of RNA for NGS. The Bioanalyzer profiles and RIN values revealed that the most efficient methods guaranteeing for RNA integrity were RNeasy and Aurum combined with an initial preservation in RNAlater. This research represents the first attempt to standardize a method for high-quality RNA extraction from sea urchin embryos at the pluteus stage, providing a new resource for this established model marine organism. PMID:28199408

Argumentation Based Joint Learning: A Novel Ensemble Learning Approach

PubMed Central

Xu, Junyi; Yao, Li; Li, Le

2015-01-01

Recently, ensemble learning methods have been widely used to improve classification performance in machine learning. In this paper, we present a novel ensemble learning method: argumentation based multi-agent joint learning (AMAJL), which integrates ideas from multi-agent argumentation, ensemble learning, and association rule mining. In AMAJL, argumentation technology is introduced as an ensemble strategy to integrate multiple base classifiers and generate a high performance ensemble classifier. We design an argumentation framework named Arena as a communication platform for knowledge integration. Through argumentation based joint learning, high quality individual knowledge can be extracted, and thus a refined global knowledge base can be generated and used independently for classification. We perform numerous experiments on multiple public datasets using AMAJL and other benchmark methods. The results demonstrate that our method can effectively extract high quality knowledge for ensemble classifier and improve the performance of classification. PMID:25966359

Optimization of simultaneous ultrasonic-assisted extraction of water-soluble and fat-soluble characteristic constituents from Forsythiae Fructus Using response surface methodology and high-performance liquid chromatography.

PubMed

Xia, Yong-Gang; Yang, Bing-You; Liang, Jun; Wang, Di; Yang, Qi; Kuang, Hai-Xue

2014-07-01

The compounds (+)-pinoresinol-β-glucoside (1) forsythiaside, (2) phillyrin (3) and phillygenin (4) were elucidated to be the characteristic constituents for quality control of Forsythiae Fructus extract by chromatographic fingerprint in 2010 edition of Chinese Pharmacopoeia due to their numerous important pharmacological actions. It is of great interest to extract these medicinally active constituents from Forsythiae Fructus simultaneously. In this study, a new ultrasound-assisted extraction (UAE) method was developed for the simultaneous extraction of biological components 1-4 in Forsythiae Fructus. The quantitative effects of extraction time, ratio of liquid to solid, extraction temperature, and methanol concentration on yield of these four important biological constituents from Forsythiae Fructus were investigated using response surface methodology with Box-Behnken design. The compounds 1-4 extracted by UAE were quantitative analysis by high-performance liquid chromatography-photodiode array detect (HPLC-PAD), and overall desirability (OD), the geometric mean of the contents of four major biological components, was used as a marker to evaluate the extraction efficiency. By solving the regression equation and analyzing 3-D plots, the optimum condition was at extraction temperature 70°C, time 60 min, ratio of liquid to solid 20, and methanol concentration 76.6%. Under these conditions, extraction yields of compounds 1-4 were 2.92 mg/g, 52.10 mg/g, 0.90 mg/g and 0.57 mg/g, respectively, which were in good agreement with the predicted OD values. In order to achieve a similar yield as UAE, soxhlet extraction required at least 6 h and maceration extraction required much longer time of 24 h. Established UAE method has been successfully applied to sample preparation for the quality control of Forsythiae Fructus. Additionally, a quadrupole time-of-flight mass spectrometry was applied to the structural confirmation of analytes from the complex matrices acquired by UAE. The results indicated that UAE is an effective alternative method for extracting bioactive constituents, which may facilitate a deeper understanding of the extract of active constituents in Forsythiae Fructus from the raw material to its extract for providing the theoretical references.

UHPLC/HRMS Analysis of African Mango (Irvingia gabonensis) Seeds, Extract and Related Dietary Supplements

PubMed Central

Sun, Jianghao; Chen, Pei

2012-01-01

Dietary Supplements based on an extract from Irvingia gabonensis (African Mango, AM for abbreviation) seeds are one of the popular herbal weight loss dietary supplements in the US market. The extract is believed to be a natural and healthy way to lose weight and improve overall health. However, the chemical composition of African mango based-dietary supplements (AMDS) has never been reported. In this study, the chemical constituents of African mango seeds, African mango seeds extract (AMSE), and different kinds of commercially available African mango based dietary supplements (AMDS) have been investigated using an ultra high-performance liquid chromatography with high resolution mass spectrometry (UHPLC-HRMS) method. Ellagic acid, mono, di, tri-O methyl-ellagic acids and their glycosides were found as major components in African Mango seeds. These compounds may be used for quality control of African Mango extract and related dietary supplements. PMID:22880691

Quantitative analysis of genomic DNA degradation in whole blood under various storage conditions for molecular diagnostic testing.

PubMed

Permenter, Jessalyn; Ishwar, Arjun; Rounsavall, Angie; Smith, Maddie; Faske, Jennifer; Sailey, Charles J; Alfaro, Maria P

2015-12-01

Proper storage of whole blood is crucial for isolating nucleic acids from leukocytes and to ensure adequate performance of downstream assays in the molecular diagnostic laboratory. Short-term and long-term storage recommendations are lacking for successful isolation of genomic DNA (gDNA). Container type (EDTA or heparin), temperature (4 °C and room temperature) and time (1-130 days) were assessed as criterion for sample acceptance policies. The percentage of integrated area (%Ti) between 150 and 10,000 bp from the 2200 TapeStation electropherogram was calculated to measure gDNA degradation. Refrigerated EDTA samples yielded gDNA with low %Ti (high quality). Heparinized samples stored at room temperature yielded gDNA of worst quality. Downstream analysis demonstrated that the quality of the gDNA correlated with the quality of the data; samples with high %Ti generated significantly lower levels of high molecular weight amplicons. Recommendations from these analyses include storing blood samples intended for nucleic acid isolation in EDTA tubes at 4 °C for long term storage (>10 days). gDNA should be extracted within 3 days when blood is stored at room temperature regardless of the container. Finally, refrigerated heparinized samples should not be stored longer than 9 days if expecting high quality gDNA isolates. Laboratories should consider many factors, in addition to the results obtained herein, to update their policies for sample acceptance for gDNA extraction intended for molecular genetic testing. Copyright © 2015 Elsevier Ltd. All rights reserved.

Essential Oil Variability and Biological Activities of Tetraclinis articulata (Vahl) Mast. Wood According to the Extraction Time.

PubMed

Djouahri, Abderrahmane; Saka, Boualem; Boudarene, Lynda; Baaliouamer, Aoumeur

2016-12-01

In the present work, the hydrodistillation (HD) and microwave-assisted hydrodistillation (MAHD) kinetics of essential oil (EO) extracted from Tetraclinis articulata (Vahl) Mast. wood was conducted, in order to assess the impact of extraction time and technique on chemical composition and biological activities. Gas chromatography (GC) and GC/mass spectrometry analyses showed significant differences between the extracted EOs, where each family class or component presents a specific kinetic according to extraction time, technique and especially for the major components: camphene, linalool, cedrol, carvacrol and α-acorenol. Furthermore, our findings showed a high variability for both antioxidant and anti-inflammatory activities, where each activity has a specific effect according to extraction time and technique. The highlighted variability reflects the high impact of extraction time and technique on chemical composition and biological activities, which led to conclude that we should select EOs to be investigated carefully depending on extraction time and technique, in order to isolate the bioactive components or to have the best quality of EO in terms of biological activities and preventive effects in food. © 2016 Wiley-VHCA AG, Zurich, Switzerland.

Diversity and relationships in key traits for functional and apparent quality in a collection of eggplant: fruit phenolics content, antioxidant activity, polyphenol oxidase activity, and browning.

PubMed

Plazas, Mariola; López-Gresa, María P; Vilanova, Santiago; Torres, Cristina; Hurtado, Maria; Gramazio, Pietro; Andújar, Isabel; Herráiz, Francisco J; Bellés, José M; Prohens, Jaime

2013-09-18

Eggplant (Solanum melongena) varieties with increased levels of phenolics in the fruit present enhanced functional quality, but may display greater fruit flesh browning. We evaluated 18 eggplant accessions for fruit total phenolics content, chlorogenic acid content, DPPH scavenging activity, polyphenol oxidase (PPO) activity, liquid extract browning, and fruit flesh browning. For all the traits we found a high diversity, with differences among accessions of up to 3.36-fold for fruit flesh browning. Variation in total content in phenolics and in chlorogenic acid content accounted only for 18.9% and 6.0% in the variation in fruit flesh browning, and PPO activity was not significantly correlated with fruit flesh browning. Liquid extract browning was highly correlated with chlorogenic acid content (r = 0.852). Principal components analysis (PCA) identified four groups of accessions with different profiles for the traits studied. Results suggest that it is possible to develop new eggplant varieties with improved functional and apparent quality.

High Efficiency DNA Extraction by Graphite Oxide/Cellulose/Magnetite Composites Under Na+ Free System

NASA Astrophysics Data System (ADS)

Akceoglu, Garbis Atam; Li, Oi Lun; Saito, Nagahiro

2016-04-01

DNA extraction is the key step at various research areas like biotechnology, diagnostic development, paternity determination, and forensic science . Solid support extraction is the most common method for DNA purification. In this method, Na+ ions have often been applied as binding buffers in order to obtain high extraction efficiency and high quality of DNA; however, the presence of Na+ ions might be interfering with the downstream DNA applications. In this study, we proposed graphite oxide (GO)/magnetite composite/cellulose as an innovative material for Na+-free DNA extraction. The total wt.% of GO was fixed at 4.15% in the GO/cellulose/magnetite composite . The concentration of magnetite within the composites were controlled at 0-3.98 wt.%. The extraction yield of DNA increased with increasing weight percentage of magnetite. The highest yield was achieved at 3.98 wt.% magnetite, where the extraction efficiency was reported to be 338.5 ng/µl. The absorbance ratios between 260 nm and 280 nm (A260/A280) of the DNA elution volume was demonstrated as 1.81, indicating the extracted DNA consisted of high purity. The mechanism of adsorption of DNA was provided by (1) π-π interaction between the aromatic ring in GO and nucleobases of DNA molecule, and (2) surface charge interaction between the positive charge magnetite and anions such as phosphates within the DNA molecules. The results proved that the GO/cellulose/magnetite composite provides a Na+-free method for selective DNA extraction with high extraction efficiency of pure DNA.

A research of road centerline extraction algorithm from high resolution remote sensing images

NASA Astrophysics Data System (ADS)

Zhang, Yushan; Xu, Tingfa

2017-09-01

Satellite remote sensing technology has become one of the most effective methods for land surface monitoring in recent years, due to its advantages such as short period, large scale and rich information. Meanwhile, road extraction is an important field in the applications of high resolution remote sensing images. An intelligent and automatic road extraction algorithm with high precision has great significance for transportation, road network updating and urban planning. The fuzzy c-means (FCM) clustering segmentation algorithms have been used in road extraction, but the traditional algorithms did not consider spatial information. An improved fuzzy C-means clustering algorithm combined with spatial information (SFCM) is proposed in this paper, which is proved to be effective for noisy image segmentation. Firstly, the image is segmented using the SFCM. Secondly, the segmentation result is processed by mathematical morphology to remover the joint region. Thirdly, the road centerlines are extracted by morphology thinning and burr trimming. The average integrity of the centerline extraction algorithm is 97.98%, the average accuracy is 95.36% and the average quality is 93.59%. Experimental results show that the proposed method in this paper is effective for road centerline extraction.

Extraction of Data from a Hospital Information System to Perform Process Mining.

PubMed

Neira, Ricardo Alfredo Quintano; de Vries, Gert-Jan; Caffarel, Jennifer; Stretton, Erin

2017-01-01

The aim of this work is to share our experience in relevant data extraction from a hospital information system in preparation for a research study using process mining techniques. The steps performed were: research definition, mapping the normative processes, identification of tables and fields names of the database, and extraction of data. We then offer lessons learned during data extraction phase. Any errors made in the extraction phase will propagate and have implications on subsequent analyses. Thus, it is essential to take the time needed and devote sufficient attention to detail to perform all activities with the goal of ensuring high quality of the extracted data. We hope this work will be informative for other researchers to plan and execute extraction of data for process mining research studies.

Quality assessment of Penthorum chinense Pursh through multicomponent qualification and fingerprint, chemometric, and antihepatocarcinoma analyses.

PubMed

Sun, Zong-Liang; Zhang, Yu-Zhen; Zhang, Feng; Zhang, Jia-Wei; Zheng, Guo-Can; Tan, Ling; Wang, Chong-Zhi; Zhou, Lian-Di; Zhang, Qi-Hui; Yuan, Chun-Su

2018-06-22

An efficient method combined with fingerprint and chemometric analyses was developed to evaluate the quality of the traditional Chinese medicine plant Penthorum chinense Pursh. Nine samples were collected from different regions during different harvest periods, and 17 components in the form of extracts were simultaneously examined to assess quality by using high-performance liquid chromatography. The hepatoprotective effects of components were investigated by assessing the inhibition of SMMC-7721 cell growth. The results indicated that the quality control method was accurate, stable, and reliable, and the hierarchical heat-map cluster and the principle component analyses confirmed that the classification of all nine samples was consistent. Quercetin and ellagitannins including pinocembrin-7-O-[3''-O-galloyl-4'',6''-hexahydroxydiphenoyl]-β-glucose (PGHG), thonningianin A, thonningianin B, and other flavonoids were abundant in the extracts, and significantly contributed to the hepatoprotective effects.

Quality evaluation of banana skin extract jellies.

PubMed

Borges, S V; Valente, W A; Figueiredo, L P; Dias, M V; Pereira, P P; Pereira, A G T; Clemente, P R

2011-04-01

Due to the great volume of banana skin resulting from the industrialization of banana and to their high pectin content, the objectives of the present study were to evaluate the effect of the following factors: extract/sugar, pectin and citric acid on the chemical, physical and sensory qualities of the jellies obtained. A complete factorial experimental design was used (2(3)) with 3 central points to evaluate the influence of the factors on the dependent variables, testing the linear models. The chemical properties underwent few alterations and the instrumental and sensory texture attributes were mainly affected by the extract/sugar ratio and the pectin level. The brittleness, elasticity and gumminess increased with increases in the extract/ sugar ratio and pectin level. According to the sensory analysis and the purchasing intention, the best formulations were those obtained using a higher extract/sugar ratio (60/40) and lower pectin level (0.5 g/ 100), combined with the highest (20 mL) or lowest volumes of citric acid (15 mL), with scores for all the attributes in the range from 'I liked slightly' to 'I liked moderately'.

Quality assessment of systematic reviews on alveolar socket preservation.

PubMed

Moraschini, V; Barboza, E Dos S P

2016-09-01

The aim of this overview was to evaluate and compare the quality of systematic reviews, with or without meta-analysis, that have evaluated studies on techniques or biomaterials used for the preservation of alveolar sockets post tooth extraction in humans. An electronic search was conducted without date restrictions using the Medline/PubMed, Cochrane Library, and Web of Science databases up to April 2015. Eligibility criteria included systematic reviews, with or without meta-analysis, focused on the preservation of post-extraction alveolar sockets in humans. Two independent authors assessed the quality of the included reviews using AMSTAR and the checklist proposed by Glenny et al. in 2003. After the selection process, 12 systematic reviews were included. None of these reviews obtained the maximum score using the quality assessment tools implemented, and the results of the analyses were highly variable. A significant statistical correlation was observed between the scores of the two checklists. A wide structural and methodological variability was observed between the systematic reviews published on the preservation of alveolar sockets post tooth extraction. None of the reviews evaluated obtained the maximum score using the two quality assessment tools implemented. Copyright © 2016 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Comparison of nutritional qualities and antioxidant properties of ready-to-eat fruit-enriched corn based breakfast cereals.

PubMed

Bhavya, S N; Prakash, J

2012-12-01

The study aimed to analyse the nutritional quality, antioxidant components and activity of three varieties of corn based ready-to- eat (RTE) breakfast cereals (BFC) enriched with strawberry, banana and mango. Fruit-enriched corn based breakfast cereals manufactured in India were purchased and ground to obtain homogeneous samples for analysis. The contents of moisture, protein, total fat, dietary fibre, iron, phosphorous, calcium, vitamin C, total carotene, thiamine, riboflavin, in vitro digestible protein, bioaccessible calcium and iron, and digestible starch fractions were determined. The antioxidant components namely, polyphenols, flavonoids and antioxidant activity in different extracts were also determined using total antioxidant, free radical scavenging (2,2-diphenyl-1-picrylhydrazyl) and reducing power assays. The protein and dietary fibre contents in all samples ranged between 4.0-4.6 and 6.4-7.6 g/ 100g respectively. Total iron and vitamin C ranged between 10.7-13.3 mg and 33.2-43.6 mg/100g respectively. Cereals with mango had high total carotene in comparison with other samples. In vitro digestible protein of the processed cereals was low, while bioaccessible calcium (50.2-59.5%) and iron (8.5-15.1%) levels were high due to low oxalates and phytic acid contents. The starch profiles of the breakfast cereals showed high rapidly available glucose and starch digestibility index. Fruit-enriched breakfast cereals showed high polyphenol content in methanol extract (48.6-71.3 mg/100g) and high total antioxidant activity in aqueous extracts. Free radical scavenging and reducing power assay showed high activity in 80% methanol extract. Fruit-enriched breakfast cereals have the potential to be a good source of iron, dietary fibre, vitamin C and total carotene. The fruit-enriched cereals also had high bioaccessible iron and antioxidant activity.

[Evaluation of social demographic aspect of life quality of coal extraction workers in Kouzbass enterprises].

PubMed

Ivoĭlov, V M; Semenikhin, V A; Odintseva, O V; Shternis, T A

2014-01-01

For assessing influence of social factors on life quality of workers in coal extraction enterpirses of Kemerovo region, the authors used questionnaire SF-36. Life quality parameters of workers engaged into coal extraction in Kemerovo region appeared to lower with age from 20 to 64 years. Life quality parameters on scales of pain, physical functioning and general health are invertedly correlated with age and length of service in hazardous work conditions for coal extraction workers. Life quality of the miners is influenced by the following factors: marital status, educational level and income level of the workers.

Combined effect of MAP and active compounds on fresh blue fish burger.

PubMed

Del Nobile, M A; Corbo, M R; Speranza, B; Sinigaglia, M; Conte, A; Caroprese, M

2009-11-15

The combined effects of three essential oils [thymol, lemon extract and grapefruit seed extract (GFSE)] and modified atmosphere packaging conditions (MAP) on quality retention of blue fish burgers was studied and discussed. In particular, samples were packaged in air and in three different gas mix compositions: 30:40:30 O(2):CO(2):N(2), 50:50 O(2):CO(2) and 5:95 O(2):CO(2). During a 28-day storage period at 4 degrees C, the nutritional, microbiological and sensorial quality of the packed products was assessed. The potential development of biogenic amines was also evaluated. The obtained results highlight the possibility to improve the microbial quality of blue fish burgers by using very small amount of thymol (110ppm), GFSE (100ppm) and lemon extract (120ppm) in combination with MAP. Based primarily on microbiological results, the combined use of the tested natural preservatives and a packaging system characterized by a high CO(2)-concentration, was able to guarantee the microbial acceptability of fish burgers until the 28th day of storage at 4 degrees C. On the other hand, results from sensory analyses showed that sensorial quality was the sub-index that limited the burgers shelf life (to about 22-23days), even if the proposed strategy was also effective in minimizing the sensory quality loss of the product having no effect on its nutritional quality.

Protein Oxidation and Sensory Quality of Brine-Injected Pork Loins Added Ascorbate or Extracts of Green Tea or Maté during Chill-Storage in High-Oxygen Modified Atmosphere.

PubMed

Jongberg, Sisse; Tørngren, Mari Ann; Skibsted, Leif H

2018-01-15

Background: Ascorbate is often applied to enhance stability and robustness of brine-injected pork chops sold for retail, but may affect protein oxidation, while plant extracts are potential substitutes. Methods: Brine-injected pork chops (weight-gain ~12%, NaCl ~0.9%) prepared with ascorbate (225 ppm), green tea extract (25 ppm gallic acid equivalents (GAE)), or maté extract (25 ppm GAE) stored (5 °C, seven days) in high-oxygen atmosphere packaging (MAP: 80% O₂ and 20% CO₂) were analyzed for color changes, sensory quality, and protein oxidation compared to a control without antioxidant. Results: No significant differences were observed for green tea and maté extracts as compared to ascorbate when evaluated based on lipid oxidation derived off-flavors, except for stale flavor, which maté significantly reduced. All treatments increased the level of the protein oxidation product, α-aminoadipic semialdehyde as compared to the control, and ascorbate was further found to increase thiol loss and protein cross-linking, with a concomitant decrease in the sensory perceived tenderness. Conclusions: Green tea and maté were found to equally protect against lipid oxidation derived off-flavors, and maté showed less prooxidative activity towards proteins as compared to ascorbate, resulting in more tender meat. Maté is a valuable substitute for ascorbate in brine-injected pork chops.

Selective extraction and determination of chlorogenic acids as combined quality markers in herbal medicines using molecularly imprinted polymers based on a mimic template.

PubMed

Ji, Wenhua; Zhang, Mingming; Yan, Huijiao; Zhao, Hengqiang; Mu, Yan; Guo, Lanping; Wang, Xiao

2017-12-01

We describe a solid-phase extraction adsorbent based on molecularly imprinted polymers (MIPs), prepared with use of a mimic template. The MIPs were used for the selective extraction and determination of three chlorogenic acids as combined quality markers for Lonicera japonica and Lianhua qingwen granules. The morphologies and surface groups of the MIPs were assessed by scanning electron microscopy, Brunauer-Emmett-Teller surface area analysis, and Fourier transform infrared spectroscopy. The adsorption isotherms, kinetics, and selectivity of the MIPs were systematically compared with those of non-molecularly imprinted polymers. The MIPs showed high selectivity toward three structurally similar chlorogenic acids (chlorogenic acid, cryptochlorogenic acid, and neochlorogenic acid). A procedure using molecularly imprinted solid-phase extraction coupled with high-performance liquid chromatography was established for the determination of three chlorogenic acids from Lonicera japonica and Lianhua qingwen granules. The recoveries of the chlorogenic acids ranged from 93.1% to 101.4%. The limits of detection and limits of quantification for the three chlorogenic acids were 0.003 mg g -1 and 0.01 mg g -1 , respectively. The newly developed method is thus a promising technique for the enrichment and determination of chlorogenic acids from herbal medicines. Graphical Abstract Mimic molecularly imprinted polymers for the selective extraction of chlorogenic acids.

Research on Methods of High Coherent Target Extraction in Urban Area Based on Psinsar Technology

NASA Astrophysics Data System (ADS)

Li, N.; Wu, J.

2018-04-01

PSInSAR technology has been widely applied in ground deformation monitoring. Accurate identification of Persistent Scatterers (PS) is key to the success of PSInSAR data processing. In this paper, the theoretic models and specific algorithms of PS point extraction methods are summarized and the characteristics and applicable conditions of each method, such as Coherence Coefficient Threshold method, Amplitude Threshold method, Dispersion of Amplitude method, Dispersion of Intensity method, are analyzed. Based on the merits and demerits of different methods, an improved method for PS point extraction in urban area is proposed, that uses simultaneously backscattering characteristic, amplitude and phase stability to find PS point in all pixels. Shanghai city is chosen as an example area for checking the improvements of the new method. The results show that the PS points extracted by the new method have high quality, high stability and meet the strong scattering characteristics. Based on these high quality PS points, the deformation rate along the line-of-sight (LOS) in the central urban area of Shanghai is obtained by using 35 COSMO-SkyMed X-band SAR images acquired from 2008 to 2010 and it varies from -14.6 mm/year to 4.9 mm/year. There is a large sedimentation funnel in the cross boundary of Hongkou and Yangpu district with a maximum sedimentation rate of more than 14 mm per year. The obtained ground subsidence rates are also compared with the result of spirit leveling and show good consistent. Our new method for PS point extraction is more reasonable, and can improve the accuracy of the obtained deformation results.

[Husk of Venezuelan cocoa as raw material of infusions].

PubMed

Sangronis, Elba; José Soto, María; Valero, Yolmar; Buscema, Ignacio

2014-06-01

In the cocoa bean industry, some by-products go underutilized. Some of these components could provide other innovative products, and such is the case with the husk of the cocoa bean. Previous studies have attributed the husk with a high antioxidant capacity, which added to its relative low cost, makes it an attractive ingredient for the production of infusions. However, prior to promoting it as such, its quality needs to be guaranteed. This study evaluated the chemical composition of the husk of cocoa, its microbiologic quality and other parameters in order to be considered raw material in the preparation of infusions. The cocoa was cultivated in two different states in Venezuela. Moisture, protein, fat, ash, carbohydrates, microbiologic quality and ochratoxin A as well antioxidant properties, content of foreign matter, insoluble ash in HCL and aqueous extract were evaluated in the husk of cocoa seeds. Applied methods were in compliance with national and international norms. Significant differences were determined between the samples through the ANOVA application. A low level in moisture content, but high in ash, along with a microbiologic quality that met the norm, and an absence of ochratoxin A were observed in the totality of the analyzed samples. Low levels of foreign matter, the high value of its aqueous extract and high phenolic compounds content with antioxidant activity allow for the recommendation of the husk of cocoa as raw material for the preparation of infusions.

Effect of Subcritical Fluid Extraction on the High Quality of Headspace Oil from Jasminum sambac (L.) Aiton.

PubMed

Ye, Qiuping; Jin, Xinyi; Wei, Shiqin; Zheng, Gongyu; Li, Xinlei

2016-05-01

Subcritical fluid extraction (SFE), as a novel method, was applied to investigate the yield, quality, and sensory evaluation of headspace oil from Jasminum sambac (L.) Aiton in comparison with petroleum ether extraction (PEE). The results indicated that the yield of the headspace oil using SFE was significantly higher (P < 0.05) than when using PEE. SFE contributed to obtaining alcohols and ethers, prevented the thermal reaction of terpenes, and reduced α-caryophyllene and β-caryophyllene in the headspace oil. The contents of linalool (21.90%) and benzyl acetate (16.31%) were higher via SFE than PEE. In addition, the sensory evaluation of SFE was superior to PEE, indicating a fresh, jasmine-like odor and green-yellow color. Thus, SFE is an improved method for obtaining natural headspace oil from jasmine flowers.

Second Iteration of Photogrammetric Pipeline to Enhance the Accuracy of Image Pose Estimation

NASA Astrophysics Data System (ADS)

Nguyen, T. G.; Pierrot-Deseilligny, M.; Muller, J.-M.; Thom, C.

2017-05-01

In classical photogrammetric processing pipeline, the automatic tie point extraction plays a key role in the quality of achieved results. The image tie points are crucial to pose estimation and have a significant influence on the precision of calculated orientation parameters. Therefore, both relative and absolute orientations of the 3D model can be affected. By improving the precision of image tie point measurement, one can enhance the quality of image orientation. The quality of image tie points is under the influence of several factors such as the multiplicity, the measurement precision and the distribution in 2D images as well as in 3D scenes. In complex acquisition scenarios such as indoor applications and oblique aerial images, tie point extraction is limited while only image information can be exploited. Hence, we propose here a method which improves the precision of pose estimation in complex scenarios by adding a second iteration to the classical processing pipeline. The result of a first iteration is used as a priori information to guide the extraction of new tie points with better quality. Evaluated with multiple case studies, the proposed method shows its validity and its high potiential for precision improvement.

A semi-blind logo watermarking scheme for color images by comparison and modification of DFT coefficients

NASA Astrophysics Data System (ADS)

Kusyk, Janusz; Eskicioglu, Ahmet M.

2005-10-01

Digital watermarking is considered to be a major technology for the protection of multimedia data. Some of the important applications are broadcast monitoring, copyright protection, and access control. In this paper, we present a semi-blind watermarking scheme for embedding a logo in color images using the DFT domain. After computing the DFT of the luminance layer of the cover image, the magnitudes of DFT coefficients are compared, and modified. A given watermark is embedded in three frequency bands: Low, middle, and high. Our experiments show that the watermarks extracted from the lower frequencies have the best visual quality for low pass filtering, adding Gaussian noise, JPEG compression, resizing, rotation, and scaling, and the watermarks extracted from the higher frequencies have the best visual quality for cropping, intensity adjustment, histogram equalization, and gamma correction. Extractions from the fragmented and translated image are identical to extractions from the unattacked watermarked image. The collusion and rewatermarking attacks do not provide the hacker with useful tools.

A rapid silica spin column-based method of RNA extraction from fruit trees for RT-PCR detection of viruses.

PubMed

Yang, Fan; Wang, Guoping; Xu, Wenxing; Hong, Ni

2017-09-01

Efficient recovery of high quality RNA is very important for successful RT-PCR detection of plant RNA viruses. High levels of polyphenols and polysaccharides in plant tissues can irreversibly bind to and/or co-precipitate with RNA, which influences RNA isolation. In this study, a silica spin column-based RNA isolation method was developed by using commercially available silica columns combined with the application of a tissue lysis solution, and binding and washing buffers with high concentration guanidinium thiocyanate (GuSCN, 50% w/v), which helps remove plant proteins, polysaccharides and polyphenolic compounds. The method was successfully used to extract high quality RNA from citrus (Citrus aurantifolia), grapevine (Vitis vinifera), peach (Prunus persica), pear (Pyrus spp.), taro (Colocosia esculenta) and tobacco (Nicotiana benthamiana) samples. The method was comparable to conventional CTAB method in RNA isolation efficiency, but it was more sample-adaptable and cost-effective than commercial kits. High quality RNA isolated using silica spin column-based method was successfully used for the RT-PCR and/or multiplex RT-PCR amplification of woody fruit tree viruses and a viroid. The study provided a useful tool for the detection and characterization of plant viruses. Copyright © 2017 Elsevier B.V. All rights reserved.

Extraction and labeling methods for microarrays using small amounts of plant tissue.

PubMed

Stimpson, Alexander J; Pereira, Rhea S; Kiss, John Z; Correll, Melanie J

2009-03-01

Procedures were developed to maximize the yield of high-quality RNA from small amounts of plant biomass for microarrays. Two disruption techniques (bead milling and pestle and mortar) were compared for the yield and the quality of RNA extracted from 1-week-old Arabidopsis thaliana seedlings (approximately 0.5-30 mg total biomass). The pestle and mortar method of extraction showed enhanced RNA quality at the smaller biomass samples compared with the bead milling technique, although the quality in the bead milling could be improved with additional cooling steps. The RNA extracted from the pestle and mortar technique was further tested to determine if the small quantity of RNA (500 ng-7 microg) was appropriate for microarray analyses. A new method of low-quantity RNA labeling for microarrays (NuGEN Technologies, Inc.) was used on five 7-day-old seedlings (approximately 2.5 mg fresh weight total) of Arabidopsis that were grown in the dark and exposed to 1 h of red light or continued dark. Microarray analyses were performed on a small plant sample (five seedlings; approximately 2.5 mg) using these methods and compared with extractions performed with larger biomass samples (approximately 500 roots). Many well-known light-regulated genes between the small plant samples and the larger biomass samples overlapped in expression changes, and the relative expression levels of selected genes were confirmed with quantitative real-time polymerase chain reaction, suggesting that these methods can be used for plant experiments where the biomass is extremely limited (i.e. spaceflight studies).

ACCELERATED SOLVENT EXTRACTION COMBINED WITH ...

EPA Pesticide Factsheets

A research project was initiated to address a recurring problem of elevated detection limits above required risk-based concentrations for the determination of semivolatile organic compounds in high moisture content solid samples. This project was initiated, in cooperation with the EPA Region 1 Laboratory, under the Regional Methods Program administered through the ORD Office of Science Policy. The aim of the project was to develop an approach for the rapid removal of water in high moisture content solids (e.g., wetland sediments) in preparation for analysis via Method 8270. Alternative methods for water removal have been investigated to enhance compound solid concentrations and improve extraction efficiency, with the use of pressure filtration providing a high-throughput alternative for removal of the majority of free water in sediments and sludges. In order to eliminate problems with phase separation during extraction of solids using Accelerated Solvent Extraction, a variation of a water-isopropanol extraction method developed at the USGS National Water Quality Laboratory in Denver, CO is being employed. The concentrations of target compounds in water-isopropanol extraction fluids are subsequently analyzed using an automated Solid Phase Extraction (SPE)-GC/MS method developed in our laboratory. The coupled approaches for dewatering, extraction, and target compound identification-quantitation provide a useful alternative to enhance sample throughput for Me

Evaluating the Impact of DNA Extraction Method on the Representation of Human Oral Bacterial and Fungal Communities

PubMed Central

Biswas, Kristi; Taylor, Michael W.; Gear, Kim

2017-01-01

The application of high-throughput, next-generation sequencing technologies has greatly improved our understanding of the human oral microbiome. While deciphering this diverse microbial community using such approaches is more accurate than traditional culture-based methods, experimental bias introduced during critical steps such as DNA extraction may compromise the results obtained. Here, we systematically evaluate four commonly used microbial DNA extraction methods (MoBio PowerSoil® DNA Isolation Kit, QIAamp® DNA Mini Kit, Zymo Bacterial/Fungal DNA Mini PrepTM, phenol:chloroform-based DNA isolation) based on the following criteria: DNA quality and yield, and microbial community structure based on Illumina amplicon sequencing of the V3–V4 region of the 16S rRNA gene of bacteria and the internal transcribed spacer (ITS) 1 region of fungi. Our results indicate that DNA quality and yield varied significantly with DNA extraction method. Representation of bacterial genera in plaque and saliva samples did not significantly differ across DNA extraction methods and DNA extraction method showed no effect on the recovery of fungal genera from plaque. By contrast, fungal diversity from saliva was affected by DNA extraction method, suggesting that not all protocols are suitable to study the salivary mycobiome. PMID:28099455

A Simple and Rapid Protocol for Producing Yeast Extract from Saccharomyces cerevisiae Suitable for Preparing Bacterial Culture Media

PubMed Central

Zarei, Omid; Dastmalchi, Siavoush; Hamzeh-Mivehroud, Maryam

2016-01-01

Yeasts, especially Saccharomyces cerevisiae, are one of the oldest organisms with broad spectrum of applications, owing to their unique genetics and physiology. Yeast extract, i.e. the product of yeast cells, is extensively used as nutritional resource in bacterial culture media. The aim of this study was to develop a simple, rapid and cost benefit process to produce the yeast extract. In this procedure mechanical methods such as high temperature and pressure were utilized to produce the yeast extract. The growth of the bacteria feed with the produced yeast extract was monitored in order to assess the quality of the product. The results showed that the quality of the produced yeast extract was very promising concluded from the growth pattern of bacterial cells in media prepared from this product and was comparable with that of the three commercial yeast extracts in terms of bacterial growth properties. One of the main advantages of the current method was that no chemicals and enzymes were used, leading to the reduced production cost. The method is very simple and cost effective, and can be performed in a reasonable time making it suitable for being adopted by research laboratories. Furthermore, it can be scaled up to produce large quantities for industrial applications. PMID:28243289

Signal extraction and wave field separation in tunnel seismic prediction by independent component analysis

NASA Astrophysics Data System (ADS)

Yue, Y.; Jiang, T.; Zhou, Q.

2017-12-01

In order to ensure the rationality and the safety of tunnel excavation, the advanced geological prediction has been become an indispensable step in tunneling. However, the extraction of signal and the separation of P and S waves directly influence the accuracy of geological prediction. Generally, the raw data collected in TSP system is low quality because of the numerous disturb factors in tunnel projects, such as the power interference and machine vibration interference. It's difficult for traditional method (band-pass filtering) to remove interference effectively as well as bring little loss to signal. The power interference, machine vibration interference and the signal are original variables and x, y, z component as observation signals, each component of the representation is a linear combination of the original variables, which satisfy applicable conditions of independent component analysis (ICA). We perform finite-difference simulations of elastic wave propagation to synthetic a tunnel seismic reflection record. The method of ICA was adopted to process the three-component data, and the results show that extract the estimates of signal and the signals are highly correlated (the coefficient correlation is up to more than 0.93). In addition, the estimates of interference that separated from ICA and the interference signals are also highly correlated, and the coefficient correlation is up to more than 0.99. Thus, simulation results showed that the ICA is an ideal method for extracting high quality data from mixed signals. For the separation of P and S waves, the conventional separation techniques are based on physical characteristics of wave propagation, which require knowledge of the near-surface P and S waves velocities and density. Whereas the ICA approach is entirely based on statistical differences between P and S waves, and the statistical technique does not require a priori information. The concrete results of the wave field separation will be presented in the meeting. In summary, we can safely draw the conclusion that ICA can not only extract high quality data from the mixed signals, but also can separate P and S waves effectively.

[Application of DNA extraction kit, 'GM quicker' for detection of genetically modified soybeans].

PubMed

Sato, Noriko; Sugiura, Yoshitsugu; Tanaka, Toshitsugu

2012-01-01

Several DNA extraction methods have been officially introduced to detect genetically modified soybeans, but the choice of DNA extraction kits depend on the nature of the samples, such as grains or processed foods. To overcome this disadvantage, we examined whether the GM quicker kit is available for both grains and processed foods. We compared GM quicker with four approved DNA extraction kits in respect of DNA purity, copy numbers of lectin gene, and working time. We found that the DNA quality of GM quicker was superior to that of the other kits for grains, and the procedure was faster. However, in the case of processed foods, GM quicker was not superior to the other kits. We therefore investigated an unapproved GM quicker 3 kit, which is available for DNA extraction from processed foods, such as tofu and boiled soybeans. The GM quicker 3 kit provided good DNA quality from both grains and processed foods, so we made a minor modification of the GM quicker-based protocol that was suitable for processed foods, using GM quicker and its reagents. The modified method enhanced the performance of GM quicker with processed foods. We believe that GM quicker with the modified protocol is an excellent tool to obtain high-quality DNA from grains and processed foods for detection of genetically modified soybeans.

Simultaneous determination of rhamnose, xylitol, arabitol, fructose, glucose, inositol, sucrose, maltose in jujube (Zizyphus jujube Mill.) extract: comparison of HPLC-ELSD, LC-ESI-MS/MS and GC-MS.

PubMed

Sun, Shihao; Wang, Hui; Xie, Jianping; Su, Yue

2016-01-01

Jujube extract is commonly used as a food additive and flavoring. The sensory properties of the extract, especially sweetness, are a critical factor determining the product quality and therefore affecting consumer acceptability. Small molecular carbohydrates make major contribution to the sweetness of the jujube extract, and their types and contents in the extract have direct influence on quality of the product. So, an appropriate qualitative and quantitative method for determination of the carbohydrates is vitally important for quality control of the product. High performance liquid chromatography-evaporative light scattering detection (HPLC-ELSD), liquid chromatography-electronic spay ionization tandem mass spectrometry (LC-ESI-MS/MS), and gas chromatography-mass spectrometry (GC-MS) methods have been developed and applied to determining small molecular carbohydrates in jujube extract, respectively. Eight sugars and alditols were identified from the extract, including rhamnose, xylitol, arabitol, fructose, glucose, inositol, sucrose, and maltose. Comparisons were carried out to investigate the performance of the methods. Although the methods have been found to perform satisfactorily, only three sugars (fructose, glucose and inositol) could be detected by all these methods. Meanwhile, a similar quantitative result for the three sugars can be obtained by the methods. Eight sugars and alditols in the jujube extract were determined by HPLC-ELSD, LC-ESI-MS/MS and GC-MS, respectively. The LC-ELSD method and the LC-ESI-MS/MS method with good precision and accuracy were suitable for quantitative analysis of carbohydrates in jujube extract; although the performance of the GC-MS method for quantitative analysis was inferior to the other methods, it has a wider scope in qualitative analysis. A multi-analysis technique should be adopted in order to obtain complete constituents of about the carbohydrates in jujube extract, and the methods should be employed according to the purpose of analysis.

Value Added Processing of Aflatoxin Contaminated Peanut Meal

USDA-ARS?s Scientific Manuscript database

Peanut meal (PM) is the solid material remaining after commercial extraction of oil. Despite being an excellent source of high quality protein, applications of PM are limited to feed markets as this material typically contains high concentrations of aflatoxin. Our research group has developed a nov...

VizieR Online Data Catalog: Hi-GAL. inner Milky Way: +68>=l>=70 (Molinari+, 2016)

NASA Astrophysics Data System (ADS)

Molinari, S.; Schisano, E.; Elia, D.; Pestalozzi, M.; Traficante, A.; Pezzuto, S.; Swinyard, B. M.; Noriega-Crespo, A.; Bally, J.; Moore, T. J. T.; Plume, R.; Zavagno, A.; di Giorgio A. M.; Liu, S. J.; Pilbratt, G. L.; Mottram, J. C.; Russeil, D.; Piazzo, L.; Veneziani, M.; Benedettini, M.; Calzoletti, L.; Faustini, F.; Natoli, P.; Piacentini, F.; Merello, M.; Palmese, A.; Del Grande, R.; Polychroni, D.; Rygl, K. L. J.; Polenta, G.; Barlow, M. J.; Bernard, J.-P.; Martin, P. G.; Testi, L.; Ali, B.; Andre, P.; Beltran, M. T.; Billot, N.; Carey, S.; Cesaroni, R.; Compiegne, M.; Eden, D.; Fukui, Y.; Garcia-Lario, P.; Hoare, M. G.; Huang, M.; Joncas, G.; Lim, T. L.; Lord, S. D.; Martinavarro-Armengol, S.; Motte, F.; Paladini, R.; Paradis, D.; Peretto, N.; Robitaille, T.; Schilke, P.; Schneider, N.; Schulz, B.; Sibthorpe, B.; Strafella, F.; Thompson, M. A.; Umana, G.; Ward-Thompson, D.; Wyrowski, F.

2016-08-01

This is the first public data release of high-quality products from the Herschel Hi-GAL survey. The release comes two years after the end of the Herschel observing campaign and is the result of extensive testing of the data reduction and extraction procedures created by members of the Hi-GAL consortium. The complexity and the large variation of the background conditions in all Herschel wavelength bands makes source extraction on the Galactic plane a challenging task. With Hi-GAL DR1, we provide access (http://vialactea.iaps.inaf.it) through a cutout service to high-quality images and compact source catalogues for the Galactic plane at 70, 160, 250, 350, and 500um in the region 68°>=l>=-70° and |b|<= 1°. (6 data files).

Beam brilliance investigation of high current ion beams at GSI heavy ion accelerator facility.

PubMed

Adonin, A A; Hollinger, R

2014-02-01

In this work the emittance measurements of high current Ta-beam provided by VARIS (Vacuum Arc Ion Source) ion source are presented. Beam brilliance as a function of beam aperture at various extraction conditions is investigated. Influence of electrostatic ion beam compression in post acceleration gap on the beam quality is discussed. Use of different extraction systems (single aperture, 7 holes, and 13 holes) in order to achieve more peaked beam core is considered. The possible ways to increase the beam brilliance are discussed.

The correlation between the quality of oral hygiene and oral HPV infection in adults: a prospective cross-sectional study.

PubMed

Dalla Torre, Daniel; Burtscher, D; Sölder, E; Rasse, M; Puelacher, W

2018-03-25

Various risk factors for oral human papillomavirus (HPV) infections have been described, including tobacco smoking and sexual behavior. However, less is known about the influence of oral health on such infections. The present study aimed to determine a possible association between the quality of oral hygiene and the presence of oral HPV. In a prospective analysis, the approximal plaque index (API), the gingival bleeding index (GBI), and the lifetime number of extracted teeth was determined in 187 patients. Additionally, the presence of oral low-risk and/or high-risk HPV was investigated by brush smear testing in all participants. Seventy-four patients had an API < 20%, 84 participants showed an API of 20-40%, and in 29 cases, an API > 40% was recorded. Ninety-six patients presented a GBI < 20%, 75 had a GBI of 20-40%, and 16 showed a GBI > 40%. One hundred four patients had experienced one to three extractions, and 36 had lost more than three teeth. Thirty-nine participants had a positive oral HPV testing (27 high-risk HPV, 26 low-risk HPV, 14 low- and high-risk HPV). A higher API respectively GBI and a greater number of extracted teeth were significantly correlated with the presence of high-risk HPV. The presence of low-risk HPV was significantly higher in patients with API > 40% and GBI > 40% (OR 7.89). Similar results were found regarding the number of extracted teeth. The present analysis confirms a relationship between the quality of oral hygiene, determined by objective markers. Thus, improvement of oral health may reduce the incidence of oral HPV infection. The present article investigates the relationship between oral hygiene and the presence of oral HPV. As a significant correlation between these two factors could be recorded, improvement of oral hygiene may reduce actively the incidence of oral HPV. Thereby, good oral hygiene may contribute oral cancer prevention.

Supercritical Carbon Dioxide Extraction of Carotenoids from Pumpkin (Cucurbita spp.): A Review

PubMed Central

Durante, Miriana; Lenucci, Marcello Salvatore; Mita, Giovanni

2014-01-01

Carotenoids are well known for their nutritional properties and health promoting effects representing attractive ingredients to develop innovative functional foods, nutraceutical and pharmaceutical preparations. Pumpkin (Cucurbita spp.) flesh has an intense yellow/orange color owing to the high level of carotenoids, mainly α-carotene, β-carotene, β-cryptoxanthin, lutein and zeaxanthin. There is considerable interest in extracting carotenoids and other bioactives from pumpkin flesh. Extraction procedures able to preserve nutritional and pharmacological properties of carotenoids are essential. Conventional extraction methods, such as organic solvent extraction (CSE), have been used to extract carotenoids from plant material for a long time. In recent years, supercritical carbon dioxide (SC-CO2) extraction has received a great deal of attention because it is a green technology suitable for the extraction of lipophylic molecules and is able to give extracts of high quality and totally free from potentially toxic chemical solvents. Here, we review the results obtained so far on SC-CO2 extraction efficiency and quali-quantitative composition of carotenoids from pumpkin flesh. In particular, we consider the effects of (1) dehydration pre-treatments; (2) extraction parameters (temperature and pressure); the use of water, ethanol and olive oil singularly or in combination as entrainers or pumpkin seeds as co-matrix. PMID:24756094

Supercritical carbon dioxide extraction of carotenoids from pumpkin (Cucurbita spp.): a review.

PubMed

Durante, Miriana; Lenucci, Marcello Salvatore; Mita, Giovanni

2014-04-21

Carotenoids are well known for their nutritional properties and health promoting effects representing attractive ingredients to develop innovative functional foods, nutraceutical and pharmaceutical preparations. Pumpkin (Cucurbita spp.) flesh has an intense yellow/orange color owing to the high level of carotenoids, mainly α-carotene, β-carotene, β-cryptoxanthin, lutein and zeaxanthin. There is considerable interest in extracting carotenoids and other bioactives from pumpkin flesh. Extraction procedures able to preserve nutritional and pharmacological properties of carotenoids are essential. Conventional extraction methods, such as organic solvent extraction (CSE), have been used to extract carotenoids from plant material for a long time. In recent years, supercritical carbon dioxide (SC-CO2) extraction has received a great deal of attention because it is a green technology suitable for the extraction of lipophylic molecules and is able to give extracts of high quality and totally free from potentially toxic chemical solvents. Here, we review the results obtained so far on SC-CO2 extraction efficiency and quali-quantitative composition of carotenoids from pumpkin flesh. In particular, we consider the effects of (1) dehydration pre-treatments; (2) extraction parameters (temperature and pressure); the use of water, ethanol and olive oil singularly or in combination as entrainers or pumpkin seeds as co-matrix.

Aviation obstacle auto-extraction using remote sensing information

NASA Astrophysics Data System (ADS)

Zimmer, N.; Lugsch, W.; Ravenscroft, D.; Schiefele, J.

2008-10-01

An Obstacle, in the aviation context, may be any natural, man-made, fixed or movable object, permanent or temporary. Currently, the most common way to detect relevant aviation obstacles from an aircraft or helicopter for navigation purposes and collision avoidance is the use of merged infrared and synthetic information of obstacle data. Several algorithms have been established to utilize synthetic and infrared images to generate obstacle information. There might be a situation however where the system is error-prone and may not be able to consistently determine the current environment. This situation can be avoided when the system knows the true position of the obstacle. The quality characteristics of the obstacle data strongly depends on the quality of the source data such as maps and official publications. In some countries such as newly industrializing and developing countries, quality and quantity of obstacle information is not available. The aviation world has two specifications - RTCA DO-276A and ICAO ANNEX 15 Ch. 10 - which describe the requirements for aviation obstacles. It is essential to meet these requirements to be compliant with the specifications and to support systems based on these specifications, e.g. 3D obstacle warning systems where accurate coordinates based on WGS-84 is a necessity. Existing aerial and satellite or soon to exist high quality remote sensing data makes it feasible to think about automated aviation obstacle data origination. This paper will describe the feasibility to auto-extract aviation obstacles from remote sensing data considering limitations of image and extraction technologies. Quality parameters and possible resolution of auto-extracted obstacle data will be discussed and presented.

A systematic review of goal directed fluid therapy: rating of evidence for goals and monitoring methods.

PubMed

Wilms, Heath; Mittal, Anubhav; Haydock, Matthew D; van den Heever, Marc; Devaud, Marcello; Windsor, John A

2014-04-01

To review the literature on goal directed fluid therapy and evaluate the quality of evidence for each combination of goal and monitoring method. A search of major digital databases and hand search of references was conducted. All studies assessing the clinical utility of a specific fluid therapy goal or set of goals using any monitoring method were included. Data was extracted using a pre-determined pro forma and papers were evaluated using GRADE principles to assess evidence quality. Eighty-one papers met the inclusion criteria, investigating 31 goals and 22 methods for monitoring fluid therapy in 13052 patients. In total there were 118 different goal/method combinations. Goals with high evidence quality were central venous lactate and stroke volume index. Goals with moderate quality evidence were sublingual microcirculation flow, the oxygen extraction ratio, cardiac index, cardiac output, and SVC collapsibility index. This review has highlighted the plethora of goals and methods for monitoring fluid therapy. Strikingly, there is scant high quality evidence, in particular for non-invasive G/M combinations in non-operative and non-intensive care settings. There is an urgent need to address this research gap, which will be helped by methodologies to compare utility of G/M combinations. Copyright © 2014 Elsevier Inc. All rights reserved.

Identification of Ginkgo biloba supplements adulteration using high performance thin layer chromatography and ultra high performance liquid chromatography-diode array detector-quadrupole time of flight-mass spectrometry.

PubMed

Avula, Bharathi; Sagi, Satyanarayanaraju; Gafner, Stefan; Upton, Roy; Wang, Yan-Hong; Wang, Mei; Khan, Ikhlas A

2015-10-01

Ginkgo biloba is one of the most widely sold herbal supplements and medicines in the world. Its popularity stems from having a positive effect on memory and the circulatory system in clinical studies. As ginkgo popularity increased, non-proprietary extracts were introduced claiming to have a similar phytochemical profile as the clinically tested extracts. The standardized commercial extracts of G. biloba leaf used in ginkgo supplements contain not less than 6% sesquiterpene lactones and 24% flavonol glycosides. While sesquiterpene lactones are unique constituents of ginkgo leaf, the flavonol glycosides are found in many other botanical extracts. Being a high value botanical, low quality ginkgo extracts may be subjected to adulteration with flavonoids to meet the requirement of 24% flavonol glycosides. Chemical analysis by ultra high performance liquid chromatography-mass spectrometry revealed that adulteration of ginkgo leaf extracts in many of these products is common, the naturally flavonol glycoside-rich extract being spiked with pure flavonoids or extracts made from another flavonoid-rich material, such as the fruit/flower of Japanese sophora (Styphnolobium japonicum), which also contains the isoflavone genistein. Recently, genistein has been proposed as an analytical marker for the detection of adulteration of ginkgo extracts with S. japonicum. This study confirms that botanically authenticated G. biloba leaf and extracts made therefrom do not contain genistein, and the presence of which even in trace amounts is suggestive of adulteration. In addition to the mass spectrometric approach, a high performance thin layer chromatography method was developed as a fast and economic method for chemical fingerprint analysis of ginkgo samples.

Acceptability, Safety, and Efficacy of Oral Administration of Extracts of Black or Red Maca (Lepidium meyenii) in Adult Human Subjects: A Randomized, Double-Blind, Placebo-Controlled Study

PubMed Central

Gonzales-Arimborgo, Carla; Yupanqui, Irma; Montero, Elsa; Alarcón-Yaquetto, Dulce E.; Zevallos-Concha, Alisson; Caballero, Lidia; Gasco, Manuel; Zhao, Jianping; Khan, Ikhlas A.; Gonzales, Gustavo F.

2016-01-01

The plant maca, grown at 4000 m altitude in the Peruvian Central Andes, contains hypocotyls that have been used as food and in traditional medicine for centuries. The aim of this research was to provide results on some health effects of oral administration of spray-dried extracts of black or red maca (Lepidium meyenii) in adult human subjects living at low (LA) and high altitude (HA). A total of 175 participants were given 3 g of either placebo, black, or red maca extract daily for 12 weeks. Primary outcomes were changes in sexual desire, mood, energy, health-related quality of life score (HRQL), and chronic mountain sickness (CMS) score, or in glycaemia, blood pressure, and hemoglobin levels. Secondary outcomes were acceptability and safety, assessed using the Likert test and side effect self-recording, respectively, and the effect of altitude. At low altitude, 32, 30, and 32 participants started the study receiving placebo, red maca, or black maca, respectively. At high altitudes, 33, 35, and 31 participants started the study receiving placebo, red maca, and black maca, respectively. Consumption of spray-dried extracts of red and black maca resulted in improvement in mood, energy, and health status, and reduced CMS score. Fatty acids and macamides were higher in spray-dried extracts of black maca than in red maca. GABA predominated in spray-dried extracts of red maca. Effects on mood, energy, and CMS score were better with red maca. Black maca and, in smaller proportions, red maca reduced hemoglobin levels only in highlanders with abnormally high hemoglobin levels; neither variety of maca reduced hemoglobin levels in lowlanders. Black maca reduced blood glucose levels. Both varieties produced similar responses in mood, and HRQL score. Maca extracts consumed at LA or HA had good acceptability and did not show serious adverse effects. In conclusion, maca extract consumption relative to the placebo improved quality of life parameters. Differences in the level of improvement between red and black maca are probably due to differences in the composition of these two plant varieties. Both maca extracts were well tolerated and safe. PMID:27548190

Acceptability, Safety, and Efficacy of Oral Administration of Extracts of Black or Red Maca (Lepidium meyenii) in Adult Human Subjects: A Randomized, Double-Blind, Placebo-Controlled Study.

PubMed

Gonzales-Arimborgo, Carla; Yupanqui, Irma; Montero, Elsa; Alarcón-Yaquetto, Dulce E; Zevallos-Concha, Alisson; Caballero, Lidia; Gasco, Manuel; Zhao, Jianping; Khan, Ikhlas A; Gonzales, Gustavo F

2016-08-18

The plant maca, grown at 4000 m altitude in the Peruvian Central Andes, contains hypocotyls that have been used as food and in traditional medicine for centuries. The aim of this research was to provide results on some health effects of oral administration of spray-dried extracts of black or red maca (Lepidium meyenii) in adult human subjects living at low (LA) and high altitude (HA). A total of 175 participants were given 3 g of either placebo, black, or red maca extract daily for 12 weeks. Primary outcomes were changes in sexual desire, mood, energy, health-related quality of life score (HRQL), and chronic mountain sickness (CMS) score, or in glycaemia, blood pressure, and hemoglobin levels. Secondary outcomes were acceptability and safety, assessed using the Likert test and side effect self-recording, respectively, and the effect of altitude. At low altitude, 32, 30, and 32 participants started the study receiving placebo, red maca, or black maca, respectively. At high altitudes, 33, 35, and 31 participants started the study receiving placebo, red maca, and black maca, respectively. Consumption of spray-dried extracts of red and black maca resulted in improvement in mood, energy, and health status, and reduced CMS score. Fatty acids and macamides were higher in spray-dried extracts of black maca than in red maca. GABA predominated in spray-dried extracts of red maca. Effects on mood, energy, and CMS score were better with red maca. Black maca and, in smaller proportions, red maca reduced hemoglobin levels only in highlanders with abnormally high hemoglobin levels; neither variety of maca reduced hemoglobin levels in lowlanders. Black maca reduced blood glucose levels. Both varieties produced similar responses in mood, and HRQL score. Maca extracts consumed at LA or HA had good acceptability and did not show serious adverse effects. In conclusion, maca extract consumption relative to the placebo improved quality of life parameters. Differences in the level of improvement between red and black maca are probably due to differences in the composition of these two plant varieties. Both maca extracts were well tolerated and safe.

Optimization of the Ultrasonic-Assisted Extraction of Bioactive Flavonoids from Ampelopsis grossedentata and Subsequent Separation and Purification of Two Flavonoid Aglycones by High-Speed Counter-Current Chromatography.

PubMed

Zhang, Hongbing; Xie, Guoyong; Tian, Mei; Pu, Qian; Qin, Minjian

2016-08-20

The fermented leaf of Ampelopsis grossedentata has been used as a beverage and folk medicine called "vine tea" in the southern region of China. In this paper, the optimum extraction conditions for the maximum recovery amounts of total flavonoids (TF), dihydromyricetin (DMY), myricitrin (MYG) and myricetin (MY) from natural Ampelopsis grossedentata leaves subjected to ultrasonic-assisted extraction (UAE) were determined and optimized by using response surface methodology. The method was employed by the Box-Behnken design (BBD) and Derringer's desirability function using methanol concentration, extraction time, liquid/solid ratio as factors and the contents of TF, DMY, MYG and MY as responses. The obtained optimum UAE conditions were as follows: a solvent of 80.87% methanol, an extraction time of 31.98 min and a liquid/solid ratio of 41.64:1 mL/g. Through analysis of the response surface, it implied that methanol concentration and the liquid/solid ratio had significant effects on TF, DMY, MYG and MY yields, whereas extraction time had relatively little effects. The established extraction and analytical methods were successfully applied to determine the contents of the total flavonoids and three individual flavonoids in 10 batches of the leaf samples of A. grossedentata from three counties in Fujian Province, China. The results suggested the variability in the quality of A. grossedentata leaves from different origins. In addition, high purities of dihydromyricetin and myricetin were simultaneously separated and purified from the extract subjected to optimized UAE, by high-speed counter-current chromatography using a solvent system of N-hexane-ethyl acetate-methanol-water (1:3:2:4; v/v/v/v). In a single operation, 200 mg of the extract were separated to yield 86.46 mg of dihydromyricetin and 3.61 mg of myricetin with the purity of 95.03% and 99.21%, respectively. The results would be beneficial for further exploiting the herbal products and controlling the quality of the herb and its derived products.

Inexpensive metagenomic DNA extraction protocol with high quality from marine sediments contaminated by petroleum hydrocarbons.

PubMed

García-Bautista, I; Toledano-Thompson, T; Dantán-González, E; González-Montilla, J; Valdez-Ojeda, R

2017-09-21

Marine environments are a reservoir of relevant information on dangerous contaminants such as hydrocarbons, as well as microbial communities with probable degradation skills. However, to access microbial diversity, it is necessary to obtain high-quality DNA. An inexpensive, reliable, and effective metagenomic DNA (mgDNA) extraction protocol from marine sediments contaminated with petroleum hydrocarbons was established in this study from modifications to Zhou's protocol. The optimization included pretreatment of sediment with saline solutions for the removal of contaminants, a second precipitation and enzymatic degradation of RNA, followed by purification of mgDNA extracted by electroelution. The results obtained indicated that the modifications applied to 12 sediments with total petroleum hydrocarbon (TPH) concentrations from 22.6-174.3 (µg/g dry sediment) yielded 20.3-321.3 ng/µL mgDNA with A 260 /A 280 and A 260 /A 230 ratios of 1.75 ± 0.08 and 1.19 ± 0.22, respectively. The 16S rRNA amplification confirmed the purity of the mgDNA. The suitability of this mgDNA extraction protocol lies in the fact that all chemical solutions utilized are common in all molecular biology laboratories, and the use of dialysis membrane does not require any sophisticated or expensive equipment, only an electrophoretic chamber.

Two-beam combined 3.36  J, 100  Hz diode-pumped high beam quality Nd:YAG laser system.

PubMed

Qiu, J S; Tang, X X; Fan, Z W; Wang, H C; Liu, H

2016-07-20

In this paper, we develop a diode-pumped all-solid-state high-energy and high beam quality Nd:YAG laser system. A master oscillator power amplifier structure is used to provide a high pulse energy laser output with a high repetition rate. In order to decrease the amplifier working current so as to reduce the impact of the thermal effect on the beam quality, a beam splitting-amplifying-combining scheme is adopted. The energy extraction efficiency of the laser system is 50.68%. We achieve 3.36 J pulse energy at a 100 Hz repetition rate with a pulse duration of 7.1 ns, a far-field beam spot 1.71 times the diffraction limit, and 1.07% energy stability (RMS).

Application of in situ ductal perfusion to facilitate isolation of high-quality RNA from mouse pancreas.

PubMed

Mullin, Anne E; Soukatcheva, Galina; Verchere, C Bruce; Chantler, Janet K

2006-05-01

A technique to isolate high-quality intact RNA from murine pancreas is described. This technique involves in situ ductal perfusion of the pancreas with an RNase inhibitor prior to removal of the organ for RNA extraction. In this way, the pancreatic RNases are inhibited in situ allowing good yields of intact RNA, suitable for studies on pancreatic gene transcription by real-time PCR or microarray analysis, to be obtained in a reliable way.

Specific immunotherapy for rhinitis and asthma with a subcutaneous hypoallergenic high-dose house dust mite extract: results of a 9-month therapy.

PubMed

El-Qutob, David; Moreno, Francisco; Subtil-Rodríguez, Alicia

2016-07-01

Effectiveness of a 9-month specific immunotherapy with a subcutaneous hypoallergenic high-dose house dust mite extract to reduce allergic symptoms as perceived by patients and physicians was assessed. An observational, retrospective, multicenter study was carried out in patients diagnosed with asthma and/or rhinitis caused by house dust mites having started specific immunotherapy with Acaroid(®). Primary end point was perceived effectiveness. A total of 409 patients were included. According to physician-completed visual analogue scale, a 58.1% clinical improvement was observed. Patient-completed visual analogue scale showed a 69.8% clinical improvement. The need for unscheduled/emergency healthcare, as an indication of poor quality of life, showed a significant reduction. Our results confirm in a real-world setting the findings from randomized clinical trials of high-dose house dust mites allergoid immunotherapy with a subcutaneous hypoallergenic high-dose house dust mite extract.

A combination of solvent extraction and freeze thaw for oil recovery from petroleum refinery wastewater treatment pond sludge.

PubMed

Hu, Guangji; Li, Jianbing; Hou, Haobo

2015-01-01

A combination of solvent extraction and freeze thaw was examined for recovering oil from the high-moisture petroleum refinery wastewater treatment pond sludge. Five solvents including cyclohexane (CHX), dichloromethane (DCM), methyl ethyl ketone (MEK), ethyl acetate (EA), and 2-propanol (2-Pro) were examined. It was found that these solvents except 2-Pro showed a promising oil recovery rate of about 40%, but the recycling of DCM solvent after oil extraction was quite low. Three solvents (CHX, MEK and EA) were then selected for examining the effect of freeze/thaw treatment on improving the quality of recovered oil. This treatment increased the total petroleum hydrocarbon (TPH) content in recovered oil from about 40% to 60% for both MEK and EA extractions, but little effect was observed for CHX extraction. Although the solid residue after oil recovery had a significantly decreased TPH content, a high concentration of heavy metals was observed, indicating that this residue may require proper management. In general, the combination of solvent extraction with freeze/thaw is effective for high-moisture oily hazardous waste treatment. Copyright © 2014 Elsevier B.V. All rights reserved.

Modified salting-out method: high-yield, high-quality genomic DNA extraction from whole blood using laundry detergent.

PubMed

Nasiri, H; Forouzandeh, M; Rasaee, M J; Rahbarizadeh, F

2005-01-01

Different approaches have been used to extract DNA from whole blood. In most of these methods enzymes (such as proteinase K and RNAse A) or toxic organic solvents (such as phenol or guanidine isothiocyanate) are used. Since these enzymes are expensive, and most of the materials that are used routinely are toxic, it is desirable to apply an efficient DNA extraction procedure that does not require the use of such materials. In this study, genomic DNA was extracted by the salting-out method, but instead of using an analytical-grade enzyme and chemical detergents, as normally used for DNA isolation, a common laundry powder was used. Different concentrations of the powder were tested, and proteins were precipitated by NaCl-saturated distilled water. Finally, DNA precipitation was performed with the use of 96% ethanol. From the results, we conclude that the optimum concentration of laundry powder for the highest yield and purity of isolated DNA is 30 mg/mL. The procedure was optimized, and a final protocol is suggested. Following the same protocol, DNA was extracted from 100 blood samples, and their amounts were found to be >50 microg/mL of whole blood. The integrity of the DNA fragments was confirmed by agarose gel electrophoresis. Furthermore, the extracted DNA was used as a template for PCR reaction. The results obtained from PCR showed that the final solutions of extracted DNA did not contain any inhibitory material for the enzyme used in the PCR reaction, and indicated that the isolated DNA was of good quality. These results show that this method is simple, fast, safe, and cost-effective, and can be used in medical laboratories and research centers. Copyright 2005 Wiley-Liss, Inc.

Learning a Health Knowledge Graph from Electronic Medical Records.

PubMed

Rotmensch, Maya; Halpern, Yoni; Tlimat, Abdulhakim; Horng, Steven; Sontag, David

2017-07-20

Demand for clinical decision support systems in medicine and self-diagnostic symptom checkers has substantially increased in recent years. Existing platforms rely on knowledge bases manually compiled through a labor-intensive process or automatically derived using simple pairwise statistics. This study explored an automated process to learn high quality knowledge bases linking diseases and symptoms directly from electronic medical records. Medical concepts were extracted from 273,174 de-identified patient records and maximum likelihood estimation of three probabilistic models was used to automatically construct knowledge graphs: logistic regression, naive Bayes classifier and a Bayesian network using noisy OR gates. A graph of disease-symptom relationships was elicited from the learned parameters and the constructed knowledge graphs were evaluated and validated, with permission, against Google's manually-constructed knowledge graph and against expert physician opinions. Our study shows that direct and automated construction of high quality health knowledge graphs from medical records using rudimentary concept extraction is feasible. The noisy OR model produces a high quality knowledge graph reaching precision of 0.85 for a recall of 0.6 in the clinical evaluation. Noisy OR significantly outperforms all tested models across evaluation frameworks (p < 0.01).

Active Semi-Supervised Community Detection Based on Must-Link and Cannot-Link Constraints

PubMed Central

Cheng, Jianjun; Leng, Mingwei; Li, Longjie; Zhou, Hanhai; Chen, Xiaoyun

2014-01-01

Community structure detection is of great importance because it can help in discovering the relationship between the function and the topology structure of a network. Many community detection algorithms have been proposed, but how to incorporate the prior knowledge in the detection process remains a challenging problem. In this paper, we propose a semi-supervised community detection algorithm, which makes full utilization of the must-link and cannot-link constraints to guide the process of community detection and thereby extracts high-quality community structures from networks. To acquire the high-quality must-link and cannot-link constraints, we also propose a semi-supervised component generation algorithm based on active learning, which actively selects nodes with maximum utility for the proposed semi-supervised community detection algorithm step by step, and then generates the must-link and cannot-link constraints by accessing a noiseless oracle. Extensive experiments were carried out, and the experimental results show that the introduction of active learning into the problem of community detection makes a success. Our proposed method can extract high-quality community structures from networks, and significantly outperforms other comparison methods. PMID:25329660

Significant Enrichment of Polyunsaturated Fatty Acids (PUFAs) in the Lipids Extracted by Supercritical CO2 from the Livers of Australian Rock Lobsters (Jasus edwardsii).

PubMed

Nguyen, Trung T; Zhang, Wei; Barber, Andrew R; Su, Peng; He, Shan

2015-05-13

Australian rock lobster (Jasus edwardsii) liver contains approximately 24.3% (w/w) lipids, which can contain a high amount of polyunsaturated fatty acids (PUFAs). However, this material has been found to be contaminated with arsenic (240 mg/kg) and cadmium (8 mg/kg). The high level of contaminants in the raw material and the large amount of PUFAs in the lipids prove a significant challenge in the extraction of high-quality lipids from this byproduct by conventional methods. Supercritical carbon dioxide (SC-CO2) extraction is a highly promising technology for lipid extraction with advantages including low contamination and low oxidation. The technique was optimized to achieve nearly 94% extraction of lipids relative to conventional Soxhlet extraction in Australian rock lobster liver at conditions of 35 MPa and 50 °C for 4 h. The extracted lipids are significantly enriched in PUFAs at 31.3% of total lipids, 4 times higher than those in the lipids recovered by Soxhlet extraction (7.8%). Specifically, the concentrations of docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) in SC-CO2 extraction are 7 times higher than those obtained by Soxhlet extraction. Moreover, very small amounts of toxic heavy metals such as lead (Pb), arsenic (As), mercury (Hg), and cadmium (Cd) were detected in the SC-CO2-extracted lipids, 0.5-27 times lower than those in the Soxhlet-extracted lipids, which are 40-200 times lower than the regulatory limit maximum values. The low levels of contaminants and the high proportion of PUFAs (dominated by DHA and EPA) found in the SC-CO2-extracted lipids from Australian rock lobster liver suggest that the material could potentially be used as a valuable source of essential fatty acids for human consumption.

Automated DNA extraction from genetically modified maize using aminosilane-modified bacterial magnetic particles.

PubMed

Ota, Hiroyuki; Lim, Tae-Kyu; Tanaka, Tsuyoshi; Yoshino, Tomoko; Harada, Manabu; Matsunaga, Tadashi

2006-09-18

A novel, automated system, PNE-1080, equipped with eight automated pestle units and a spectrophotometer was developed for genomic DNA extraction from maize using aminosilane-modified bacterial magnetic particles (BMPs). The use of aminosilane-modified BMPs allowed highly accurate DNA recovery. The (A(260)-A(320)):(A(280)-A(320)) ratio of the extracted DNA was 1.9+/-0.1. The DNA quality was sufficiently pure for PCR analysis. The PNE-1080 offered rapid assay completion (30 min) with high accuracy. Furthermore, the results of real-time PCR confirmed that our proposed method permitted the accurate determination of genetically modified DNA composition and correlated well with results obtained by conventional cetyltrimethylammonium bromide (CTAB)-based methods.

[Quality comparison of Hirudo before and after processed by French chalk].

PubMed

Zhang, Yong-Tai

2008-04-01

To evaluate the effects of processing methods of Hirudo. Both water and alcohol extracts of Hirudo were studied according to Chinese Pharmacopeia (Edition 2005). The content of hypoxanthine in Hirudo was measured by high performance liquid chromatography (HPLC) and Hirudin was determined by thrombin. The contents of water, water soluble extraction, ethanol soluble extraction and hirudin in crude Hirudo are higher than those in processed Hirudo. But the contents of hypoxanthine in processed Hirudo is higher than in crude Hirudo. Hirudo fried by French chalk can decrease the active components with high intensive drug property, accordingly the toxicity of Hirudo was decreased. As a result, the effects of Hirudo as invigorate the circulation of blood and stimulate the menstrual flow were abated.

Use of Moringa oleifera Flower Pod Extract as Natural Preservative and Development of SCAR Marker for Its DNA Based Identification.

PubMed

Gull, Iram; Javed, Attia; Aslam, Muhammad Shahbaz; Mushtaq, Roohi; Athar, Muhammad Amin

2016-01-01

The use of Moringa oleifera as natural food preservative has been evaluated in the present study. In addition, for quality assurance, the study has also been focused on the shelf life of product to authenticate the identification of plant by development of DNA based marker. Among the different extracts prepared from flower pods of Moringa oleifera, methanol and aqueous extract exhibited high antibacterial and antioxidant activity, respectively. The high phenolic contents (53.5 ± 0.169 mg GAE/g) and flavonoid contents (10.9 ± 0.094 mg QE/g) were also recorded in methanol and aqueous extract, respectively. Due to instability of bioactive compounds in aqueous extract, methanol extract is considered as potent natural preservative. The shelf life of methanol extract was observed for two months at 4°C under dark conditions. The developed SCAR primers (MOF217/317/MOR317) specifically amplified a fragment of 317 bp from DNA of Moringa oleifera samples collected from different regions of Punjab province of Pakistan. The methanol extract of Moringa oleifera flower pods has great potential to be used as natural preservative and nutraceutical in food industry.

Use of Moringa oleifera Flower Pod Extract as Natural Preservative and Development of SCAR Marker for Its DNA Based Identification

PubMed Central

Gull, Iram; Javed, Attia; Aslam, Muhammad Shahbaz; Mushtaq, Roohi; Athar, Muhammad Amin

2016-01-01

The use of Moringa oleifera as natural food preservative has been evaluated in the present study. In addition, for quality assurance, the study has also been focused on the shelf life of product to authenticate the identification of plant by development of DNA based marker. Among the different extracts prepared from flower pods of Moringa oleifera, methanol and aqueous extract exhibited high antibacterial and antioxidant activity, respectively. The high phenolic contents (53.5 ± 0.169 mg GAE/g) and flavonoid contents (10.9 ± 0.094 mg QE/g) were also recorded in methanol and aqueous extract, respectively. Due to instability of bioactive compounds in aqueous extract, methanol extract is considered as potent natural preservative. The shelf life of methanol extract was observed for two months at 4°C under dark conditions. The developed SCAR primers (MOF217/317/MOR317) specifically amplified a fragment of 317 bp from DNA of Moringa oleifera samples collected from different regions of Punjab province of Pakistan. The methanol extract of Moringa oleifera flower pods has great potential to be used as natural preservative and nutraceutical in food industry. PMID:27471732

Optimization of simultaneous ultrasonic-assisted extraction of water-soluble and fat-soluble characteristic constituents from Forsythiae Fructus Using response surface methodology and high-performance liquid chromatography

PubMed Central

Xia, Yong-Gang; Yang, Bing-You; Liang, Jun; Wang, Di; Yang, Qi; Kuang, Hai-Xue

2014-01-01

Background: The compounds (+)-pinoresinol-β-glucoside (1) forsythiaside, (2) phillyrin (3) and phillygenin (4) were elucidated to be the characteristic constituents for quality control of Forsythiae Fructus extract by chromatographic fingerprint in 2010 edition of Chinese Pharmacopoeia due to their numerous important pharmacological actions. It is of great interest to extract these medicinally active constituents from Forsythiae Fructus simultaneously. Materials and Methods: In this study, a new ultrasound-assisted extraction (UAE) method was developed for the simultaneous extraction of biological components 1-4 in Forsythiae Fructus. The quantitative effects of extraction time, ratio of liquid to solid, extraction temperature, and methanol concentration on yield of these four important biological constituents from Forsythiae Fructus were investigated using response surface methodology with Box-Behnken design. The compounds 1-4 extracted by UAE were quantitative analysis by high-performance liquid chromatography-photodiode array detect (HPLC-PAD), and overall desirability (OD), the geometric mean of the contents of four major biological components, was used as a marker to evaluate the extraction efficiency. Results: By solving the regression equation and analyzing 3-D plots, the optimum condition was at extraction temperature 70°C, time 60 min, ratio of liquid to solid 20, and methanol concentration 76.6%. Under these conditions, extraction yields of compounds 1-4 were 2.92 mg/g, 52.10 mg/g, 0.90 mg/g and 0.57 mg/g, respectively, which were in good agreement with the predicted OD values. In order to achieve a similar yield as UAE, soxhlet extraction required at least 6 h and maceration extraction required much longer time of 24 h. Established UAE method has been successfully applied to sample preparation for the quality control of Forsythiae Fructus. Additionally, a quadrupole time-of-flight mass spectrometry was applied to the structural confirmation of analytes from the complex matrices acquired by UAE. Conclusion: The results indicated that UAE is an effective alternative method for extracting bioactive constituents, which may facilitate a deeper understanding of the extract of active constituents in Forsythiae Fructus from the raw material to its extract for providing the theoretical references. PMID:25210317

Comparison of DNA extraction methods for human gut microbial community profiling.

PubMed

Lim, Mi Young; Song, Eun-Ji; Kim, Sang Ho; Lee, Jangwon; Nam, Young-Do

2018-03-01

The human gut harbors a vast range of microbes that have significant impact on health and disease. Therefore, gut microbiome profiling holds promise for use in early diagnosis and precision medicine development. Accurate profiling of the highly complex gut microbiome requires DNA extraction methods that provide sufficient coverage of the original community as well as adequate quality and quantity. We tested nine different DNA extraction methods using three commercial kits (TianLong Stool DNA/RNA Extraction Kit (TS), QIAamp DNA Stool Mini Kit (QS), and QIAamp PowerFecal DNA Kit (QP)) with or without additional bead-beating step using manual or automated methods and compared them in terms of DNA extraction ability from human fecal sample. All methods produced DNA in sufficient concentration and quality for use in sequencing, and the samples were clustered according to the DNA extraction method. Inclusion of bead-beating step especially resulted in higher degrees of microbial diversity and had the greatest effect on gut microbiome composition. Among the samples subjected to bead-beating method, TS kit samples were more similar to QP kit samples than QS kit samples. Our results emphasize the importance of mechanical disruption step for a more comprehensive profiling of the human gut microbiome. Copyright © 2017 The Authors. Published by Elsevier GmbH.. All rights reserved.

Supercritical Carbon Dioxide Extraction of Selected Herbal Leaves: An Overview

NASA Astrophysics Data System (ADS)

Hamid, I. A. Abd; Ismail, N.; Rahman, N. Abd

2018-05-01

Supercritical fluid extraction of carbon dioxide (SC-CO2) is one of new alternative extraction method that has been widely used to isolate bioactive components from variety of plant materials. The method was proved to be clean and safe, compatible for the extraction of edible products such as spices, food additives, medicines and nutritional supplement products compared to traditional extraction techniques such as solvent extraction, hydro distillation and steam distillation. The SC-CO2 extraction was known as highly influenced by its process parameter such as temperature and pressure for obtaining maximum yield. Therefore, a clear review on the optimum range of temperature and pressure for herbal leaves extraction using SC-CO2 is necessary for future reference. The aim of this work is to analyze the effect of temperature and pressure of SC-CO2 process without modifier on extraction yield of some selected herbal leaves i.e clubmoss, drumstick leaves, kratom leaves, mallee and myrtle leaves. The values of investigated parameters were; pressure from 8.9 to 50 MPa and temperature from 35 to 80°C. The results showed that the highest extraction yields were obtained when the pressure and temperature were above 30 MPa and 40°C. The interaction between pressure and temperature for SC-CO2 extraction of plant leaves are crucial since the values cannot be very high or very low in order to preserve the quality of the extracts.

Chemical Analysis and Study of Phenolics, Antioxidant Activity, and Antibacterial Effect of the Wood and Bark of Maclura tinctoria (L.) D. Don ex Steud.

PubMed Central

Lamounier, K. C.; Cunha, L. C. S.; de Morais, S. A. L.; de Aquino, F. J. T.; Chang, R.; do Nascimento, E. A.; de Souza, M. G. M.; Martins, C. H. G.; Cunha, W. R.

2012-01-01

Maclura tinctoria (L.) D. Don ex Steud. has one of the highest qualities among the coefficients for Brazilian woods (up to 9.6) and resistance rates equivalent to Indian teak (Tectona grandis). In this study, the macromolecular constituents and total phenols compounds as well as the antioxidant and antibacterial activities of this wood were evaluated. Total phenols and proanthocyanidin levels were higher in wood when compared with bark levels. The antioxidant activity of wood extracts (IC50 = 18.7 μg/mL) was more effective than that of bark extracts (IC50 = 20.9 μg/mL). Wood and bark extracts revealed a high potential for inhibition of aerobic and anaerobic bacteria. The bark extracts were the most active (MIC from 20 to 60 μg/mL). Both antioxidant activity and high potential for bacteria inhibition turn these extracts promising for drug formulations, especially as antibacterial agent. PMID:22454666

Protein Oxidation and Sensory Quality of Brine-Injected Pork Loins Added Ascorbate or Extracts of Green Tea or Maté during Chill-Storage in High-Oxygen Modified Atmosphere

PubMed Central

Tørngren, Mari Ann

2018-01-01

Background: Ascorbate is often applied to enhance stability and robustness of brine-injected pork chops sold for retail, but may affect protein oxidation, while plant extracts are potential substitutes. Methods: Brine-injected pork chops (weight-gain ~12%, NaCl ~0.9%) prepared with ascorbate (225 ppm), green tea extract (25 ppm gallic acid equivalents (GAE)), or maté extract (25 ppm GAE) stored (5 °C, seven days) in high-oxygen atmosphere packaging (MAP: 80% O2 and 20% CO2) were analyzed for color changes, sensory quality, and protein oxidation compared to a control without antioxidant. Results: No significant differences were observed for green tea and maté extracts as compared to ascorbate when evaluated based on lipid oxidation derived off-flavors, except for stale flavor, which maté significantly reduced. All treatments increased the level of the protein oxidation product, α-aminoadipic semialdehyde as compared to the control, and ascorbate was further found to increase thiol loss and protein cross-linking, with a concomitant decrease in the sensory perceived tenderness. Conclusions: Green tea and maté were found to equally protect against lipid oxidation derived off-flavors, and maté showed less prooxidative activity towards proteins as compared to ascorbate, resulting in more tender meat. Maté is a valuable substitute for ascorbate in brine-injected pork chops. PMID:29342928

A comparative study on composition and antioxidant activities of supercritical carbon dioxide, hexane and ethanol extracts from blackberry (Rubus fruticosus) growing in Poland.

PubMed

Wajs-Bonikowska, Anna; Stobiecka, Agnieszka; Bonikowski, Radosław; Krajewska, Agnieszka; Sikora, Magdalena; Kula, Józef

2017-08-01

Large quantities of blackberry seeds are produced as a pomace during the processing of juice and jam production; this by-product is a very interesting raw material both for oil manufacturing and as a source of bioactive compounds. In this work the composition, yield and antioxidant activity of three types of Rubus fructicosus pomace extracts isolated by liquid extraction using solvents of different polarity, as well with supercritical CO 2 fluid extraction have been compared. The highest extract yield was reported for Soxhlet extraction using ethanol as a solvent (14.2%). Supercritical carbon dioxide and hexane extracts were characterised by the highest content of phytosterols (1445 and 1583 mg 100 g -1 of extract, respectively) among which β-sitosterol was the main one, while the concentration of tocopherols, with predominant γ-isomer, was the highest for both hexane and ethanol extracts, being 2364 and 2334 mg 100 g -1 , respectively. Using a GC-MS method 95 volatiles, in which non-saturated aldehydes were predominant, were identified in the essential oil of seed pomace and in the volatile oil isolated from supercritical extract. The ethanolic extract which is characterised by the highest phenolic content (9443 mg GAE 100 g -1 ) exhibited the highest antioxidant activity (according to the ABTS •+ and DPPH • assays). All pomace extracts examined were of high quality, rich in essential omega fatty acids and with a very high content of bioactive compounds, such as phytosterols and tocopherols. The high nutritional value of extracts from berry seed pomace could justify the commercialisation of specific extracts not only as food additives but also as cosmetic components. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Comparation of Hypolipidemic and Antioxidant Effects of Aqueous and Ethanol Extracts of Crataegus pinnatifida Fruit in High-Fat Emulsion-Induced Hyperlipidemia Rats

PubMed Central

Shao, Feng; Gu, Lifei; Chen, Huijuan; Liu, Ronghua; Huang, Huilian; Ren, Gang

2016-01-01

Background: Hawthorn (Crataegus pinnatifida) is a Chinese medicinal plant traditionally used in the treatment of hyperlipidemia. Recently, studies indicated free radical scavenging was one of the major pathways to alleviate hyperlipidemia. Moreover, hawthorn fruit is a rich source of phenols, which quench free radical and attenuate hyperlipidemia. However, the phenols vary with processing methods, especially solvent type. Objective: Our aim was to compare hypolipidemic and antioxidant effects of aqueous and ethanol extracts of hawthorn fruit in hyperlipidemia rats. Materials and Methods: After a 4-week treatment of high-fat emulsion, lipid profile levels and antioxidant levels of two extracts were determined using commercial analysis. Total phenols content in the extract of hawthorn fruit was determined colorimetrically by the Folin–Ciocalteu method. Results: Both ethanol and aqueous extracts of hawthorn fruit possessed hypolipidemic and antioxidant activities. Simultaneously, stronger activities were observed in ethanol extract. Besides, total phenols content in ethanol extract from the same quality of hawthorn fruit was 3.9 times more than that in aqueous extract. Conclusion: The obvious difference of hypolipidemic and antioxidant effects between ethanol extract and aqueous extract of hawthorn fruit was probably due to the presence of total phenols content, under the influence of extraction solvent. SUMMARY Ethanol extract of hawthorn fruit exhibited more favorable hypolipidemic and antioxidant effects than aqueous extract. The higher effects could be due to the higher content of total phenols that varies with extraction solvent. Abbreviations used: TC: Total cholesterol, TG: Triglyceride, LDL-C: Low-density lipoprotein cholesterol, HDL-C: High-density lipoprotein cholesterol, GSH-Px: Glutathione peroxidase, SOD: Superoxide dismutase, MDA: Malondialdehyde, CAT: Catalase, NO: Nitric oxide, NOS: Nitric oxide synthase, SR-BI: Scavenger receptor Class B Type I PMID:27019563

Comparation of Hypolipidemic and Antioxidant Effects of Aqueous and Ethanol Extracts of Crataegus pinnatifida Fruit in High-Fat Emulsion-Induced Hyperlipidemia Rats.

PubMed

Shao, Feng; Gu, Lifei; Chen, Huijuan; Liu, Ronghua; Huang, Huilian; Ren, Gang

2016-01-01

Hawthorn (Crataegus pinnatifida) is a Chinese medicinal plant traditionally used in the treatment of hyperlipidemia. Recently, studies indicated free radical scavenging was one of the major pathways to alleviate hyperlipidemia. Moreover, hawthorn fruit is a rich source of phenols, which quench free radical and attenuate hyperlipidemia. However, the phenols vary with processing methods, especially solvent type. Our aim was to compare hypolipidemic and antioxidant effects of aqueous and ethanol extracts of hawthorn fruit in hyperlipidemia rats. After a 4-week treatment of high-fat emulsion, lipid profile levels and antioxidant levels of two extracts were determined using commercial analysis. Total phenols content in the extract of hawthorn fruit was determined colorimetrically by the Folin-Ciocalteu method. Both ethanol and aqueous extracts of hawthorn fruit possessed hypolipidemic and antioxidant activities. Simultaneously, stronger activities were observed in ethanol extract. Besides, total phenols content in ethanol extract from the same quality of hawthorn fruit was 3.9 times more than that in aqueous extract. The obvious difference of hypolipidemic and antioxidant effects between ethanol extract and aqueous extract of hawthorn fruit was probably due to the presence of total phenols content, under the influence of extraction solvent. Ethanol extract of hawthorn fruit exhibited more favorable hypolipidemic and antioxidant effects than aqueous extract. The higher effects could be due to the higher content of total phenols that varies with extraction solvent. Abbreviations used: TC: Total cholesterol, TG: Triglyceride, LDL-C: Low-density lipoprotein cholesterol, HDL-C: High-density lipoprotein cholesterol, GSH-Px: Glutathione peroxidase, SOD: Superoxide dismutase, MDA: Malondialdehyde, CAT: Catalase, NO: Nitric oxide, NOS: Nitric oxide synthase, SR-BI: Scavenger receptor Class B Type I.

Photomask quality evaluation using lithography simulation and precision SEM image contour data

NASA Astrophysics Data System (ADS)

Murakawa, Tsutomu; Fukuda, Naoki; Shida, Soichi; Iwai, Toshimichi; Matsumoto, Jun; Nakamura, Takayuki; Hagiwara, Kazuyuki; Matsushita, Shohei; Hara, Daisuke; Adamov, Anthony

2012-11-01

To evaluate photomask quality, the current method uses spatial imaging by optical inspection tools. This technique at 1Xnm node has a resolution limit because small defects will be difficult to extract. To simulate the mask error-enhancement factor (MEEF) influence for aggressive OPC in 1Xnm node, wide FOV contour data and tone information are derived from high precision SEM images. For this purpose we have developed a new contour data extraction algorithm with sub-nanometer accuracy resulting in a wide Field of View (FOV) SEM image: (for example, more than 10um x 10um square). We evaluated MEEF influence of high-end photomask pattern using the wide FOV contour data of "E3630 MVM-SEMTM" and lithography simulator "TrueMaskTM DS" of D2S, Inc. As a result, we can detect the "invisible defect" as the MEEF influence using the wide FOV contour data and lithography simulator.

Synthesis of microspheres of triuranium octaoxide by simultaneous water and nitrate extraction from ascorbate-uranyl sols.

PubMed

Brykala, M; Deptula, A; Rogowski, M; Lada, W; Olczak, T; Wawszczak, D; Smolinski, T; Wojtowicz, P; Modolo, G

A new method for synthesis of uranium oxide microspheres (diameter <100 μm) has been developed. It is a variant of our patented Complex Sol-Gel Process, which has been used to synthesize high-quality powders of a wide variety of complex oxides. Starting uranyl-nitrate-ascorbate sols were prepared by addition of ascorbic acid to uranyl nitrate hexahydrate solution and alkalizing by aqueous ammonium hydroxide and then emulsified in 2-ethylhexanol-1 containing 1v/o SPAN-80. Drops of emulsion were firstly gelled by extraction of water by the solvent. Destruction of the microspheres during thermal treatment, owing to highly reactive components in the gels, requires modification of the gelation step by Double Extraction Process-simultaneously extraction of water and nitrates using Primene JMT, which completely eliminates these problem. Final step was calcination in air of obtained microspheres of gels to triuranium octaoxide.

The effect of non-structural components and lignin on hemicellulose extraction.

PubMed

Liu, Kai-Xuan; Li, Hong-Qiang; Zhang, Jie; Zhang, Zhi-Guo; Xu, Jian

2016-08-01

As the important structural component of corn stover, hemicellulose could be converted into a variety of high value-added products. However, high quality hemicellulose extraction is not an easy issue. The present study aims to investigate the effects of non-structural components (NSCs) and lignin removal on alkaline extraction of hemicellulose. Although NSCs were found to have a minimal effect on hemicellulose dissolution, they affected the color values of the hemicellulose extracts. The lignin limited the hemicellulose dissolution and increased the color value by binding to hemicellulose molecules and forming lignin-carbohydrate complexes. Sodium chlorite method can remove about 90% lignin from corn stover, especially the lignin connected to hemicellulose through p-coumaric and ferulic acids. Which increased the hemicellulose dissolution ratio to 93% and reduced the color value 14-28%, but the cost is about 20% carbohydrates lost. Copyright © 2016 Elsevier Ltd. All rights reserved.

Extraction and analysis of carotenoids from the New Zealand sea urchin Evechinus chloroticus gonads.

PubMed

Garama, Daniel; Bremer, Phil; Carne, Alan

2012-01-01

Sea urchin gonad (roe) is a highly valued food in Japan and North America. Gonad price is strongly influenced by quality, with appearance, especially colour being a major determinant. Previous attempts to extract a carotenoid profile from the New Zealand sea urchin species Evechinus chloroticus have been challenging due to the large amount of lipid present in the gonad. A carotenoid extraction and high performance liquid chromatography (HPLC) analysis method was developed to reduce lipid contamination by incorporating a saponification and lipid cold precipitation in the extraction procedure. This method enabled greater carotenoid purity and enhanced analysis by HPLC. Echinenone was found to be the main carotenoid present in all E. chloroticus gonads. Dark coloured gonads contained higher levels of fucoxanthin/fucoxanthinol, β-carotene and xanthophylls such as astaxanthin and canthaxanthin. This information on the modification and deposition of carotenoids will help in the development of diets to enhance gonad colour.

Extraction of space-charge-dominated ion beams from an ECR ion source: Theory and simulation

NASA Astrophysics Data System (ADS)

Alton, G. D.; Bilheux, H.

2004-05-01

Extraction of high quality space-charge-dominated ion beams from plasma ion sources constitutes an optimization problem centered about finding an optimal concave plasma emission boundary that minimizes half-angular divergence for a given charge state, independent of the presence or lack thereof of a magnetic field in the extraction region. The curvature of the emission boundary acts to converge/diverge the low velocity beam during extraction. Beams of highest quality are extracted whenever the half-angular divergence, ω, is minimized. Under minimum half-angular divergence conditions, the plasma emission boundary has an optimum curvature and the perveance, P, current density, j+ext, and extraction gap, d, have optimum values for a given charge state, q. Optimum values for each of the independent variables (P, j+ext and d) are found to be in close agreement with those derived from elementary analytical theory for extraction with a simple two-electrode extraction system, independent of the presence of a magnetic field. The magnetic field only increases the emittances of beams through additional aberrational effects caused by increased angular divergences through coupling of the longitudinal to the transverse velocity components of particles as they pass though the mirror region of the electron cyclotron resonance (ECR) ion source. This article reviews the underlying theory of elementary extraction optics and presents results derived from simulation studies of extraction of space-charge dominated heavy-ion beams of varying mass, charge state, and intensity from an ECR ion source with emphasis on magnetic field induced effects.

High Throughput Multispectral Image Processing with Applications in Food Science.

PubMed

Tsakanikas, Panagiotis; Pavlidis, Dimitris; Nychas, George-John

2015-01-01

Recently, machine vision is gaining attention in food science as well as in food industry concerning food quality assessment and monitoring. Into the framework of implementation of Process Analytical Technology (PAT) in the food industry, image processing can be used not only in estimation and even prediction of food quality but also in detection of adulteration. Towards these applications on food science, we present here a novel methodology for automated image analysis of several kinds of food products e.g. meat, vanilla crème and table olives, so as to increase objectivity, data reproducibility, low cost information extraction and faster quality assessment, without human intervention. Image processing's outcome will be propagated to the downstream analysis. The developed multispectral image processing method is based on unsupervised machine learning approach (Gaussian Mixture Models) and a novel unsupervised scheme of spectral band selection for segmentation process optimization. Through the evaluation we prove its efficiency and robustness against the currently available semi-manual software, showing that the developed method is a high throughput approach appropriate for massive data extraction from food samples.

Investigation on the supercritical CO(2) extraction of the volatile constituents from Juniperus communis obtained under different treatments of the "berries" (cones).

PubMed

Chatzopoulou, Paschalina; de Haan, Andre; Katsiotis, Stavros T

2002-09-01

The present investigation reports the experimental data a) from the recovery and the composition of the extract under super critical fluid extraction from Juniperus communis L. "berries" (cones), and b) their comparison with those of the essential oil obtained by hydrodistillation. For the extraction of the juniper oil different values of temperature and pressure were applied; furthermore, the degree of comminution of the plant material was also considered - a) integral "berries" and b) comminuted "berries". The quality of the oil recovered from the "berries" by supercritical carbon dioxide extraction was found to be highly dependent on the applied conditions. The comminution affected greatly the oil recovery and consequently the final composition of the extracts. Significant differences were recorded between the supercritical CO(2) extract and the distilled oil, the latter being more enriched in monoterpenoid hydrocarbons.

Choice of solvent extraction technique affects fatty acid composition of pistachio (Pistacia vera L.) oil.

PubMed

Abdolshahi, Anna; Majd, Mojtaba Heydari; Rad, Javad Sharifi; Taheri, Mehrdad; Shabani, Aliakbar; Teixeira da Silva, Jaime A

2015-04-01

Pistachio (Pistacia vera L.) oil has important nutritional and therapeutic properties because of its high concentration of essential fatty acids. The extraction method used to obtain natural compounds from raw material is critical for product quality, in particular to protect nutritional value. This study compared the fatty acid composition of pistachio oil extracted by two conventional procedures, Soxhlet extraction and maceration, analyzed by a gas chromatography-flame ionization detector (GC-FID). Four solvents with different polarities were tested: n-hexane (Hx), dichloromethane (DCM), ethyl acetate (EtAc) and ethanol (EtOH). The highest unsaturated fatty acid content (88.493 %) was obtained by Soxhlet extraction with EtAc. The Soxhlet method extracted the most oleic and linolenic acids (51.99 % and 0.385 %, respectively) although a higher concentration (36.32 %) of linoleic acid was extracted by maceration.

Human DNA extraction from whole saliva that was fresh or stored for 3, 6 or 12 months using five different protocols

PubMed Central

GARBIERI, Thais Francini; BROZOSKI, Daniel Thomas; DIONÍSIO, Thiago José; SANTOS, Carlos Ferreira; NEVES, Lucimara Teixeira das

2017-01-01

Abstract Saliva when compared to blood collection has the following advantages: it requires no specialized personnel for collection, allows for remote collection by the patient, is painless, well accepted by participants, has decreased risks of disease transmission, does not clot, can be frozen before DNA extraction and possibly has a longer storage time. Objective and Material and Methods This study aimed to compare the quantity and quality of human DNA extracted from saliva that was fresh or frozen for three, six and twelve months using five different DNA extraction protocols: protocol 1 – Oragene™ commercial kit, protocol 2 – QIAamp DNA mini kit, protocol 3 – DNA extraction using ammonium acetate, protocol 4 – Instagene™ Matrix and protocol 5 – Instagene™ Matrix diluted 1:1 using proteinase K and 1% SDS. Briefly, DNA was analyzed using spectrophotometry, electrophoresis and PCR. Results Results indicated that time spent in storage typically decreased the DNA quantity with the exception of protocol 1. The purity of DNA was generally not affected by storage times for the commercial based protocols, while the purity of the DNA samples extracted by the noncommercial protocols typically decreased when the saliva was stored longer. Only protocol 1 consistently extracted unfragmented DNA samples. In general, DNA samples extracted through protocols 1, 2, 3 and 4, regardless of storage time, were amplified by human specific primers whereas protocol 5 produced almost no samples that were able to be amplified by human specific primers. Depending on the protocol used, it was possible to extract DNA in high quantities and of good quality using whole saliva, and furthermore, for the purposes of DNA extraction, saliva can be reliably stored for relatively long time periods. Conclusions In summary, a complicated picture emerges when taking into account the extracted DNA’s quantity, purity and quality; depending on a given researchers needs, one protocol’s particular strengths and costs might be the deciding factor for its employment. PMID:28403355

Extracting Information about the Electronic Quality of Organic Solar-Cell Absorbers from Fill Factor and Thickness

NASA Astrophysics Data System (ADS)

Kaienburg, Pascal; Rau, Uwe; Kirchartz, Thomas

2016-08-01

Understanding the fill factor in organic solar cells remains challenging due to its complex dependence on a multitude of parameters. By means of drift-diffusion simulations, we thoroughly analyze the fill factor of such low-mobility systems and demonstrate its dependence on a collection coefficient defined in this work. We systematically discuss the effect of different recombination mechanisms, space-charge regions, and contact properties. Based on these findings, we are able to interpret the thickness dependence of the fill factor for different experimental studies from the literature. The presented model provides a facile method to extract the photoactive layer's electronic quality which is of particular importance for the fill factor. We illustrate that over the past 15 years, the electronic quality has not been continuously improved, although organic solar-cell efficiencies increased steadily over the same period of time. Only recent reports show the synthesis of polymers for semiconducting films of high electronic quality that are able to produce new efficiency records.

Interpretation of fingerprint image quality features extracted by self-organizing maps

NASA Astrophysics Data System (ADS)

Danov, Ivan; Olsen, Martin A.; Busch, Christoph

2014-05-01

Accurate prediction of fingerprint quality is of significant importance to any fingerprint-based biometric system. Ensuring high quality samples for both probe and reference can substantially improve the system's performance by lowering false non-matches, thus allowing finer adjustment of the decision threshold of the biometric system. Furthermore, the increasing usage of biometrics in mobile contexts demands development of lightweight methods for operational environment. A novel two-tier computationally efficient approach was recently proposed based on modelling block-wise fingerprint image data using Self-Organizing Map (SOM) to extract specific ridge pattern features, which are then used as an input to a Random Forests (RF) classifier trained to predict the quality score of a propagated sample. This paper conducts an investigative comparative analysis on a publicly available dataset for the improvement of the two-tier approach by proposing additionally three feature interpretation methods, based respectively on SOM, Generative Topographic Mapping and RF. The analysis shows that two of the proposed methods produce promising results on the given dataset.

Study on Quality Standard of Processed Curcuma Longa Radix

PubMed Central

Zhao, Yongfeng; Quan, Liang; Zhou, Haiting; Cao, Dong; Li, Wenbing; Yang, Zhuo

2017-01-01

To control the quality of Curcuma Longa Radix by establishing quality standards, this paper increased the contents of extract and volatile oil determination. Meanwhile, the curcumin was selected as the internal marker, and the relative correlation factors (RCFs) of demethoxycurcumin and bisdemethoxycurcumin were established by high performance liquid chromatography (HPLC). The contents of multicomponents were calculated based on their RCFs. The rationality and feasibility of the methods were evaluated by comparison of the quantitative results between external standard method (ESM) and quantitative analysis of multicomponents by single-marker (QAMS). Ethanol extracts ranged from 9.749 to 15.644% and the mean value was 13.473%. The volatile oil ranged from 0.45 to 0.90 mL/100 g and the mean value was 0.66 mL/100 g. This method was accurate and feasible and could provide a reference for further comprehensive and effective control of the quality standard of Curcuma Longa Radix and its processed products. PMID:29375640

How the variance of some extraction variables may affect the quality of espresso coffees served in coffee shops.

PubMed

Severini, Carla; Derossi, Antonio; Fiore, Anna G; De Pilli, Teresa; Alessandrino, Ofelia; Del Mastro, Arcangela

2016-07-01

To improve the quality of espresso coffee, the variables under the control of the barista, such as grinding grade, coffee quantity and pressure applied to the coffee cake, as well as their variance, are of great importance. A nonlinear mixed effect modeling was used to obtain information on the changes in chemical attributes of espresso coffee (EC) as a function of the variability of extraction conditions. During extraction, the changes in volume were well described by a logistic model, whereas the chemical attributes were better fit by a first-order kinetic. The major source of information was contained in the grinding grade, which accounted for 87-96% of the variance of the experimental data. The variability of the grinding produced changes in caffeine content in the range of 80.03 mg and 130.36 mg when using a constant grinding grade of 6.5. The variability in volume and chemical attributes of EC is large. Grinding had the most important effect as the variability in particle size distribution observed for each grinding level had a profound effect on the quality of EC. Standardization of grinding would be of crucial importance for obtaining all espresso coffees with a high quality. © 2015 Society of Chemical Industry. © 2015 Society of Chemical Industry.

Jussara berry (Euterpe edulis M.) oil-in-water emulsions are highly stable: the role of natural antioxidants in the fruit oil.

PubMed

Carvalho, Aline G A; Silva, Kelly A; Silva, Laís O; Costa, André M M; Akil, Emília; Coelho, Maria A Z; Torres, Alexandre G

2018-05-23

Antioxidants help prevent lipid oxidation, and therefore are critical to maintain sensory quality and chemical characteristics of edible oils. Jussara berry (Euterpe edulis M.) oil is a source of minor compounds with potential antioxidant activity. The aim of this work was to investigate the role of such compounds on the effectiveness to prevent or delay oxidation of oil present in oil-in-water emulsions, and how the emulsions physical stability would be affected. Jussara berry oil extracted by ethanol extraction, its stripped variations (partially stripped, highly stripped and highly stripped with added BHT), and expeller pressed oil were used to prepare oil-in-water emulsions. Jussara berry oils were analyzed before emulsions preparation to ensure its initial quality and composition, and oil-in-water emulsions were analyzed regarding their oxidative and physical stability. Ethanol extracted oil emulsion presented higher oxidative stability when compared to highly stripped oil emulsion with added synthetic antioxidant BHT (oxidative stability index 45% lower, after 60 days, and reached undetectable levels after 90 days). All emulsions maintained physically stable for up to 120 days of storage. Our results indicate that natural antioxidants in jussara berry oil protect emulsions from oxidation while keeping physical stability unchanged. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Downstream Processing of Synechocystis for Biofuel Production

NASA Astrophysics Data System (ADS)

Sheng, Jie

Lipids and free fatty acids (FFA) from cyanobacterium Synechocystis can be used for biofuel (e.g. biodiesel or renewable diesel) production. In order to utilize and scale up this technique, downstream processes including culturing and harvest, cell disruption, and extraction were studied. Several solvents/solvent systems were screened for lipid extraction from Synechocystis. Chloroform + methanol-based Folch and Bligh & Dyer methods were proved to be "gold standard" for small-scale analysis due to their highest lipid recoveries that were confirmed by their penetration of the cell membranes, higher polarity, and stronger interaction with hydrogen bonds. Less toxic solvents, such as methanol and MTBE, or direct transesterification of biomass (without preextraction step) gave only slightly lower lipid-extraction yields and can be considered for large-scale application. Sustained exposure to high and low temperature extremes severely lowered the biomass and lipid productivity. Temperature stress also triggered changes of lipid quality such as the degree of unsaturation; thus, it affected the productivities and quality of Synechocystis-derived biofuel. Pulsed electric field (PEF) was evaluated for cell disruption prior to lipid extraction. A treatment intensity > 35 kWh/m3 caused significant damage to the plasma membrane, cell wall, and thylakoid membrane, and it even led to complete disruption of some cells into fragments. Treatment by PEF enhanced the potential for the low-toxicity solvent isopropanol to access lipid molecules during subsequent solvent extraction, leading to lower usage of isopropanol for the same extraction efficiency. Other cell-disruption methods also were tested. Distinct disruption effects to the cell envelope, plasma membrane, and thylakoid membranes were observed that were related to extraction efficiency. Microwave and ultrasound had significant enhancement of lipid extraction. Autoclaving, ultrasound, and French press caused significant release of lipid into the medium, which may increase solvent usage and make medium recycling difficult. Production of excreted FFA by mutant Synechocystis has the potential of reducing the complexity of downstream processing. Major problems, such as FFA precipitation and biodegradation by scavengers, account for FFA loss in operation. Even a low concentration of FFA scavengers could consume FFA at a high rate that outpaced FFA production rate. Potential strategies to overcome FFA loss include high pH, adsorptive resin, and sterilization techniques.

Use of Embryos Extracted from Individual Cannabis sativa Seeds for Genetic Studies and Forensic Applications.

PubMed

Soler, Salvador; Borràs, Dionís; Vilanova, Santiago; Sifres, Alicia; Andújar, Isabel; Figàs, Maria R; Llosa, Ernesto R; Prohens, Jaime

2016-03-01

Legal limits on the psychoactive tetrahydrocannabinol (THC) content in Cannabis sativa plants have complicated genetic and forensic studies in this species. However, Cannabis seeds present very low THC levels. We developed a method for embryo extraction from seeds and an improved protocol for DNA extraction and tested this method in four hemp and six marijuana varieties. This embryo extraction method enabled the recovery of diploid embryos from individual seeds. An improved DNA extraction protocol (CTAB3) was used to obtain DNA from individual embryos at a concentration and quality similar to DNA extracted from leaves. DNA extracted from embryos was used for SSR molecular characterization in individuals from the 10 varieties. A unique molecular profile for each individual was obtained, and a clear differentiation between hemp and marijuana varieties was observed. The combined embryo extraction-DNA extraction methodology and the new highly polymorphic SSR markers facilitate genetic and forensic studies in Cannabis. © 2015 American Academy of Forensic Sciences.

RP-HPTLC densitometric determination and validation of vanillin and related phenolic compounds in accelerated solvent extract of Vanilla planifolia*.

PubMed

Sharma, Upendra Kumar; Sharma, Nandini; Gupta, Ajai Prakash; Kumar, Vinod; Sinha, Arun Kumar

2007-12-01

A simple, fast and sensitive RP-HPTLC method is developed for simultaneous quantitative determination of vanillin and related phenolic compounds in ethanolic extracts of Vanilla planifolia pods. In addition to this, the applicability of accelerated solvent extraction (ASE) as an alternative to microwave-assisted extraction (MAE), ultrasound-assisted extraction (UAE) and Soxhlet extraction was also explored for the rapid extraction of phenolic compounds in vanilla pods. Good separation was achieved on aluminium plates precoated with silica gel RP-18 F(254S) in the mobile phase of methanol/water/isopropanol/acetic acid (30:65:2:3, by volume). The method showed good linearity, high precision and good recovery of compounds of interest. ASE showed good extraction efficiency in less time as compared to other techniques for all the phenolic compounds. The present method would be useful for analytical research and for routine analysis of vanilla extracts for their quality control.

Improved collagen extraction from jellyfish (Acromitus hardenbergi) with increased physical-induced solubilization processes.

PubMed

Khong, Nicholas M H; Yusoff, Fatimah Md; Jamilah, B; Basri, Mahiran; Maznah, I; Chan, Kim Wei; Armania, Nurdin; Nishikawa, Jun

2018-06-15

Efficiency and effectiveness of collagen extraction process contribute to huge impacts to the quality, supply and cost of the collagen produced. Jellyfish is a potential sustainable source of collagen where their applications are not limited by religious constraints and threats of transmittable diseases. The present study compared the extraction yield, physico-chemical properties and toxicology in vitro of collagens obtained by the conventional acid-assisted and pepsin-assisted extraction to an improved physical-aided extraction process. By increasing physical intervention, the production yield increased significantly compared to the conventional extraction processes (p < .05). Collagen extracted using the improved process was found to possess similar proximate and amino acids composition to those extracted using pepsin (p > .05) while retaining high molecular weight distributions and polypeptide profiles similar to those extracted using only acid. Moreover, they exhibited better appearance, instrumental colour and were found to be non-toxic in vitro and free of heavy metal contamination. Copyright © 2017 Elsevier Ltd. All rights reserved.

A proteomics performance standard to support measurement quality in proteomics.

PubMed

Beasley-Green, Ashley; Bunk, David; Rudnick, Paul; Kilpatrick, Lisa; Phinney, Karen

2012-04-01

The emergence of MS-based proteomic platforms as a prominent technology utilized in biochemical and biomedical research has increased the need for high-quality MS measurements. To address this need, National Institute of Standards and Technology (NIST) reference material (RM) 8323 yeast protein extract is introduced as a proteomics quality control material for benchmarking the preanalytical and analytical performance of proteomics-based experimental workflows. RM 8323 yeast protein extract is based upon the well-characterized eukaryote Saccharomyces cerevisiae and can be utilized in the design and optimization of proteomics-based methodologies from sample preparation to data analysis. To demonstrate its utility as a proteomics quality control material, we coupled LC-MS/MS measurements of RM 8323 with the NIST MS Quality Control (MSQC) performance metrics to quantitatively assess the LC-MS/MS instrumentation parameters that influence measurement accuracy, repeatability, and reproducibility. Due to the complexity of the yeast proteome, we also demonstrate how NIST RM 8323, along with the NIST MSQC performance metrics, can be used in the evaluation and optimization of proteomics-based sample preparation methods. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Determination by high performance chromatography, steroid saponins in a biologically active food supplements containing the extract of Tribulus terrestris].

PubMed

Kozlova, O I; Perederiaev, O I; Ramenskaia, G V

2011-01-01

Steroidal saponins are bioactive substances of Tribulus terrestris and can be used to assess the quality of raw materials and processed products from them. For this purpose has been developed the method of qualitative and quantitative determination of steroidal saponins by high performance liquid chromatography with spectrophotometric and mass-selective detection and optimal conditions of sample preparation (70% methanol extraction with sonication and heating); also has been studied steroidal saponins composition of Tribulus terrestris (protodioscin, tribulosaponin B, metilprotodiostsin, terrestrozin H, prototribestin, gracillin and others were found).

Has the use of talc an effect on yield and extra virgin olive oil quality?

PubMed

Caponio, Francesco; Squeo, Giacomo; Difonzo, Graziana; Pasqualone, Antonella; Summo, Carmine; Paradiso, Vito Michele

2016-08-01

The maximization of both extraction yield and extra virgin olive oil quality during olive processing are the main objectives of the olive oil industry. As regards extraction yield, it can be improved by both acting on time/temperature of malaxation and using physical coadjuvants. It is well known that, generally, increasing temperature of malaxation gives an increase in oil extraction yield due to a reduction in oily phase viscosity; however, high malaxation temperature can compromise the nutritional and health values of extra virgin olive oil, leading to undesirable effects such as accelerated oxidative process and loss of volatile compounds responsible for oil flavor and fragrance. The addition of physical coadjuvants in olive oil processing during the malaxation phase, not excluded by EC regulations owing to its exclusively physical action, is well known to promote the breakdown of oil/water emulsions and consequently make oil extraction easier, thus increasing the yield. Among physical coadjuvants, micronized natural talc is used for olive oil processing above all for Spanish and Italian olive cultivars. The quality of extra virgin olive oil depends on numerous variables such as olive cultivar, ripeness degree and quality, machines utilized for processing, oil storage conditions, etc. However, the coadjuvants utilized in olive processing can also influence virgin olive oil characteristics. The literature highlights an increase in oil yield by micronized natural talc addition during olive processing, whereas no clear trend was observed as regards the chemical, nutritional and sensory characteristics of extra virgin olive oil. Although an increase in oil stability was reported, no effect of talc was found on the evolution of virgin olive oil quality indices during storage. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

A unified framework for physical print quality

NASA Astrophysics Data System (ADS)

Eid, Ahmed; Cooper, Brian; Rippetoe, Ed

2007-01-01

In this paper we present a unified framework for physical print quality. This framework includes a design for a testbed, testing methodologies and quality measures of physical print characteristics. An automatic belt-fed flatbed scanning system is calibrated to acquire L* data for a wide range of flat field imagery. Testing methodologies based on wavelet pre-processing and spectral/statistical analysis are designed. We apply the proposed framework to three common printing artifacts: banding, jitter, and streaking. Since these artifacts are directional, wavelet based approaches are used to extract one artifact at a time and filter out other artifacts. Banding is characterized as a medium-to-low frequency, vertical periodic variation down the page. The same definition is applied to the jitter artifact, except that the jitter signal is characterized as a high-frequency signal above the banding frequency range. However, streaking is characterized as a horizontal aperiodic variation in the high-to-medium frequency range. Wavelets at different levels are applied to the input images in different directions to extract each artifact within specified frequency bands. Following wavelet reconstruction, images are converted into 1-D signals describing the artifact under concern. Accurate spectral analysis using a DFT with Blackman-Harris windowing technique is used to extract the power (strength) of periodic signals (banding and jitter). Since streaking is an aperiodic signal, a statistical measure is used to quantify the streaking strength. Experiments on 100 print samples scanned at 600 dpi from 10 different printers show high correlation (75% to 88%) between the ranking of these samples by the proposed metrologies and experts' visual ranking.

RNA Extraction from Animal and Human's Cancerous Tissues: Does Tissue Matter?

PubMed

Samadani, Ali Akbar; Nikbakhsh, Novin; Fattahi, Sadegh; Pourbagher, Roghayeh; Aghajanpour Mir, Seyyed Mohsen; Mousavi Kani, Narges; Abedian, Zeinab; Akhavan-Niaki, Haleh

2015-01-01

The reliability of gene expression profiling, based technologies and methods to find transcriptional differences representative of the original samples is influenced by the quality of the extracted RNA. Hence, RNA extraction is the first step to investigate the gene expression and its function. Consequently, the quality of extracted RNA is really significant. Correspondingly, this research was accomplished to optimize the RNA extraction methods and compare the amounts of tissue or quality of tissue. Relatively, the cancerous tissue of human stomach in fresh and frozen conditions and also the mouse fresh tissue were studied. Some factors like the amount of samples, efficacy differences of diverse extraction buffers (TriPure, Trizol) and also the efficacy of b-mercaptoethanol were compared and investigated. The results indicated that the less amount (1-2 mg) compared to other amounts (2-5 mg, 5-15 mg) yielded the best quality and the RNA bands (5S, 18S, 28S) were observed perfectly. Relatively, comparing and measuring some kinds of buffers (Trizol, TriPure) indicated no difference in RNA extraction quality. The last investigated factor was the effect of b- mercaptoethanol which was used along with TriPure to remove the RNAse. Conclusively, no effective impression was observed.

Quality of life improvement after a three-year course of sublingual immunotherapy in patients with house dust mite and grass pollen induced allergic rhinitis: results from real-life.

PubMed

Novakova, Silviya Mihaylova; Staevska, Maria Toncheva; Novakova, Plamena Ivanova; Yoncheva, Manuela Dimitrova; Bratoycheva, Maria Stoykova; Musurlieva, Nina Mihaylova; Tzekov, Valeri Dimitrov; Nicolov, Dimitar Georgiev

2017-09-29

Along with its high prevalence, the burden of allergic rhinitis rests upon the serious impact on quality of life of patients. Allergic rhinitis is associated with impairments in daily activities, work and school performance, and practical problems. Patients suffer from sleep disorders and emotional problems. Тhe advantages of sublingual immunotherapy on quality of life have only recently begun to emerge. The objective of this prospective real-life study was to evaluate the effect of a three-year course of sublingual immunotherapy with house dust mite (HDM) and grass pollen extracts on quality of life in adults with allergic rhinitis. A total number of 191 adult patients [105 (54,979%) men; mean age 27.3 years (SD-6.14)] with moderate to severe allergic rhinitis and clinically relevant sensitization to house dust mites or grass pollen were prospectively evaluated in the course of management of their disease. Health-related quality of life was assessed by Rhinoconjunctivitis Quality of Life Questionnaire at baseline and after three-year course of sublingual immunotherapy. The mean overall Qol score assessed at baseline and at the end of the third year of treatment decreased significantly in patients treated with HDM extract (from 2.95 to 0.76) as well as with Grass pollen extract (from 2.83 to 1.22) (р < 0.001). The improvements in treated with HDM extract were as followed: activities - 3.52 to 0.68; sleep- 2.48 to 0.31; general problems - 1.79 to 0.49; practical problems - 3.57 to 0.68; nasal symptoms - 3.91 to 0.74; eye symptoms - 2.92 to 0.39; emotions - 3.03 to 0.39. The improvements in grass pollen group were: activities - 3.68 to 1.69; sleep- 1.85 to 0.84; general problems - 1.74 to 0.97; practical problems - 3.52 to 1.37; nasal symptoms - 3.72 to 1.57; eye symptoms - 3.58 to 1.3; emotions - 2.48 to 1.19. Our study conducted in real life provided evidence that a three-year course of SLIT with HDM extract as well as with grass pollen extract significantly increased QoL in patients with allergic rhinitis.

Extraction of GBH Film Medicine and Influence on Quality Evaluation of The Film

NASA Astrophysics Data System (ADS)

Ji, Y. B.; Lu, L.; Ru, X.; Guo, S. Z.; Qiao, A. N.; Wang, S. W.

2017-12-01

To know the extraction effects of GBH film medicine and the influence on film quality evaluation. Ultrasonic extraction and reflux extraction were used to extract the two methods with the traditional water decocting method to contrast. They were used to determining the content of total flavonoids. The same method was used to separate the root of the main medicinal herbs and the decoction of the water decoction of the other drug powder. They were used to determine the content of total flavonoids. The effect of extraction method on the preparation of membrane was investigated. The membrane preparation, evaluation and flexibility, respectively, film-forming property, smoothness and disintegration time are used to evaluating separately the effect of extraction method. The results showed that the extraction effect of 70% ethanol concentration of total flavonoids. The best extraction method had no effect on the film quality initial evaluation. This experiment provides a method for membrane extraction agent, has a certain practical significance.

Predicting nucleic acid binding interfaces from structural models of proteins

PubMed Central

Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

2011-01-01

The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared to patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. PMID:22086767

High resolution mapping of development in the wildland-urban interface using object based image extraction.

PubMed

Caggiano, Michael D; Tinkham, Wade T; Hoffman, Chad; Cheng, Antony S; Hawbaker, Todd J

2016-10-01

The wildland-urban interface (WUI), the area where human development encroaches on undeveloped land, is expanding throughout the western United States resulting in increased wildfire risk to homes and communities. Although census based mapping efforts have provided insights into the pattern of development and expansion of the WUI at regional and national scales, these approaches do not provide sufficient detail for fine-scale fire and emergency management planning, which requires maps of individual building locations. Although fine-scale maps of the WUI have been developed, they are often limited in their spatial extent, have unknown accuracies and biases, and are costly to update over time. In this paper we assess a semi-automated Object Based Image Analysis (OBIA) approach that utilizes 4-band multispectral National Aerial Image Program (NAIP) imagery for the detection of individual buildings within the WUI. We evaluate this approach by comparing the accuracy and overall quality of extracted buildings to a building footprint control dataset. In addition, we assessed the effects of buffer distance, topographic conditions, and building characteristics on the accuracy and quality of building extraction. The overall accuracy and quality of our approach was positively related to buffer distance, with accuracies ranging from 50 to 95% for buffer distances from 0 to 100 m. Our results also indicate that building detection was sensitive to building size, with smaller outbuildings (footprints less than 75 m 2 ) having detection rates below 80% and larger residential buildings having detection rates above 90%. These findings demonstrate that this approach can successfully identify buildings in the WUI in diverse landscapes while achieving high accuracies at buffer distances appropriate for most fire management applications while overcoming cost and time constraints associated with traditional approaches. This study is unique in that it evaluates the ability of an OBIA approach to extract highly detailed data on building locations in a WUI setting.

High resolution mapping of development in the wildland-urban interface using object based image extraction

USGS Publications Warehouse

Caggiano, Michael D.; Tinkham, Wade T.; Hoffman, Chad; Cheng, Antony S.; Hawbaker, Todd J.

2016-01-01

The wildland-urban interface (WUI), the area where human development encroaches on undeveloped land, is expanding throughout the western United States resulting in increased wildfire risk to homes and communities. Although census based mapping efforts have provided insights into the pattern of development and expansion of the WUI at regional and national scales, these approaches do not provide sufficient detail for fine-scale fire and emergency management planning, which requires maps of individual building locations. Although fine-scale maps of the WUI have been developed, they are often limited in their spatial extent, have unknown accuracies and biases, and are costly to update over time. In this paper we assess a semi-automated Object Based Image Analysis (OBIA) approach that utilizes 4-band multispectral National Aerial Image Program (NAIP) imagery for the detection of individual buildings within the WUI. We evaluate this approach by comparing the accuracy and overall quality of extracted buildings to a building footprint control dataset. In addition, we assessed the effects of buffer distance, topographic conditions, and building characteristics on the accuracy and quality of building extraction. The overall accuracy and quality of our approach was positively related to buffer distance, with accuracies ranging from 50 to 95% for buffer distances from 0 to 100 m. Our results also indicate that building detection was sensitive to building size, with smaller outbuildings (footprints less than 75 m2) having detection rates below 80% and larger residential buildings having detection rates above 90%. These findings demonstrate that this approach can successfully identify buildings in the WUI in diverse landscapes while achieving high accuracies at buffer distances appropriate for most fire management applications while overcoming cost and time constraints associated with traditional approaches. This study is unique in that it evaluates the ability of an OBIA approach to extract highly detailed data on building locations in a WUI setting.

Noninvasive extraction of fetal electrocardiogram based on Support Vector Machine

NASA Astrophysics Data System (ADS)

Fu, Yumei; Xiang, Shihan; Chen, Tianyi; Zhou, Ping; Huang, Weiyan

2015-10-01

The fetal electrocardiogram (FECG) signal has important clinical value for diagnosing the fetal heart diseases and choosing suitable therapeutics schemes to doctors. So, the noninvasive extraction of FECG from electrocardiogram (ECG) signals becomes a hot research point. A new method, the Support Vector Machine (SVM) is utilized for the extraction of FECG with limited size of data. Firstly, the theory of the SVM and the principle of the extraction based on the SVM are studied. Secondly, the transformation of maternal electrocardiogram (MECG) component in abdominal composite signal is verified to be nonlinear and fitted with the SVM. Then, the SVM is trained, and the training results are compared with the real data to ensure the effect of the training. Meanwhile, the parameters of the SVM are optimized to achieve the best performance so that the learning machine can be utilized to fit the unknown samples. Finally, the FECG is extracted by removing the optimal estimation of MECG component from the abdominal composite signal. In order to evaluate the performance of FECG extraction based on the SVM, the Signal-to-Noise Ratio (SNR) and the visual test are used. The experimental results show that the FECG with good quality can be extracted, its SNR ratio is significantly increased as high as 9.2349 dB and the time cost is significantly decreased as short as 0.802 seconds. Compared with the traditional method, the noninvasive extraction method based on the SVM has a simple realization, the shorter treatment time and the better extraction quality under the same conditions.

Rapid and quantitative determination of 10 major active components in Lonicera japonica Thunb. by ultrahigh pressure extraction-HPLC/DAD

NASA Astrophysics Data System (ADS)

Fan, Li; Lin, Changhu; Duan, Wenjuan; Wang, Xiao; Liu, Jianhua; Liu, Feng

2015-01-01

An ultrahigh pressure extraction (UPE)-high performance liquid chromatography (HPLC)/diode array detector (DAD) method was established to evaluate the quality of Lonicera japonica Thunb. Ten active components, including neochlorogenic acid, chlorogenic acid, 4-dicaffeoylquinic acid, caffeic acid, rutin, luteoloside, isochlorogenic acid B, isochlorogenic acid A, isochlorogenic acid C, and quercetin, were qualitatively evaluated and quantitatively determined. Scanning electron microscope images elucidated the bud surface microstructure and extraction mechanism. The optimal extraction conditions of the UPE were 60% methanol solution, 400 MPa of extraction pressure, 3 min of extraction time, and 1:30 (g/mL) solid:liquid ratio. Under the optimized conditions, the total extraction yield of 10 active components was 57.62 mg/g. All the components showed good linearity (r2 ≥ 0.9994) and recoveries. This method was successfully applied to quantify 10 components in 22 batches of L. japonica samples from different areas. Compared with heat reflux extraction and ultrasonic-assisted extraction, UPE can be considered as an alternative extraction technique for fast extraction of active ingredient from L. japonica.

DeTEXT: A Database for Evaluating Text Extraction from Biomedical Literature Figures

PubMed Central

Yin, Xu-Cheng; Yang, Chun; Pei, Wei-Yi; Man, Haixia; Zhang, Jun; Learned-Miller, Erik; Yu, Hong

2015-01-01

Hundreds of millions of figures are available in biomedical literature, representing important biomedical experimental evidence. Since text is a rich source of information in figures, automatically extracting such text may assist in the task of mining figure information. A high-quality ground truth standard can greatly facilitate the development of an automated system. This article describes DeTEXT: A database for evaluating text extraction from biomedical literature figures. It is the first publicly available, human-annotated, high quality, and large-scale figure-text dataset with 288 full-text articles, 500 biomedical figures, and 9308 text regions. This article describes how figures were selected from open-access full-text biomedical articles and how annotation guidelines and annotation tools were developed. We also discuss the inter-annotator agreement and the reliability of the annotations. We summarize the statistics of the DeTEXT data and make available evaluation protocols for DeTEXT. Finally we lay out challenges we observed in the automated detection and recognition of figure text and discuss research directions in this area. DeTEXT is publicly available for downloading at http://prir.ustb.edu.cn/DeTEXT/. PMID:25951377

Design and analysis of a radio frequency extractor in an S-band relativistic klystron amplifier.

PubMed

Zhang, Zehai; Zhang, Jun; Shu, Ting; Qi, Zumin

2012-09-01

A radio frequency (RF) extractor converts the energy of a strongly modulated intense relativistic electron beam (IREB) into the energy of high power microwave in relativistic klystron amplifier (RKA). In the aim of efficiently extracting the energy of the modulated IREB, a RF extractor with all round coupling structure is proposed. Due to the all round structure, the operating transverse magnetic mode can be established easily and its resonant property can be investigated with an approach of group delay time. Furthermore, the external quality factor can be low enough. The design and analysis of the extractor applied in an S-band RKA are carried out, and the performance of the extractor is validated with three-dimensional (3D) particle-in-cell simulations. The extraction efficiency reaches 27% in the simulation with a totally 3D model of the whole RKA. The primary experiments are also carried out and the results show that the RF extractor with the external quality factor of 7.9 extracted 22% of the beam power and transformed it into the high power microwave. Better results are expected after the parasitic mode between the input and middle cavities is suppressed.

Design and analysis of a radio frequency extractor in an S-band relativistic klystron amplifier

NASA Astrophysics Data System (ADS)

Zhang, Zehai; Zhang, Jun; Shu, Ting; Qi, Zumin

2012-09-01

A radio frequency (RF) extractor converts the energy of a strongly modulated intense relativistic electron beam (IREB) into the energy of high power microwave in relativistic klystron amplifier (RKA). In the aim of efficiently extracting the energy of the modulated IREB, a RF extractor with all round coupling structure is proposed. Due to the all round structure, the operating transverse magnetic mode can be established easily and its resonant property can be investigated with an approach of group delay time. Furthermore, the external quality factor can be low enough. The design and analysis of the extractor applied in an S-band RKA are carried out, and the performance of the extractor is validated with three-dimensional (3D) particle-in-cell simulations. The extraction efficiency reaches 27% in the simulation with a totally 3D model of the whole RKA. The primary experiments are also carried out and the results show that the RF extractor with the external quality factor of 7.9 extracted 22% of the beam power and transformed it into the high power microwave. Better results are expected after the parasitic mode between the input and middle cavities is suppressed.

Yield and quality of pectins extractable from the peels of thai mango cultivars depending on fruit ripeness.

PubMed

Sirisakulwat, Suparat; Nagel, Andreas; Sruamsiri, Pittaya; Carle, Reinhold; Neidhart, Sybille

2008-11-26

Pectins, recovered from the peels of four mango ( Mangifera indica L.) cultivars by mimicking industrial techniques, were evaluated in terms of yield, composition, macromolecular properties, and technofunctional quality. Freeze-dried peels of mature-green fruits, after major mesocarp softening, and at full ripeness were extracted using hot acid. The pectins were precipitated in propan-2-ol and their crude yields quantified as alcohol-insoluble substance. Like apple pomace, the dried peels provided hardly acetylated (DAc < 6.3%) rapid-set to ultrarapid-set high-methoxyl pectins at starch-adjusted yields of 11-21 g/100 g. However, despite similar high molecular weight fractions and galacturonic acid/rhamnose ratios, their average molecular weight was markedly reduced by a characteristic, almost monodisperse fraction of 16000-19000. Expanded galactans, indicated by galactose/rhamnose ratios of 15-24 mol/mol, probably represented arabinogalactan side-chain fragments withstanding hot-acid extraction at pH 1.5 and 2.0, as implied by arabinose/galactose ratios of 8-15 and 33-56 mol/100 mol, respectively. Limited galacturonic acid contents made the mango peel pectins less valuable than commercial apple pectins with regard to gelling capacity and thickening properties. Whereas starch and matrix glycan fragments almost completely degraded during ripening, depolymerization of pectins and galactans was insignificant. Technofunctional properties, modulated by extraction at different pH values, were ascribed to structural differences influencing macromolecular entanglements.

Green synthesis of silver nanoparticles using Mentha pulegium and investigation of their antibacterial, antifungal and anticancer activity.

PubMed

Kelkawi, Ali Hamad Abd; Abbasi Kajani, Abolghasem; Bordbar, Abdol-Khalegh

2017-06-01

A simple and eco-friendly method for efficient synthesis of stable colloidal silver nanoparticles (AgNPs) using Mentha pulegium extracts is described. A series of reactions was conducted using different types and concentrations of plant extract as well as metal ions to optimize the reaction conditions. AgNPs were characterized by using UV-vis spectroscopy, transmission electron microscopy, atomic force microscopy, dynamic light scattering, zetasizer, energy-dispersive X-ray spectroscopy (EDAX) and Fourier transform infrared spectroscopy (FTIR). At the optimized conditions, plate shaped AgNPs with zeta potential value of -15.7 and plasmon absorption maximum at 450 nm were obtained using high concentration of aqueous extract. Efficient adsorption of organic compounds on the nanoparticles was confirmed by FTIR and EDAX. The biogenic AgNPs displayed promising antibacterial activity on Escherichia coli , Staphylococcus aureus , and Streptococcus pyogenes . The highest antibacterial activity of 25 µg mL-1 was obtained for all the strains using aqueous extract synthesized AgNPs. The aqueous extract synthesised AgNPs also showed considerable antifungal activity against fluconazole resistant Candida albicans . The cytotoxicity assay revealed considerable anticancer activity of AgNPs on HeLa and MCF-7 cancer cells. Overall results indicated high potential of M. pulegium extract to synthesis high quality AgNPs for biomedical applications.

Comparative analysis of prodigiosin isolated from endophyte Serratia marcescens.

PubMed

Khanam, B; Chandra, R

2018-03-01

Extraction of pigments from endophytes is an uphill task. Up till now, there are no efficient methods available to extract the maximum amount of prodigiosin from Serratia marcescens. This is one of the important endophytes of Beta vulgaris L. The present work was carried out for the comparative study of six different extraction methods such as homogenization, ultrasonication, freezing and thawing, heat treatment, organic solvents and inorganic acids to evaluate the efficiency of prodigiosin yield. Our results demonstrated that highest extraction was observed in ultrasonication (98·1 ± 1·7%) while the lowest extraction by freezing and thawing (31·8 ± 3·8%) methods. However, thin layer chromatography, high-performance liquid chromatography and Fourier transform infrared data suggest that bioactive pigment in the extract was prodigiosin. To the best of our knowledge, this is the first comprehensive study of extraction methods and identification and purification of prodigiosin from cell biomass of Ser. marcescens isolated from Beta vulgaris L. The prodigiosin family is a potent drug with anticancer, antimalarial, antibacterial, antifungal, antiproliferative and immunosuppressive activities. Moreover, it has immense potential in pharmaceutical, food and textile industries. For the industrial perspective, it is essential to achieve purified, high yield and cost-effective extraction of prodigiosin. To the best of our knowledge, this is the first comprehensive study on prodigiosin extraction and also the first report on endophyte Serratia marcescens isolated from Beta vulgaris L. The significance of our results is to extract high amount and good quality prodigiosin for commercial application. © 2017 The Society for Applied Microbiology.

A combined microwave pretreatment/solvent extraction process for the production of oil from palm fruit: optimisation, oil quality and effect of prolonged exposure.

PubMed

Tan, Jason Cx; Chuah, Cheng-Hock; Cheng, Sit-Foon

2017-04-01

Conventional palm oil milling involves multiple stages after fruit collection; in particular, oil clarification introduces water into the pressed oil, which results in a large quantity of wastewater. A combined process of microwave pretreatment and solvent extraction to mill crude palm oil, without introducing water or steam, is described. An excellent yield (up to 30%) of oil was obtained with pretreatment in a 42 L, 1000 W and 2450 MHz microwave oven followed by hexane extraction. The optimum conditions (10 min microwave pretreatment and 12 h solvent extraction) yielded an oil with a low free fatty acid content (<1.0%) and an acceptable anisidine value (<3.0 meq kg -1 ). The oil had a fatty acid composition not resembling those of conventional crude palm oil and crude palm kernel oil. In the pretreatment, the leached oil had 6.3% lauric acid whereas the solvent extracted oil had only 1.5% lauric acid. Among the factors affecting the oil quality, microwave pretreatment affected the oil quality significantly; however, an optimised duration that would ensure high efficiency in solvent extraction also resulted in ruptured fruitlets, although not to the extent of causing excessive oxidation. In fact, microwave pretreatment should exceed 12 min; after only 15 min, the oil had 1-methylcyclopentanol (12.96%), 1-tetradecanol (9.44%), 1-nonadecene (7.22%), nonanal (7.13%) and 1-tridecene (5.09%), which probably arose from the degradation of fibres. Microwave pretreatment represents an alternative milling process for crude palm oil compared with conventional processes in the omission of wet treatment with steam. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

ON-SITE SOLID-PHASE EXTRACTION AND LABORATORY ...

EPA Pesticide Factsheets

Fragrance materials such as synthetic musks in aqueous samples, are normally determined by gas chromatography/mass spectrometry in the selected ion monitoring (SIM) mode to provide maximum sensitivity after liquid-liquid extraction of I -L samples. Full-scan mass spectra are required to verify that a target analyte has been found by comparison with the mass spectra of fragrance compounds in the NIST mass spectral library. A I -L sample usually provides insufficient analyte for full scan data acquisition. This paper describes an on-site extraction method developed at the U.S. Environmental Protection Agency (USEPA)- Las Vegas Nevada - for synthetic musks from 60 L of wastewater effluent. Such a large sample volume permits high-quality, full-scan mass spectra to be obtained for a wide array of synthetic musks. Quantification of these compounds was achieved from the full-scan data directly, without the need to acquire SIM data. The detection limits obtained with this method are an order of magnitude lower than those obtained from liquid-liquid and other solid phase extraction methods. This method is highly reproducible, and recoveries ranged from 80 to 97% in spiked sewage treatment plant effluent. The high rate of sorbent-sample mass transfer eliminated the need for a methanolic activation step, which reduced extraction time, labor, and solvent use, More samples could be extracted in the field at lower cost. After swnple extraction, the light- weight cartridges ar

Low-Cost 3D Printers Enable High-Quality and Automated Sample Preparation and Molecular Detection

PubMed Central

Chan, Kamfai; Coen, Mauricio; Hardick, Justin; Gaydos, Charlotte A.; Wong, Kah-Yat; Smith, Clayton; Wilson, Scott A.; Vayugundla, Siva Praneeth; Wong, Season

2016-01-01

Most molecular diagnostic assays require upfront sample preparation steps to isolate the target’s nucleic acids, followed by its amplification and detection using various nucleic acid amplification techniques. Because molecular diagnostic methods are generally rather difficult to perform manually without highly trained users, automated and integrated systems are highly desirable but too costly for use at point-of-care or low-resource settings. Here, we showcase the development of a low-cost and rapid nucleic acid isolation and amplification platform by modifying entry-level 3D printers that cost between $400 and $750. Our modifications consisted of replacing the extruder with a tip-comb attachment that houses magnets to conduct magnetic particle-based nucleic acid extraction. We then programmed the 3D printer to conduct motions that can perform high-quality extraction protocols. Up to 12 samples can be processed simultaneously in under 13 minutes and the efficiency of nucleic acid isolation matches well against gold-standard spin-column-based extraction technology. Additionally, we used the 3D printer’s heated bed to supply heat to perform water bath-based polymerase chain reactions (PCRs). Using another attachment to hold PCR tubes, the 3D printer was programmed to automate the process of shuttling PCR tubes between water baths. By eliminating the temperature ramping needed in most commercial thermal cyclers, the run time of a 35-cycle PCR protocol was shortened by 33%. This article demonstrates that for applications in resource-limited settings, expensive nucleic acid extraction devices and thermal cyclers that are used in many central laboratories can be potentially replaced by a device modified from inexpensive entry-level 3D printers. PMID:27362424

Enhancing Phenolic Contents and Antioxidant Potentials of Antidesma thwaitesianum by Supercritical Carbon Dioxide Extraction

PubMed Central

Poontawee, Warut; Natakankitkul, Surapol; Wongmekiat, Orawan

2015-01-01

Supercritical fluid extraction (SFE) has increasingly gained attention as an alternative technique for extraction of natural products without leaving toxic residues in extracts. Antidesma thwaitesianum Muell. Arg. (Phyllanthaceae), or ma mao, has been reported to exhibit antioxidant health benefits due to its phenolic constituents. To determine whether SFE technique could impact on phenolic contents and associated antioxidant potentials, ripe fruits of Antidesma thwaitesianum (Phyllanthaceae) were extracted using supercritical carbon dioxide (SC-CO2) and conventional solvents (ethanol, water). The results showed that the SC-CO2 extract contained significantly higher yield, total phenolic, flavonoid, and proanthocyanidin contents than those obtained from ethanol and water. It also demonstrated the greatest antioxidant activities as assessed by ABTS radical cation decolorization, DPPH radical scavenging, and ferric reducing antioxidant power (FRAP) assays. Further analysis using high-performance liquid chromatography with diode array and mass spectrometry detectors (HPLC-DAD/MSD) revealed the presence of catechin as a major phenolic compound of Antidesma thwaitesianum (Phyllanthaceae), with the maximum amount detected in the SC-CO2 extract. These data indicate that SFE technology improves both quantity and quality of Antidesma thwaitesianum fruit extract. The findings added more reliability of using this technique to produce high added value products from this medicinal plant. PMID:25977832

Postsecondary Plans of High-School Seniors in 1972 and 1980: Implications for Student Quality. AIR Forum 1982 Paper.

ERIC Educational Resources Information Center

Brown, Kenneth G.

The postsecondary educational plans of black and white high school seniors in the class of 1972 were compared with those in the same racial classification in the class of 1980. Data were extracted from the National Longitudinal Study of the High School Class of 1972 and from the survey entitled, "High School and Beyond." In order to test…

Climatic factors directly impact the volatile organic compound fingerprint in green Arabica coffee bean as well as coffee beverage quality.

PubMed

Bertrand, B; Boulanger, R; Dussert, S; Ribeyre, F; Berthiot, L; Descroix, F; Joët, T

2012-12-15

Coffee grown at high elevations fetches a better price than that grown in lowland regions. This study was aimed at determining whether climatic conditions during bean development affected sensory perception of the coffee beverage and combinations of volatile compounds in green coffee. Green coffee samples from 16 plots representative of the broad range of climatic variations in Réunion Island were compared by sensory analysis. Volatiles were extracted by solid phase micro-extraction and the volatile compounds were analysed by GC-MS. The results revealed that, among the climatic factors, the mean air temperature during seed development greatly influenced the sensory profile. Positive quality attributes such as acidity, fruity character and flavour quality were correlated and typical of coffees produced at cool climates. Two volatile compounds (ethanal and acetone) were identified as indicators of these cool temperatures. Among detected volatiles, most of the alcohols, aldehydes, hydrocarbons and ketones appeared to be positively linked to elevated temperatures and high solar radiation, while the sensory profiles displayed major defects (i.e. green, earthy flavour). Two alcohols (butan-1,3-diol and butan-2,3-diol) were closely correlated with a reduction in aromatic quality, acidity and an increase in earthy and green flavours. We assumed that high temperatures induce accumulation of these compounds in green coffee, and would be detected as off-flavours, even after roasting. Climate change, which generally involves a substantial increase in average temperatures in mountainous tropical regions, could be expected to have a negative impact on coffee quality. Copyright © 2012 Elsevier Ltd. All rights reserved.

Highly Selective and Considerable Subcritical Butane Extraction to Separate Abamectin in Green Tea.

PubMed

Zhang, Yating; Gu, Lingbiao; Wang, Fei; Kong, Lingjun; Pang, Huili; Qin, Guangyong

2017-06-01

We specially carried out the subcritical butane extraction to separate abamectin from tea leaves. Four parameters, such as extraction temperature, extraction time, number of extraction cycles, and solid-liquid ratio were studied and optimized through the response surface methodology with design matrix developed by Box-Behnken. Seventeen experiments with three various factors and three variable levels were employed to investigate the effect of these parameters on the extraction of abamectin. Besides, catechins, theanine, caffeine, and aroma components were determined by both high-performance liquid chromatography and gas chromatography-mass spectrometry to evaluate the tea quality before and after the extraction. The results showed that the extraction temperature was the uppermost parameter compared with others. The optimal extraction conditions selected as follows: extraction temperature, 42°C; number of extraction cycles and extraction time, 1 and 30 min, respectively; and solid-liquid ratio, 1:10. Based on the above study, the separation efficiency of abamectin was up to 93.95%. It is notable that there has a quite low loss rate, including the negligible damage of aroma components, the bits reduce of catechins within the range of 0.7%-13.1%, and a handful lessen of caffeine and theanine of 1.81% and 2.6%, respectively. The proposed method suggested subcritical butane possesses solubility for lipid-soluble pesticides, and since most of the pesticides are attached to the surfaces of tea, thus the as-applied method was successfully effective to separate abamectin because of the so practical and promising method.

A simple and rapid method for isolation of high quality genomic DNA from fruit trees and conifers using PVP.

PubMed

Kim, C S; Lee, C H; Shin, J S; Chung, Y S; Hyung, N I

1997-03-01

Because DNA degradation is mediated by secondary plant products such as phenolic terpenoids, the isolation of high quality DNA from plants containing a high content of polyphenolics has been a difficult problem. We demonstrate an easy extraction process by modifying several existing ones. Using this process we have found it possible to isolate DNAs from four fruit trees, grape (Vitis spp.), apple (Malus spp.), pear (Pyrus spp.) and persimmon (Diospyros spp.) and four species of conifer, Pinus densiflora, Pinus koraiensis,Taxus cuspidata and Juniperus chinensis within a few hours. Compared with the existing method, we have isolated high quality intact DNAs (260/280 = 1.8-2.0) routinely yielding 250-500 ng/microl (total 7.5-15 microg DNA from four to five tissue discs).

A simple and rapid method for isolation of high quality genomic DNA from fruit trees and conifers using PVP.

PubMed Central

Kim, C S; Lee, C H; Shin, J S; Chung, Y S; Hyung, N I

1997-01-01

Because DNA degradation is mediated by secondary plant products such as phenolic terpenoids, the isolation of high quality DNA from plants containing a high content of polyphenolics has been a difficult problem. We demonstrate an easy extraction process by modifying several existing ones. Using this process we have found it possible to isolate DNAs from four fruit trees, grape (Vitis spp.), apple (Malus spp.), pear (Pyrus spp.) and persimmon (Diospyros spp.) and four species of conifer, Pinus densiflora, Pinus koraiensis,Taxus cuspidata and Juniperus chinensis within a few hours. Compared with the existing method, we have isolated high quality intact DNAs (260/280 = 1.8-2.0) routinely yielding 250-500 ng/microl (total 7.5-15 microg DNA from four to five tissue discs). PMID:9023124

Complementary and Alternative Medicine Treatments for Generalized Anxiety Disorder: Systematic Review and Meta-analysis of Randomized Controlled Trials.

PubMed

Barić, Hrvoje; Đorđević, Veljko; Cerovečki, Ivan; Trkulja, Vladimir

2018-03-01

The objective was to evaluate efficacy/safety of complementary and alternative medicine (CAM) methods for generalized anxiety disorder (GAD) based on randomized controlled trials in adults. Data sources. Six electronic databases ("generalized anxiety (disorder)" and "randomized trial") and reference lists of identified publications were searched to March 2017. Eligibility: full-text publications (English, German language); CAM versus conventional treatment, placebo/sham or no treatment; GAD diagnosed according to standard criteria; and a validated scale for disease severity. Of the 6693 screened records, 32 were included (18 on biologically-based therapies, exclusively herbal preparations; eight on manipulative and body-based therapies; and three on alternative medical systems and three on mind-body therapies). Cochrane Collaboration methodology was used for quality assessment and data extraction. Direct comparisons of Kava Kava (Piper methysticum) extracts to placebo (4 quality trials, n = 233) were highly heterogeneous. Network meta-regression reduced heterogeneity and suggested a modest Kava effect [end-of-treatment Hamilton Anxiety scale score difference adjusted for baseline scores and trial duration: - 3.24 (95% CI - 6.65, 0.17; P = 0.059), Kava Kava 4 arms, n = 139; placebo 5 arms, n = 359]. Lavender (Lavandula angustifolia) extract (1 quality trial, 10 weeks, n = 523) and a combination of extracts of C. oxycantha, E. californica and magnesium (1 quality trial, 12 weeks, n = 264) were superior to placebo and balneotherapy was superior to paroxetine (1 quality trial, 8 weeks, n = 237) indicating efficacy. All other trials were small and/or of modest/low quality and/or lacked assay sensitivity. Safety reporting was poor. Evidence about efficacy/safety of most CAM methods in GAD is limited. Apparent efficacy of certain herbal preparations and body-based therapies requires further confirmation.

Enzymatic treatment to improve the quality of black tea extracts.

PubMed

Chandini, S K; Rao, L Jaganmohan; Gowthaman, M K; Haware, D J; Subramanian, R

2011-08-01

Enzymatic extraction was investigated to improve the quality of black tea extracts with pretreatment of pectinase and tannase independently, successively and simultaneously. Pectinase improved the extractable-solids-yield (ESY) up to 11.5%, without much of an improvement in polyphenols recovery, while tannase pre-treatment showed a significant improvement in polyphenols recovery (14.3%) along with an 11.1% improvement in ESY. Among the four treatments, tannase-alone treatment showed the maximum improvement in tea quality, with higher polyphenols-in-extracted solids. Treatments involving tannase resulted in the significant release of gallic acid, due to its hydrolytic activity, leading to greater solubility besides favourably improving TF/TR ratio. The results suggested that employing a single enzyme, tannase, for the pre-treatment of black tea is desirable. Enzymatic extraction may be preferred over enzymatic clarification as it not only displayed reduction in tea cream and turbidity but also improved the recovery of polyphenols and ESY in the extract, as well as maintaining a good balance of tea quality. Copyright © 2011 Elsevier Ltd. All rights reserved.

Direct analysis of 18 flavonol glycosides, aglycones and terpene trilactones in Ginkgo biloba tablets by matrix solid phase dispersion coupled with ultra-high performance liquid chromatography tandem triple quadrupole mass spectrometry.

PubMed

Liu, Xin-Guang; Yang, Hua; Cheng, Xiao-Lan; Liu, Lei; Qin, Yong; Wang, Qi; Qi, Lian-Wen; Li, Ping

2014-08-01

Analysis and quality control of Ginkgo biloba have been comprehensively studied. However, little attention has been devoted to the simultaneous extraction and analysis of flavonols and terpene trilactones, especially for direct quantification of flavonol glycosides. This work described a rapid strategy for one-step extraction and quantification of the components. A matrix solid phase dispersion (MSPD) method was designed for the extraction of ginkgo ingredients and compared with the heat-reflux and ultrasonic extraction methods. An ultra-high performance liquid chromatography (UHPLC)-tandem-triple-quadrupole-mass spectrometry (QQQ-MS) method was developed for detection of the 18 components, including 10 original flavonol glycosides, 3 aglycones, and 5 lactones. Subsequently, the proposed strategy was used for the analysis of 12 G. biloba tablets. Results showed that MSPD produced comparable extraction efficiency but consumed less time and required lower solvent volumes compared with conventional methods. Without hydrolysis, the concentration detected was much closer to the original in the sample. The total flavonol glycoside contents in ginkgo tablets ranged from 3.59 to 125.21μgmg(-1), and the terpene trilactone varied from 3.45 to 57.8μgmg(-1) among different manufacturers. In conclusion, the proposed MSPD and UHPLC-QQQ-MS is rapid and sensitive in providing comprehensive profile of chemical constituents especially the genuine flavonol glycosides for improved quality control of ginkgo products. Copyright © 2014 Elsevier B.V. All rights reserved.

Optimization protocol for the extraction of 6-gingerol and 6-shogaol from Zingiber officinale var. rubrum Theilade and improving antioxidant and anticancer activity using response surface methodology.

PubMed

Ghasemzadeh, Ali; Jaafar, Hawa Z E; Rahmat, Asmah

2015-07-30

Analysis and extraction of plant matrices are important processes for the development, modernization, and quality control of herbal formulations. Response surface methodology is a collection of statistical and mathematical techniques that are used to optimize the range of variables in various experimental processes to reduce the number of experimental runs, cost , and time, compared to other methods. Response surface methodology was applied for optimizing reflux extraction conditions for achieving high 6-gingerol and 6-shogaol contents, and high antioxidant activity in Zingiber officinale var. rubrum Theilade . The two-factor central composite design was employed to determine the effects of two independent variables, namely extraction temperature (X1: 50-80 °C) and time (X2: 2-4 h), on the properties of the extracts. The 6-gingerol and 6-shogaol contents were measured using ultra-performance liquid chromatography. The antioxidant activity of the rhizome extracts was determined by means of the 1,1-diphenyl-2-picrylhydrazyl assay. Anticancer activity of optimized extracts against HeLa cancer cell lines was measured using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay. Increasing the extraction temperature and time induced significant response of the variables. The optimum extraction condition for all responses was at 76.9 °C for 3.4 h. Under the optimum condition, the corresponding predicted response values for 6-gingerol, 6-shogaol, and the antioxidant activity were 2.89 mg/g DW, 1.85 mg/g DW, and 84.3%, respectively. 6-gingerol and 6-shogaol were extracted under optimized condition to check the viability of the models. The values were 2.92 and 1.88 mg/g DW, and 84.0% for 6-gingerol, 6-shogaol, and the antioxidant activity respectively. The experimental values agreed with those predicted, thus indicating suitability of the models employed and the success of RSM in optimizing the extraction condition. With optimizing of reflux extraction anticancer activity of extracts against HeLa cancer cells enhanced about 16.8%. The half inhibition concentration (IC50) value of optimized and unoptimized extract was found at concentration of 20.9 and 38.4 μg/mL respectively. Optimized extract showed more distinct anticancer activities against HeLa cancer cells in a concentration of 40 μg/mL (P < 0.01) without toxicity to normal cells. The results indicated that the pharmaceutical quality of ginger could be improved significantly by optimizing of extraction process using response surface methodology.

A solvent-extraction module for cyclotron production of high-purity technetium-99m.

PubMed

Martini, Petra; Boschi, Alessandra; Cicoria, Gianfranco; Uccelli, Licia; Pasquali, Micòl; Duatti, Adriano; Pupillo, Gaia; Marengo, Mario; Loriggiola, Massimo; Esposito, Juan

2016-12-01

The design and fabrication of a fully-automated, remotely controlled module for the extraction and purification of technetium-99m (Tc-99m), produced by proton bombardment of enriched Mo-100 molybdenum metallic targets in a low-energy medical cyclotron, is here described. After dissolution of the irradiated solid target in hydrogen peroxide, Tc-99m was obtained under the chemical form of 99m TcO 4 - , in high radionuclidic and radiochemical purity, by solvent extraction with methyl ethyl ketone (MEK). The extraction process was accomplished inside a glass column-shaped vial especially designed to allow for an easy automation of the whole procedure. Recovery yields were always >90% of the loaded activity. The final pertechnetate saline solution Na 99m TcO 4 , purified using the automated module here described, is within the Pharmacopoeia quality control parameters and is therefore a valid alternative to generator-produced 99m Tc. The resulting automated module is cost-effective and easily replicable for in-house production of high-purity Tc-99m by cyclotrons. Copyright © 2016 Elsevier Ltd. All rights reserved.

Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive

PubMed Central

Nakazato, Takeru; Ohta, Tazro; Bono, Hidemasa

2013-01-01

High-throughput sequencing technology, also called next-generation sequencing (NGS), has the potential to revolutionize the whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary data archive, the Sequence Read Archive (SRA). As of January 2013, data from more than 14,000 projects have been submitted to SRA, which is double that of the previous year. Researchers can download raw sequence data from SRA website to perform further analyses and to compare with their own data. However, it is extremely difficult to search entries and download raw sequences of interests with SRA because the data structure is complicated, and experimental conditions along with raw sequences are partly described in natural language. Additionally, some sequences are of inconsistent quality because anyone can submit sequencing data to SRA with no quality check. Therefore, as a criterion of data quality, we focused on SRA entries that were cited in journal articles. We extracted SRA IDs and PubMed IDs (PMIDs) from SRA and full-text versions of journal articles and retrieved 2748 SRA ID-PMID pairs. We constructed a publication list referring to SRA entries. Since, one of the main themes of -omics analyses is clarification of disease mechanisms, we also characterized SRA entries by disease keywords, according to the Medical Subject Headings (MeSH) extracted from articles assigned to each SRA entry. We obtained 989 SRA ID-MeSH disease term pairs, and constructed a disease list referring to SRA data. We previously developed feature profiles of diseases in a system called “Gendoo”. We generated hyperlinks between diseases extracted from SRA and the feature profiles of it. The developed project, publication and disease lists resulting from this study are available at our web service, called “DBCLS SRA” (http://sra.dbcls.jp/). This service will improve accessibility to high-quality data from SRA. PMID:24167589

Published methodological quality of randomized controlled trials does not reflect the actual quality assessed in protocols

PubMed Central

Mhaskar, Rahul; Djulbegovic, Benjamin; Magazin, Anja; Soares, Heloisa P.; Kumar, Ambuj

2011-01-01

Objectives To assess whether reported methodological quality of randomized controlled trials (RCTs) reflect the actual methodological quality, and to evaluate the association of effect size (ES) and sample size with methodological quality. Study design Systematic review Setting Retrospective analysis of all consecutive phase III RCTs published by 8 National Cancer Institute Cooperative Groups until year 2006. Data were extracted from protocols (actual quality) and publications (reported quality) for each study. Results 429 RCTs met the inclusion criteria. Overall reporting of methodological quality was poor and did not reflect the actual high methodological quality of RCTs. The results showed no association between sample size and actual methodological quality of a trial. Poor reporting of allocation concealment and blinding exaggerated the ES by 6% (ratio of hazard ratio [RHR]: 0.94, 95%CI: 0.88, 0.99) and 24% (RHR: 1.24, 95%CI: 1.05, 1.43), respectively. However, actual quality assessment showed no association between ES and methodological quality. Conclusion The largest study to-date shows poor quality of reporting does not reflect the actual high methodological quality. Assessment of the impact of quality on the ES based on reported quality can produce misleading results. PMID:22424985

Chemical and sensorial aroma characterization of freshly distilled Calvados. 1. Evaluation of quality and defects on the basis of key odorants by olfactometry and sensory analysis.

PubMed

Guichard, Hugues; Lemesle, Stéphane; Ledauphin, Jérôme; Barillier, Daniel; Picoche, Bernard

2003-01-15

Eight freshly distilled samples of Calvados, a fermented and distilled apple juice, were analyzed by sensory evaluation and direct injection GC to determine the composition of higher alcohols, esters, and aldehydes. The composition determined by direct injection was tentatively related to sensory descriptors. Esters have a probable maximum level around 500 g/hl of pure alcohol (PA). This level also corresponds to the threshold of the main ester constituent, ethyl acetate. A high ratio of esters to ethyl acetate seems to be of prime importance for good quality. Total aldehydes, with a maximum level between 8 and 11 g/hl of PA and mainly comprising acetal (maximum between 5 and 9 g/hl of PA), were related to a "green" descriptor. Higher alcohols do not have a direct impact on quality, but other volatile compounds with a positive impact on flavor should probably be present at a high level. As overall quality was not well related to sensory quality, it was necessary to perform more a precise analysis to determine the key odorants. The Calvados samples were thus extracted using pentane. Gas chromatography, employing both a flame ionization detector and an olfactometry port, was used to analyze the obtained extracts. Seventy-one odors were detected and distributed according to Calvados quality determined by sensory evaluation. Nineteen odors common to all Calvados samples constituted the "skeleton" of the aroma. Twenty-eight odors were specific to a quality class: 6 for good quality, 4 for neutral, and 18 for defective. Twenty-four other odors had either too low an odor impact or no evident specificity.

An efficient and scalable extraction and quantification method for algal derived biofuel.

PubMed

Lohman, Egan J; Gardner, Robert D; Halverson, Luke; Macur, Richard E; Peyton, Brent M; Gerlach, Robin

2013-09-01

Microalgae are capable of synthesizing a multitude of compounds including biofuel precursors and other high value products such as omega-3-fatty acids. However, accurate analysis of the specific compounds produced by microalgae is important since slight variations in saturation and carbon chain length can affect the quality, and thus the value, of the end product. We present a method that allows for fast and reliable extraction of lipids and similar compounds from a range of algae, followed by their characterization using gas chromatographic analysis with a focus on biodiesel-relevant compounds. This method determines which range of biologically synthesized compounds is likely responsible for each fatty acid methyl ester (FAME) produced; information that is fundamental for identifying preferred microalgae candidates as a biodiesel source. Traditional methods of analyzing these precursor molecules are time intensive and prone to high degrees of variation between species and experimental conditions. Here we detail a new method which uses microwave energy as a reliable, single-step cell disruption technique to extract lipids from live cultures of microalgae. After extractable lipid characterization (including lipid type (free fatty acids, mono-, di- or tri-acylglycerides) and carbon chain length determination) by GC-FID, the same lipid extracts are transesterified into FAMEs and directly compared to total biodiesel potential by GC-MS. This approach provides insight into the fraction of total FAMEs derived from extractable lipids compared to FAMEs derived from the residual fraction (i.e. membrane bound phospholipids, sterols, etc.). This approach can also indicate which extractable lipid compound, based on chain length and relative abundance, is responsible for each FAME. This method was tested on three species of microalgae; the marine diatom Phaeodactylum tricornutum, the model Chlorophyte Chlamydomonas reinhardtii, and the freshwater green alga Chlorella vulgaris. The method is shown to be robust, highly reproducible, and fast, allowing for multiple samples to be analyzed throughout the time course of culturing, thus providing time-resolved information regarding lipid quantity and quality. Total time from harvesting to obtaining analytical results is less than 2h. © 2013.

Oil extraction from Scenedesmus obliquus using a continuous microwave system--design, optimization, and quality characterization.

PubMed

Balasubramanian, Sundar; Allen, James D; Kanitkar, Akanksha; Boldor, Dorin

2011-02-01

A 1.2 kW, 2450 MHz resonant continuous microwave processing system was designed and optimized for oil extraction from green algae (Scenedesmus obliquus). Algae-water suspension (1:1 w/w) was heated to 80 and 95°C, and subjected to extraction for up to 30 min. Maximum oil yield was achieved at 95°C and 30 min. The microwave system extracted 76-77% of total recoverable oil at 20-30 min and 95°C, compared to only 43-47% for water bath control. Extraction time and temperature had significant influence (p<0.0001) on extraction yield. Oil analysis indicated that microwaves extracted oil containing higher percentages of unsaturated and essential fatty acids (indicating higher quality). This study validates for the first time the efficiency of a continuous microwave system for extraction of lipids from algae. Higher oil yields, faster extraction rates and superior oil quality demonstrate this system's feasibility for oil extraction from a variety of feedstock. Copyright © 2010 Elsevier Ltd. All rights reserved.

Sampling methods for the study of volatile profile of PDO wine vinegars. A comparison using multivariate data analysis.

PubMed

Ríos-Reina, Rocío; Morales, M Lourdes; García-González, Diego L; Amigo, José M; Callejón, Raquel M

2018-03-01

High-quality wine vinegars have been registered in Spain under protected designation of origin (PDO): "Vinagre de Jerez", "Vinagre de Condado de Huelva" and "Vinagre de Montilla-Moriles". The raw material, production and aging processes determine their quality and their aromatic composition. Vinegar volatile profile is usually analyzed by gas chromatography-mass spectrometry (GC-MS), being necessary a previous extraction step. Thus, three different sampling methods (Headspace solid phase microextraction "HS-SPME", Headspace stir bar sorptive extraction "HSSE" and Dynamic headspace extraction "DHS") were studied for the analysis of the volatile composition of Spanish PDO wine vinegars. Multivariate curve resolution (MCR) was used to solve chromatographic problems, improving the results obtained. Principal component analysis (PCA) showed that not all the sampling methods were equally suitable for the characterization and differentiation between PDOs and categories, being HSSE the technique that made able the best vinegar characterization. Copyright © 2017 Elsevier Ltd. All rights reserved.

Herbal Extract Incorporated Nanofiber Fabricated by an Electrospinning Technique and its Application to Antimicrobial Air Filtration.

PubMed

Choi, Jeongan; Yang, Byeong Joon; Bae, Gwi-Nam; Jung, Jae Hee

2015-11-18

Recently, with the increased attention to indoor air quality, antimicrobial air filtration techniques have been studied widely to inactivate hazardous airborne microorganisms effectively. In this study, we demonstrate herbal extract incorporated (HEI) nanofibers synthesized by an electrospinning technique and their application to antimicrobial air filtration. As an antimicrobial herbal material, an ethanolic extract of Sophora flavescens, which exhibits great antibacterial activity against pathogens, was mixed with the polymer solution for the electrospinning process. We measured various characteristics of the synthesized HEI nanofibers, such as fiber morphology, fiber size distribution, and thermal stability. For application of the electrospun HEI nanofibers, we made highly effective air filters with 99.99% filtration efficiency and 99.98% antimicrobial activity against Staphylococcus epidermidis. The pressure drop across the HEI nanofiber air filter was 4.75 mmH2O at a face air velocity of 1.79 cm/s. These results will facilitate the implementation of electrospun HEI nanofiber techniques to control air quality and protect against hazardous airborne microorganisms.

Vaccinium meridionale Swartz extracts and their addition in beef burgers as antioxidant ingredient.

PubMed

López-Padilla, Alexis; Martín, Diana; Villanueva Bermejo, David; Jaime, Laura; Ruiz-Rodriguez, Alejandro; Restrepo Flórez, Claudia Estela; Rivero Barrios, Diana Marsela; Fornari, Tiziana

2018-01-01

Vaccinium meridionale Swartz (mortiño) constitutes a source of bioactive phytochemicals, but reports related to its efficient and green production are scarce. In this study, pressurized liquid extraction (PLE) and ultrasound-assisted extraction of mortiño were compared. Total phenolic content (TPC) and antioxidant capacity (ABTS •+ ) were determined. Beef burgers with 20 g kg -1 of mortiño (MM) or its PLE extract (ME) were manufactured. Lipid oxidation (TBARS) and instrumental color changes were measured after refrigerated storage. High TPC (up to 72 g gallic acid equivalent kg -1 extract) was determined in mortiño extracts, which was positively correlated with antioxidant activity. TBARS values of beef burgers containing either MM or ME did not change after refrigerated storage, whereas lipid oxidation of control burgers increased significantly. The color of burgers with added MM or ME was different (lower b* and a* values) from that of control burgers. However, the evolution of color after storage was similar between control and ME samples. Mortiño extracts with high TPC can be obtained by PLE. Both mortiño and its PLE extract are able to control lipid oxidation of beef burgers, but the extract is preferred from the color quality point of view. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Analysis of lignans in Magnoliae Flos by turbulent flow chromatography with online solid-phase extraction and high-performance liquid chromatography with tandem mass spectrometry.

PubMed

Zhou, Xuan; Chen, Cen; Ye, Xiaolan; Song, Fenyun; Fan, Guorong; Wu, Fuhai

2016-04-01

In this study, a method coupling turbulent flow chromatography with online solid-phase extraction and high-performance liquid chromatography with tandem mass spectrometry was developed for analyzing the lignans in Magnoliae Flos. By the online pretreatment of turbulent flow chromatography solid-phase extraction, the impurities removal and analytes concentration were automatically processed, and the lignans were separated rapidly and well. Seven lignans of Magnoliae Flos including epieudesmin, magnolin, 1-irioresinol-B-dimethyl ether, epi-magnolin, fargesin aschantin, and demethoxyaschantin were identified by comparing their retention behavior, UV spectra, and mass spectra with those of reference substances or literature data. The developed method was validated, and the good results showed that the method was not only automatic and rapid, but also accurate and reliable. The turbulent flow chromatography with online solid-phase extraction and high-performance liquid chromatography with tandem mass spectrometry method holds a high potential to become an effective method for the quality control of lignans in Magnoliae Flos and a useful tool for the analysis of other complex mixtures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Impact of a packing medium with alga Bifurcaria bifurcata extract on canned Atlantic mackerel (Scomber scombrus) quality.

PubMed

Barbosa, Roberta G; Trigo, Marcos; Fett, Roseane; Aubourg, Santiago P

2018-01-03

The present research focused on the quality of canned fish. Its primary objective was the quality enhancement of canned Atlantic mackerel (Scomber scombrus) by including an aqueous Bifurcaria bifurcata extract in the packing medium. Various alga extract concentrations were tested and compared with a control without alga extract. After 3 months of canned storage, the cans were opened and quality changes in fish white muscle were analyzed. An inhibitory effect on lipid oxidation development (tertiary compound formation) and color parameter (L* and b*) values was observed as a result of the alga presence in the packing medium. On the contrary, the presence of the alga extract did not produce any effect on volatile compound (total and trimethylamine) formation and lipid hydrolysis (free fatty acid formation) development. A preservative effect derived from the use of an aqueous B. bifurcata extract as packing medium is concluded, and this result is primarily linked to the presence of hydrophilic preservative molecules. The packing system proposed in this work constitutes a novel and promising strategy to enhance the quality of commercial canned fish products. © 2018 Society of Chemical Industry. © 2018 Society of Chemical Industry.

Metatranscriptomics of Soil Eukaryotic Communities.

PubMed

Yadav, Rajiv K; Bragalini, Claudia; Fraissinet-Tachet, Laurence; Marmeisse, Roland; Luis, Patricia

2016-01-01

Functions expressed by eukaryotic organisms in soil can be specifically studied by analyzing the pool of eukaryotic-specific polyadenylated mRNA directly extracted from environmental samples. In this chapter, we describe two alternative protocols for the extraction of high-quality RNA from soil samples. Total soil RNA or mRNA can be converted to cDNA for direct high-throughput sequencing. Polyadenylated mRNA-derived full-length cDNAs can also be cloned in expression plasmid vectors to constitute soil cDNA libraries, which can be subsequently screened for functional gene categories. Alternatively, the diversity of specific gene families can also be explored following cDNA sequence capture using exploratory oligonucleotide probes.

Pectin from Opuntia ficus indica: Optimization of microwave-assisted extraction and preliminary characterization.

PubMed

Lefsih, Khalef; Giacomazza, Daniela; Dahmoune, Farid; Mangione, Maria Rosalia; Bulone, Donatella; San Biagio, Pier Luigi; Passantino, Rosa; Costa, Maria Assunta; Guarrasi, Valeria; Madani, Khodir

2017-04-15

Optimization of microwave-assisted extraction (MAE) of water-soluble pectin (WSP) from Opuntia ficus indica cladodes was performed using Response Surface Methodology. The effect of extraction time (X 1 ), microwave power (X 2 ), pH (X 3 ) and solid-to-liquid ratio (X 4 ) on the extraction yield was examined. The optimum conditions of MAE were as follows: X 1 =2.15min; X 2 =517W; X 3 =2.26 and X 4 =2g/30.6mL. The maximum obtained yield of pectin extraction was 12.57%. Total carbohydrate content of WSP is about 95.5% including 34.4% of Galacturonic acid. Pectin-related proteins represent only the 0.66% of WSP mass. HPSEC and light scattering analyses reveal that WSP is mostly constituted of high molecular pectin and FTIR measurements show that the microwave treatment does not alter the chemical structure of WSP, in which Galacturonic acid content and yield are 34.4% and 4.33%, respectively. Overall, application of MAE can give rise to high quality pectin. Copyright © 2016 Elsevier Ltd. All rights reserved.

Synthesis of High-Quality Biodiesel Using Feedstock and Catalyst Derived from Fish Wastes.

PubMed

Madhu, Devarapaga; Arora, Rajan; Sahani, Shalini; Singh, Veena; Sharma, Yogesh Chandra

2017-03-15

A low-cost and high-purity calcium oxide (CaO) was prepared from waste crab shells, which were extracted from the dead crabs, was used as an efficient solid base catalyst in the synthesis of biodiesel. Raw fish oil was extracted from waste parts of fish through mechanical expeller followed by solvent extraction. Physical as well as chemical properties of raw fish oil were studied, and its free fatty acid composition was analyzed with GC-MS. Stable and high-purity CaO was obtained when the material was calcined at 800 °C for 4 h. Prepared catalyst was characterized by XRD, FT-IR, and TGA/DTA. The surface structure of the catalyst was analyzed with SEM, and elemental composition was determined by EDX spectra. Esterification followed by transesterification reactions were conducted for the synthesis of biodiesel. The effect of cosolvent on biodiesel yield was studied in each experiment using different solvents such as toluene, diethyl ether, hexane, tetrahydrofuran, and acetone. High-quality and pure biodiesel was synthesized and characterized by 1 H NMR and FT-IR. Biodiesel yield was affected by parameters such as reaction temperature, reaction time, molar ratio (methanol:oil), and catalyst loading. Properties of synthesized biodiesel such as density, kinematic viscosity, and cloud point were determined according to ASTM standards. Reusability of prepared CaO catalyst was checked, and the catalyst was found to be stable up to five runs without significant loss of catalytic activity.

Assessment of the effluent quality from a gold mining industry in Ghana.

PubMed

Acheampong, Mike A; Paksirajan, Kannan; Lens, Piet N L

2013-06-01

The physical and chemical qualities of the process effluent and the tailings dam wastewater of AngloGold-Ashanti Limited, a gold mining company in Ghana, were studied from June to September, 2010. The process effluent from the gold extraction plant contains high amounts of suspended solids and is therefore highly turbid. Arsenic, copper and cyanide were identified as the major pollutants in the process effluent with average concentrations of 10.0, 3.1 and 21.6 mg L(-1), respectively. Arsenic, copper, iron and free cyanide (CN(-)) concentrations in the process effluent exceeded the Ghana EPA discharge limits; therefore, it is necessary to treat the process effluent before it can be discharged into the environment. Principal component analysis of the data indicated that the process effluent characteristics were influenced by the gold extraction process as well as the nature of the gold-bearing ore processed. No significant correlation was observed between the wastewater characteristics themselves, except for the dissolved oxygen and the biochemical oxygen demand. The process effluent is fed to the Sansu tailings dam, which removes 99.9 % of the total suspended solids and 99.7 % of the turbidity; but copper, arsenic and cyanide concentrations were still high. The effluent produced can be classified as inorganic with a high load of non-biodegradable compounds. It was noted that, though the Sansu tailings dam stores the polluted effluent from the gold extraction plant, there will still be serious environmental problems in the event of failure of the dam.

Sci-Thur PM: YIS - 07: Monte Carlo simulations to obtain several parameters required for electron beam dosimetry.

PubMed

Muir, B; Rogers, D; McEwen, M

2012-07-01

When current dosimetry protocols were written, electron beam data were limited and had uncertainties that were unacceptable for reference dosimetry. Protocols for high-energy reference dosimetry are currently being updated leading to considerable interest in accurate electron beam data. To this end, Monte Carlo simulations using the EGSnrc user-code egs_chamber are performed to extract relevant data for reference beam dosimetry. Calculations of the absorbed dose to water and the absorbed dose to the gas in realistic ion chamber models are performed as a function of depth in water for cobalt-60 and high-energy electron beams between 4 and 22 MeV. These calculations are used to extract several of the parameters required for electron beam dosimetry - the beam quality specifier, R 50 , beam quality conversion factors, k Q and k R50 , the electron quality conversion factor, k' R50 , the photon-electron conversion factor, k ecal , and ion chamber perturbation factors, P Q . The method used has the advantage that many important parameters can be extracted as a function of depth instead of determination at only the reference depth as has typically been done. Results obtained here are in good agreement with measured and other calculated results. The photon-electron conversion factors obtained for a Farmer-type NE2571 and plane-parallel PTW Roos, IBA NACP-02 and Exradin A11 chambers are 0.903, 0.896, 0.894 and 0.906, respectively. These typically differ by less than 0.7% from the contentious TG-51 values but have much smaller systematic uncertainties. These results are valuable for reference dosimetry of high-energy electron beams. © 2012 American Association of Physicists in Medicine.

Activated charcoal-mediated RNA extraction method for Azadirachta indica and plants highly rich in polyphenolics, polysaccharides and other complex secondary compounds

PubMed Central

2013-01-01

Background High quality RNA is a primary requisite for numerous molecular biological applications but is difficult to isolate from several plants rich in polysaccharides, polyphenolics and other secondary metabolites. These compounds either bind with nucleic acids or often co-precipitate at the final step and many times cannot be removed by conventional methods and kits. Addition of vinyl-pyrollidone polymers in extraction buffer efficiently removes polyphenolics to some extent, but, it failed in case of Azadirachta indica and several other medicinal and aromatic plants. Findings Here we report the use of adsorption property of activated charcoal (0.03%–0.1%) in RNA isolation procedures to remove complex secondary metabolites and polyphenolics to yield good quality RNA from Azadirachta indica. We tested and validated our modified RNA isolation method across 21 different plants including Andrographis paniculata, Aloe vera, Rosa damascena, Pelargonium graveolens, Phyllanthus amarus etc. from 13 other different families, many of which are considered as tough system for isolating RNA. The A260/280 ratio of the extracted RNA ranged between 1.8-2.0 and distinct 28S and 18S ribosomal RNA bands were observed in denaturing agarose gel electrophoresis. Analysis using Agilent 2100 Bioanalyzer revealed intact total RNA yield with very good RNA Integrity Number. Conclusions The RNA isolated by our modified method was found to be of high quality and amenable for sensitive downstream molecular applications like subtractive library construction and RT-PCR. This modified RNA isolation procedure would aid and accelerate the biotechnological studies in complex medicinal and aromatic plants which are extremely rich in secondary metabolic compounds. PMID:23537338

Author-paper affiliation network architecture influences the methodological quality of systematic reviews and meta-analyses of psoriasis.

PubMed

Sanz-Cabanillas, Juan Luis; Ruano, Juan; Gomez-Garcia, Francisco; Alcalde-Mellado, Patricia; Gay-Mimbrera, Jesus; Aguilar-Luque, Macarena; Maestre-Lopez, Beatriz; Gonzalez-Padilla, Marcelino; Carmona-Fernandez, Pedro J; Velez Garcia-Nieto, Antonio; Isla-Tejera, Beatriz

2017-01-01

Moderate-to-severe psoriasis is associated with significant comorbidity, an impaired quality of life, and increased medical costs, including those associated with treatments. Systematic reviews (SRs) and meta-analyses (MAs) of randomized clinical trials are considered two of the best approaches to the summarization of high-quality evidence. However, methodological bias can reduce the validity of conclusions from these types of studies and subsequently impair the quality of decision making. As co-authorship is among the most well-documented forms of research collaboration, the present study aimed to explore whether authors' collaboration methods might influence the methodological quality of SRs and MAs of psoriasis. Methodological quality was assessed by two raters who extracted information from full articles. After calculating total and per-item Assessment of Multiple Systematic Reviews (AMSTAR) scores, reviews were classified as low (0-4), medium (5-8), or high (9-11) quality. Article metadata and journal-related bibliometric indices were also obtained. A total of 741 authors from 520 different institutions and 32 countries published 220 reviews that were classified as high (17.2%), moderate (55%), or low (27.7%) methodological quality. The high methodological quality subnetwork was larger but had a lower connection density than the low and moderate methodological quality subnetworks; specifically, the former contained relatively fewer nodes (authors and reviews), reviews by authors, and collaborators per author. Furthermore, the high methodological quality subnetwork was highly compartmentalized, with several modules representing few poorly interconnected communities. In conclusion, structural differences in author-paper affiliation network may influence the methodological quality of SRs and MAs on psoriasis. As the author-paper affiliation network structure affects study quality in this research field, authors who maintain an appropriate balance between scientific quality and productivity are more likely to develop higher quality reviews.

Extraction of Oil from Flaxseed (Linum usitatissimum L.) Using Enzyme-Assisted Three-Phase Partitioning.

PubMed

Tan, Zhi-Jian; Yang, Zi-Zhen; Yi, Yong-Jian; Wang, Hong-Ying; Zhou, Wan-Lai; Li, Fen-Fang; Wang, Chao-Yun

2016-08-01

In this study, enzyme-assisted three-phase partitioning (EATPP) was used to extract oil from flaxseed. The whole procedure is composed of two parts: the enzymolysis procedure in which the flaxseed was hydrolyzed using an enzyme solution (the influencing parameters such as the type and concentration of enzyme, temperature, and pH were optimized) and three-phase partitioning (TPP), which was conducted by adding salt and t-butanol to the crude flaxseed slurry, resulting in the extraction of flaxseed oil into alcohol-rich upper phase. The concentration of t-butanol, concentration of salt, and the temperature were optimized to maximize the extraction yield. Under optimized conditions of a 49.29 % t-butanol concentration, 30.43 % ammonium sulfate concentration, and 35 °C extraction temperature, a maximum extraction yield of 71.68 % was obtained. This simple and effective EATPP can be used to achieve high extraction yields and oil quality, and thus, it is potential for large-scale oil production.

Supercritical CO2 extraction of candlenut oil: process optimization using Taguchi orthogonal array and physicochemical properties of the oil.

PubMed

Subroto, Erna; Widjojokusumo, Edward; Veriansyah, Bambang; Tjandrawinata, Raymond R

2017-04-01

A series of experiments was conducted to determine optimum conditions for supercritical carbon dioxide extraction of candlenut oil. A Taguchi experimental design with L 9 orthogonal array (four factors in three levels) was employed to evaluate the effects of pressure of 25-35 MPa, temperature of 40-60 °C, CO 2 flow rate of 10-20 g/min and particle size of 0.3-0.8 mm on oil solubility. The obtained results showed that increase in particle size, pressure and temperature improved the oil solubility. The supercritical carbon dioxide extraction at optimized parameters resulted in oil yield extraction of 61.4% at solubility of 9.6 g oil/kg CO 2 . The obtained candlenut oil from supercritical carbon dioxide extraction has better oil quality than oil which was extracted by Soxhlet extraction using n-hexane. The oil contains high unsaturated oil (linoleic acid and linolenic acid), which have many beneficial effects on human health.

The Application of Clove Extract Protects Chinese-style Sausages against Oxidation and Quality Deterioration

PubMed Central

Peng, Xinyan

2017-01-01

This study was conducted to evaluate the effects of clove extract (CE) (0.25%, 0.5%, 1%, and 2%) on the oxidative stability and quality deterioration of Chinese-style sausage stored for 21 d at 4°C. The addition of clove extract to sausages significantly retarded increases in Thiobarbituric Reactive Substances (TBARS) values (p<0.05), while also controlling the production of protein carbonyls (p<0.05). However, the addition of clove extract promoted reduced thiol group content in sausages (p<0.05). Sausages amended with clove extract also had decreased L* values (p<0.05) and increased a* values (p<0.05) when compared with the control. Similarly, texture deterioration was retarded in sausage containing added clove extract when compared with the control during refrigerated storage. Moreover, the addition of clove extract had no negative effects on the sensory properties of sausages. These results suggested that clove extract was effective at protecting sausages from oxidation and quality deterioration during refrigerated storage for 21 d. PMID:28316478

The Application of Clove Extract Protects Chinese-style Sausages against Oxidation and Quality Deterioration.

PubMed

Zhang, Huiyun; Peng, Xinyan; Li, Xinling; Wu, Jingjuan; Guo, Xinyu

2017-01-01

This study was conducted to evaluate the effects of clove extract (CE) (0.25%, 0.5%, 1%, and 2%) on the oxidative stability and quality deterioration of Chinese-style sausage stored for 21 d at 4°C. The addition of clove extract to sausages significantly retarded increases in Thiobarbituric Reactive Substances (TBARS) values ( p <0.05), while also controlling the production of protein carbonyls ( p <0.05). However, the addition of clove extract promoted reduced thiol group content in sausages ( p <0.05). Sausages amended with clove extract also had decreased L* values ( p <0.05) and increased a* values ( p <0.05) when compared with the control. Similarly, texture deterioration was retarded in sausage containing added clove extract when compared with the control during refrigerated storage. Moreover, the addition of clove extract had no negative effects on the sensory properties of sausages. These results suggested that clove extract was effective at protecting sausages from oxidation and quality deterioration during refrigerated storage for 21 d.

Purification of High Molecular Weight Genomic DNA from Powdery Mildew for Long-Read Sequencing.

PubMed

Feehan, Joanna M; Scheibel, Katherine E; Bourras, Salim; Underwood, William; Keller, Beat; Somerville, Shauna C

2017-03-31

The powdery mildew fungi are a group of economically important fungal plant pathogens. Relatively little is known about the molecular biology and genetics of these pathogens, in part due to a lack of well-developed genetic and genomic resources. These organisms have large, repetitive genomes, which have made genome sequencing and assembly prohibitively difficult. Here, we describe methods for the collection, extraction, purification and quality control assessment of high molecular weight genomic DNA from one powdery mildew species, Golovinomyces cichoracearum. The protocol described includes mechanical disruption of spores followed by an optimized phenol/chloroform genomic DNA extraction. A typical yield was 7 µg DNA per 150 mg conidia. The genomic DNA that is isolated using this procedure is suitable for long-read sequencing (i.e., > 48.5 kbp). Quality control measures to ensure the size, yield, and purity of the genomic DNA are also described in this method. Sequencing of the genomic DNA of the quality described here will allow for the assembly and comparison of multiple powdery mildew genomes, which in turn will lead to a better understanding and improved control of this agricultural pathogen.

Evaluation of DNA extraction methods for the analysis of microbial community in biological activated carbon.

PubMed

Zheng, Lu; Gao, Naiyun; Deng, Yang

2012-01-01

It is difficult to isolate DNA from biological activated carbon (BAC) samples used in water treatment plants, owing to the scarcity of microorganisms in BAC samples. The aim of this study was to identify DNA extraction methods suitable for a long-term, comprehensive ecological analysis of BAC microbial communities. To identify a procedure that can produce high molecular weight DNA, maximizes detectable diversity and is relatively free from contaminants, the microwave extraction method, the cetyltrimethylammonium bromide (CTAB) extraction method, a commercial DNA extraction kit, and the ultrasonic extraction method were used for the extraction of DNA from BAC samples. Spectrophotometry, agarose gel electrophoresis and polymerase chain reaction (PCR)-restriction fragment length polymorphisms (RFLP) analysis were conducted to compare the yield and quality of DNA obtained using these methods. The results showed that the CTAB method produce the highest yield and genetic diversity of DNA from BAC samples, but DNA purity was slightly less than that obtained with the DNA extraction-kit method. This study provides a theoretical basis for establishing and selecting DNA extraction methods for BAC samples.

Simultaneous analysis of guaiacol and vanillin in a vanilla extract by using high-performance liquid chromatography with electrochemical detection.

PubMed

Takahashi, Makoto; Sakamaki, Shizuka; Fujita, Akira

2013-01-01

We developed and validated a new high-performance liquid chromatographic analysis for electrochemically detecting guaiacol and vanillin as important components in vanilla extract. Separation was achieved with Capcell Pak C-18 MG, the potential of the working electrode being set at +1000 mV. The respective calibration curves for guaiacol and vanillin were linear in the range of 1.60-460 µg/L and 5.90-1180 µg/L. The respective limits for the quantities of guaiacol and vanillin were 1.60 µg/L and 2.36 µg/L. The related standard deviations of the intra- and inter-day precision of the retention time and peak area were all less than 4%. The recovery of guaiacol and vanillin was both more than 97%, all of the validation data being within an acceptable range. This analysis method is well suited for the simultaneous and convenient analysis of guaiacol and vanillin in a vanilla extract to evaluate the quality of the vanilla extract.

Application of machine vision to pup loaf bread evaluation

NASA Astrophysics Data System (ADS)

Zayas, Inna Y.; Chung, O. K.

1996-12-01

Intrinsic end-use quality of hard winter wheat breeding lines is routinely evaluated at the USDA, ARS, USGMRL, Hard Winter Wheat Quality Laboratory. Experimental baking test of pup loaves is the ultimate test for evaluating hard wheat quality. Computer vision was applied to developing an objective methodology for bread quality evaluation for the 1994 and 1995 crop wheat breeding line samples. Computer extracted features for bread crumb grain were studied, using subimages (32 by 32 pixel) and features computed for the slices with different threshold settings. A subsampling grid was located with respect to the axis of symmetry of a slice to provide identical topological subimage information. Different ranking techniques were applied to the databases. Statistical analysis was run on the database with digital image and breadmaking features. Several ranking algorithms and data visualization techniques were employed to create a sensitive scale for porosity patterns of bread crumb. There were significant linear correlations between machine vision extracted features and breadmaking parameters. Crumb grain scores by human experts were correlated more highly with some image features than with breadmaking parameters.

A data-driven approach for quality assessment of radiologic interpretations.

PubMed

Hsu, William; Han, Simon X; Arnold, Corey W; Bui, Alex At; Enzmann, Dieter R

2016-04-01

Given the increasing emphasis on delivering high-quality, cost-efficient healthcare, improved methodologies are needed to measure the accuracy and utility of ordered diagnostic examinations in achieving the appropriate diagnosis. Here, we present a data-driven approach for performing automated quality assessment of radiologic interpretations using other clinical information (e.g., pathology) as a reference standard for individual radiologists, subspecialty sections, imaging modalities, and entire departments. Downstream diagnostic conclusions from the electronic medical record are utilized as "truth" to which upstream diagnoses generated by radiology are compared. The described system automatically extracts and compares patient medical data to characterize concordance between clinical sources. Initial results are presented in the context of breast imaging, matching 18 101 radiologic interpretations with 301 pathology diagnoses and achieving a precision and recall of 84% and 92%, respectively. The presented data-driven method highlights the challenges of integrating multiple data sources and the application of information extraction tools to facilitate healthcare quality improvement. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

High impact technologies for natural products screening.

PubMed

Koehn, Frank E

2008-01-01

Natural products have historically been a rich source of lead molecules in drug discovery. However, natural products have been de-emphasized as high throughput screening resources in the recent past, in part because of difficulties in obtaining high quality natural products screening libraries, or in applying modern screening assays to these libraries. In addition, natural products programs based on screening of extract libraries, bioassay-guided isolation, structure elucidation and subsequent production scale-up are challenged to meet the rapid cycle times that are characteristic of the modern HTS approach. Fortunately, new technologies in mass spectrometry, NMR and other spectroscopic techniques can greatly facilitate the first components of the process - namely the efficient creation of high-quality natural products libraries, bimolecular target or cell-based screening, and early hit characterization. The success of any high throughput screening campaign is dependent on the quality of the chemical library. The construction and maintenance of a high quality natural products library, whether based on microbial, plant, marine or other sources is a costly endeavor. The library itself may be composed of samples that are themselves mixtures - such as crude extracts, semi-pure mixtures or single purified natural products. Each of these library designs carries with it distinctive advantages and disadvantages. Crude extract libraries have lower resource requirements for sample preparation, but high requirements for identification of the bioactive constituents. Pre-fractionated libraries can be an effective strategy to alleviate interferences encountered with crude libraries, and may shorten the time needed to identify the active principle. Purified natural product libraries require substantial resources for preparation, but offer the advantage that the hit detection process is reduced to that of synthetic single component libraries. Whether the natural products library consists of crude or partially fractionated mixtures, the library contents should be profiled to identify the known components present - a process known as dereplication. The use of mass spectrometry and HPLC-mass spectrometry together with spectral databases is a powerful tool in the chemometric profiling of bio-sources for natural product production. High throughput, high sensitivity flow NMR is an emerging tool in this area as well. Whether by cell based or biomolecular target based assays, screening of natural product extract libraries continues to furnish novel lead molecules for further drug development, despite challenges in the analysis and prioritization of natural products hits. Spectroscopic techniques are now being used to directly screen natural product and synthetic libraries. Mass spectrometry in the form of methods such as ESI-ICRFTMS, and FACS-MS as well as NMR methods such as SAR by NMR and STD-NMR have been utilized to effectively screen molecular libraries. Overall, emerging advances in mass spectrometry, NMR and other technologies are making it possible to overcome the challenges encountered in screening natural products libraries in today's drug discovery environment. As we apply these technologies and develop them even further, we can look forward to increased impact of natural products in the HTS based drug discovery.

Predicting nucleic acid binding interfaces from structural models of proteins.

PubMed

Dror, Iris; Shazman, Shula; Mukherjee, Srayanta; Zhang, Yang; Glaser, Fabian; Mandel-Gutfreund, Yael

2012-02-01

The function of DNA- and RNA-binding proteins can be inferred from the characterization and accurate prediction of their binding interfaces. However, the main pitfall of various structure-based methods for predicting nucleic acid binding function is that they are all limited to a relatively small number of proteins for which high-resolution three-dimensional structures are available. In this study, we developed a pipeline for extracting functional electrostatic patches from surfaces of protein structural models, obtained using the I-TASSER protein structure predictor. The largest positive patches are extracted from the protein surface using the patchfinder algorithm. We show that functional electrostatic patches extracted from an ensemble of structural models highly overlap the patches extracted from high-resolution structures. Furthermore, by testing our pipeline on a set of 55 known nucleic acid binding proteins for which I-TASSER produces high-quality models, we show that the method accurately identifies the nucleic acids binding interface on structural models of proteins. Employing a combined patch approach we show that patches extracted from an ensemble of models better predicts the real nucleic acid binding interfaces compared with patches extracted from independent models. Overall, these results suggest that combining information from a collection of low-resolution structural models could be a valuable approach for functional annotation. We suggest that our method will be further applicable for predicting other functional surfaces of proteins with unknown structure. Copyright © 2011 Wiley Periodicals, Inc.

Seed oil extraction from red prickly pear using hexane and supercritical CO2 : assessment of phenolic compound composition, antioxidant and antibacterial activities.

PubMed

Koubaa, Mohamed; Mhemdi, Houcine; Barba, Francisco J; Angelotti, Armel; Bouaziz, Fatma; Chaabouni, Semia Ellouz; Vorobiev, Eugène

2017-01-01

Investigating Opuntia species for their seed oil content is of much importance owing to their potential use for food and in cosmetic applications. These oils have an important content in unsaturated fatty acids as well as antioxidant compounds (e.g. polyphenols, vitamin E), which have been associated with the prevention of some chronic diseases. Moreover, Opuntia stricta oils possess important antimicrobial activities. For instance, the main focus of this study was to compare the effectiveness of conventional (hexane extraction) and novel (supercritical (SC)-CO 2 ) extraction methods for the recovery of oil and phenolic compounds from O. stricta seeds. The oil yield of both extracts was then compared and the polyphenol content and composition of both extracts were determined by liquid chromatography-high-resolution mass spectrometry. Additionally, antioxidant (DPPH assay) and antimicrobial activities (disc diffusion method) of O. stricta seed oils were determined. The oil yield (based on Soxhlet's method) of O. stricta seeds was determined using SC-CO 2 (49.9 ± 2.2%), and hexane (49.0 ± 1.5%). Although obtaining similar oil extraction yields using the two methods, the extracted oil using SC-CO 2 was more enriched in polyphenols (172.2 ± 11.9 µg gallic acid equivalents (GAE) g -1 oil) than that extracted using hexane (76.0 ± 6.9 µg GAE g -1 of oil). Polyphenol profiles showed that the SC-CO 2 process led to the yield of more compounds (45) than that using hexane extraction (11). Moreover, the antioxidant and antimicrobial activities of SC-CO 2 extract showed a high percentage of inhibition. SC-CO 2 extraction of O. stricta seed oil led to extraction of oil with a similar yield to that with hexane extraction, but with higher polyphenol content. The extract containing polyphenols exhibited high antioxidant and antibacterial properties, demonstrating their great potential as feedstock for high-oil quality. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

[Rapid identification of micro-constituents in monoammonium glycyrrhizinate raw materials by high-pressure solid phase extraction-high performance liquid chromatography-mass spectrometry].

PubMed

Yang, Xue-Dong; Tang, Xu-Yan; Sang, Lin

2012-11-01

To establish a method for rapid identification of micro-constituents in monoammonium glycyrrhizinate by high-pressure solid phase extraction-high performance liquid chromatography-mass spectrometry. HPLC preparative chromatograph was adopted for determining the optimal method for high-pressure solid phase extraction under optimal conditions. 5C18-MS-II column (20.0 mm x 20.0 mm) was used as the extraction column, with 35% acetonitrile-acetic acid solution (pH 2. 20) as eluent at the speed of 16 mL x min(-1). The sample size was 0.5 mL, and the extraction cycle was 4.5 min. Then, extract liquid was analyzed by high performance liquid chromatography-mass spectrometry (HPLC-MS) after being concentrated by 100 times. Under the optimal condition of high-pressure solid phase extraction-high performance liquid chromatography-mass spectrometry, 10 components were rapidly identified from monoammonium glycyrrhizinate raw materials. Among them, the chemical structures of six micro-constituents were identified as 3-O-[beta-D-glucuronopyranosyl-beta-D-glucuronopyranosyl]-30-0-beta-D-apiopyranosylglycyrrhetic/3-O- [P-D-glucuronopyranosyl-beta-D-glucuronopyranosyl]-30-O-beta-D-arabinopyranosylglycyrrhetic, glycyrrhizic saponin F3, 22-hydroxyglycyrrhizin/18alpha-glycyrrhizic saponin G2, 3-O-[beta-D-rhamnopyranosyl]-24-hydroxyglycyrrhizin, glycyrrhizic saponin J2, and glycyrrhizic saponin B2 by MS(n) spectra analysis and reference to literatures. Four main chemical components were identified as glycyrrhizic saponin G2, 18beta-glycyrrhizic acid, uralglycyrrhizic saponin B and 18alpha-glycyrrhizic acid by liquid chromatography, MS(n) and ultraviolet spectra information and comparison with reference substances. The method can be used to identify chemical constituents in monoammonium glycyrrhizinate quickly and effectively, without any reference substance, which provides basis for quality control and safe application of monoammonium glycyrrhizinate-related products.

[Hygienic assessment of a recirculatory combined air-conditioning extract-and-input system in office building].

PubMed

Malysheva, A G; Abramov, E G

2006-01-01

The high concentrations of lead were reveled in the air and dust of some premises and on the filters of a combined air-conditioning extract-and-input system in the high-rise office buildings located in the ecologically lead favorable environment. The dust content of lead in some premises on the first floors dust was as high as 200 mg/kg, which was more than 6 times higher than that in the soil at the highway near the office buildings. The use of new technologies and devices for cleaning and optimizing the air in the premises requires analytical studies to assess the quality of the environment, by taking into account the optimal conditions of their operation.

In vitro propagation of peanut (Arachis hypogaea L.) by shoot tip culture.

PubMed

Ozudogru, Elif Aylin; Kaya, Ergun; Lambardi, Maurizio

2013-01-01

Peanut (Arachis hypogaea L.), also known as groundnut, is the most important species of Arachis genus, originating from Brazil and Peru. Peanut seeds contain high seed oil, proteins, amino acids, and vitamin E, and are consumed worldwide as edible nut, peanut butter, or candy, and peanut oil extracted from the seeds. The meal remaining after oil extraction is also used for animal feed. However, its narrow germplasm base, together with susceptibility to diseases, pathogens, and weeds, decreases yield and seed quality and causes great economic losses annually. Hence, the optimization of efficient in vitro propagation procedures would be highly effective for peanut propagation, as it would raise yield and improve seed quality and flavor. Earlier reports on traditional micropropagation methods, based on axillary bud proliferation which guarantees the multiplication of true-to-type plants, are still limited. This chapter describes a micropropagation protocol to improve multiple shoot formation from shoot-tip explants by using AgNO(3) in combination with plant growth regulators.

Hdr Imaging for Feature Detection on Detailed Architectural Scenes

NASA Astrophysics Data System (ADS)

Kontogianni, G.; Stathopoulou, E. K.; Georgopoulos, A.; Doulamis, A.

2015-02-01

3D reconstruction relies on accurate detection, extraction, description and matching of image features. This is even truer for complex architectural scenes that pose needs for 3D models of high quality, without any loss of detail in geometry or color. Illumination conditions influence the radiometric quality of images, as standard sensors cannot depict properly a wide range of intensities in the same scene. Indeed, overexposed or underexposed pixels cause irreplaceable information loss and degrade digital representation. Images taken under extreme lighting environments may be thus prohibitive for feature detection/extraction and consequently for matching and 3D reconstruction. High Dynamic Range (HDR) images could be helpful for these operators because they broaden the limits of illumination range that Standard or Low Dynamic Range (SDR/LDR) images can capture and increase in this way the amount of details contained in the image. Experimental results of this study prove this assumption as they examine state of the art feature detectors applied both on standard dynamic range and HDR images.

Towards evidence-based medicine in specific grass pollen immunotherapy.

PubMed

Calderon, M; Mösges, R; Hellmich, M; Demoly, P

2010-04-01

When initiating grass pollen immunotherapy for seasonal allergic rhinoconjunctivitis, specialist physicians in many European countries must choose between modalities of differing pharmaceutical and regulatory status. We applied an evidence-based medicine (EBM) approach to commercially available subcutaneous and sublingual Gramineae grass pollen immunotherapies (SCIT and SLIT) by evaluating study design, populations, pollen seasons, treatment doses and durations, efficacy, quality of life, safety and compliance. After searching MEDLINE, Embase and the Cochrane Library up until January 2009, we identified 33 randomized, double-blind, placebo-controlled trials (including seven paediatric trials) with a total of 440 specific immunotherapy (SIT)-treated subjects in seven trials (0 paediatric) for SCIT with natural pollen extracts, 168 in three trials (0 paediatric) for SCIT with allergoids, 906 in 16 trials (five paediatric) for natural extract SLIT drops, 41 in two trials (one paediatric) for allergoid SLIT tablets and 1605 in five trials (two paediatric) for natural extract SLIT tablets. Trial design and quality varied significantly within and between SIT modalities. The multinational, rigorous trials of natural extract SLIT tablets correspond to a high level of evidence in adult and paediatric populations. The limited amount of published data on allergoids prevented us from judging the level of evidence for this modality.

Strawberry Achenes Are an Important Source of Bioactive Compounds for Human Health

PubMed Central

Ariza, María Teresa; Reboredo-Rodríguez, Patricia; Mazzoni, Luca; Forbes-Hernández, Tamara Yuliett; Giampieri, Francesca; Afrin, Sadia; Gasparrini, Massimiliano; Soria, Carmen; Martínez-Ferri, Elsa; Battino, Maurizio; Mezzetti, Bruno

2016-01-01

Strawberries are highly appreciated for their taste, nutritional value and antioxidant compounds, mainly phenolics. Fruit antioxidants derive from achenes and flesh, but achene contribution to the total fruit antioxidant capacity and to the bioaccessibility after intake is still unknown. In this work, the content of total phenolic compounds, flavonoids, anthocyanins and antioxidant capacity (TEAC, FRAP and DPPH) of achenes and flesh were compared in non-digested as well as in gastric and intestinal extracts after in vitro digestion. Results showed that, despite strawberry achenes represent a small fraction of the fruit, their contribution to total fruit antioxidant content was more than 41% and accounted for 81% of antioxidant capacity (TEAC). Achenes have higher quantity and different quality of antioxidants in non-digested and digested extracts. Antioxidant release was higher in the in vitro gastric digested extracts, but digestion conditions did not only affect quantity but quality, resulting in differences in antioxidant capacity and highlighting the importance of simulating physiological-like extraction conditions for assessing fruit antioxidant properties on human health. These results give new insights into the use of strawberry achenes as a source of bioactive compounds to be considered in strawberry breeding programs for improving human health. PMID:27409612

Evaluating variation in human gut microbiota profiles due to DNA extraction method and inter-subject differences.

PubMed

Wagner Mackenzie, Brett; Waite, David W; Taylor, Michael W

2015-01-01

The human gut contains dense and diverse microbial communities which have profound influences on human health. Gaining meaningful insights into these communities requires provision of high quality microbial nucleic acids from human fecal samples, as well as an understanding of the sources of variation and their impacts on the experimental model. We present here a systematic analysis of commonly used microbial DNA extraction methods, and identify significant sources of variation. Five extraction methods (Human Microbiome Project protocol, MoBio PowerSoil DNA Isolation Kit, QIAamp DNA Stool Mini Kit, ZR Fecal DNA MiniPrep, phenol:chloroform-based DNA isolation) were evaluated based on the following criteria: DNA yield, quality and integrity, and microbial community structure based on Illumina amplicon sequencing of the V4 region of bacterial and archaeal 16S rRNA genes. Our results indicate that the largest portion of variation within the model was attributed to differences between subjects (biological variation), with a smaller proportion of variation associated with DNA extraction method (technical variation) and intra-subject variation. A comprehensive understanding of the potential impact of technical variation on the human gut microbiota will help limit preventable bias, enabling more accurate diversity estimates.

Microencapsulation of Garcinia fruit extract by spray drying and its effect on bread quality.

PubMed

Ezhilarasi, Perumal Natarajan; Indrani, Dasappa; Jena, Bhabani Sankar; Anandharamakrishnan, Chinnaswamy

2014-04-01

(-)-Hydroxycitric acid (HCA) is the major acid present in the fruit rinds of certain species of Garcinia. HCA has been reported to have several health benefits. As HCA is highly hygroscopic in nature and thermally sensitive, it is difficult to incorporate in foodstuffs. Hence, Garcinia cowa fruit extract was microencapsulated using three different wall materials such as whey protein isolate (WPI), maltodextrin (MD) and a combination of whey protein isolate and maltodextrin (WPI + MD) by spray drying. Further, these microencapsulated powders were evaluated for their impact on bread quality and HCA retention. Maltodextrin (MD) encapsulates had higher free (86%) and net HCA (90%) recovery. Microencapsulates incorporated breads had enhanced qualitative characteristics and higher HCA content than water extract incorporated bread due to efficient encapsulation during bread baking. Comparatively, bread with MD encapsulates showed softer crumb texture, desirable sensory attributes with considerable volume and higher HCA content. The higher HCA contents of encapsulate incorporated breads were sufficient to claim for functionality of HCA in bread. Comparatively, MD had efficiently encapsulated Garcinia fruit extract during spray drying and bread baking. Spray drying proved to be an excellent encapsulation technique for incorporation into the food system. © 2013 Society of Chemical Industry.

Strawberry Achenes Are an Important Source of Bioactive Compounds for Human Health.

PubMed

Ariza, María Teresa; Reboredo-Rodríguez, Patricia; Mazzoni, Luca; Forbes-Hernández, Tamara Yuliett; Giampieri, Francesca; Afrin, Sadia; Gasparrini, Massimiliano; Soria, Carmen; Martínez-Ferri, Elsa; Battino, Maurizio; Mezzetti, Bruno

2016-07-11

Strawberries are highly appreciated for their taste, nutritional value and antioxidant compounds, mainly phenolics. Fruit antioxidants derive from achenes and flesh, but achene contribution to the total fruit antioxidant capacity and to the bioaccessibility after intake is still unknown. In this work, the content of total phenolic compounds, flavonoids, anthocyanins and antioxidant capacity (TEAC, FRAP and DPPH) of achenes and flesh were compared in non-digested as well as in gastric and intestinal extracts after in vitro digestion. Results showed that, despite strawberry achenes represent a small fraction of the fruit, their contribution to total fruit antioxidant content was more than 41% and accounted for 81% of antioxidant capacity (TEAC). Achenes have higher quantity and different quality of antioxidants in non-digested and digested extracts. Antioxidant release was higher in the in vitro gastric digested extracts, but digestion conditions did not only affect quantity but quality, resulting in differences in antioxidant capacity and highlighting the importance of simulating physiological-like extraction conditions for assessing fruit antioxidant properties on human health. These results give new insights into the use of strawberry achenes as a source of bioactive compounds to be considered in strawberry breeding programs for improving human health.

Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications

PubMed Central

Peña-Llopis, Samuel; Brugarolas, James

2014-01-01

Genomic technologies have revolutionized our understanding of complex Mendelian diseases and cancer. Solid tumors present several challenges for genomic analyses, such as tumor heterogeneity and tumor contamination with surrounding stroma and infiltrating lymphocytes. We developed a protocol to (i) select tissues of high cellular purity on the basis of histological analyses of immediately flanking sections and (ii) simultaneously extract genomic DNA (gDNA), messenger RNA (mRNA), noncoding RNA (ncRNA; enriched in microRNA (miRNA)) and protein from the same tissues. After tissue selection, about 12–16 extractions of DNA/RNA/protein can be obtained per day. Compared with other similar approaches, this fast and reliable methodology allowed us to identify mutations in tumors with remarkable sensitivity and to perform integrative analyses of whole-genome and exome data sets, DNA copy numbers (by single-nucleotide polymorphism (SNP) arrays), gene expression data (by transcriptome profiling and quantitative PCR (qPCR)) and protein levels (by western blotting and immunohistochemical analysis) from the same samples. Although we focused on renal cell carcinoma, this protocol may be adapted with minor changes to any human or animal tissue to obtain high-quality and high-yield nucleic acids and proteins. PMID:24136348

Using time-frequency analysis to determine time-resolved detonation velocity with microwave interferometry.

PubMed

Kittell, David E; Mares, Jesus O; Son, Steven F

2015-04-01

Two time-frequency analysis methods based on the short-time Fourier transform (STFT) and continuous wavelet transform (CWT) were used to determine time-resolved detonation velocities with microwave interferometry (MI). The results were directly compared to well-established analysis techniques consisting of a peak-picking routine as well as a phase unwrapping method (i.e., quadrature analysis). The comparison is conducted on experimental data consisting of transient detonation phenomena observed in triaminotrinitrobenzene and ammonium nitrate-urea explosives, representing high and low quality MI signals, respectively. Time-frequency analysis proved much more capable of extracting useful and highly resolved velocity information from low quality signals than the phase unwrapping and peak-picking methods. Additionally, control of the time-frequency methods is mainly constrained to a single parameter which allows for a highly unbiased analysis method to extract velocity information. In contrast, the phase unwrapping technique introduces user based variability while the peak-picking technique does not achieve a highly resolved velocity result. Both STFT and CWT methods are proposed as improved additions to the analysis methods applied to MI detonation experiments, and may be useful in similar applications.

Using the CER Hub to ensure data quality in a multi-institution smoking cessation study.

PubMed

Walker, Kari L; Kirillova, Olga; Gillespie, Suzanne E; Hsiao, David; Pishchalenko, Valentyna; Pai, Akshatha Kalsanka; Puro, Jon E; Plumley, Robert; Kudyakov, Rustam; Hu, Weiming; Allisany, Art; McBurnie, MaryAnn; Kurtz, Stephen E; Hazlehurst, Brian L

2014-01-01

Comparative effectiveness research (CER) studies involving multiple institutions with diverse electronic health records (EHRs) depend on high quality data. To ensure uniformity of data derived from different EHR systems and implementations, the CER Hub informatics platform developed a quality assurance (QA) process using tools and data formats available through the CER Hub. The QA process, implemented here in a study of smoking cessation services in primary care, used the 'emrAdapter' tool programmed with a set of quality checks to query large samples of primary care encounter records extracted in accord with the CER Hub common data framework. The tool, deployed to each study site, generated error reports indicating data problems to be fixed locally and aggregate data sharable with the central site for quality review. Across the CER Hub network of six health systems, data completeness and correctness issues were prevalent in the first iteration and were considerably improved after three iterations of the QA process. A common issue encountered was incomplete mapping of local EHR data values to those defined by the common data framework. A highly automated and distributed QA process helped to ensure the correctness and completeness of patient care data extracted from EHRs for a multi-institution CER study in smoking cessation. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Batch and Continuous Ultrasound Assisted Extraction of Boldo Leaves (Peumus boldus Mol.).

PubMed

Petigny, Loïc; Périno-Issartier, Sandrine; Wajsman, Joël; Chemat, Farid

2013-03-12

Vegetal extracts are widely used as primary ingredients for various products from creams to perfumes in the pharmaceutical, nutraceutic and cosmetic industries. Having concentrated and active extract is essential, as the process must extract as much soluble material as possible in a minimum time, using the least possible volume of solvent. The boldo leaves extract is of great interest for the industry as it holds a great anti-oxidant activity due to high levels of flavonoids and alkaloids such as boldine. Ultrasound Assisted Extraction (UAE) has been used to improve the efficiency of the plant extraction, reducing extraction time, increasing the concentration of the extract with the same amount of solvent and plant material. After a preliminary study, a response surface method has been used to optimize the extraction of soluble material from the plant. The results provided by the statistical analysis revealed that the optimized conditions were: sonication power 23 W/cm2 for 40 min and a temperature of 36 °C. The optimized parameters of the UAE provide a better extraction compared to a conventional maceration in terms of process time (30 min instead of 120 min), higher yield, more energy saving, cleanliness, safety and product quality.

Batch and Continuous Ultrasound Assisted Extraction of Boldo Leaves (Peumus boldus Mol.)

PubMed Central

Petigny, Loïc; Périno-Issartier, Sandrine; Wajsman, Joël; Chemat, Farid

2013-01-01

Vegetal extracts are widely used as primary ingredients for various products from creams to perfumes in the pharmaceutical, nutraceutic and cosmetic industries. Having concentrated and active extract is essential, as the process must extract as much soluble material as possible in a minimum time, using the least possible volume of solvent. The boldo leaves extract is of great interest for the industry as it holds a great anti-oxidant activity due to high levels of flavonoids and alkaloids such as boldine. Ultrasound Assisted Extraction (UAE) has been used to improve the efficiency of the plant extraction, reducing extraction time, increasing the concentration of the extract with the same amount of solvent and plant material. After a preliminary study, a response surface method has been used to optimize the extraction of soluble material from the plant. The results provided by the statistical analysis revealed that the optimized conditions were: sonication power 23 W/cm2 for 40 min and a temperature of 36 °C. The optimized parameters of the UAE provide a better extraction compared to a conventional maceration in terms of process time (30 min instead of 120 min), higher yield, more energy saving, cleanliness, safety and product quality. PMID:23481637

Extraction fatty acid as a source to produce biofuel in microalgae Chlorella sp. and Spirulina sp. using supercritical carbon dioxide

NASA Astrophysics Data System (ADS)

Tai, Do Chiem; Hai, Dam Thi Thanh; Vinh, Nguyen Hanh; Phung, Le Thi Kim

2016-06-01

In this research, the fatty acids of isolated microalgae were extracted by some technologies such as maceration, Soxhlet, ultrasonic-assisted extraction and supercritical fluid extraction; and analyzed for biodiesel production using GC-MS. This work deals with the extraction of microalgae oil from dry biomass by using supercritical fluid extraction method. A complete study at laboratory of the influence of some parameters on the extraction kinetics and yields and on the composition of the oil in terms of lipid classes and profiles is proposed. Two types of microalgae were studied: Chlorella sp. and Spirulina sp. For the extraction of oil from microalgae, supercritical CO2 (SC-CO2) is regarded with interest, being safer than n-hexane and offering a negligible environmental impact, a short extraction time and a high-quality final product. Whilst some experimental papers are available on the supercritical fluid extraction (SFE) of oil from microalgae, only limited information exists on the kinetics of the process. These results demonstrate that supercritical CO2 extraction is an efficient method for the complete recovery of the neutral lipid phase.

Extraction and preparation of high-aroma and low-caffeine instant green teas by the novel column chromatographic extraction method with gradient elution.

PubMed

Li, Qing-Rong; Wu, Min; Huang, Rui-Jie; Chen, Ya-Fei; Chen, Chan-Jian; Li, Hui; Ni, He; Li, Hai-Hang

2017-06-01

The lack of aroma and natural taste is a critical problem in production and consumption of instant green teas. A method to prepare instant green teas high in-natural-aroma and low-caffeine by the novel column chromatographic extraction with gradient elution is reported. This method simultaneously extracted aroma (or volatile) and non-aroma compounds from green tea. Green tea was loaded into columns with 2.0-fold of petroleum ether (PE): ethanol (8:2). After standing for 3 h until the aroma compounds dissolved, the column was sequentially eluted with 3.0-fold 40% ethanol and 3.5-fold water. The eluant was collected together and automatically separated into PE and ethanol aqueous phases. The aroma extracts was obtained by vacuum-evaporation of PE phase at 45 °C. The ethanol aqueous phase was vacuum-concentrated to aqueous and partially or fully decaffeinated with 4% or 9% charcoal at 70 °C. A regular instant green tea with epigallocatechin-3-gallate: caffeine of 3.5:1 and a low-caffeine instant green tea (less than 1% caffeine) with excellent aroma and taste were prepared, by combining the aroma and non-aroma extracts at a 1:10 ratio. This work provides a practical approach to solve the low-aroma and low-taste problems in the production of high quality instant green teas.

Photovoltaic panel extraction from very high-resolution aerial imagery using region-line primitive association analysis and template matching

NASA Astrophysics Data System (ADS)

Wang, Min; Cui, Qi; Sun, Yujie; Wang, Qiao

2018-07-01

In object-based image analysis (OBIA), object classification performance is jointly determined by image segmentation, sample or rule setting, and classifiers. Typically, as a crucial step to obtain object primitives, image segmentation quality significantly influences subsequent feature extraction and analyses. By contrast, template matching extracts specific objects from images and prevents shape defects caused by image segmentation. However, creating or editing templates is tedious and sometimes results in incomplete or inaccurate templates. In this study, we combine OBIA and template matching techniques to address these problems and aim for accurate photovoltaic panel (PVP) extraction from very high-resolution (VHR) aerial imagery. The proposed method is based on the previously proposed region-line primitive association framework, in which complementary information between region (segment) and line (straight line) primitives is utilized to achieve a more powerful performance than routine OBIA. Several novel concepts, including the mutual fitting ratio and best-fitting template based on region-line primitive association analyses, are proposed. Automatic template generation and matching method for PVP extraction from VHR imagery are designed for concept and model validation. Results show that the proposed method can successfully extract PVPs without any user-specified matching template or training sample. High user independency and accuracy are the main characteristics of the proposed method in comparison with routine OBIA and template matching techniques.

Determination of Wastewater Compounds in Sediment and Soil by Pressurized Solvent Extraction, Solid-Phase Extraction, and Capillary-Column Gas Chromatography/Mass Spectrometry

USGS Publications Warehouse

Burkhardt, Mark R.; Zaugg, Steven D.; Smith, Steven G.; ReVello, Rhiannon C.

2006-01-01

A method for the determination of 61 compounds in environmental sediment and soil samples is described. The method was developed in response to increasing concern over the effects of endocrine-disrupting chemicals in wastewater and wastewater-impacted sediment on aquatic organisms. This method also may be used to evaluate the effects of combined sanitary and storm-sewer overflow on the water and sediment quality of urban streams. Method development focused on the determination of compounds that were chosen on the basis of their endocrine-disrupting potential or toxicity. These compounds include the alkylphenol ethoxylate nonionic surfactants and their degradates, food additives, fragrances, antioxidants, flame retardants, plasticizers, industrial solvents, disinfectants, fecal sterols, polycyclic aromatic hydrocarbons, and high-use domestic pesticides. Sediment and soil samples are extracted using a pressurized solvent extraction system. The compounds of interest are extracted from interfering matrix components by high-pressure water/isopropyl alcohol extraction. The compounds were isolated using disposable solid-phase extraction (SPE) cartridges containing chemically modified polystyrene-divinylbenzene resin. The cartridges were dried with nitrogen gas, and then sorbed compounds were eluted with methylene chloride (80 percent)-diethyl ether (20 percent) through Florisil/sodium sulfate SPE cartridge, and then determined by capillary-column gas chromatography/mass spectrometry. Recoveries in reagent-sand samples fortified at 4 to 72 micrograms averaged 76 percent ?13 percent relative standard deviation for all method compounds. Initial method reporting levels for single-component compounds ranged from 50 to 500 micrograms per kilogram. The concentrations of 20 out of 61 compounds initially will be reported as estimated with the 'E' remark code for one of three reasons: (1) unacceptably low-biased recovery (less than 60 percent) or highly variable method performance (greater than 25 percent relative standard deviation), (2) reference standards prepared from technical mixtures, or (3) potential blank contamination. Samples were preserved by freezing to -20 degrees Celsius. The U.S. Geological Survey National Water Quality Laboratory has established a 1-year sample-holding time limit (prior to sample extraction) from the date of sample collection (if the sample is kept at -20?C) until a statistically accepted method can be used to determine the effectiveness of the sample-freezing procedure.

The Product Quality Research Institute (PQRI) Leachables and Extractables Working Group Initiatives for Parenteral and Ophthalmic Drug Product (PODP).

PubMed

Paskiet, Diane; Jenke, Dennis; Ball, Douglas; Houston, Christopher; Norwood, Daniel L; Markovic, Ingrid

2013-01-01

The Product Quality Research Institute (PQRI) is a non-profit consortium of organizations working together to generate and share timely, relevant, and impactful information that advances drug product quality and development. The collaborative activities of PQRI participants have, in the case of orally inhaled and nasal drug products (OINDPs), resulted in comprehensive and widely-accepted recommendations for leachables assessments to help ensure patient safety with respect to this class of packaged drug products. These recommendations, which include scientifically justified safety thresholds for leachables, represent a significant milestone towards establishing standardized approaches for safety qualification of leachables in OINDP. To build on the success of the OINDP effort, PQRI's Parenteral and Ophthalmic Drug Products (PODP) Leachables and Extractables Working Group was formed to extrapolate the OINDP threshold concepts and best practice recommendations to other dosage forms with high concern for interaction with packaging/delivery systems. This article considers the general aspects of leachables and their safety assessment, introduces the PODP Work Plan and initial study Protocol, discusses the laboratory studies being conducted by the PODP Chemistry Team, outlines the strategy being developed by the PODP Toxicology Team for the safety qualification of PODP leachables, and considers the issues associated with application of the safety thresholds, particularly with respect to large-volume parenterals. Lastly, the unique leachables issues associated with biologics are described. The Product Quality Research Institute (PQRI) is a non-profit consortium involving industry organizations, academia, and regulatory agencies that together provide recommendations in support of regulatory guidance to advance drug product quality. The collaborative activities of the PQRI Orally Inhaled and Nasal Drug Products Leachables and Extractables Working Group resulted in a systematic and science-based approach to identify and qualify leachables, including the concept of safety thresholds. Concepts from this widely accepted approach, formally publicized in 2006, are being extrapolated to parenteral and ophthalmic drug products. This article provides an overview of extractables and leachables in drug products and biologics and discusses the PQRI Work Plan and Protocols developed by the PQRI Parenteral and Ophthalmic Drug Products Leachables and Extractables Working Group.

An Improved Total RNA Extraction Method for White Jelly Mushroom Tremella fuciformis Rich in Polysaccharides

PubMed Central

Zhu, Hanyu; Sun, Xueyan; Liu, Dongmei; Zheng, Liesheng; Chen, Liguo

2017-01-01

An improved method for extracting high quality and quantity RNA from a jelly mushroom and a dimorphic fungus—Tremella fuciformis which is especially rich in polysaccharides, is described. RNA was extracted from T. fuciformis mycelium M1332 and its parental monokaryotic yeast-like cells Y13 and Y32. The A260/280 and A260/230 ratios were both approximately 2, and the RNA integrity number was larger than 8.9. The yields of RNA were between 108 and 213 µg/g fresh wt. Downstream molecular applications including reverse transcriptional PCR and quantitative real-time PCR were also performed. This protocol is reliable and may be widely applicable for total RNA extraction from other jelly mushrooms or filamentous fungi rich in polysaccharides. PMID:29371814

A graph-Laplacian-based feature extraction algorithm for neural spike sorting.

PubMed

Ghanbari, Yasser; Spence, Larry; Papamichalis, Panos

2009-01-01

Analysis of extracellular neural spike recordings is highly dependent upon the accuracy of neural waveform classification, commonly referred to as spike sorting. Feature extraction is an important stage of this process because it can limit the quality of clustering which is performed in the feature space. This paper proposes a new feature extraction method (which we call Graph Laplacian Features, GLF) based on minimizing the graph Laplacian and maximizing the weighted variance. The algorithm is compared with Principal Components Analysis (PCA, the most commonly-used feature extraction method) using simulated neural data. The results show that the proposed algorithm produces more compact and well-separated clusters compared to PCA. As an added benefit, tentative cluster centers are output which can be used to initialize a subsequent clustering stage.

Quantum random number generation for loophole-free Bell tests

NASA Astrophysics Data System (ADS)

Mitchell, Morgan; Abellan, Carlos; Amaya, Waldimar

2015-05-01

We describe the generation of quantum random numbers at multi-Gbps rates, combined with real-time randomness extraction, to give very high purity random numbers based on quantum events at most tens of ns in the past. The system satisfies the stringent requirements of quantum non-locality tests that aim to close the timing loophole. We describe the generation mechanism using spontaneous-emission-driven phase diffusion in a semiconductor laser, digitization, and extraction by parity calculation using multi-GHz logic chips. We pay special attention to experimental proof of the quality of the random numbers and analysis of the randomness extraction. In contrast to widely-used models of randomness generators in the computer science literature, we argue that randomness generation by spontaneous emission can be extracted from a single source.

Simultaneous determination of five bioactive components in radix glycyrrhizae by pressurised liquid extraction combined with UPLC-PDA and UPLC/ESI-QTOF-MS confirmation.

PubMed

Zhou, Shujun; Cao, Jiliang; Qiu, Feng; Kong, Weijun; Yang, Shihai; Yang, Meihua

2013-01-01

Glycyrrhizae species are popular ingredients of herbal medicine in most traditional Chinese medicine prescriptions, and they mainly contain flavonoids and triterpene saponins. The contents of these bioactive compounds may vary in different batches and affect the therapeutic effects. Thus comprehensive quality control and monitoring of their herbal formulation are of paramount concern. To establish a rapid, effective pressurised liquid extraction (PLE) and ultra-performance liquid chromatography coupled with photodiode array (UPLC-PDA) method to evaluate the quality of Glycyrrhizae species. Radix Glycyrrhizae was extracted by PLE using 70% ethanol at 100°C for 15 min during three static extraction cycles. Separation was performed using an UPLC system to quantify five bioactive compounds, namely liquiritin apioside, liquiritin, liquiritigenin, glycyrrhizic acid and glycyrrhetinic acid, in 12 batches of samples of different origins in China. Furthermore, the samples were analysed using an ultra-performance liquid chromatography coupled with electrospray ionisation and time-of-flight mass spectrometry (UPLC/ESI-QTOF-MS) system to confirm the results. The calibration curves of all five analytes showed good linearity (R(2)  > 0.9997). Accuracy, precision and repeatability were all within required limits. The mean recoveries measured at the three concentrations were higher than 93.7% with RSDs lower than < 3.33% for the targets. The established PLE and UPLC-PDA method could serve as a rapid and effective method for quality evaluation of Radix Glycyrrhizae. The UPLC technique can be considered as an attractive alternative to HPLC in routine quality control of Chinese medicine, especially in situations where high sample throughput and fast analytical speed are required. Copyright © 2013 John Wiley & Sons, Ltd.

Optimization of preservation and storage time of sponge tissues to obtain quality mRNA for next-generation sequencing.

PubMed

Riesgo, Ana; Pérez-Porro, Alicia R; Carmona, Susana; Leys, Sally P; Giribet, Gonzalo

2012-03-01

Transcriptome sequencing with next-generation sequencing technologies has the potential for addressing many long-standing questions about the biology of sponges. Transcriptome sequence quality depends on good cDNA libraries, which requires high-quality mRNA. Standard protocols for preserving and isolating mRNA often require optimization for unusual tissue types. Our aim was assessing the efficiency of two preservation modes, (i) flash freezing with liquid nitrogen (LN₂) and (ii) immersion in RNAlater, for the recovery of high-quality mRNA from sponge tissues. We also tested whether the long-term storage of samples at -80 °C affects the quantity and quality of mRNA. We extracted mRNA from nine sponge species and analysed the quantity and quality (A260/230 and A260/280 ratios) of mRNA according to preservation method, storage time, and taxonomy. The quantity and quality of mRNA depended significantly on the preservation method used (LN₂) outperforming RNAlater), the sponge species, and the interaction between them. When the preservation was analysed in combination with either storage time or species, the quantity and A260/230 ratio were both significantly higher for LN₂-preserved samples. Interestingly, individual comparisons for each preservation method over time indicated that both methods performed equally efficiently during the first month, but RNAlater lost efficiency in storage times longer than 2 months compared with flash-frozen samples. In summary, we find that for long-term preservation of samples, flash freezing is the preferred method. If LN₂ is not available, RNAlater can be used, but mRNA extraction during the first month of storage is advised. © 2011 Blackwell Publishing Ltd.

Simultaneous quantification of eight organic acid components in Artemisia capillaris Thunb (Yinchen) extract using high-performance liquid chromatography coupled with diode array detection and high-resolution mass spectrometry.

PubMed

Yu, Fangjun; Qian, Hao; Zhang, Jiayu; Sun, Jie; Ma, Zhiguo

2018-04-01

We aim to determine the chemical constituents of Yinchen extract and Yinchen herbs using high-performance liquid chromatography coupled with diode array detection and high-resolution mass spectrometry. The method was developed to analyze of eight organic acid components of Yinchen extract (including neochlorogenic acid, chlorogenic acid, cryptochlorogenic acid, caffeic acid, 1,3-dicaffeoylquinic acid, 3,4-dicaffeoylquinic acid, 3,5-dicaffeoylquinic acid and 4,5-dicaffeoylquinic acid). The separation was conducted using an Agilent TC-C18 column with acetonitrile - 0.2% formic acid solution as the mobile phases under gradient elution. The analytical method was fully validated in terms of linearity, sensitivity, precision, repeatability as well as recovery, and subsequently the method was performed for the quantitative assessment of Yinchen extracts and Yinchen herbs. In addition, the changes of selected markers were studied when Yinchen herbs decocting in water and isomerization occurred between the chlorogenic acids. The proposed method enables both qualitative and quantitative analyses and could be developed as a new tool for the quality evaluation of Yinchen extract and Yinchen herbs. The changes of selected markers in water decoction process could give us some novel idea when studying the link between substances and drug efficacy. Copyright © 2017. Published by Elsevier B.V.

Determination of Four Major Saponins in Skin and Endosperm of Seeds of Horse Chestnut (Aesculus Hippocastanum L.) Using High Performance Liquid Chromatography with Positive Confirmation by Thin Layer Chromatography.

PubMed

Abudayeh, Zead Helmi Mahmoud; Al Azzam, Khaldun Mohammad; Naddaf, Ahmad; Karpiuk, Uliana Vladimirovna; Kislichenko, Viktoria Sergeevna

2015-11-01

To separate and quantify four major saponins in the extracts of the skin and the endosperm of seeds of horse chestnut (Aesculus hippocastanum L.) using ultrasonic solvent extraction followed by a high performance liquid chromatography-diode array detector (HPLC-DAD) with positive confirmation by thin layer chromatography (TLC). The saponins: escin Ia, escin Ib, isoescin Ia and isoescin Ib were extracted using ultrasonic extraction method. The optimized extraction conditions were: 70% methanol as extraction solvent, 80 °C as extraction temperature, and the extraction time was achieved in 4 hours. The HPLC conditions used: Zorbax SB-ODS-(150 mm × 2.1 mm, 3 μm) column, acetonitrile and 0.10% phosphoric acid solution (39:61 v/v) as mobile phase, flow rate was 0.5 mL min(-1) at 210 nm and 230 nm detection. The injection volume was 10 μL, and the separation was carried out isothermally at 30 °C in a heated chamber. The results indicated that the developed HPLC method is simple, sensitive and reliable. Moreover, the content of escins in seeds decreased by more than 30% in endosperm and by more than 40% in skin upon storage for two years. This assay can be readily utilized as a quality control method for horse chestnut and other related medicinal plants.

Microwave-assisted extraction with water for fast extraction and simultaneous RP-HPLC determination of phenolic acids in radix Salviae Miltiorrhizae.

PubMed

Fang, Xinsheng; Wang, Jianhua; Zhou, Hongying; Jiang, Xingkai; Zhu, Lixiang; Gao, Xin

2009-07-01

An optimized microwave-assisted extraction method using water (MAE-W) as the extractant and an efficient HPLC analysis method were first developed for the fast extraction and simultaneous determination of D(+)-(3,4-dihydroxyphenyl) lactic acid (Dla), salvianolic acid B (SaB), and lithospermic acid (La) in radix Salviae Miltiorrhizae. The key parameters of MAE-W were optimized. It was found that the degradation of SaB was inhibited when using the optimized MAE-W and the stable content of Dla, La, and SaB in danshen was obtained. Furthermore, compared to the conventional extraction methods, the proposed MAE-W is a more rapid method with higher yield and lower solvent consumption with a reproducibility (RSD <6%). In addition, using water as extractant is safe and helpful for environment protection, which could be referred to as green extraction. The separation and quantitative determination of the three compounds was carried out by a developed reverse-phase high-performance liquid chromatographic (RP-HPLC) method with UV detection. Highly efficient separation was obtained using gradient solvent system. The optimized HPLC analysis method was validated to have specificity, linearity, precision, and accuracy. The results indicated that MAE-W followed by HPLC-UV determination is an appropriate alternative to previously proposed method for quality control of radix Salviae Miltiorrhizae.

Impact of pecan nut shell aqueous extract on the oxidative properties of margarines during storage.

PubMed

Engler Ribeiro, Paula Cristina; de Britto Policarpi, Priscila; Dal Bo, Andrea; Barbetta, Pedro Alberto; Block, Jane Mara

2017-07-01

The oxidative properties of margarines supplemented with pecan nut shell extract, rosemary extract and butylated hydroxytoluene (BHT) were investigated. The extracts of pecan nut shell and rosemary showed a high content of total phenolics and condensed tannins (93 and 102.9 mg GAE g -1 and 46 and 38.9 mg CE g -1 respectively) as well as a high antioxidant activity (1257 and 2306 µmol TEAC g -1 and 293 and 856 mg TEAC g -1 by ABTS and DPPH methods respectively). Gallic acid, chlorogenic acid, p-hydroxybenzoic acid, epicatechin and epicatechin gallate were identified in the pecan nut shell extract. Peroxide and p-anisidine values of 3.75-4.43 meq kg -1 and 1.22-2.73 respectively, Totox values of 9.88-10.8 and specific extinction values of 4.38-4.59 and 0.92-0.94 at 232 and 268 nm respectively were observed after 8 months of storage in the studied samples. Margarines supplemented with pecan nut shell extract, rosemary extract or BHT during prolonged storage were found to be of equal quality within the degree of confidence limits. The extract of pecan nut shell may be considered as a natural product replacement for the synthetic antioxidant BHT. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

Comparison of methods for the extraction of DNA from formalin-fixed, paraffin-embedded archival tissues.

PubMed

Sengüven, Burcu; Baris, Emre; Oygur, Tulin; Berktas, Mehmet

2014-01-01

Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE.

Algal Proteins: Extraction, Application, and Challenges Concerning Production

PubMed Central

Bleakley, Stephen; Hayes, Maria

2017-01-01

Population growth combined with increasingly limited resources of arable land and fresh water has resulted in a need for alternative protein sources. Macroalgae (seaweed) and microalgae are examples of under-exploited “crops”. Algae do not compete with traditional food crops for space and resources. This review details the characteristics of commonly consumed algae, as well as their potential for use as a protein source based on their protein quality, amino acid composition, and digestibility. Protein extraction methods applied to algae to date, including enzymatic hydrolysis, physical processes, and chemical extraction and novel methods such as ultrasound-assisted extraction, pulsed electric field, and microwave-assisted extraction are discussed. Moreover, existing protein enrichment methods used in the dairy industry and the potential of these methods to generate high value ingredients from algae, such as bioactive peptides and functional ingredients are discussed. Applications of algae in human nutrition, animal feed, and aquaculture are examined. PMID:28445408

Multiaperture ion beam extraction from gas-dynamic electron cyclotron resonance source of multicharged ions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sidorov, A.; Dorf, M.; Zorin, V.

2008-02-15

Electron cyclotron resonance ion source with quasi-gas-dynamic regime of plasma confinement (ReGIS), constructed at the Institute of Applied Physics, Russia, provides opportunities for extracting intense and high-brightness multicharged ion beams. Despite the short plasma lifetime in a magnetic trap of a ReGIS, the degree of multiple ionization may be significantly enhanced by the increase in power and frequency of the applied microwave radiation. The present work is focused on studying the intense beam quality of this source by the pepper-pot method. A single beamlet emittance measured by the pepper-pot method was found to be {approx}70 {pi} mm mrad, and themore » total extracted beam current obtained at 14 kV extraction voltage was {approx}25 mA. The results of the numerical simulations of ion beam extraction are found to be in good agreement with experimental data.« less

Stabilization of Pb and Cd contaminated soils and soil quality improvements using waste oyster shells.

PubMed

Ok, Yong Sik; Lim, Jung Eun; Moon, Deok Hyun

2011-02-01

Large amounts of oyster shells are produced as a by-product of shellfish farming in coastal regions without beneficial use options. Accordingly, this study was conducted to evaluate the potential for the use of waste oyster shells (WOS) containing a high amount of CaCO₃ to improve soil quality and to stabilize heavy metals in soil. To accomplish this, an incubation experiment was conducted to evaluate the ability of the addition of 1-5 wt% WOS to stabilize the Pb (total 1,246 mg/kg) and Cd (total 17 mg/kg) in a contaminated soil. The effectiveness of the WOS treatments was evaluated using various single extraction techniques. Soil amended with WOS was cured for 30 days complied with the Korean Standard Test method (0.1 M·HCl extraction). The Pb and Cd concentrations were less than the Korean warning and countermeasure standards following treatment with 5 wt% WOS. Moreover, the concentrations of Cd were greatly reduced in response to WOS treatment following extraction using 0.01 M·CaCl₂, which is strongly associated with phytoavailability. Furthermore, the soil pH and exchangeable Ca increased significantly in response to WOS treatment. Taken together, the results of this study indicated that WOS amendments improved soil quality and stabilized Pb and Cd in contaminated soil. However, extraction with 0.43 M·CH₃ COOH revealed that remobilization of heavy metals can occur when the soil reaches an acidic condition.

The effect of filler addition and oven temperature to the antioxidant quality in the drying of Physalis angulata leaf extract obtained by subcritical water extraction

NASA Astrophysics Data System (ADS)

Susanti, R. F.; Natalia, Desy

2016-11-01

In traditional medicine, Physalis angulata which is well known as ceplukan in Indonesia, has been utilized to cure several diseases by conventional extraction in hot water. The investigation of the Swietenia mahagoni extract activity in modern medicine typically utilized organic solvents such as ethanol, methanol, chloroform and hexane in extraction. In this research, subcritical water was used as a solvent instead of organic solvent to extract the Pysalis angulata leaf part. The focus of this research was the investigation of extract drying condition in the presence of filler to preserve the quality of antioxidant in Swietenia mahagoni extract. Filler, which is inert, was added to the extract during drying to help absorb the water while protect the extract from exposure in heat during drying. The effects of filler types, concentrations and oven drying temperatures were investigated to the antioxidant quality covering total phenol and antioxidant activity. Aerosil and microcrystalline cellulose (MCC) were utilized as fillers with concentration was varied from 0-30 wt% for MCC and 0-15 wt% for aerosil. The oven drying temperature was varied from 40-60 oC. The results showed that compare to extract dried without filler, total phenol and antioxidant activity were improved upon addition of filler. The higher the concentration of filler, the better the antioxidant; however it was limited by the homogeneity of filler in the extract. Both of the variables (oven temperature and concentration) played an important role in the improvement of extract quality of Swietenia mahagoni leaf. It was related to the drying time which can be minimized to protect the deterioration of extract from heat. In addition, filler help to provide the powder form of extract instead of the typical extract form which is sticky and oily.

Exploitation of Digital Surface Models Generated from WORLDVIEW-2 Data for SAR Simulation Techniques

NASA Astrophysics Data System (ADS)

Ilehag, R.; Auer, S.; d'Angelo, P.

2017-05-01

GeoRaySAR, an automated SAR simulator developed at DLR, identifies buildings in high resolution SAR data by utilizing geometric knowledge extracted from digital surface models (DSMs). Hitherto, the simulator has utilized DSMs generated from LiDAR data from airborne sensors with pre-filtered vegetation. Discarding the need for pre-optimized model input, DSMs generated from high resolution optical data (acquired with WorldView-2) are used for the extraction of building-related SAR image parts in this work. An automatic preprocessing of the DSMs has been developed for separating buildings from elevated vegetation (trees, bushes) and reducing the noise level. Based on that, automated simulations are triggered considering the properties of real SAR images. Locations in three cities, Munich, London and Istanbul, were chosen as study areas to determine advantages and limitations related to WorldView-2 DSMs as input for GeoRaySAR. Beyond, the impact of the quality of the DSM in terms of building extraction is evaluated as well as evaluation of building DSM, a DSM only containing buildings. The results indicate that building extents can be detected with DSMs from optical satellite data with various success, dependent on the quality of the DSM as well as on the SAR imaging perspective.

Recovery of Oil with Unsaturated Fatty Acids and Polyphenols from Chaenomelessinensis (Thouin) Koehne: Process Optimization of Pilot-Scale Subcritical Fluid Assisted Extraction.

PubMed

Zhu, Zhenzhou; Zhang, Rui; Zhan, Shaoying; He, Jingren; Barba, Francisco J; Cravotto, Giancarlo; Wu, Weizhong; Li, Shuyi

2017-10-22

The potential effects of three modern extraction technologies (cold-pressing, microwaves and subcritical fluids) on the recovery of oil from Chaenomelessinensis (Thouin) Koehne seeds have been evaluated and compared to those of conventional chemical extraction methods (Soxhlet extraction). This oil contains unsaturated fatty acids and polyphenols. Subcritical fluid extraction (SbFE) provided the highest yield-25.79 g oil/100 g dry seeds-of the three methods. Moreover, the fatty acid composition in the oil samples was analysed using gas chromatography-mass spectrometry. This analysis showed that the percentages of monounsaturated (46.61%), and polyunsaturated fatty acids (42.14%), after applying SbFE were higher than those obtained by Soxhlet, cold-pressing or microwave-assisted extraction. In addition, the oil obtained under optimized SbFE conditions (35 min extraction at 35 °C with four extraction cycles), showed significant polyphenol (527.36 mg GAE/kg oil), and flavonoid (15.32 mg RE/kg oil), content, had a good appearance and was of high quality.

Protocol: a rapid and economical procedure for purification of plasmid or plant DNA with diverse applications in plant biology

PubMed Central

2010-01-01

Research in plant molecular biology involves DNA purification on a daily basis. Although different commercial kits enable convenient extraction of high-quality DNA from E. coli cells, PCR and agarose gel samples as well as plant tissues, each kit is designed for a particular type of DNA extraction work, and the cost of purchasing these kits over a long run can be considerable. Furthermore, a simple method for the isolation of binary plasmid from Agrobacterium tumefaciens cells with satisfactory yield is lacking. Here we describe an easy protocol using homemade silicon dioxide matrix and seven simple solutions for DNA extraction from E. coli and A. tumefaciens cells, PCR and restriction digests, agarose gel slices, and plant tissues. Compared with the commercial kits, this protocol allows rapid DNA purification from diverse sources with comparable yield and purity at negligible cost. Following this protocol, we have demonstrated: (1) DNA fragments as small as a MYC-epitope tag coding sequence can be successfully recovered from an agarose gel slice; (2) Miniprep DNA from E. coli can be eluted with as little as 5 μl water, leading to high DNA concentrations (>1 μg/μl) for efficient biolistic bombardment of Arabidopsis seedlings, polyethylene glycol (PEG)-mediated Arabidopsis protoplast transfection and maize protoplast electroporation; (3) Binary plasmid DNA prepared from A. tumefaciens is suitable for verification by restriction analysis without the need for large scale propagation; (4) High-quality genomic DNA is readily isolated from several plant species including Arabidopsis, tobacco and maize. Thus, the silicon dioxide matrix-based DNA purification protocol offers an easy, efficient and economical way to extract DNA for various purposes in plant research. PMID:20180960

Peptidomic strategy for purification and identification of potential ACE-inhibitory and antioxidant peptides in Tetradesmus obliquus microalgae.

PubMed

Montone, Carmela Maria; Capriotti, Anna Laura; Cavaliere, Chiara; La Barbera, Giorgia; Piovesana, Susy; Zenezini Chiozzi, Riccardo; Laganà, Aldo

2018-06-01

Microalgae are unicellular marine organisms that have promoted complex biochemical pathways to survive in greatly competitive marine environments. They could contain significant amounts of high-quality proteins which, because of their structural diversity, contain a range of yet undiscovered novel bioactive peptides. In this work, a peptidomic platform was developed for the separation and identification of bioactive peptides in protein hydrolysates. In this work, a peptidomic platform was developed for the extraction, separation, and identification of bioactive peptides in protein hydrolysates. Indeed, extraction of proteins from recalcitrant tissues is still a challenge due to their strong cell walls and high levels of non-protein interfering compounds. Therefore, seven different protein extraction protocols, based on mechanical and chemical methods, were tested in order to produce high-quality protein extracts. Proteins obtained by means of the best protocol, consisting of milling the recalcitrant tissue with glass beads, were subjected to enzymatic digestion with Alcalase® and subsequently the hydrolysate was purified by two-dimensional semi-preparative reversed phase liquid chromatography. Fractions were assayed for antioxidant and antihypertensive activities and only the most active ones were finally analyzed by RP nanoHPLC-MS/MS. Around 500 peptide sequences were identified in these fractions. The identified peptides were subjected to an in silico analysis by PeptideRanker algorithm in order to assign a score of bioactivity probability. Twenty-five sequenced peptides were found with potential antioxidant and angiotensin-converting-enzyme-inhibitory activities. Four of these peptides, WPRGYFL, GPDRPKFLGPF, WYGPDRPKFL, SDWDRF, were selected for synthesis and in vitro tested for specific bioactivity, exhibiting good values of antioxidant and ACE-inhibitory activity. Graphical abstract Workflow showing the entire peptidomic approach developed for identification of bioactive peptides in microalgae.

Negative ion-driven associated particle neutron generator

DOE PAGES

Antolak, A. J.; Leung, K. N.; Morse, D. H.; ...

2015-10-09

We describe an associated particle neutron generator that employs a negative ion source to produce high neutron flux from a small source size. Furthermore, negative ions produced in an rf-driven plasma source are extracted through a small aperture to form a beam which bombards a positively biased, high voltage target electrode. Electrons co-extracted with the negative ions are removed by a permanent magnet electron filter. The use of negative ions enables high neutron output (100% atomic ion beam), high quality imaging (small neutron source size), and reliable operation (no high voltage breakdowns). Finally, the neutron generator can operate in eithermore » pulsed or continuous-wave (cw) mode and has been demonstrated to produce 10 6 D-D n/s (equivalent to similar to 10 8 D-T n/s) from a 1 mm-diameter neutron source size to facilitate high fidelity associated particle imaging.« less

Microwave-assisted extraction, HPLC analysis, and inhibitory effects on carbonic anhydrase I, II, VA, and VII isoforms of 14 blueberry Italian cultivars.

PubMed

Mollica, Adriano; Locatelli, Marcello; Macedonio, Giorgia; Carradori, Simone; Sobolev, Anatoly P; De Salvador, Roberto F; Monti, Simona M; Buonanno, Martina; Zengin, Gokhan; Angeli, Andrea; Supuran, Claudiu T

2016-01-01

The multi-component fingerprint and the biological evaluation of plant-derived material are indispensable for the pharmaceutical field, in food quality control procedures, and in all plant-based products. We investigated the quantitative content of biologically active compounds (anthocyanins and chlorogenic acid) of microwave-assisted blueberry extracts from 14 different Italian cultivars, using validated high-performance liquid chromatography-photodiode array detector (HPLC-PDA) method and routinely instrument configuration. The carbonic anhydrase (CA, EC 4.2.1.1) inhibition profiles against several pharmacologically relevant CA isoforms of blueberry extracts and some bioactive compounds were also investigated. The various cultivars showed a highly variable content in anthocyanins and chlorogenic acid, and their CA inhibitory effects were also highly variable. Overall these data prove that antioxidant natural products found in blueberries may be useful for designing pharmacological agents in which various CAs are involved, e.g., antiobesity, antitumor, or anticonvulsants agents.

Determination of fatty acid composition and quality characteristics of oils from palm fruits using solvent extraction

NASA Astrophysics Data System (ADS)

Kasmin, Hasimah; Lazim, Azwan Mat; Awang, Roila

2015-09-01

Palm oil contains about 45% of saturated palmitic acid and 39% of mono-unsaturated oleic acid. Investigations made in the past to trace the fatty acid composition in palm revealed that ripeness of fresh fruit bunch (FFB) affect oil composition. However, there is no evidence that processing operations affect oil composition, although different stage of processing does affect the quality of oil extracted. An improved method for sterilizing the oil palm fruits by dry heating, followed by oil extraction has been studied. This method eliminates the use of water, thus, increasing the extraction of lipid soluble. The objective of this study is to determine the possibility production of palm oil with different fatty acid composition (FAC) as well as the changes in quality from conventional milling. The unripe and ripe FFB were collected, sterilized and extracted using different method of solvent extraction. Preliminary data have shown that variation in FAC will also alter the physical and chemical properties of the oil extracted.

Transglycosylation of stevioside to improve the edulcorant quality by lower substitution using cornstarch hydrolyzate and CGTase.

PubMed

Li, Sha; Li, Wei; Xiao, Qiu-yan; Xia, Yongmei

2013-06-01

Stevioside is an abundant sweetener extracted from Stevia rebaudiana leaf with a bitter aftertaste. Enzymatic transglycosylation of stevioside is a solution to improve the edulcorant quality of stevioside, but highly derivatised stevioside coming with high conversion of stevioside is undesired. In this experiment, the transglycosylation of stevioside was investigated by using a commercial cyclodextrin glucanotransferase and cornstarch hydrolyzate. With controlled parameters, the product was mainly composed of mono- and di-glucosylated stevioside while the highest stevioside conversion reached 77.11%. Neither kinetic nor thermodynamic factor stimulated the formation of high substituted steviosides. The simultaneous hydrolysis in the reaction might inhibit the yield of highly substituted steviosides. Copyright © 2012 Elsevier Ltd. All rights reserved.

Arrhenius equation modeling for the shelf life prediction of tomato paste containing a natural preservative.

PubMed

Jafari, Seid Mahdi; Ganje, Mohammad; Dehnad, Danial; Ghanbari, Vahid; Hajitabar, Javad

2017-12-01

The shelf life of tomato paste with microencapsulated olive leaf extract was compared with that of samples containing a commercial preservative by accelerated shelf life testing. Based on previous studies showing that olive leaf extract as a rich source of phenolic compounds can have antimicrobial properties, application of its encapsulated form to improve the storage stability of tomato paste is proposed here. Regarding total soluble solids, the control and the sample containing 1000 µg g -1 sodium benzoate had the lowest (Q 10  = 1.63) and highest (Q 10  = 1.88) sensitivity to temperature changes respectively; also, the microencapsulated sample containing 1000 µg g -1 encapsulated olive leaf extract (Q 10  = 1.83) followed the sample containing 1000 µg g -1 sodium benzoate in terms of the highest kinetic rates. In the case of consistency, the lowest and highest activation energies (E a ) corresponded to samples containing 1000 µg g -1 non-encapsulated olive leaf extract and 1000 µg g -1 microencapsulated olive leaf extract respectively. Interestingly, samples containing microencapsulated olive leaf extract could maintain the original quality of the tomato paste very well, while those with non-encapsulated olive leaf extract rated the worst performance (among all specimens) in terms of maintaining their quality indices for a long time period. Overall, the shelf life equation was able to predict the consistency index of all tomato paste samples during long-time storage with high precision. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Uniform competency-based local feature extraction for remote sensing images

NASA Astrophysics Data System (ADS)

Sedaghat, Amin; Mohammadi, Nazila

2018-01-01

Local feature detectors are widely used in many photogrammetry and remote sensing applications. The quantity and distribution of the local features play a critical role in the quality of the image matching process, particularly for multi-sensor high resolution remote sensing image registration. However, conventional local feature detectors cannot extract desirable matched features either in terms of the number of correct matches or the spatial and scale distribution in multi-sensor remote sensing images. To address this problem, this paper proposes a novel method for uniform and robust local feature extraction for remote sensing images, which is based on a novel competency criterion and scale and location distribution constraints. The proposed method, called uniform competency (UC) local feature extraction, can be easily applied to any local feature detector for various kinds of applications. The proposed competency criterion is based on a weighted ranking process using three quality measures, including robustness, spatial saliency and scale parameters, which is performed in a multi-layer gridding schema. For evaluation, five state-of-the-art local feature detector approaches, namely, scale-invariant feature transform (SIFT), speeded up robust features (SURF), scale-invariant feature operator (SFOP), maximally stable extremal region (MSER) and hessian-affine, are used. The proposed UC-based feature extraction algorithms were successfully applied to match various synthetic and real satellite image pairs, and the results demonstrate its capability to increase matching performance and to improve the spatial distribution. The code to carry out the UC feature extraction is available from href="https://www.researchgate.net/publication/317956777_UC-Feature_Extraction.

Study of optimal extraction conditions for achieving high yield and antioxidant activity of tomato seed oil.

PubMed

Shao, Dongyan; Atungulu, Griffiths G; Pan, Zhongli; Yue, Tianli; Zhang, Ang; Li, Xuan

2012-08-01

Value of tomato seed has not been fully recognized. The objectives of this research were to establish suitable processing conditions for extracting oil from tomato seed by using solvent, determine the impact of processing conditions on yield and antioxidant activity of extracted oil, and elucidate kinetics of the oil extraction process. Four processing parameters, including time, temperature, solvent-to-solid ratio and particle size were studied. A second order model was established to describe the oil extraction process. Based on the results, increasing temperature, solvent-to-solid ratio, and extraction time increased oil yield. In contrast, larger particle size reduced the oil yield. The recommended oil extraction conditions were 8 min of extraction time at temperature of 25 °C, solvent-to-solids ratio of 5/1 (v/w) and particle size of 0.38 mm, which gave oil yield of 20.32% with recovery rate of 78.56%. The DPPH scavenging activity of extracted oil was not significantly affected by the extraction parameters. The inhibitory concentration (IC(50) ) of tomato seed oil was 8.67 mg/mL which was notably low compared to most vegetable oils. A 2nd order model successfully described the kinetics of tomato oil extraction process and parameters of extraction kinetics including initial extraction rate (h), equilibrium concentration of oil (C(s) ), and the extraction rate constant (k) could be precisely predicted with R(2) of at least 0.957. The study revealed that tomato seed which is typically treated as a low value byproduct of tomato processing has great potential in producing oil with high antioxidant capability. The impact of processing conditions including time, temperature, solvent-to-solid ratio and particle size on yield, and antioxidant activity of extracted tomato seed oil are reported. Optimal conditions and models which describe the extraction process are recommended. The information is vital for determining the extraction processing conditions for industrial production of high quality tomato seed oil. Journal of Food Science © 2012 Institute of Food Technologists® No claim to original US government works.

xMSanalyzer: automated pipeline for improved feature detection and downstream analysis of large-scale, non-targeted metabolomics data.

PubMed

Uppal, Karan; Soltow, Quinlyn A; Strobel, Frederick H; Pittard, W Stephen; Gernert, Kim M; Yu, Tianwei; Jones, Dean P

2013-01-16

Detection of low abundance metabolites is important for de novo mapping of metabolic pathways related to diet, microbiome or environmental exposures. Multiple algorithms are available to extract m/z features from liquid chromatography-mass spectral data in a conservative manner, which tends to preclude detection of low abundance chemicals and chemicals found in small subsets of samples. The present study provides software to enhance such algorithms for feature detection, quality assessment, and annotation. xMSanalyzer is a set of utilities for automated processing of metabolomics data. The utilites can be classified into four main modules to: 1) improve feature detection for replicate analyses by systematic re-extraction with multiple parameter settings and data merger to optimize the balance between sensitivity and reliability, 2) evaluate sample quality and feature consistency, 3) detect feature overlap between datasets, and 4) characterize high-resolution m/z matches to small molecule metabolites and biological pathways using multiple chemical databases. The package was tested with plasma samples and shown to more than double the number of features extracted while improving quantitative reliability of detection. MS/MS analysis of a random subset of peaks that were exclusively detected using xMSanalyzer confirmed that the optimization scheme improves detection of real metabolites. xMSanalyzer is a package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. The program was designed to integrate with existing packages such as apLCMS and XCMS, but the framework can also be used to enhance data extraction for other LC/MS data software.

Chemical investigation of commercial grape seed derived products to assess quality and detect adulteration.

PubMed

Villani, Tom S; Reichert, William; Ferruzzi, Mario G; Pasinetti, Giulio M; Simon, James E; Wu, Qingli

2015-03-01

Fundamental concerns in quality control arise due to increasing use of grape seed extract (GSE) and the complex chemical composition of GSE. Proanthocyanidin monomers and oligomers are the major bioactive compounds in GSE. Given no standardized criteria for quality, large variation exists in the composition of commercial GSE supplements. Using HPLC/UV/MS, 21 commercial GSE containing products were purchased and chemically profiled, major compounds quantitated, and compared against authenticated grape seed extract, peanut skin extract, and pine bark extract. The antioxidant capacity and total polyphenol content for each sample was also determined and compared using standard techniques. Nine products were adulterated, found to contain peanut skin extract. A wide degree of variability in chemical composition was detected in commercial products, demonstrating the need for development of quality control standards for GSE. A TLC method was developed to allow for rapid and inexpensive detection of adulteration in GSE by peanut skin. Copyright © 2014 Elsevier Ltd. All rights reserved.

A method for the evaluation of image quality according to the recognition effectiveness of objects in the optical remote sensing image using machine learning algorithm.

PubMed

Yuan, Tao; Zheng, Xinqi; Hu, Xuan; Zhou, Wei; Wang, Wei

2014-01-01

Objective and effective image quality assessment (IQA) is directly related to the application of optical remote sensing images (ORSI). In this study, a new IQA method of standardizing the target object recognition rate (ORR) is presented to reflect quality. First, several quality degradation treatments with high-resolution ORSIs are implemented to model the ORSIs obtained in different imaging conditions; then, a machine learning algorithm is adopted for recognition experiments on a chosen target object to obtain ORRs; finally, a comparison with commonly used IQA indicators was performed to reveal their applicability and limitations. The results showed that the ORR of the original ORSI was calculated to be up to 81.95%, whereas the ORR ratios of the quality-degraded images to the original images were 65.52%, 64.58%, 71.21%, and 73.11%. The results show that these data can more accurately reflect the advantages and disadvantages of different images in object identification and information extraction when compared with conventional digital image assessment indexes. By recognizing the difference in image quality from the application effect perspective, using a machine learning algorithm to extract regional gray scale features of typical objects in the image for analysis, and quantitatively assessing quality of ORSI according to the difference, this method provides a new approach for objective ORSI assessment.

Acoustic correlates of Japanese expressions associated with voice quality of male adults

NASA Astrophysics Data System (ADS)

Kido, Hiroshi; Kasuya, Hideki

2004-05-01

Japanese expressions associated with the voice quality of male adults were extracted by a series of questionnaire surveys and statistical multivariate analysis. One hundred and thirty-seven Japanese expressions were collected through the first questionnaire and careful investigations of well-established Japanese dictionaries and articles. From the second questionnaire about familiarity with each of the expressions and synonymity that were addressed to 249 subjects, 25 expressions were extracted. The third questionnaire was about an evaluation of their own voice quality. By applying a statistical clustering method and a correlation analysis to the results of the questionnaires, eight bipolar expressions and one unipolar expression were obtained. They constituted high-pitched/low-pitched, masculine/feminine, hoarse/clear, calm/excited, powerful/weak, youthful/elderly, thick/thin, tense/lax, and nasal, respectively. Acoustic correlates of each of the eight bipolar expressions were extracted by means of perceptual evaluation experiments that were made with sentence utterances of 36 males and by a statistical decision tree method. They included an average of the fundamental frequency (F0) of the utterance, speaking rate, spectral tilt, formant frequency parameter, standard deviation of F0 values, and glottal noise, when SPL of each of the stimuli was maintained identical in the perceptual experiments.

Published methodological quality of randomized controlled trials does not reflect the actual quality assessed in protocols.

PubMed

Mhaskar, Rahul; Djulbegovic, Benjamin; Magazin, Anja; Soares, Heloisa P; Kumar, Ambuj

2012-06-01

To assess whether the reported methodological quality of randomized controlled trials (RCTs) reflects the actual methodological quality and to evaluate the association of effect size (ES) and sample size with methodological quality. Systematic review. This is a retrospective analysis of all consecutive phase III RCTs published by eight National Cancer Institute Cooperative Groups up to 2006. Data were extracted from protocols (actual quality) and publications (reported quality) for each study. Four hundred twenty-nine RCTs met the inclusion criteria. Overall reporting of methodological quality was poor and did not reflect the actual high methodological quality of RCTs. The results showed no association between sample size and actual methodological quality of a trial. Poor reporting of allocation concealment and blinding exaggerated the ES by 6% (ratio of hazard ratio [RHR]: 0.94; 95% confidence interval [CI]: 0.88, 0.99) and 24% (RHR: 1.24; 95% CI: 1.05, 1.43), respectively. However, actual quality assessment showed no association between ES and methodological quality. The largest study to date shows that poor quality of reporting does not reflect the actual high methodological quality. Assessment of the impact of quality on the ES based on reported quality can produce misleading results. Copyright © 2012 Elsevier Inc. All rights reserved.

[Application of genetic algorithm in blending technology for extractions of Cortex Fraxini].

PubMed

Yang, Ming; Zhou, Yinmin; Chen, Jialei; Yu, Minying; Shi, Xiufeng; Gu, Xijun

2009-10-01

To explore the feasibility of genetic algorithm (GA) on multiple objective blending technology for extractions of Cortex Fraxini. According to that the optimization objective was the combination of fingerprint similarity and the root-mean-square error of multiple key constituents, a new multiple objective optimization model of 10 batches extractions of Cortex Fraxini was built. The blending coefficient was obtained by genetic algorithm. The quality of 10 batches extractions of Cortex Fraxini that after blending was evaluated with the finger print similarity and root-mean-square error as indexes. The quality of 10 batches extractions of Cortex Fraxini that after blending was well improved. Comparing with the fingerprint of the control sample, the similarity was up, but the degree of variation is down. The relative deviation of the key constituents was less than 10%. It is proved that genetic algorithm works well on multiple objective blending technology for extractions of Cortex Fraxini. This method can be a reference to control the quality of extractions of Cortex Fraxini. Genetic algorithm in blending technology for extractions of Chinese medicines is advisable.

Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis

PubMed Central

Jiang, Zhijian; Kumar, Manoj; Padula, Matthew P.; Pernice, Mathieu; Kahlke, Tim; Kim, Mikael; Ralph, Peter J.

2017-01-01

The availability of the first complete genome sequence of the marine flowering plant Zostera marina (commonly known as seagrass) in early 2016, is expected to significantly raise the impact of seagrass proteomics. Seagrasses are marine ecosystem engineers that are currently declining worldwide at an alarming rate due to both natural and anthropogenic disturbances. Seagrasses (especially species of the genus Zostera) are compromised for proteomic studies primarily due to the lack of efficient protein extraction methods because of their recalcitrant cell wall which is rich in complex polysaccharides and a high abundance of secondary metabolites in their cells. In the present study, three protein extraction methods that are commonly used in plant proteomics i.e., phenol (P); trichloroacetic acid/acetone/SDS/phenol (TASP); and borax/polyvinyl-polypyrrolidone/phenol (BPP) extraction, were evaluated quantitatively and qualitatively based on two dimensional isoelectric focusing (2D-IEF) maps and LC-MS/MS analysis using the two most abundant Australian seagrass species, namely Zostera muelleri and Posidonia australis. All three tested methods produced high quality protein extracts with excellent 2D-IEF maps in P. australis. However, the BPP method produces better results in Z. muelleri compared to TASP and P. Therefore, we further modified the BPP method (M-BPP) by homogenizing the tissue in a modified protein extraction buffer containing both ionic and non-ionic detergents (0.5% SDS; 1.5% Triton X-100), 2% PVPP and protease inhibitors. Further, the extracted proteins were solubilized in 0.5% of zwitterionic detergent (C7BzO) instead of 4% CHAPS. This slight modification to the BPP method resulted in a higher protein yield, and good quality 2-DE maps with a higher number of protein spots in both the tested seagrasses. Further, the M-BPP method was successfully utilized in western-blot analysis of phosphoenolpyruvate carboxylase (PEPC—a key enzyme for carbon metabolism). This optimized protein extraction method will be a significant stride toward seagrass proteome mining and identifying the protein biomarkers to stress response of seagrasses under the scenario of global climate change and anthropogenic perturbations. PMID:28861098

Development of an Efficient Protein Extraction Method Compatible with LC-MS/MS for Proteome Mapping in Two Australian Seagrasses Zostera muelleri and Posidonia australis.

PubMed

Jiang, Zhijian; Kumar, Manoj; Padula, Matthew P; Pernice, Mathieu; Kahlke, Tim; Kim, Mikael; Ralph, Peter J

2017-01-01

The availability of the first complete genome sequence of the marine flowering plant Zostera marina (commonly known as seagrass) in early 2016, is expected to significantly raise the impact of seagrass proteomics. Seagrasses are marine ecosystem engineers that are currently declining worldwide at an alarming rate due to both natural and anthropogenic disturbances. Seagrasses (especially species of the genus Zostera ) are compromised for proteomic studies primarily due to the lack of efficient protein extraction methods because of their recalcitrant cell wall which is rich in complex polysaccharides and a high abundance of secondary metabolites in their cells. In the present study, three protein extraction methods that are commonly used in plant proteomics i.e., phenol (P); trichloroacetic acid/acetone/SDS/phenol (TASP); and borax/polyvinyl-polypyrrolidone/phenol (BPP) extraction, were evaluated quantitatively and qualitatively based on two dimensional isoelectric focusing (2D-IEF) maps and LC-MS/MS analysis using the two most abundant Australian seagrass species, namely Zostera muelleri and Posidonia australis . All three tested methods produced high quality protein extracts with excellent 2D-IEF maps in P. australis . However, the BPP method produces better results in Z. muelleri compared to TASP and P. Therefore, we further modified the BPP method (M-BPP) by homogenizing the tissue in a modified protein extraction buffer containing both ionic and non-ionic detergents (0.5% SDS; 1.5% Triton X-100), 2% PVPP and protease inhibitors. Further, the extracted proteins were solubilized in 0.5% of zwitterionic detergent (C7BzO) instead of 4% CHAPS. This slight modification to the BPP method resulted in a higher protein yield, and good quality 2-DE maps with a higher number of protein spots in both the tested seagrasses. Further, the M-BPP method was successfully utilized in western-blot analysis of phosphoenolpyruvate carboxylase (PEPC-a key enzyme for carbon metabolism). This optimized protein extraction method will be a significant stride toward seagrass proteome mining and identifying the protein biomarkers to stress response of seagrasses under the scenario of global climate change and anthropogenic perturbations.

Simultaneous quantification of the major bile acids in artificial Calculus bovis by high-performance liquid chromatography with precolumn derivatization and its application in quality control.

PubMed

Shi, Yan; Xiong, Jing; Sun, Dongmei; Liu, Wei; Wei, Feng; Ma, Shuangcheng; Lin, Ruichao

2015-08-01

An accurate and sensitive high-performance liquid chromatography method coupled with ultralviolet detection and precolumn derivatization was developed for the simultaneous quantification of the major bile acids in Artificial Calculus bovis, including cholic acid, hyodeoxycholic acid, chenodeoxycholic acid, and deoxycholic acid. The extraction, derivatization, chromatographic separation, and detection parameters were fully optimized. The samples were extracted with methanol by ultrasonic extraction. Then, 2-bromine-4'-nitroacetophenone and 18-crown ether-6 were used for derivatization. The chromatographic separation was performed on an Agilent SB-C18 column (250 × 4.6 mm id, 5 μm) at a column temperature of 30°C and liquid flow rate of 1.0 mL/min using water and methanol as the mobile phase with a gradient elution. The detection wavelength was 263 nm. The method was extensively validated by evaluating the linearity (r(2) ≥ 0.9980), recovery (94.24-98.91%), limits of detection (0.25-0.31 ng) and limits of quantification (0.83-1.02 ng). Seventeen samples were analyzed using the developed and validated method. Then, the amounts of bile acids were analyzed by hierarchical agglomerative clustering analysis and principal component analysis. The results of the chemometric analysis showed that the contents of these compounds reflect the intrinsic quality of artificial Calculus bovis, and two compounds (hyodeoxycholic acid and chenodeoxycholic acid) were the most important markers for quality evaluating. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-throughput simultaneous analysis of RNA, protein, and lipid biomarkers in heterogeneous tissue samples.

PubMed

Reiser, Vladimír; Smith, Ryan C; Xue, Jiyan; Kurtz, Marc M; Liu, Rong; Legrand, Cheryl; He, Xuanmin; Yu, Xiang; Wong, Peggy; Hinchcliffe, John S; Tanen, Michael R; Lazar, Gloria; Zieba, Renata; Ichetovkin, Marina; Chen, Zhu; O'Neill, Edward A; Tanaka, Wesley K; Marton, Matthew J; Liao, Jason; Morris, Mark; Hailman, Eric; Tokiwa, George Y; Plump, Andrew S

2011-11-01

With expanding biomarker discovery efforts and increasing costs of drug development, it is critical to maximize the value of mass-limited clinical samples. The main limitation of available methods is the inability to isolate and analyze, from a single sample, molecules requiring incompatible extraction methods. Thus, we developed a novel semiautomated method for tissue processing and tissue milling and division (TMAD). We used a SilverHawk atherectomy catheter to collect atherosclerotic plaques from patients requiring peripheral atherectomy. Tissue preservation by flash freezing was compared with immersion in RNAlater®, and tissue grinding by traditional mortar and pestle was compared with TMAD. Comparators were protein, RNA, and lipid yield and quality. Reproducibility of analyte yield from aliquots of the same tissue sample processed by TMAD was also measured. The quantity and quality of biomarkers extracted from tissue prepared by TMAD was at least as good as that extracted from tissue stored and prepared by traditional means. TMAD enabled parallel analysis of gene expression (quantitative reverse-transcription PCR, microarray), protein composition (ELISA), and lipid content (biochemical assay) from as little as 20 mg of tissue. The mean correlation was r = 0.97 in molecular composition (RNA, protein, or lipid) between aliquots of individual samples generated by TMAD. We also demonstrated that it is feasible to use TMAD in a large-scale clinical study setting. The TMAD methodology described here enables semiautomated, high-throughput sampling of small amounts of heterogeneous tissue specimens by multiple analytical techniques with generally improved quality of recovered biomolecules.

High performance thin layer chromatography (HPTLC) and high performance liquid chromatography (HPLC) for the qualitative and quantitative analysis of Calendula officinalis-advantages and limitations.

PubMed

Loescher, Christine M; Morton, David W; Razic, Slavica; Agatonovic-Kustrin, Snezana

2014-09-01

Chromatography techniques such as HPTLC and HPLC are commonly used to produce a chemical fingerprint of a plant to allow identification and quantify the main constituents within the plant. The aims of this study were to compare HPTLC and HPLC, for qualitative and quantitative analysis of the major constituents of Calendula officinalis and to investigate the effect of different extraction techniques on the C. officinalis extract composition from different parts of the plant. The results found HPTLC to be effective for qualitative analysis, however, HPLC was found to be more accurate for quantitative analysis. A combination of the two methods may be useful in a quality control setting as it would allow rapid qualitative analysis of herbal material while maintaining accurate quantification of extract composition. Copyright © 2014 Elsevier B.V. All rights reserved.

An efficient method for purifying high quality RNA from wheat pistils.

PubMed

Manickavelu, A; Kambara, Kumiko; Mishina, Kohei; Koba, Takato

2007-02-15

Many methods are available for total RNA extraction from plants, except the floral organs like wheat pistils containing high levels of polysaccharides that bind/or co-precipitate with RNA. In this protocol, a simple and effective method for extracting total RNA from small and feathery wheat pistils has been developed. Lithium chloride (LiCl) and phenol:chloroform:isoamylalcohol (PCI) were employed and the samples were ground in microcentrifuge tube using plastic pestle. A jacket of liquid nitrogen and simplified procedures were applied to ensure thorough grinding of the pistils and to minimize the samples loss. These measures substantially increased the recovery of total RNA (approximately 50%) in the extraction process. Reliable differential display by cDNA-AFLP was successfully achieved with the total RNA after DNase treatment and reverse transcription. This method is also practicable for gene expression and gene regulation studies in floral parts of other plants.

Compositional Changes and Baking Performance of Rye Dough As Affected by Microbial Transglutaminase and Xylanase.

PubMed

Grossmann, Isabel; Döring, Clemens; Jekle, Mario; Becker, Thomas; Koehler, Peter

2016-07-20

Doughs supplemented with endoxylanase (XYL) and varying amounts of microbial transglutaminase (TG) were analyzed by sequential protein extraction, quantitation of protein fractions and protein types, and determination of water-extractable arabinoxylans. With increasing TG activity, the concentration of prolamins and glutelins decreased and increased, respectively, and the prolamin-to-glutelin ratio strongly declined. The overall amount of extractable protein decreased with increasing TG level showing that cross-linking by TG provided high-molecular-weight protein aggregates. The decrease of the high-molecular-weight arabinoxylan fraction and the concurrent increase of the medium-molecular-weight fraction confirmed the degradation of arabinoxylans by XYL. However, XYL addition did not lead to significant improved cross-linking of rye proteins by TG. Volume and crumb hardness measurements of bread showed increased protein connectivity induced by XYL and TG. Significant positive effects on the final bread quality were especially obtained by XYL addition.

Untargeted NMR Spectroscopic Analysis of the Metabolic Variety of New Apple Cultivars

PubMed Central

Eisenmann, Philipp; Ehlers, Mona; Weinert, Christoph H.; Tzvetkova, Pavleta; Silber, Mara; Rist, Manuela J.; Luy, Burkhard; Muhle-Goll, Claudia

2016-01-01

Metabolome analyses by NMR spectroscopy can be used in quality control by generating unique fingerprints of different species. Hundreds of components and their variation between different samples can be analyzed in a few minutes/hours with high accuracy and low cost of sample preparation. Here, apple peel and pulp extracts of a variety of apple cultivars were studied to assess their suitability to discriminate between the different varieties. The cultivars comprised mainly newly bred varieties or ones that were brought onto the market in recent years. Multivariate analyses of peel and pulp extracts were able to unambiguously identify all cultivars, with peel extracts showing a higher discriminative power. The latter was increased if the highly concentrated sugar metabolites were omitted from the analysis. Whereas sugar concentrations lay within a narrow range, polyphenols, discussed as potential health promoting substances, and acids varied remarkably between the cultivars. PMID:27657148

Untargeted NMR Spectroscopic Analysis of the Metabolic Variety of New Apple Cultivars.

PubMed

Eisenmann, Philipp; Ehlers, Mona; Weinert, Christoph H; Tzvetkova, Pavleta; Silber, Mara; Rist, Manuela J; Luy, Burkhard; Muhle-Goll, Claudia

2016-09-19

Metabolome analyses by NMR spectroscopy can be used in quality control by generating unique fingerprints of different species. Hundreds of components and their variation between different samples can be analyzed in a few minutes/hours with high accuracy and low cost of sample preparation. Here, apple peel and pulp extracts of a variety of apple cultivars were studied to assess their suitability to discriminate between the different varieties. The cultivars comprised mainly newly bred varieties or ones that were brought onto the market in recent years. Multivariate analyses of peel and pulp extracts were able to unambiguously identify all cultivars, with peel extracts showing a higher discriminative power. The latter was increased if the highly concentrated sugar metabolites were omitted from the analysis. Whereas sugar concentrations lay within a narrow range, polyphenols, discussed as potential health promoting substances, and acids varied remarkably between the cultivars.

Ultrasonic-Assisted Extraction of Raspberry Seed Oil and Evaluation of Its Physicochemical Properties, Fatty Acid Compositions and Antioxidant Activities

PubMed Central

Huang, Qun; Wang, Jinli; Lin, Qiyang; Liu, Mingxin; Lee, Won Young; Song, Hongbo

2016-01-01

Ultrasonic-assisted extraction was employed for highly efficient separation of aroma oil from raspberry seeds. A central composite design with two variables and five levels was employed and effects of process variables of sonication time and extraction temperature on oil recovery and quality were investigated. Optimal conditions predicted by response surface methodology were sonication time of 37 min and extraction temperature of 54°C. Specifically, ultrasonic-assisted extraction (UAE) was able to provide a higher content of beneficial unsaturated fatty acids, whereas conventional Soxhlet extraction (SE) resulted in a higher amount of saturated fatty acids. Moreover, raspberry seed oil contained abundant amounts of edible linoleic acid and linolenic acid, which suggest raspberry seeds could be valuable edible sources of natural γ-linolenic acid products. In comparison with SE, UAE exerted higher free radical scavenging capacities. In addition, UAE significantly blocked H2O2-induced intracellular reactive oxygen species (ROS) generation. PMID:27120053

Extraction of urban vegetation with Pleiades multiangular images

NASA Astrophysics Data System (ADS)

Lefebvre, Antoine; Nabucet, Jean; Corpetti, Thomas; Courty, Nicolas; Hubert-Moy, Laurence

2016-10-01

Vegetation is essential in urban environments since it provides significant services in terms of health, heat, property value, ecology ... As part of the European Union Biodiversity Strategy Plan for 2020, the protection and development of green-infrastructures is strengthened in urban areas. In order to evaluate and monitor the quality of the green infra-structures, this article investigates contributions of Pléiades multi-angular images to extract and characterize low and high urban vegetation. From such images one can extract both spectral and elevation information from optical images. Our method is composed of 3 main steps : (1) the computation of a normalized Digital Surface Model from the multi-angular images ; (2) Extraction of spectral and contextual features ; (3) a classification of vegetation classes (tree and grass) performed with a random forest classifier. Results performed in the city of Rennes in France show the ability of multi-angular images to extract DEM in urban area despite building height. It also highlights its importance and its complementarity with contextual information to extract urban vegetation.

Extraction of saponifiable lipids from wet microalgal biomass for biodiesel production.

PubMed

Jiménez Callejón, María J; Robles Medina, Alfonso; Macías Sánchez, María D; Hita Peña, Estrella; Esteban Cerdán, Luis; González Moreno, Pedro A; Molina Grima, Emilio

2014-10-01

Saponifiable lipids (SLs) were extracted with hexane from wet biomass (86 wt% water) of the microalga Nannochloropsis gaditana in order to transform them into fatty acid methyl esters (FAMEs, biodiesel). The influence of homogenization pressure on SL extraction yield at low temperature (20-22 °C) was studied. Homogenization at 1700 bar tripled the SL extraction yield. Two biomass batches with similar total lipid content but different lipidic compositions were used. Batch 1 contained fewer SLs (12.0 wt%) and neutral saponifiable lipids (NSLs, 7.9 wt%) than batch 2 (21.6 and 17.2 wt%, respectively). For this reason, and due to the selectivity of hexane toward NSLs, high SL yield (69.1 wt%) and purity (71.0 wt%) were obtained from batch 2. Moreover, this extract contains a small percentage of polyunsaturated fatty acids (16.9 wt%), thereby improving the biodiesel quality. Finally, up to 97.0% of extracted SLs were transformed to FAMEs by acid catalyzed transesterification. Copyright © 2014 Elsevier Ltd. All rights reserved.

A comprehensive review on vanilla flavor: extraction, isolation and quantification of vanillin and others constituents.

PubMed

Sinha, Arun K; Sharma, Upendra K; Sharma, Nandini

2008-06-01

Vanilla, being the world's most popular flavoring materials, finds extensive applications in food, beverages, perfumery and pharmaceutical industry. With the high demand and limited supply of vanilla pods and the continuing increase in their cost, numerous efforts of blending and adulteration in natural vanilla extracts have been reported. Thus, to ensure the quality of vanilla extracts and vanilla-containing products, it is important to develop techniques to verify their authenticity. Quantitatively, vanillin is the major compound present in the vanilla pods and the determination of vanillin is a vital consideration in natural vanilla extracts. This paper provides a comprehensive account of different extraction processes and chromatographic techniques applied for the separation, identification and determination of chemical constituents of vanilla. The review also provides an account of different methods applied for the quantification and the authentification of chemical constituents of vanilla extract. As the various properties of vanilla are attributed to its main constituent vanillin, its physico-chemical and bioactive properties have also been outlined.

Oil extraction from sheanut (Vitellaria paradoxa Gaertn C.F.) kernels assisted by microwaves.

PubMed

Nde, Divine B; Boldor, Dorin; Astete, Carlos; Muley, Pranjali; Xu, Zhimin

2016-03-01

Shea butter, is highly solicited in cosmetics, pharmaceuticals, chocolates and biodiesel formulations. Microwave assisted extraction (MAE) of butter from sheanut kernels was carried using the Doehlert's experimental design. Factors studied were microwave heating time, temperature and solvent/solute ratio while the responses were the quantity of oil extracted and the acid number. Second order models were established to describe the influence of experimental parameters on the responses studied. Under optimum MAE conditions of heating time 23 min, temperature 75 °C and solvent/solute ratio 4:1 more than 88 % of the oil with a free fatty acid (FFA) value less than 2, was extracted compared to the 10 h and solvent/solute ratio of 10:1 required for soxhlet extraction. Scanning electron microscopy was used to elucidate the effect of microwave heating on the kernels' microstructure. Substantial reduction in extraction time and volumes of solvent used and oil of suitable quality are the main benefits derived from the MAE process.

ON-SITE SOLID PHRASE EXTRACTION AND LABORATORY ...

EPA Pesticide Factsheets

Fragrance materials, such as synthetic musks in aqueous samples, are normally analyzed by GC/MS in the selected ion monitoring (SIM) mode to provide maximum sensitivity after liquid-liquid extraction of I -L samples. A I -L sample, however, usually provides too little analyte for full-scan data acquisition. An on-site extraction method for extracting synthetic musks from 60 L of wastewater effluent has been developed. Such a large sample volume permits high-quality, full-scan mass spectra to be obtained for various synthetic musk compounds. Quantification of these compounds was conveniently achieved from the full-scan data directly, without preparing SIM descriptors for each compound to acquire SIM data. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support of this Task and more in-depth coverage of each project. Briefly, each project's objective is stated below.Subtask 1: To integrate state-of-the-art technologies (polar organic chemical integrative samplers, advanced solid-phase extraction methodologies with liquid chromatography/electrospray/mass spectrometry) and apply them to studying the sources and fate of a select list of PPCPs. Application and improvement of analytical methodologies that can detect non-volatile, polar, water-sol

IN SITU SOLID-PHASE EXTRACTION AND ANALYSIS OF ...

EPA Pesticide Factsheets

Fragrance materials, such as synthetic musks in aqueous samples, are normally analyzed by GC/MS in the selected ion monitoring (SIM) mode to provide maximum sensitivity after liquid-liquid extraction of 1-L samples. A 1-L sample, however, usually provides too little analyte for full-scan data acquisition.We have developed an on-site extraction method for extracting synthetic musks from 60 L of wastewater effluent. Such a large sample volume permits high-quality, full-scan mass spectra to be obtained for various synthetic musk compounds. Quantification of these compounds was conveniently achieved from the full-scan data directly, without preparing SIM descriptors for each compound to acquire SIM data. The research focused on in the subtasks is the development and application of state-of the-art technologies to meet the needs of the public, Office of Water, and ORD in the area of Water Quality. Located In the subtasks are the various research projects being performed in support of this Task and more in-depth coverage of each project. Briefly, each project's objective is stated below.Subtask 1: To integrate state-of-the-art technologies (polar organic chemical integrative samplers, advanced solid-phase extraction methodologies with liquid chromatography/electrospray/mass spectrometry) and apply them to studying the sources and fate of a select list of PPCPs. Application and improvement of analytical methodologies that can detect non-volatile, polar, water-s

Expression analysis and identification of antimicrobial peptide transcripts from six North American frog species

USGS Publications Warehouse

Robertson, Laura S.; Fellers, Gary M.; Marranca, Jamie Marie; Kleeman, Patrick M.

2013-01-01

Frogs secrete antimicrobial peptides onto their skin. We describe an assay to preserve and analyze antimicrobial peptide transcripts from field-collected skin secretions that will complement existing methods for peptide analysis. We collected skin secretions from 4 North American species in the field in California and 2 species in the laboratory. Most frogs appeared healthy after release; however, Rana boylii in the Sierra Nevada foothills, but not the Coast Range, showed signs of morbidity and 2 died after handling. The amount of total RNA extracted from skin secretions was higher in R. boylii and R. sierrae compared to R. draytonii, and much higher compared to Pseudacris regilla. Interspecies variation in amount of RNA extracted was not explained by size, but for P. regilla it depended upon collection site and date. RNA extracted from skin secretions from frogs handled with bare hands had poor quality compared to frogs handled with gloves or plastic bags. Thirty-four putative antimicrobial peptide precursor transcripts were identified. This study demonstrates that RNA extracted from skin secretions collected in the field is of high quality suitable for use in sequencing or quantitative PCR (qPCR). However, some species do not secrete profusely, resulting in very little extracted RNA. The ability to measure transcript abundance of antimicrobial peptides in field-collected skin secretions complements proteomic analyses and may provide insight into transcriptional mechanisms that could affect peptide abundance.

Refining of metallurgical-grade silicon

NASA Technical Reports Server (NTRS)

Dietl, J.

1986-01-01

A basic requirement of large scale solar cell fabrication is to provide low cost base material. Unconventional refining of metallurical grade silicon represents one of the most promising ways of silicon meltstock processing. The refining concept is based on an optimized combination of metallurgical treatments. Commercially available crude silicon, in this sequence, requires a first pyrometallurgical step by slagging, or, alternatively, solvent extraction by aluminum. After grinding and leaching, high purity qualtiy is gained as an advanced stage of refinement. To reach solar grade quality a final pyrometallurgical step is needed: liquid-gas extraction.

Root yield and quality of sugarbeet hybrids with pollinators selected for sodium, potassium, or amino-nitrogen concentration

USDA-ARS?s Scientific Manuscript database

Sodium, potassium, and amino-nitrogen, collectively referred to as impurities, are natural constituents of sugarbeet that impede sucrose extraction during factory operations. Lines selected specifically for low or high concentration of a single impurity component were crossed as pollinators with a ...

Radioactive Decay: Audio Data Collection

ERIC Educational Resources Information Center

Struthers, Allan

2009-01-01

Many phenomena generate interesting audible time series. This data can be collected and processed using audio software. The free software package "Audacity" is used to demonstrate the process by recording, processing, and extracting click times from an inexpensive radiation detector. The high quality of the data is demonstrated with a simple…

Valorization of Waste Obtained from Oil Extraction in Moringa Oleifera Seeds: Coagulation of Reactive Dyes in Textile Effluents.

PubMed

Vilaseca, Mercè; López-Grimau, Víctor; Gutiérrez-Bouzán, Carmen

2014-09-12

Moringa oleifera seeds contain about 40% of highly valued oil due to its wide range of applications, from nutritional issues to cosmetics or biodiesel production. The extraction of Moringa oil generates a waste (65%-75% of seeds weight) which contains a water soluble protein able to be used either in drinking water clarification or wastewater treatment. In this paper, the waste of Moringa oleifera extraction was used as coagulant to remove five reactive dyes from synthetic textile effluents. This waste constitutes a natural coagulant which was demonstrated to be effective for the treatment of industrial reactive dyestuff effluents, characterized by alkaline pH, high NaCl content and hydrolyzed dyes. The coagulation yield increased at high NaCl concentration, whereas the pH did not show any significant effect on dye removal. Moringa oleifera showed better results for dye removal than the conventional treatment of coagulation-flocculation with FeCl₃ and polyelectrolyte. Treated water can be reused in new dyeing processes of cotton fabrics with high quality results.

Valorization of Waste Obtained from Oil Extraction in Moringa Oleifera Seeds: Coagulation of Reactive Dyes in Textile Effluents

PubMed Central

Vilaseca, Mercè; López-Grimau, Víctor; Gutiérrez-Bouzán, Carmen

2014-01-01

Moringa oleifera seeds contain about 40% of highly valued oil due to its wide range of applications, from nutritional issues to cosmetics or biodiesel production. The extraction of Moringa oil generates a waste (65%–75% of seeds weight) which contains a water soluble protein able to be used either in drinking water clarification or wastewater treatment. In this paper, the waste of Moringa oleifera extraction was used as coagulant to remove five reactive dyes from synthetic textile effluents. This waste constitutes a natural coagulant which was demonstrated to be effective for the treatment of industrial reactive dyestuff effluents, characterized by alkaline pH, high NaCl content and hydrolyzed dyes. The coagulation yield increased at high NaCl concentration, whereas the pH did not show any significant effect on dye removal. Moringa oleifera showed better results for dye removal than the conventional treatment of coagulation-flocculation with FeCl3 and polyelectrolyte. Treated water can be reused in new dyeing processes of cotton fabrics with high quality results. PMID:28788199

Monitoring the quality of welding based on welding current and ste analysis

NASA Astrophysics Data System (ADS)

Mazlan, Afidatusshimah; Daniyal, Hamdan; Izzani Mohamed, Amir; Ishak, Mahadzir; Hadi, Amran Abdul

2017-10-01

Qualities of welding play an important part in industry especially in manufacturing field. Post-welding non-destructive test is one of the importance process to ensure the quality of welding but it is time consuming and costly. To reduce the chance of defects, online monitoring had been utilized by continuously sense some of welding parameters and predict welding quality. One of the parameters is welding current, which is rich of information but lack of study focus on extract them at signal analysis level. This paper presents the analysis of welding current using Short Time Energy (STE) signal processing to quantify the pattern of the current. GMAW set with carbon steel specimens are used in this experimental study with high-bandwidth and high sampling rate oscilloscope capturing the welding current. The results indicate welding current as signatures have high correlation with the welding process. Continue with STE analysis, the value below 5000 is declare as good welding, meanwhile the STE value more than 6000 is contained defect.

Simultaneous determination of secondary metabolites from Vinca rosea plant extractives by reverse phase high performance liquid chromatography

PubMed Central

Siddiqui, Mohammad Jamshed Ahmad; Ismail, Zhari; Saidan, Noor Hafizoh

2011-01-01

Background: Vinca rosea (Apocynaceae) is one of the most important and high value medicinal plants known for its anticancer alkaloids. It is the iota of the isolated secondary metabolites used in chemotherapy to treat diverse cancers. Several high performance liquid chromatography (HPLC) methods have been developed to quantify the active alkaloids in the plant. However, this method may serve the purpose in quantification of V. rosea plant extracts in totality. Objective: To develop and validate the reverse phase (RP)-HPLC method for simultaneous determination of secondary metabolites, namely alkaloids from V. rosea plant extracts. Materials and Methods: The quantitative determination was conducted by RP-HPLC equipped with ultraviolet detector. Optimal separation was achieved by isocratic elution with mobile phase consisting of methanol:acetonitrile:ammonium acetate buffer (25 mM) with 0.1% triethylamine (15:45:40 v/v) on a column (Zorbax Eclipse plus C18, 250 mm % 4.6 mm; 5 μm). The standard markers (vindoline, vincristine, catharanthine, and vinblastine) were identified by retention time and co-injected with reference standard and quantified by external standard method at 297 nm. Results: The precision of the method was confirmed by the relative standard deviation (R.S.D.), which was lower than 2.68%. The recoveries were in the range of 98.09%-108%. The limits of detection (LOD) for each marker alkaloids were lower than 0.20 μg. Different parts of the V. rosea extracts shows different concentrations of markers, flower samples were high in vinblastine content, while methanol extract from the leaves contains all the four alkaloids in good yield, and there is no significant presence of markers in water extracts. Conclusion: HPLC method established is appropriate for the standardization and quality assurance of V. rosea plant extracts. PMID:21716929

Qualitative characterization of Desmodium adscendens constituents by high-performance liquid chromatography-diode array ultraviolet-electrospray ionization multistage mass spectrometry.

PubMed

Baiocchi, Claudio; Medana, Claudio; Giancotti, Valeria; Aigotti, Riccardo; Dal Bello, Frederica; Massolino, Cristina; Gastaldi, Daniela; Grandi, Maurizio

2013-01-01

The many effects of the African medicinal herb Desmodium adscendens were studied in the 1980s and 1990s. In spite of this, a comprehensive analytical protocol for the quality control of its constituents (soyasaponins, alkaloids and flavonoids) has not yet been formulated and reported. This study deals with the optimization of extraction conditions from the plant and qualitative identification of the constituents by HPLC-diode array UV and multistage mass spectrometry. Plant constituents were extracted from leaves by liquid-liquid and solid matrix dispersion extraction. Separation was achieved via RP-C18 liquid chromatographywith UV and MS(n) detection and mass spectrometry analysis was conducted by electrospray ionization ion trap or orbitrap mass spectrometry. High resolution mass spectrometry (HRMS) was used for structural identification of active molecules relating to soyasaponins and alkaloids. The flavonoid fragmentations were preliminarily studied by HRMS in order to accurately characterize the more common neutral losses. However, the high number of isomeric species induced us to make recourse to a more extended chromatographic separation in order to enable useful tandem mass spectrometry and ultraviolet spectral interpretation to propose a reasonable chemical classification of these polyphenols. 35 compounds of this class were identified herein with respect to the five reported in literature in this way we made up a comprehensive protocol for the qualitative analysis of the high complexity content of this plant. This result paves the way for both reliable quality control of potential phytochemical medicaments and possible future systematic clinical studies.

Other factors to consider in the formation of chloropropandiol fatty esters in oil processes.

PubMed

Ramli, Muhamad Roddy; Siew, Wai Lin; Ibrahim, Nuzul Amri; Kuntom, Ainie; Abd Razak, Raznim Arni

2015-01-01

This paper examines the processing steps of extracting palm oil from fresh fruit bunches in a way that may impact on the formation of chloropropandiol fatty esters (3-MCPD esters), particularly during refining. Diacylglycerols (DAGs) do not appear to be a critical factor when crude palm oils are extracted from various qualities of fruit bunches. Highly hydrolysed oils, in spite of the high free fatty acid (FFA) contents, did not show exceptionally high DAGs, and the oils did not display a higher formation of 3-MCPD esters upon heat treatment. However, acidity measured in terms of pH appears to have a strong impact on 3-MCPD ester formation in the crude oil when heated at high temperatures. The differences in the extraction process of crude palm oil from current commercial processes and that from a modified experimental process showed clearly the effect of acidity of the oil on the formation of 3-MCPD esters. This paper concludes that the washing or dilution step in palm oil mills removes the acidity of the vegetative materials and that a well-optimised dilution/washing step in the extraction process will play an important role in reducing formation of 3-MCPD esters in crude palm oil upon further heat processing.

Validation of green-solvent extraction combined with chromatographic chemical fingerprint to evaluate quality of Stevia rebaudiana Bertoni.

PubMed

Teo, Chin Chye; Tan, Swee Ngin; Yong, Jean Wan Hong; Hew, Choy Sin; Ong, Eng Shi

2009-02-01

An approach that combined green-solvent methods of extraction with chromatographic chemical fingerprint and pattern recognition tools such as principal component analysis (PCA) was used to evaluate the quality of medicinal plants. Pressurized hot water extraction (PHWE) and microwave-assisted extraction (MAE) were used and their extraction efficiencies to extract two bioactive compounds, namely stevioside (SV) and rebaudioside A (RA), from Stevia rebaudiana Bertoni (SB) under different cultivation conditions were compared. The proposed methods showed that SV and RA could be extracted from SB using pure water under optimized conditions. The extraction efficiency of the methods was observed to be higher or comparable to heating under reflux with water. The method precision (RSD, n = 6) was found to vary from 1.91 to 2.86% for the two different methods on different days. Compared to PHWE, MAE has higher extraction efficiency with shorter extraction time. MAE was also found to extract more chemical constituents and provide distinctive chemical fingerprints for quality control purposes. Thus, a combination of MAE with chromatographic chemical fingerprints and PCA provided a simple and rapid approach for the comparison and classification of medicinal plants from different growth conditions. Hence, the current work highlighted the importance of extraction method in chemical fingerprinting for the classification of medicinal plants from different cultivation conditions with the aid of pattern recognition tools used.

Rapid method to extract DNA from Cryptococcus neoformans.

PubMed Central

Varma, A; Kwon-Chung, K J

1991-01-01

A rapid and easy method for the extraction of total cellular DNA from Cryptococcus neoformans is described. This procedure modifies and considerably simplifies previously reported methods. Numerous steps were either eliminated or replaced, including preincubations with cell wall permeability agents such as beta-mercaptoethanol and dithiothreitol. The commercially available enzyme preparation Novozyme 234 was found to contain a potent concentration of DNases which actively degrade DNA. Degradation and loss of DNA was prevented by maintaining a high concentration of EDTA in the lysing solution. This procedure resulted in high yields (150 to 200 micrograms of DNA from 100 ml of culture) of good-quality (undegraded), high-molecular-weight DNA which was readily digested by restriction endonucleases, making it suitable for use in various molecular applications. Images PMID:1909713

Persistent-current magnetizations of Nb3Sn Rutherford cables and extracted strands

NASA Astrophysics Data System (ADS)

Collings, E. W.; Sumption, M. D.; Myers, C. S.; Wang, X.; Dietderich, D. R.; Yagotyntsev, K.; Nijhuis, A.

2017-12-01

The magnetizations of eight high-gradient quadrupole cables designated HQ and QXF and a pair of strands, identical in architecture but with different effective strand diameters extracted from an HQ and a related QXF cable, were measured. In the service of field quality assessment, the cable magnetizations and losses were measured by pickup coil magnetometry at 4.2 K in face-on fields, B m , of ± 400 mT at frequencies, f, of up to 60 mHz. Based on the coupling component of loss, Q coup , the coupling magnetization M coup = Q coup /4B m was derived for a ramp rate of 7.5 mT/s. Persistent current (shielding) magnetization and loss (M sh and Q h,strand ) were measured on short pieces of extracted strand by vibrating sample magnetometry at 4.2 K. Unpenetrated M-B loops to ± 400 mT and fully penetrated loops to ± 14 T were obtained. M coup can be easily controlled and reduced to relatively small values by introducing cores and adjusting the preparation conditions. But in low fields near injection Nb3Sn’s high J c and correspondingly high M sh,cable may call for magnetic compensation to preserve field quality. The suitably adjusted cable and strand fully penetrated M-B loops were in reasonable accord leading to the conclusion that strand magnetization is a useful measure of cable magnetization, and that when suitably manipulated can provide input to magnet field error calculations.

Comparison of four DNA extraction methods for the detection of Mycobacterium leprae from Ziehl-Neelsen-stained microscopic slides.

PubMed

Ruiz-Fuentes, Jenny Laura; Díaz, Alexis; Entenza, Anayma Elena; Frión, Yahima; Suárez, Odelaisy; Torres, Pedro; de Armas, Yaxsier; Acosta, Lucrecia

2015-12-01

The diagnosis of leprosy has been a challenge due to the low sensibility of the conventional methods and the impossibility of culturing the causative organism. In this study, four methods for Mycobacterium leprae nucleic-acid extraction from Ziehl-Neelsen-stained slides (ZNS slides) were compared: Phenol/chloroform, Chelex 100 resin, and two commercial kits (Wizard Genomic DNA Purification Kit and QIAamp DNA Mini Kit). DNA was extracted from four groups of slides: a high-codification-slide group (bacteriological index [BI]⩾4), a low-codification-slide group (BI=1), a negative-slide group (BI=0), and a negative-control-slide group (BI=0). Quality DNA was evidenced by the amplification of specific repetitive element present in M. leprae genomic DNA (RLEP) using a nested polymerase chain reaction. This is the first report comparing four different extraction methods for obtaining M. leprae DNA from ZNS slides in Cuban patients, and applied in molecular diagnosis. Good-quality DNA and positive amplification were detected in the high-codification-slide group with the four methods, while from the low-codification-slide group only the QIAGEN and phenol-chloroform methods obtained amplification of M. leprae. In the negative-slide group, only the QIAGEN method was able to obtain DNA with sufficient quality for positive amplification of the RLEP region. No amplification was observed in the negative-control-slide group by any method. Patients with ZNS negative slides can still transmit the infection, and molecular methods can help identify and treat them, interrupting the chain of transmission and preventing the onset of disabilities. The ZNS slides can be sent easily to reference laboratories for later molecular analysis that can be useful not only to improve the diagnosis, but also for the application of other molecular techniques. Copyright © 2015 Asian-African Society for Mycobacteriology. Published by Elsevier Ltd. All rights reserved.

A robust method for RNA extraction and purification from a single adult mouse tendon.

PubMed

Grinstein, Mor; Dingwall, Heather L; Shah, Rishita R; Capellini, Terence D; Galloway, Jenna L

2018-01-01

Mechanistic understanding of tendon molecular and cellular biology is crucial toward furthering our abilities to design new therapies for tendon and ligament injuries and disease. Recent transcriptomic and epigenomic studies in the field have harnessed the power of mouse genetics to reveal new insights into tendon biology. However, many mouse studies pool tendon tissues or use amplification methods to perform RNA analysis, which can significantly increase the experimental costs and limit the ability to detect changes in expression of low copy transcripts. Single Achilles tendons were harvested from uninjured, contralateral injured, and wild type mice between three and five months of age, and RNA was extracted. RNA Integrity Number (RIN) and concentration were determined, and RT-qPCR gene expression analysis was performed. After testing several RNA extraction approaches on single adult mouse Achilles tendons, we developed a protocol that was successful at obtaining high RIN and sufficient concentrations suitable for RNA analysis. We found that the RNA quality was sensitive to the time between tendon harvest and homogenization, and the RNA quality and concentration was dependent on the duration of homogenization. Using this method, we demonstrate that analysis of Scx gene expression in single mouse tendons reduces the biological variation caused by pooling tendons from multiple mice. We also show successful use of this approach to analyze Sox9 and Col1a2 gene expression changes in injured compared with uninjured control tendons. Our work presents a robust, cost-effective, and straightforward method to extract high quality RNA from a single adult mouse Achilles tendon at sufficient amounts for RT-qPCR as well as RNA-seq. We show this can reduce variation and decrease the overall costs associated with experiments. This approach can also be applied to other skeletal tissues, as well as precious human samples.

Automated extraction of natural drainage density patterns for the conterminous United States through high performance computing

USGS Publications Warehouse

Stanislawski, Larry V.; Falgout, Jeff T.; Buttenfield, Barbara P.

2015-01-01

Hydrographic networks form an important data foundation for cartographic base mapping and for hydrologic analysis. Drainage density patterns for these networks can be derived to characterize local landscape, bedrock and climate conditions, and further inform hydrologic and geomorphological analysis by indicating areas where too few headwater channels have been extracted. But natural drainage density patterns are not consistently available in existing hydrographic data for the United States because compilation and capture criteria historically varied, along with climate, during the period of data collection over the various terrain types throughout the country. This paper demonstrates an automated workflow that is being tested in a high-performance computing environment by the U.S. Geological Survey (USGS) to map natural drainage density patterns at the 1:24,000-scale (24K) for the conterminous United States. Hydrographic network drainage patterns may be extracted from elevation data to guide corrections for existing hydrographic network data. The paper describes three stages in this workflow including data pre-processing, natural channel extraction, and generation of drainage density patterns from extracted channels. The workflow is concurrently implemented by executing procedures on multiple subbasin watersheds within the U.S. National Hydrography Dataset (NHD). Pre-processing defines parameters that are needed for the extraction process. Extraction proceeds in standard fashion: filling sinks, developing flow direction and weighted flow accumulation rasters. Drainage channels with assigned Strahler stream order are extracted within a subbasin and simplified. Drainage density patterns are then estimated with 100-meter resolution and subsequently smoothed with a low-pass filter. The extraction process is found to be of better quality in higher slope terrains. Concurrent processing through the high performance computing environment is shown to facilitate and refine the choice of drainage density extraction parameters and more readily improve extraction procedures than conventional processing.

Inhibitory Effects of Spices on Biogenic Amine Accumulation during Fish Sauce Fermentation.

PubMed

Zhou, Xuxia; Qiu, Mengting; Zhao, Dandan; Lu, Fei; Ding, Yuting

2016-04-01

The presence of high levels of biogenic amines is detrimental to the quality and safety of fish sauce. This study investigated the effects of ethanol extracts of spices, including garlic, ginger, cinnamon, and star anise extracts, in reducing the accumulation of biogenic amines during fish sauce fermentation. The concentrations of biogenic amines, which include histamine, putrescine, tyramine, and spermidine, all increased during fish sauce fermentation. When compared with the samples without spices, the garlic and star anise extracts significantly reduced these increases. The greatest inhibitory effect was observed for the garlic ethanolic extracts. When compared with controls, the histamine, putrescine, tyramine, and spermidine contents and the overall biogenic amine levels of the garlic extract-treated samples were reduced by 30.49%, 17.65%, 26.03%, 37.20%, and 27.17%, respectively. The garlic, cinnamon, and star anise extracts showed significant inhibitory effects on aerobic bacteria counts. Furthermore, the garlic and star anise extracts showed antimicrobial activity against amine producers. These findings may be helpful for enhancing the safety of fish sauce. © 2016 Institute of Food Technologists®

A comparison of sediment quality results with acid volatile sulfide (AVS) and simultaneously extracted metals (SEM) ratio in Vojvodina (Serbia) sediments.

PubMed

Prica, M; Dalmacija, B; Roncević, S; Krcmar, D; Becelić, M

2008-01-25

The acid-volatile sulfide (AVS), simultaneously extracted metals (SEM), total metals, and pore-water metal concentrations were studied in Vojvodina (Serbia) sediments. In Serbia, there are no regulations concerning sediment quality standards and sediment management. Harmonization of legislation in the domain of environmental protection with EU requirements will increase the significance of the sediment issue. Sediment quality was assessed according to Dutch standards, but the results were also compared with Canadian and USEPA (United States Environmental Protection Agency) guidelines for sediment quality. A comparison of the results based on different criteria for sediment quality assessment shows that they are sometimes contradictory. Therefore, a single approach to quality assessment may be insufficient. The Sigma[SEM]/[AVS] ratio was found to be greater than one at several locations that were already recognized as places of high risk based on Dutch standards. Some other samples had Sigma[SEM]/[AVS]<1, despite of the high risk classification based on the Dutch evaluation. However, not all sediments with Sigma[SEM]/[AVS]>1 can cause increased toxicity because there are many other metal-binding phases in sediments. Metals that are associated with AVS may be released within sediments through storms, dredging activities, oxidation, etc., and may have adverse environmental impacts. This has to be taken into account during dredging, which is for some sediments necessary because the sediment is of class 4 (Dutch evaluation), because the dredging process will certainly increase the concentration of bioavailable heavy metals and disturb the sedimentation dynamics. The obtained results will be invaluable for future activities regarding dredging and sediment management in the country.

Quality components and antidepressant-like effects of GABA green tea.

PubMed

Teng, Jie; Zhou, Wen; Zeng, Zhen; Zhao, Wenfang; Huang, Yahui; Zhang, Xu

2017-09-20

Gamma (γ)-aminobutyric acid (GABA) green tea, with high GABA content, is a kind of special green tea. The goals of this study are to analyze the changes in quality components of green tea during anaerobic treatment, and to investigate whether or not the extract of GABA present in green tea can prevent depression or improve the depressive state of animals. Results showed that GABA content in green tea had increased significantly after anaerobic treatment. The contents of tea polysaccharides, total free amino acids, and water extracts were also increased whereas tea polyphenols were reduced. More importantly, the extract of GABA green tea could alleviate mouse depression and stress from desperate environments through the forced swim test (FST), tail suspension test (TST), mRNA and protein expression levels of GABA A receptors. Therefore, these results indicate that GABA green tea may have a health effect on prevention and alleviation of depression, and it works on the GABAergic neurotransmission of mouse cerebral cortex via up-regulating expression of the GABA A receptor α1 subunit, thus ameliorating depression.

Effectiveness of health and safety in small enterprises: a systematic review of quantitative evaluations of interventions.

PubMed

Breslin, F Curtis; Kyle, Natasha; Bigelow, Philip; Irvin, Emma; Morassaei, Sara; MacEachen, Ellen; Mahood, Quenby; Couban, Rachel; Shannon, Harry; Amick, Benjamin C

2010-06-01

This systematic review was conducted to identify effective occupational health and safety interventions for small businesses. The review focused on peer-reviewed intervention studies conducted in small businesses with 100 or fewer employees, that were published in English and several other languages, and that were not limited by publication date. Multidisciplinary members of the review team identified relevant articles and assessed their quality. Studies assessed as medium or high quality had data extracted, which was then synthesized. Five studies were deemed of medium or high quality, and proceeded to data extraction and evidence synthesis. The types of interventions identified: a combination of training and safety audits; and a combination of engineering, training, safety audits, and a motivational component, showed a limited amount of evidence in improving safety outcomes. Overall, this evidence synthesis found a moderate level of evidence for intervention effectiveness, and found no evidence that any intervention had adverse effects. Even though there were few studies that adequately evaluated small business intervention, several studies demonstrate that well-designed evaluations are possible with small businesses. While stronger levels of evidence are required to make recommendations, these interventions noted above were associated with positive changes in safety-related attitudes and beliefs and workplace parties should be aware of them.

Improvement of seawater salt quality by hydro-extraction and re-crystallization methods

NASA Astrophysics Data System (ADS)

Sumada, K.; Dewati, R.; Suprihatin

2018-01-01

Indonesia is one of the salt producing countries that use sea water as a source of raw materials, the quality of salt produced is influenced by the quality of sea water. The resulting average salt quality contains 85-90% NaCl. The Indonesian National Standard (SNI) for human salt’s consumption sodium chloride content is 94.7 % (dry base) and for industrial salt 98,5 %. In this study developed the re-crystallization without chemical and hydro-extraction method. The objective of this research to choose the best methods based on efficiency. The results showed that re-crystallization method can produce salt with NaCl content 99,21%, while hydro-extraction method content 99,34 % NaCl. The salt produced through both methods can be used as a consumption and industrial salt, Hydro-extraction method is more efficient than re-crystallization method because re-crystallization method requires heat energy.

Extraction of respiratory signals from the electrocardiogram and photoplethysmogram: technical and physiological determinants.

PubMed

Charlton, Peter H; Bonnici, Timothy; Tarassenko, Lionel; Alastruey, Jordi; Clifton, David A; Beale, Richard; Watkinson, Peter J

2017-05-01

Breathing rate (BR) can be estimated by extracting respiratory signals from the electrocardiogram (ECG) or photoplethysmogram (PPG). The extracted respiratory signals may be influenced by several technical and physiological factors. In this study, our aim was to determine how technical and physiological factors influence the quality of respiratory signals. Using a variety of techniques 15 respiratory signals were extracted from the ECG, and 11 from PPG signals collected from 57 healthy subjects. The quality of each respiratory signal was assessed by calculating its correlation with a reference oral-nasal pressure respiratory signal using Pearson's correlation coefficient. Relevant results informing device design and clinical application were obtained. The results informing device design were: (i) seven out of 11 respiratory signals were of higher quality when extracted from finger PPG compared to ear PPG; (ii) laboratory equipment did not provide higher quality of respiratory signals than a clinical monitor; (iii) the ECG provided higher quality respiratory signals than the PPG; (iv) during downsampling of the ECG and PPG significant reductions in quality were first observed at sampling frequencies of  <250 Hz and  <16 Hz respectively. The results informing clinical application were: (i) frequency modulation-based respiratory signals were generally of lower quality in elderly subjects compared to young subjects; (ii) the qualities of 23 out of 26 respiratory signals were reduced at elevated BRs; (iii) there were no differences associated with gender. Recommendations based on the results are provided regarding device designs for BR estimation, and clinical applications. The dataset and code used in this study are publicly available.

Rapid extraction and determination of 25 bioactive constituents in Alpinia oxyphylla using microwave extraction with ultra high performance liquid chromatography with tandem mass spectrometry.

PubMed

Sun, Zhi; Kong, Xiangzhen; Zuo, Lihua; Kang, Jian; Hou, Lei; Zhang, Xiaojian

2016-02-01

A novel and rapid microwave extraction and ultra high performance liquid chromatography with tandem mass spectrometry method was developed and validated for the simultaneous determination of 25 bioactive constituents (including two new constituents) in Fructus Alpinia oxyphylla. The optimized conditions of the microwave extraction was a microwave power of 300 W, extraction temperature of 80°C, solvent-to-solid ratio of 30 mL/g and extraction time of 8 min. Separation was achieved on a Waters ACQUITY UPLC(®) HSS C18 column (2.1 mm× 50 mm, 1.8 μm) using gradient elution with a mobile phase consisting of acetonitrile and 1 mM ammonium acetate at a flow rate of 0.2 mL/min. This is the first report of the simultaneous determination of 25 bioactive constituents in Fructus Alpinia oxyphylla by ultra high performance liquid chromatography with tandem mass spectrometry. The method was validated with good linearity, acceptable precision and accuracy. The validated method was successfully applied to determine the contents of 25 bioactive constituents in Fructus Alpinia oxyphylla from different sources and the analysis results were classified by hierarchical cluster analysis, which indicated the effect of different cultivation regions on the contents of constituents. This study provides powerful and practical guidance in the quality control of Alpinia oxyphylla and lays the foundation for further research of Alpinia oxyphylla. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect on quality of life of the mixed house dust mite/weed pollen extract immunotherapy.

PubMed

Li, Lisha; Guan, Kai

2016-07-01

Although many patients with allergic rhinitis have symptoms due to sensitization to more than one kind of allergens, and mixed allergen extracts are widely used for immunotherapy, there are few published trials. Our study aimed to evaluate the effect of multiple-allergen immunotherapy on improving the symptoms and quality of life of allergic rhinitis patients. We performed a 1-year single-center observation study of subcutaneous immunotherapy using house dust mite extract (n = 12), weed pollen extract (n = 21), or mixed house dust mite/weed pollen extract (n = 11) in 44 allergic rhinitis patients. All the allergens responsible for the symptom of each patient were included in his immunotherapy. Symptom score, medication score, and quality of life of the patients were evaluated before and after 1-year immunotherapy. Quality of life was evaluated with the Rhinoconjunctivitis Quality of Life Questionnaire. In all 3 groups receiving subcutaneous immunotherapy, significant improvement of symptom score, medication score, and quality of life was found vs. baseline at 1 year, irrespective of the allergen used. In the weed pollen season, the changes of quality of life questionnaire score after 1-year treatment were not significantly different between the weed pollen group (1.55 ± 1.24) and the mixed house dust mite/weed pollen group (1.14 ± 1.01). The same happened in the nonpollen seasons, during which dust mite immunotherapy (1.23 ± 1.63) and mixed immunotherapy (0.60 ± 0.47) did not show significantly different effect on the quality of life. The multiple-allergen immunotherapy might be effective in polysensitized allergic rhinitis patients, and could improve their quality of life. Our result did not show significant difference between the effects of multiple-allergen immunotherapy and mono-allergen immunotherapy.

Determination of Four Major Saponins in Skin and Endosperm of Seeds of Horse Chestnut (Aesculus Hippocastanum L.) Using High Performance Liquid Chromatography with Positive Confirmation by Thin Layer Chromatography

PubMed Central

Abudayeh, Zead Helmi Mahmoud; Al Azzam, Khaldun Mohammad; Naddaf, Ahmad; Karpiuk, Uliana Vladimirovna; Kislichenko, Viktoria Sergeevna

2015-01-01

Purpose: To separate and quantify four major saponins in the extracts of the skin and the endosperm of seeds of horse chestnut (Aesculus hippocastanum L.) using ultrasonic solvent extraction followed by a high performance liquid chromatography-diode array detector (HPLC-DAD) with positive confirmation by thin layer chromatography (TLC). Methods: The saponins: escin Ia, escin Ib, isoescin Ia and isoescin Ib were extracted using ultrasonic extraction method. The optimized extraction conditions were: 70% methanol as extraction solvent, 80 °C as extraction temperature, and the extraction time was achieved in 4 hours. The HPLC conditions used: Zorbax SB-ODS-(150 mm × 2.1 mm, 3 μm) column, acetonitrile and 0.10% phosphoric acid solution (39:61 v/v) as mobile phase, flow rate was 0.5 mL min−1 at 210 nm and 230 nm detection. The injection volume was 10 μL, and the separation was carried out isothermally at 30 °C in a heated chamber. Results: The results indicated that the developed HPLC method is simple, sensitive and reliable. Moreover, the content of escins in seeds decreased by more than 30% in endosperm and by more than 40% in skin upon storage for two years. Conclusion: This assay can be readily utilized as a quality control method for horse chestnut and other related medicinal plants. PMID:26819933

Aesthetic quality inference for online fashion shopping

NASA Astrophysics Data System (ADS)

Chen, Ming; Allebach, Jan

2014-03-01

On-line fashion communities in which participants post photos of personal fashion items for viewing and possible purchase by others are becoming increasingly popular. Generally, these photos are taken by individuals who have no training in photography with low-cost mobile phone cameras. It is desired that photos of the products have high aesthetic quality to improve the users' online shopping experience. In this work, we design features for aesthetic quality inference in the context of online fashion shopping. Psychophysical experiments are conducted to construct a database of the photos' aesthetic evaluation, specifically for photos from an online fashion shopping website. We then extract both generic low-level features and high-level image attributes to represent the aesthetic quality. Using a support vector machine framework, we train a predictor of the aesthetic quality rating based on the feature vector. Experimental results validate the efficacy of our approach. Metadata such as the product type are also used to further improve the result.

Using Lagrangian Coherent Structures to understand coastal water quality

NASA Astrophysics Data System (ADS)

Fiorentino, L. A.; Olascoaga, M. J.; Reniers, A.; Feng, Z.; Beron-Vera, F. J.; MacMahan, J. H.

2012-09-01

The accumulation of pollutants near the shoreline can result in low quality coastal water with negative effects on human health. To understand the role of mixing by tidal flows in coastal water quality we study the nearshore Lagrangian circulation. Specifically, we reveal Lagrangian Coherent Structures (LCSs), i.e., distinguished material curves which shape global mixing patterns and thus act as skeletons of the Lagrangian circulation. This is done using the recently developed geodesic theory of transport barriers. Particular focus is placed on Hobie Beach, a recreational subtropical marine beach located in Virginia Key, Miami, Florida. According to studies of water quality, Hobie Beach is characterized by high microbial levels. Possible sources of pollution in Hobie Beach include human bather shedding, dog fecal matter, runoff, and sand efflux at high tides. Consistent with the patterns formed by satellite-tracked drifter trajectories, the LCSs extracted from simulated currents reveal a Lagrangian circulation favoring the retention near the shoreline of pollutants released along the shoreline, which can help explain the low quality water registered at Hobie Beach.

Chemical-quality reconnaissance of the water and surficial bed material in the Delaware River estuary and adjacent New Jersey tributaries, 1980-81

USGS Publications Warehouse

Hochreiter, Joseph J.

1982-01-01

This report presents chemical-quality data collected from May 1980 to January 1981 at several locations within the Delaware River estuary and selected New Jersey tributaries. Samples of surface water were analyzed Environmental Protection Agency ' priority pollutants, ' including acid extractable, base/neutral extractable and volatile organic compounds, in addition to selected dissolved inorganic constituents. Surficial bed material at selected locations was examined for trace metals, insecticides, polychlorinated biphenyls, and base/neutral extractable organic compounds. Trace levels (1-50 micrograms per liter) of purgeable organic compounds, particularly those associated with the occurrence of hydrocarbons, were found in about 60% of the water samples taken. DDT, DDD, DDE, PCB 's and chlordane are present in most surficial bed material samples. Diazinon was the only organophosphorous insecticide detected in the study (1.6 micrograms per kilogram at one location). High values for select trace metals in bed material were discovered at two locations. Of the 10 sites sampled, the surficial bed material containing the most contamination was found along one cross section of Raccoon Creek at Bridgeport. An additional analysis of Raccoon Creek revealed bed material containing toluene, oil and grease, and trace quantities of 15 base/neutral extractable organic compounds, including polynuclear aromatic hydrocarbons, phthalate esters, and chlorinated benzenes.

Improvement in botanical standardization of commercial freeze-dried herbal extracts by using the combination of antioxidant capacity and constituent marker concentrations.

PubMed

Ninfali, Paolino; Gennari, Lorenzo; Biagiotti, Enrica; Cangi, Francesca; Mattoli, Luisa; Maidecchi, Anna

2009-01-01

Botanical extracts are standardized to > or = 1 marker compounds (MCs). This standardization provides a certain level of quality control, but not complete quality assurance. Thus, industries are looking for other satisfactory systems to improve standardization. This study focuses on the standardization of herbal medicines by combining 2 parameters: the concentration of the MC and antioxidant capacity. Antioxidant capacity was determined with the oxygen radical absorbance capacity (ORAC) method and the concentrations of the MCs, by high-performance liquid chromatography. Total phenols were also determined by the Folin-Ciocolteau method. The ORAC values, expressed as micromol Trolox equivalents/100 g (ORAC %), of 12 commercial herbal extracts were related to the ORAC values of the respective pure MCs at the concentrations at which the MCs occur in products (ORAC-MC %). The ORAC % values of 11 extracts were higher than those of the respective MCs and the ratios ORAC-MC %/ORAC % ranged from 0.007 to 0.7, whereas in the case of Olea europaea leaves, the same ratio was 1.36. The ORAC parameters and their ratios, as well as the linear relationship between ORAC-MC % and ORAC %, are described and discussed as tools for improving the standardization of herbal products and detecting modifications due to herb processing and storage.

Review of clinical trials evaluating safety and efficacy of milk thistle (Silybum marianum [L.] Gaertn.).

PubMed

Tamayo, Carmen; Diamond, Suzanne

2007-06-01

Milk thistle extracts have been used as traditional herbal remedies for almost 2000 years. The extracts are still widely used to protect the liver against toxins and to control chronic liver diseases. Recent experimental and clinical studies suggest that milk thistle extracts also have anticancer, antidiabetic, and cardioprotective effects. This article reviews clinical trials of milk thistle conducted in the past 5 years including pharmacokinetic and toxicity studies, herb-drug interactions, and other safety issues. Several trials have studied the effects of milk thistle for patients with liver diseases, cancer, hepatitis C, HIV, diabetes, and hypercholesterolemia. Promising results have been reported in the protective effect of milk thistle in certain types of cancer, and ongoing trials will provide more evidence about this effect. In addition, new established doses and improvement on the quality and standardization of this herb will provide the much-awaited evidence about the efficacy of milk thistle in the treatment of liver diseases. Milk thistle extracts are known to be safe and well tolerated, and toxic or adverse effects observed in the reviewed clinical trials seem to be minimal. The future of milk thistle research is promising, and high-quality randomized clinical trials on milk thistle versus placebo may be needed to further demonstrate the safety and efficacy of this herb.

Author-paper affiliation network architecture influences the methodological quality of systematic reviews and meta-analyses of psoriasis

PubMed Central

Gomez-Garcia, Francisco; Alcalde-Mellado, Patricia; Gay-Mimbrera, Jesus; Aguilar-Luque, Macarena; Maestre-Lopez, Beatriz; Gonzalez-Padilla, Marcelino; Carmona-Fernandez, Pedro J.; Velez Garcia-Nieto, Antonio; Isla-Tejera, Beatriz

2017-01-01

Moderate-to-severe psoriasis is associated with significant comorbidity, an impaired quality of life, and increased medical costs, including those associated with treatments. Systematic reviews (SRs) and meta-analyses (MAs) of randomized clinical trials are considered two of the best approaches to the summarization of high-quality evidence. However, methodological bias can reduce the validity of conclusions from these types of studies and subsequently impair the quality of decision making. As co-authorship is among the most well-documented forms of research collaboration, the present study aimed to explore whether authors’ collaboration methods might influence the methodological quality of SRs and MAs of psoriasis. Methodological quality was assessed by two raters who extracted information from full articles. After calculating total and per-item Assessment of Multiple Systematic Reviews (AMSTAR) scores, reviews were classified as low (0-4), medium (5-8), or high (9-11) quality. Article metadata and journal-related bibliometric indices were also obtained. A total of 741 authors from 520 different institutions and 32 countries published 220 reviews that were classified as high (17.2%), moderate (55%), or low (27.7%) methodological quality. The high methodological quality subnetwork was larger but had a lower connection density than the low and moderate methodological quality subnetworks; specifically, the former contained relatively fewer nodes (authors and reviews), reviews by authors, and collaborators per author. Furthermore, the high methodological quality subnetwork was highly compartmentalized, with several modules representing few poorly interconnected communities. In conclusion, structural differences in author-paper affiliation network may influence the methodological quality of SRs and MAs on psoriasis. As the author-paper affiliation network structure affects study quality in this research field, authors who maintain an appropriate balance between scientific quality and productivity are more likely to develop higher quality reviews. PMID:28403245

Extracting Rayleigh wave dispersion from ambient noise across the Indian Ocean

NASA Astrophysics Data System (ADS)

Ma, Z.; Dalton, C. A.

2016-12-01

Rayleigh wave dispersion extracted from ambient seismic noise has been widely used to image crustal and uppermost mantle structure. Applications of this approach in continental settings are abundant, but there have been relatively few studies within ocean basins. In this presentation, we will first demonstrate the feasibility of extracting high quality Rayleigh wave dispersion information from ambient noise across the entire Indian Ocean basin. Phase arrival times measured from ambient noise are largely consistent with the ones predicted from 2-D phase velocity maps that were determined from earthquake data alone. Secondly, we show that adding dispersion information extracted from ambient noise to existing earthquake data can indeed improve the resolution of phase velocity maps by about 20% in the western Indian Ocean region where the station distribution is the densest. High quality Rayleigh wave dispersion information can be obtained from stacking waveforms over less than two years at land stations and less than four years at island stations. After removing the age dependent average velocities, the 2-D phase velocity maps show slow anomalies associated with the Seychelles-Mascarene plateau. Forward modeling suggests that the crust is about 15-25 km thick in this area, which agrees with previous estimates obtained from gravity data. We also observe that the slow anomaly related to the Central Indian Ridge is asymmetric. The center of this slow anomaly lies to the west side of ridge, which is opposite to the ridge migration direction. This asymmetry probably reflects the interactions between the ridge and nearby hotspots.

A novel high-throughput method for supported liquid extraction of retinol and alpha-tocopherol from human serum and simultaneous quantitation by liquid chromatography tandem mass spectrometry.

PubMed

Hinchliffe, Edward; Rudge, James; Reed, Paul

2016-07-01

Measurement of vitamin A (retinol) and E (alpha-tocopherol) in UK clinical laboratories is currently performed exclusively by high-performance liquid chromatography with ultraviolet detection. We investigated whether retinol and alpha-tocopherol could be measured simultaneously by liquid chromatography tandem mass spectrometry. Serum samples (100 μL) were extracted using Isolute + Supported Liquid Extraction plates. Chromatography was performed on a Phenomenex Kinetex Biphenyl 2.6 μm, 50 × 2.1 mm column, and liquid chromatography tandem mass spectrometry on a Waters Acquity TQD. Injection-to-injection time was 4.3 min. The assay was validated according to published guidelines. Patient samples were used to compare liquid chromatography tandem mass spectrometry and high-performance liquid chromatography with ultraviolet detection methods. For retinol and alpha-tocopherol, respectively, the assay was linear up to 6.0 and 80.0 μmol/L, and lower limit of quantification was 0.07 and 0.26 μmol/L. Intra and interassay imprecision were within desirable analytical specifications. Analysis of quality control material aligned to NIST SRM 968e, and relative spiked recovery from human serum, both yielded results within 15% of target values. Method comparison with high-performance liquid chromatography with ultraviolet detection methodology demonstrated a negative bias for retinol and alpha-tocopherol by the liquid chromatography tandem mass spectrometry method. Analysis of United Kingdom National External Quality Assurance Scheme samples yielded mean bias from the target value of +3.0% for retinol and -11.2% for alpha-tocopherol. We have developed a novel, high-throughput method for extraction of retinol and alpha-tocopherol from human serum followed by simultaneous quantitation by liquid chromatography tandem mass spectrometry. The method offers a rapid, sensitive, specific and cost-effective alternative to high-performance liquid chromatography with ultraviolet detection methodology, and is suitable for routine clinical monitoring of patients predisposed to fat-soluble vitamin malabsorption. © The Author(s) 2015.

Development of quality indicators for low-risk labor care provided by midwives using a RAND-modified Delphi method.

PubMed

Ueda, Kayo; Ohtera, Shosuke; Kaso, Misato; Nakayama, Takeo

2017-09-22

In childbirth, most deliveries are low-risk, defined as spontaneous labor at full term without special high-risk facts or complications, especially in high-resource countries where maternal and perinatal mortality rates are very low. Indeed, the majority of mothers and infants have no serious conditions during labor. However, the quality of care provided is not assured, and performance may vary by birthing facility and provider. The overuse of technology in childbirth in some parts of the world is almost certainly based on assumptions like, "something can go wrong at any minute." There is a need to assess the quality of care provided for mothers and infants in low-risk labor. We aimed to develop specific quality indicators for low-risk labor care provided primarily by midwives in Japan. We used a RAND-modified Delphi method, which integrates evidence review with expert consensus development. The procedure comprises five steps: (1) literature review, including clinical practice guidelines, to extract and develop quality indicator candidates; (2) formation of a multidisciplinary panel; (3) independent panel ratings (Round 1); (4) panel meeting and independent panel ratings (Round 2); and (5) independent panel ratings (Round 3). The three independent panel ratings (Rounds 1-3) were held between July and December 2012. The assembled multidisciplinary panel comprised eight clinicians (two pediatricians, three obstetricians, and three midwives) and three mothers who were nonclinicians. Evidentiary review extracted 166 key recommendations from 32 clinical practice guidelines, and 31 existing quality indicators were added. After excluding duplicate recommendations and quality indicators, the panel discussed 25 candidate indicators. Of these, 18 were adopted, one was modified, six were not adopted, and four were added during the meeting, respectively. We established 23 quality indicators for low-risk labor care provided by midwives in labor units in Japan.

The effect of St John’s wort extracts on CYP3A: a systematic review of prospective clinical trials

PubMed Central

Whitten, D L; Myers, S P; Hawrelak, J A; Wohlmuth, H

2006-01-01

Aim The aim of this systematic review was to assess the quality and outcomes of clinical trials investigating the effect of St John’s wort extracts on the metabolism of drugs by CYP3A. Methods Prospective clinical trials assessing the effect of St John’s wort (SJW) extracts on metabolism by CYP3A were identified through computer-based searches (from their inception to May 2005) of Medline, Cinahl, PsycINFO, AMED, Current Contents and Embase, hand-searches of bibliographies of relevant papers and consultation with manufacturers and researchers in the field. Two reviewers selected trials for inclusion, independently extracted data and recorded details on study design. Results Thirty-one studies met the eligibility criteria. More than two-thirds of the studies employed a before-and-after design, less than one-third of the studies used a crossover design, and only three studies were double-blind and placebo controlled. In 12 studies the SJW extract had been assayed, and 14 studies stated the specific SJW extract used. Results from 26 studies, including all of the 19 studies that used high-dose hyperforin extracts (>10 mg day−1), had outcomes consistent with CYP3A induction. The three studies using low-dose hyperforin extracts (<4 mg day−1) demonstrated no significant effect on CYP3A. Conclusion There is reasonable evidence to suggest that high-dose hyperforin SJW extracts induce CYP3A. More studies are required to determine whether decreased CYP3A induction occurs after low-dose hyperforin extracts. Future studies should adopt study designs with a control phase or control group, identify the specific SJW extract employed and provide quantitative analyses of key constituents. PMID:17010103

Rapid Solid-Liquid Dynamic Extraction (RSLDE): a New Rapid and Greener Method for Extracting Two Steviol Glycosides (Stevioside and Rebaudioside A) from Stevia Leaves.

PubMed

Gallo, Monica; Vitulano, Manuela; Andolfi, Anna; DellaGreca, Marina; Conte, Esterina; Ciaravolo, Martina; Naviglio, Daniele

2017-06-01

Stevioside and rebaudioside A are the main diterpene glycosides present in the leaves of the Stevia rebaudiana plant, which is used in the production of foods and low-calorie beverages. The difficulties associated with their extraction and purification are currently a problem for the food processing industries. The objective of this study was to develop an effective and economically viable method to obtain a high-quality product while trying to overcome the disadvantages derived from the conventional transformation processes. For this reason, extractions were carried out using a conventional maceration (CM) and a cyclically pressurized extraction known as rapid solid-liquid dynamic extraction (RSLDE) by the Naviglio extractor (NE). After only 20 min of extraction using the NE, a quantity of rebaudioside A and stevioside equal to 1197.8 and 413.6 mg/L was obtained, respectively, while for the CM, the optimum time was 90 min. From the results, it can be stated that the extraction process by NE and its subsequent purification developed in this study is a simple, economical, environmentally friendly method for producing steviol glycosides. Therefore, this method constitutes a valid alternative to conventional extraction by reducing the extraction time and the consumption of toxic solvents and favouring the use of the extracted metabolites as food additives and/or nutraceuticals. As an added value and of local interest, the experiment was carried out on stevia leaves from the Benevento area (Italy), where a high content of rebaudioside A was observed, which exhibits a sweet taste compared to stevioside, which has a significant bitter aftertaste.

Isolation of high-quality total RNA from leaves of Myrciaria dubia "CAMU CAMU".

PubMed

Gómez, Juan Carlos Castro; Reátegui, Alina Del Carmen Egoavil; Flores, Julián Torres; Saavedra, Roberson Ramírez; Ruiz, Marianela Cobos; Correa, Sixto Alfredo Imán

2013-01-01

Myrciaria dubia is a main source of vitamin C for people in the Amazon region. Molecular studies of M. dubia require high-quality total RNA from different tissues. So far, no protocols have been reported for total RNA isolation from leaves of this species. The objective of this research was to develop protocols for extracting high-quality total RNA from leaves of M. dubia. Total RNA was purified following two modified protocols developed for leaves of other species (by Zeng and Yang, and by Reid et al.) and one modified protocol developed for fruits of the studied species (by Silva). Quantity and quality of purified total RNA were assessed by spectrophotometric and electrophoretic analysis. Additionally, quality of total RNA was evaluated with reverse-transcription polymerase chain reaction (RT-PCR). With these three modified protocols we were able to isolate high-quality RNA (A260nm/A280nm >1.9 and A260nm/A230nm >2.0). Highest yield was produced with the Zeng and Yang modified protocol (384±46µg ARN/g fresh weight). Furthermore, electrophoretic analysis showed the integrity of isolated RNA and the absence of DNA. Another proof of the high quality of our purified RNA was the successful cDNA synthesis and amplification of a segment of the M. dubia actin 1 gene. We report three modified protocols for isolation total RNA from leaves of M. dubia. The modified protocols are easy, rapid, low in cost, and effective for high-quality and quantity total RNA isolation suitable for cDNA synthesis and polymerase chain reaction.

DIE-RNA: A Reproducible Strategy for the Digestion of Normal and Injured Pancreas, Isolation of Pancreatic Cells from Genetically Engineered Mouse Models and Extraction of High Quality RNA

PubMed Central

Assi, Mohamad; Dauguet, Nicolas; Jacquemin, Patrick

2018-01-01

The isolation of ribonucleic acid (RNA) suitable for gene expression studies is challenging in the pancreas, due to its high ribonuclease activity. This is even more complicated during pancreatitis, a condition associated with inflammation and fibrosis. Our aim was to implement a time-effective and reproducible protocol to isolate high quality RNA from specific pancreatic cell subtypes, in normal and inflammatory conditions. We used two genetically engineered mouse models (GEMM), Ela-CreER/YFP and Sox9-CreER/YFP, to isolate acinar and ductal cells, respectively. To induce pancreatitis, mice received a caerulein treatment (125 μg/kg) for 8 and 72 h. We alternatively used EGTA and calcium buffers that contain collagenase P (0.6 mg/mL) to rapidly digest the pancreas into individual cells. Most of the cells from normal and injured pancreas were single-dissociated, exhibited a round morphology and did not incorporate trypan blue dye. Cell suspensions from Ela- and Sox9-CreER/YFP pancreas were then sorted by flow cytometry to isolate the YFP-positive acinar and ductal cells, respectively. Sorted cells kept a round shape and emitted fluorescence detected by the 38 HE green fluorescence filter. RNA was isolated by column-based purification approach. The RNA integrity number (RIN) was high in sorted acinar cell fractions treated with or without caerulein (8.6 ± 0.17 and 8.4 ± 0.09, respectively), compared to the whole pancreas fraction (4.8 ± 1.1). Given the low number of sorted ductal cells, the RIN value was slightly lower compared to acini (7.4 ± 0.4). Quantitative-PCR experiments indicated that sorted acinar and ductal cells express the specific acinar and ductal markers, respectively. Additionally, RNA preparations from caerulein-treated acinar cells were free from significant contamination with immune cell RNA. We thus validated the DIE (Digestion, Isolation, and Extraction)-RNA tool as a reproducible and efficient protocol to isolate pure acinar and ductal cells in vivo and to extract high quality RNA from these cells. PMID:29535635

DIE-RNA: A Reproducible Strategy for the Digestion of Normal and Injured Pancreas, Isolation of Pancreatic Cells from Genetically Engineered Mouse Models and Extraction of High Quality RNA.

PubMed

Assi, Mohamad; Dauguet, Nicolas; Jacquemin, Patrick

2018-01-01

The isolation of ribonucleic acid (RNA) suitable for gene expression studies is challenging in the pancreas, due to its high ribonuclease activity. This is even more complicated during pancreatitis, a condition associated with inflammation and fibrosis. Our aim was to implement a time-effective and reproducible protocol to isolate high quality RNA from specific pancreatic cell subtypes, in normal and inflammatory conditions. We used two genetically engineered mouse models (GEMM), Ela-CreER/YFP and Sox9-CreER/YFP, to isolate acinar and ductal cells, respectively. To induce pancreatitis, mice received a caerulein treatment (125 μg/kg) for 8 and 72 h. We alternatively used EGTA and calcium buffers that contain collagenase P (0.6 mg/mL) to rapidly digest the pancreas into individual cells. Most of the cells from normal and injured pancreas were single-dissociated, exhibited a round morphology and did not incorporate trypan blue dye. Cell suspensions from Ela- and Sox9-CreER/YFP pancreas were then sorted by flow cytometry to isolate the YFP-positive acinar and ductal cells, respectively. Sorted cells kept a round shape and emitted fluorescence detected by the 38 HE green fluorescence filter. RNA was isolated by column-based purification approach. The RNA integrity number (RIN) was high in sorted acinar cell fractions treated with or without caerulein (8.6 ± 0.17 and 8.4 ± 0.09, respectively), compared to the whole pancreas fraction (4.8 ± 1.1). Given the low number of sorted ductal cells, the RIN value was slightly lower compared to acini (7.4 ± 0.4). Quantitative-PCR experiments indicated that sorted acinar and ductal cells express the specific acinar and ductal markers, respectively. Additionally, RNA preparations from caerulein-treated acinar cells were free from significant contamination with immune cell RNA. We thus validated the DIE (Digestion, Isolation, and Extraction)-RNA tool as a reproducible and efficient protocol to isolate pure acinar and ductal cells in vivo and to extract high quality RNA from these cells.

Separation of switchgrass bio-oil by water/organic solvent addition and pH adjustment

DOE PAGES

Park, Lydia Kyoung-Eun; Ren, Shoujie; Yiacoumi, Sotira; ...

2016-01-29

Applications of bio-oil are limited by its challenging properties including high moisture content, low pH, high viscosity, high oxygen content, and low heating value. Separation of switchgrass bio-oil components by adding water, organic solvents (hexadecane and octane), and sodium hydroxide may help to overcome these issues. Acetic acid and phenolic compounds were extracted in aqueous and organic phases, respectively. Polar chemicals, such as acetic acid, did not partition in the organic solvent phase. Acetic acid in the aqueous phase after extraction is beneficial for a microbial-electrolysis-cell application to produce hydrogen as an energy source for further hydrodeoxygenation of bio-oil. Organicmore » solvents extracted more chemicals from bio-oil in combined than in sequential extraction; however, organic solvents partitioned into the aqueous phase in combined extraction. When sodium hydroxide was added to adjust the pH of aqueous bio-oil, organic-phase precipitation occurred. As the pH was increased, a biphasic aqueous/organic dispersion was formed, and phase separation was optimized at approximately pH 6. The neutralized organic bio-oil had approximately 37% less oxygen and 100% increased heating value than the initial centrifuged bio-oil. In conclusion, the less oxygen content and increased heating value indicated a significant improvement of the bio-oil quality through neutralization.« less

Separation of switchgrass bio-oil by water/organic solvent addition and pH adjustment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Lydia Kyoung-Eun; Ren, Shoujie; Yiacoumi, Sotira

Applications of bio-oil are limited by its challenging properties including high moisture content, low pH, high viscosity, high oxygen content, and low heating value. Separation of switchgrass bio-oil components by adding water, organic solvents (hexadecane and octane), and sodium hydroxide may help to overcome these issues. Acetic acid and phenolic compounds were extracted in aqueous and organic phases, respectively. Polar chemicals, such as acetic acid, did not partition in the organic solvent phase. Acetic acid in the aqueous phase after extraction is beneficial for a microbial-electrolysis-cell application to produce hydrogen as an energy source for further hydrodeoxygenation of bio-oil. Organicmore » solvents extracted more chemicals from bio-oil in combined than in sequential extraction; however, organic solvents partitioned into the aqueous phase in combined extraction. When sodium hydroxide was added to adjust the pH of aqueous bio-oil, organic-phase precipitation occurred. As the pH was increased, a biphasic aqueous/organic dispersion was formed, and phase separation was optimized at approximately pH 6. The neutralized organic bio-oil had approximately 37% less oxygen and 100% increased heating value than the initial centrifuged bio-oil. In conclusion, the less oxygen content and increased heating value indicated a significant improvement of the bio-oil quality through neutralization.« less

Quality enhancement in the Japanese sea bass (Lateolabrax japonicas) fillets stored at 4°C by chitosan coating incorporated with citric acid or licorice extract.

PubMed

Qiu, Xujian; Chen, Shengjun; Liu, Guangming; Yang, Qiuming

2014-11-01

The preserving effects of chitosan, chitosan and citric acid, chitosan and licorice extract on fresh Japanese sea bass fillets stored at 4 °C for 12 days were studied. Results showed that citric acid or licorice extract can enhance the preserving function of chitosan significantly by retarding lipid oxidation and inhibiting microbial growth as reflected in thiobarbituric acid reactive substances and total plate count, respectively. Both total volatile basic nitrogen values and sensory scores indicated chitosan and citric acid or licorice extract can significantly reduce the quality loss and extend the shelf life of Japanese sea bass fish fillets during refrigerated storage. Citric acid or licorice extract with chitosan could thus be applied in the seafood industry to enhance quality of fish fillets as natural preservatives. Copyright © 2014 Elsevier Ltd. All rights reserved.

Enzyme assisted extraction of biomolecules as an approach to novel extraction technology: A review.

PubMed

Nadar, Shamraja S; Rao, Priyanka; Rathod, Virendra K

2018-06-01

An interest in the development of extraction techniques of biomolecules from various natural sources has increased in recent years due to their potential applications particularly for food and nutraceutical purposes. The presence of polysaccharides such as hemicelluloses, starch, pectin inside the cell wall, reduces the extraction efficiency of conventional extraction techniques. Conventional techniques also suffer from low extraction yields, time inefficiency and inferior extract quality due to traces of organic solvents present in them. Hence, there is a need of the green and novel extraction methods to recover biomolecules. The present review provides a holistic insight to various aspects related to enzyme aided extraction. Applications of enzymes in the recovery of various biomolecules such as polyphenols, oils, polysaccharides, flavours and colorants have been highlighted. Additionally, the employment of hyphenated extraction technologies can overcome some of the major drawbacks of enzyme based extraction such as longer extraction time and immoderate use of solvents. This review also includes hyphenated intensification techniques by coupling conventional methods with ultrasound, microwave, high pressure and supercritical carbon dioxide. The last section gives an insight on application of enzyme immobilization as a strategy for large scale extraction. Immobilization of enzymes on magnetic nanoparticles can be employed to enhance the operational performance of the system by multiple use of expensive enzymes making them industrially and economically feasible. Copyright © 2018 Elsevier Ltd. All rights reserved.

Absence of carious lesions at margins of glass-ionomer cement and amalgam restorations: An update of systematic review evidence

PubMed Central

2011-01-01

Background This article aims to update the existing systematic review evidence elicited by Mickenautsch et al. up to 18 January 2008 (published in the European Journal of Paediatric Dentistry in 2009) and addressing the review question of whether, in the same dentition and same cavity class, glass-ionomer cement (GIC) restored cavities show less recurrent carious lesions on cavity margins than cavities restored with amalgam. Methods The systematic literature search was extended beyond the original search date and a further hand-search and reference check was done. The quality of accepted trials was assessed, using updated quality criteria, and the risk of bias was investigated in more depth than previously reported. In addition, the focus of quantitative synthesis was shifted to single datasets extracted from the accepted trials. Results The database search (up to 10 August 2010) identified 1 new trial, in addition to the 9 included in the original systematic review, and 11 further trials were included after a hand-search and reference check. Of these 21 trials, 11 were excluded and 10 were accepted for data extraction and quality assessment. Thirteen dichotomous datasets of primary outcomes and 4 datasets with secondary outcomes were extracted. Meta-analysis and cumulative meta-analysis were used in combining clinically homogenous datasets. The overall results of the computed datasets suggest that GIC has a higher caries-preventive effect than amalgam for restorations in permanent teeth. No difference was found for restorations in the primary dentition. Conclusion This outcome is in agreement with the conclusions of the original systematic review. Although the findings of the trials identified in this update may be considered to be less affected by attrition- and publication bias, their risk of selection- and detection/performance bias is high. Thus, verification of the currently available results requires further high-quality randomised control trials. PMID:21396097

A Systematic Review and Taxonomy of Published Quality Criteria Related to the Evaluation of User-Facing eHealth Programs.

PubMed

Baumel, Amit; Birnbaum, Michael L; Sucala, Madalina

2017-08-01

The purpose of this review was to identify and classify key criteria concepts related to the evaluation of user-facing eHealth programs. In line with the PRISMA statement methodology, computer searches of relevant databases were conducted for studies published between January 1, 2000 and March 1, 2016 that contained explicit quality criteria related to mHealth and eHealth products. Reference lists of included articles, review articles, and grey literature (e.g., books, websites) were searched for additional sources. A team of nine experts led by the first author was gathered to support the classification of these criteria. Identified criteria were extracted, grouped and organized using an inductive thematic analysis. Eighty-four sources - emanating from 26 different courtiers - were included in this review. The team extracted 454 criteria that were grouped into 11 quality domains, 58 criteria concepts and 134 concepts' sub-groups. Quality domains were: Usability, Visual Design, User Engagement, Content, Behavior Change/Persuasive Design, Influence of Social Presence, Therapeutic Alliance, Classification, Credibility/Accountability, and Privacy/Security. Findings suggest that authors around the globe agree on key criteria concepts when evaluating user-facing eHealth products. The high proportion of new published criteria in the second half of this review time-frame (2008-2016), and more specifically, the high proportion of criteria relating to persuasive design, therapeutic alliance and privacy/security within this time-frame, points to the advancements made in recent years within this field.

How to Conduct a Good Meta-Analysis in Gifted Education

ERIC Educational Resources Information Center

Steenbergen-Hu, Saiying; Olszewski-Kubilius, Paula

2016-01-01

This methodological brief introduces basic procedures and issues for conducting a high-quality meta-analysis in gifted education. Specifically, we discuss issues such as how to select a topic and formulate research problems, search for and identify qualified studies, code studies and extract data, choose and calculate effect sizes, analyze data,…

Effect of RNA Integrity Determined With the Agilent 2100 Bioanalyzer on Bacterial RNA Quantification with RT-PCR

USDA-ARS?s Scientific Manuscript database

RNA integrity is critical for successful RNA quantification. The level of integrity required differs among sources and extraction procedures and has not been determined for bacterial RNA. Three RNA isolation methods were evaluated for their ability to produce high quality RNA from D. dadantii. The i...

Determination of free fatty acids in beer wort.

PubMed

Bravi, Elisabetta; Benedetti, Paolo; Marconi, Ombretta; Perretti, Giuseppe

2014-05-15

The importance of free fatty acids (FFAs) in wort has been known for a long time because of their influence on beer quality and yeast metabolism. Lipids have a beneficial effect on yeast growth during fermentation as well as negative effects on beer quality. Lipids content of beer affects the ability to form a stable head of foam and plays an important role in beer staling. Moreover, the ratio of unsaturated and saturated fatty acids seems to be related to gushing problems. A novel, simple, and reliable procedure for quantitative analysis of FFAs in wort was developed and validated. The determination of FFAs in wort was achieved via liquid-liquid cartridge extraction, purification of FFA fraction by solid phase extraction, boron trifluoride in methanol methylation, and injection into GC-FID system. The proposed method has high accuracy (<0.3%, expressed as the bias), high precision (<1.2%, RSD), and recoveries ranging from 74% to 98%. The method was tested on two different wort samples (9° and 12° Plato). Copyright © 2013 Elsevier Ltd. All rights reserved.

Fast filtration sampling protocol for mammalian suspension cells tailored for phosphometabolome profiling by capillary ion chromatography - tandem mass spectrometry.

PubMed

Kvitvang, Hans F N; Bruheim, Per

2015-08-15

Capillary ion chromatography (capIC) is the premium separation technology for low molecular phosphometabolites and nucleotides in biological extracts. Removal of excessive amounts of salt during sample preparation stages is a prerequisite to enable high quality capIC separation in combination with reproducible and sensitive MS detection. Existing sampling protocols for mammalian cells used for GC-MS and LC-MS metabolic profiling can therefore not be directly applied to capIC separations. Here, the development of a fast filtration sampling protocol for mammalian suspension cells tailored for quantitative profiling of the phosphometabolome on capIC-MS/MS is presented. The whole procedure from sampling the culture to transfer of filter to quenching and extraction solution takes less than 10s. To prevent leakage it is critical that a low vacuum pressure is applied, and satisfactorily reproducibility was only obtained by usage of a vacuum pressure controlling device. A vacuum of 60mbar was optimal for filtration of multiple myeloma Jjn-3 cell cultures through 5μm polyvinylidene (PVDF) filters. A quick deionized water (DI-water) rinse step prior to extraction was tested, and significantly higher metabolite yields were obtained during capIC-MS/MS analyses in this extract compared to extracts prepared by saline and reduced saline (25%) washing steps only. In addition, chromatographic performance was dramatically improved. Thus, it was verified that a quick DI-water rinse is tolerated by the cells and can be included as the final stage during filtration. Over 30 metabolites were quantitated in JJN-3 cell extracts by using the optimized sampling protocol with subsequent capIC-MS/MS analysis, and up to 2 million cells can be used in a single filtration step for the chosen filter and vacuum pressure. The technical set-up is also highly advantageous for microbial metabolome filtration protocols after optimization of vacuum pressure and washing solutions, and the reduced salt content of the extract will also improve the quality of LC-MS analysis due to lower salt adduct ion formation. Copyright © 2015 Elsevier B.V. All rights reserved.

Rapid non-enzymatic extraction method for isolating PCR-quality camelpox virus DNA from skin.

PubMed

Yousif, A Ausama; Al-Naeem, A Abdelmohsen; Al-Ali, M Ahmad

2010-10-01

Molecular diagnostic investigations of orthopoxvirus (OPV) infections are performed using a variety of clinical samples including skin lesions, tissues from internal organs, blood and secretions. Skin samples are particularly convenient for rapid diagnosis and molecular epidemiological investigations of camelpox virus (CMLV). Classical extraction procedures and commercial spin-column-based kits are time consuming, relatively expensive, and require multiple extraction and purification steps in addition to proteinase K digestion. A rapid non-enzymatic procedure for extracting CMLV DNA from dried scabs or pox lesions was developed to overcome some of the limitations of the available DNA extraction techniques. The procedure requires as little as 10mg of tissue and produces highly purified DNA [OD(260)/OD(280) ratios between 1.47 and 1.79] with concentrations ranging from 6.5 to 16 microg/ml. The extracted CMLV DNA was proven suitable for virus-specific qualitative and, semi-quantitative PCR applications. Compared to spin-column and conventional viral DNA extraction techniques, the two-step extraction procedure saves money and time, and retains the potential for automation without compromising CMLV PCR sensitivity. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Physicochemical and Antioxidant Properties of Rice Bran Oils Produced from Colored Rice Using Different Extraction Methods.

PubMed

Mingyai, Sukanya; Kettawan, Aikkarach; Srikaeo, Khongsak; Singanusong, Riantong

2017-06-01

This study investigated the physicochemical and antioxidant properties of rice bran oil (RBO) produced from the bran of three rice varities; Khao Dawk Mali 105 (white rice), Red Jasmine rice (red rice) and Hom-nin rice (black rice) using three extraction methods including cold-press extraction (CPE), solvent extraction (SE) and supercritical CO 2 extraction (SC-CO 2 ). Yields, color, acid value (AV), free fatty acid (FFA), peroxide value (PV), iodine value (IV), total phenolic compound (TPC), γ-oryzanol, α-tocopherol and fatty acid profile were analyzed. It was found that the yields obtained from SE, SC-CO 2 and CPE extractions were 17.35-20.19%, 14.76-18.16% and 3.22-6.22%, respectively. The RBO from the bran of red and black rice samples exhibited high antioxidant activities. They also contained higher amount of γ-oryzanol and α-tocopherol than those of white rice sample. In terms of extraction methods, SC-CO 2 provided better qualities of RBO as evidenced by their physicochemical and antioxidant properties. This study found that RBO produced from the bran of black rice samples using SC-CO 2 extraction method showed the best physicochemical and antioxidant properties.

Plant extracts: sense or nonsense?

PubMed

Madersbacher, Stephan; Berger, Ingrid; Ponholzer, Anton; Marszalek, Martin

2008-01-01

To assess the current role of plant extracts in the medical management of lower urinary tract symptoms due to benign prostatic enlargement/benign prostatic obstruction. In 2006, two clinical trials meeting the WHO benign prostatic hyperplasia consensus conference criteria (randomized against placebo/standard therapy, study duration 12 months) were published. One trial compared a saw palmetto extract with placebo. This industry-independent trial published in the New England Journal of Medicine was negative, that is, this saw palmetto extract had no effect on symptoms, Qmax and postvoid residual volume. In another trial, a saw palmetto/urtica combination was compared with tamsulosin. After 12 months, the improvement of symptoms was identical in both study arms. No detailed data were presented, however, on Qmax, postvoid residual or prostate volume. The biological mechanisms of plant extracts in vivo are still unknown and the numerous metaanalyses cannot supplement high-quality prospective trials. Further prospective studies according to WHO benign prostatic hyperplasia standards are required to reliably determine the role of plant extracts in contemporary lower urinary tract symptoms management and to be able to answer the question in the title: 'plant extracts: sense or nonsense?' Plant extracts are currently not recommended by the American and European Association of Urology benign prostatic hyperplasia guidelines.

Quality measurement in physician-staffed emergency medical services: a systematic literature review.

PubMed

Haugland, Helge; Uleberg, Oddvar; Klepstad, Pål; Krüger, Andreas; Rehn, Marius

2018-05-15

Quality measurement of physician-staffed emergency medical services (P-EMS) is necessary to improve service quality. Knowledge and consensus on this topic are scarce, making quality measurement of P-EMS a high-priority research area. The aim of this review was to identify, describe and evaluate studies of quality measurement in P-EMS. The databases of MEDLINE and Embase were searched initially, followed by a search for included article citations in Scopus. The study eligibility criteria were: (1) articles describing the use of one quality indicator (QI) or more in P-EMS, (2) original manuscripts, (3) articles published from 1 January 1968 until 5 October 2016. The literature search identified 4699 records. 4543 were excluded after reviewing title and abstract. An additional 129 were excluded based on a full-text review. The remaining 27 papers were included in the analysis. Methodological quality was assessed using an adapted critical appraisal tool. The description of used QIs and methods of quality measurement was extracted. Variables describing the involved P-EMSs were extracted as well. In the included papers, a common understanding of which QIs to use in P-EMS did not exist. Fifteen papers used only a single QI. The most widely used QIs were 'Adherence to medical protocols', 'Provision of advanced interventions', 'Response time' and 'Adverse events'. The review demonstrated a lack of shared understanding of which QIs to use in P-EMS. Moreover, papers using only one QI dominated the literature, thus increasing the risk of a narrow perspective in quality measurement. Future quality measurement in P-EMS should rely on a set of consensus-based QIs, ensuring a comprehensive approach to quality measurement.

Fractionation and reconstitution experiments provide insight into the role of starch gelatinization and pasting properties in pasta quality.

PubMed

Delcour, J A; Vansteelandt, J; Hythier, M; Abécassis, J

2000-09-01

Commercial durum wheat semolina was fractionated into protein, starch, water-extractable, and sludge fractions. The starch fraction was hydroxypropylated, annealed, or cross-linked to change its gelatinization and pasting properties. Spaghettis were made by reconstitution of the fractions, and their quality was assessed. Hydroxypropylated starches were detrimental for cooked pasta quality. Cross-linked starches made the reconstituted pasta firmer and even brittle when the degree of cross-linking was too high. These results indicate that starch properties play a role in pasta quality, although the gluten remains very important as an ultrastructure agent. It was concluded that, given a certain gluten ultrastructure, starch water uptake and gel properties and/or its interference with or breakdown of the continuous gluten network during cooking determine pasta quality.

White organic light emitting diodes with enhanced internal and external outcoupling for ultra-efficient light extraction and Lambertian emission.

PubMed

Bocksrocker, Tobias; Preinfalk, Jan Benedikt; Asche-Tauscher, Julian; Pargner, Andreas; Eschenbaum, Carsten; Maier-Flaig, Florian; Lemme, Uli

2012-11-05

White organic light emitting diodes (WOLEDs) suffer from poor outcoupling efficiencies. The use of Bragg-gratings to enhance the outcoupling efficiency is very promising for light extraction in OLEDs, but such periodic structures can lead to angular or spectral dependencies in the devices. Here we present a method which combines highly efficient outcoupling by a TiO(2)-Bragg-grating leading to a 104% efficiency enhancement and an additional high quality microlens diffusor at the substrate/air interface. With the addition of this diffusor, we achieved not only a uniform white emission, but also further increased the already improved device efficiency by another 94% leading to an overall enhancement factor of about 4.

Road Extraction from AVIRIS Using Spectral Mixture and Q-Tree Filter Techniques

NASA Technical Reports Server (NTRS)

Gardner, Margaret E.; Roberts, Dar A.; Funk, Chris; Noronha, Val

2001-01-01

Accurate road location and condition information are of primary importance in road infrastructure management. Additionally, spatially accurate and up-to-date road networks are essential in ambulance and rescue dispatch in emergency situations. However, accurate road infrastructure databases do not exist for vast areas, particularly in areas with rapid expansion. Currently, the US Department of Transportation (USDOT) extends great effort in field Global Positioning System (GPS) mapping and condition assessment to meet these informational needs. This methodology, though effective, is both time-consuming and costly, because every road within a DOT's jurisdiction must be field-visited to obtain accurate information. Therefore, the USDOT is interested in identifying new technologies that could help meet road infrastructure informational needs more effectively. Remote sensing provides one means by which large areas may be mapped with a high standard of accuracy and is a technology with great potential in infrastructure mapping. The goal of our research is to develop accurate road extraction techniques using high spatial resolution, fine spectral resolution imagery. Additionally, our research will explore the use of hyperspectral data in assessing road quality. Finally, this research aims to define the spatial and spectral requirements for remote sensing data to be used successfully for road feature extraction and road quality mapping. Our findings will facilitate the USDOT in assessing remote sensing as a new resource in infrastructure studies.

Gynecomastia: A systematic review.

PubMed

Fagerlund, Anders; Lewin, Richard; Rufolo, Guglielmo; Elander, Anna; Santanelli di Pompeo, Fabio; Selvaggi, Gennaro

2015-01-01

Gynecomastia is a common medical problem presenting in nearly a third of the male population. Treatment for gynecomastia can be either pharmacological or surgical. Patients with gynecomastia often experience affected quality-of-life. The aim of this systematic review was to analyze the quality of evidence of the current literature in relation to different treatment modalities and Quality-of-Life in patients with gynecomastia. A systematic search of the literature was performed in PubMed, Medline, Scopus, The Cochrane Library, and SveMed+ in accordance with the PRISMA statement. All searches were undertaken between September-November 2014. The PICOS (patients, intervention, comparator, outcomes, and study design) approach was used to specify inclusion criteria. Methodological quality was graded according to MINORS. Quality of evidence was rated according to GRADE. Data from the included studies were extracted based on study characteristics, participants specifics, type of intervention/treatment, and type of outcome measures into data extraction forms. A total of 134 abstracts were identified in the literature search. Seventeen studies met inclusion criteria, 14 concerning treatment and three concerning Quality-of-Life. All studies were non-randomised with a high risk of bias and very low quality of evidence according to GRADE. Several different surgical methods have been described with good results, minimal scars, and various levels of complications. Traditional surgical excision of glandular tissue combined with liposuction provides most consistent results and a low rate of complications. Pubertal gynecomastia may safely be managed by pharmacological anti-oestrogen treatment.

[Extraction of management information from the national quality assurance program].

PubMed

Stausberg, Jürgen; Bartels, Claus; Bobrowski, Christoph

2007-07-15

Starting with clinically motivated projects, the national quality assurance program has established a legislative obligatory framework. Annual feedback of results is an important means of quality control. The annual reports cover quality-related information with high granularity. A synopsis for corporate management is missing, however. Therefore, the results of the University Clinics in Greifswald, Germany, have been analyzed and aggregated to support hospital management. Strengths were identified by the ranking of results within the state for each quality indicator, weaknesses by the comparison with national reference values. The assessment was aggregated per clinical discipline and per category (indication, process, and outcome). A composition of quality indicators was claimed multiple times. A coherent concept is still missing. The method presented establishes a plausible summary of strengths and weaknesses of a hospital from the point of view of the national quality assurance program. Nevertheless, further adaptation of the program is needed to better assist corporate management.

Comparison of Methods for the Extraction of DNA from Formalin-Fixed, Paraffin-Embedded Archival Tissues

PubMed Central

Sengüven, Burcu; Baris, Emre; Oygur, Tulin; Berktas, Mehmet

2014-01-01

Aim: Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. Methods: DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. Results: The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. Conclusion: Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE. PMID:24688314

Driver drowsiness classification using fuzzy wavelet-packet-based feature-extraction algorithm.

PubMed

Khushaba, Rami N; Kodagoda, Sarath; Lal, Sara; Dissanayake, Gamini

2011-01-01

Driver drowsiness and loss of vigilance are a major cause of road accidents. Monitoring physiological signals while driving provides the possibility of detecting and warning of drowsiness and fatigue. The aim of this paper is to maximize the amount of drowsiness-related information extracted from a set of electroencephalogram (EEG), electrooculogram (EOG), and electrocardiogram (ECG) signals during a simulation driving test. Specifically, we develop an efficient fuzzy mutual-information (MI)- based wavelet packet transform (FMIWPT) feature-extraction method for classifying the driver drowsiness state into one of predefined drowsiness levels. The proposed method estimates the required MI using a novel approach based on fuzzy memberships providing an accurate-information content-estimation measure. The quality of the extracted features was assessed on datasets collected from 31 drivers on a simulation test. The experimental results proved the significance of FMIWPT in extracting features that highly correlate with the different drowsiness levels achieving a classification accuracy of 95%-- 97% on an average across all subjects.

Recovery of Tungsten and Molybdenum from Low-Grade Scheelite

NASA Astrophysics Data System (ADS)

Li, Yongli; Yang, Jinhong; Zhao, Zhongwei

2017-10-01

With most high-quality tungsten ores being exhausted, the enhancement of low-grade scheelite concentrates processing has attracted a great deal of attention. The objective of this study is to develop a method to maximize the recovery tungsten and molybdenum from a low-grade scheelite via a new acid leaching process followed by solvent extraction. Under optimal conditions (350 g/L H2SO4, 95°C, and 2 h), approximately 99.8% of tungsten and 98% of molybdenum were leached out. In the subsequent solvent extraction process, more than 99% of the tungsten and molybdenum were extracted with a co-extraction system (50% TBP, 30% HDEHP, and 10% 2-octanol in kerosene) using a three-stage cross-flow extraction. The raffinate can be recycled for the next leaching process after replenishing the H2SO4 to the initial value (approximately 350 g/L). Based on these results, a conceptual flowsheet is presented to recover tungsten and molybdenum from the low-grade scheelite.

[Physical fingerprint for quality control of traditional Chinese medicine extract powders].

PubMed

Zhang, Yi; Xu, Bing; Sun, Fei; Wang, Xin; Zhang, Na; Shi, Xin-Yuan; Qiao, Yan-Jiang

2016-06-01

The physical properties of both raw materials and excipients are closely correlated with the quality of traditional Chinese medicine preparations in oral solid dosage forms. In this paper, based on the concept of the chemical fingerprint for quality control of traditional Chinese medicine products, the method of physical fingerprint for quality evaluation of traditional Chinese medicine extract powders was proposed. This novel physical fingerprint was built by the radar map, and consisted of five primary indexes (i.e. stackablity, homogeneity, flowability, compressibility and stability) and 12 secondary indexes (i.e. bulk density, tap density, particle size<50 μm percentage, relative homogeneity index, hausner ratio, angle of repose, powder flow time, inter-particle porosity, Carr index, cohesion index, loss on drying, hygroscopicity). Panax notoginseng saponins (PNS) extract was taken for an example. This paper introduced the application of physical fingerprint in the evaluation of source-to-source and batch-to-batch quality consistence of PNS extract powders. Moreover, the physical fingerprint of PNS was built by calculating the index of parameters, the index of parametric profile and the index of good compressibility, in order to successfully predict the compressibility of the PNS extract powder and relevant formulations containing PNS extract powder and conventional pharmaceutical excipients. The results demonstrated that the proposed method could not only provide new insights into the development and process control of traditional Chinese medicine solid dosage forms. Copyright© by the Chinese Pharmaceutical Association.

Mini-implants for orthodontic anchorage.

PubMed

Reynders, Reint Meursinge; Ladu, Luisa

2017-10-27

Data sourcesPubmed, Embase, Cochrane Central Register of Controlled Trials and the Web of Science databases. Hand searches of the journals European Journal of Orthodontics, Journal of Orthodontics, Journal of Clinical Orthodontics, Seminars in Orthodontics, American Journal of Orthodontics & Dentofacial Orthopaedics and Angle Orthodontist.Study selectionTwo reviewers independently selected studies. Randomised controlled trials (RCTs) and controlled clinical trials (CCTs) of orthodontic patients requiring extraction of the maxillary first premolars and closure of the spaces without anchorage loss were considered.Data extraction and synthesisData extraction and risk of bias assessment were carried out independently by two reviewers. Meta-analysis and sensitivity analysis were conducted.ResultsFourteen studies; seven RCTS and seven CCTs were included. In total 303 patients received TISADs with 313 control patients. Overall the quality of the studies was considered to be moderate. Overall the TISAD group had significantly less anchorage loss than the control group. On average, TISADs enabled 1.86mm more anchorage preservation than did conventional methods.ConclusionsThe results of the meta-analysis showed that TISADs are more effective than conventional methods of anchorage reinforcement. The average difference of 2mm seems not only statistically but also clinically significant. However, the results should be interpreted with caution because of the moderate quality of the included studies. More high-quality studies on this issue are necessary to enable drawing more reliable conclusions.

Isolation of Mitochondrial DNA from Single, Short Hairs without Roots Using Pressure Cycling Technology.

PubMed

Harper, Kathryn A; Meiklejohn, Kelly A; Merritt, Richard T; Walker, Jessica; Fisher, Constance L; Robertson, James M

2018-02-01

Hairs are commonly submitted as evidence to forensic laboratories, but standard nuclear DNA analysis is not always possible. Mitochondria (mt) provide another source of genetic material; however, manual isolation is laborious. In a proof-of-concept study, we assessed pressure cycling technology (PCT; an automated approach that subjects samples to varying cycles of high and low pressure) for extracting mtDNA from single, short hairs without roots. Using three microscopically similar donors, we determined the ideal PCT conditions and compared those yields to those obtained using the traditional manual micro-tissue grinder method. Higher yields were recovered from grinder extracts, but yields from PCT extracts exceeded the requirements for forensic analysis, with the DNA quality confirmed through sequencing. Automated extraction of mtDNA from hairs without roots using PCT could be useful for forensic laboratories processing numerous samples.

A new organic-rich soil reference material certified for its EDTA- and acetic acid- extractable contents of Cd, Cr, Cu, Ni, Pb and Zn, following collaboratively tested and harmonised procedures.

PubMed

Pueyo, M; Rauret, G; Bacon, J R; Gomez, A; Muntau, H; Quevauviller, P; López-Sánchez, J F

2001-02-01

There is an increasing requirement for assessment of the bioavailable metal fraction and the mobility of trace elements in soils upon disposal. One of the approaches is the use of leaching procedures, but the results obtained are operationally defined; therefore, their significance is highly dependent on the extraction protocol performed. So, for this type of study, there is a need for reference materials that allow the quality of measurements to be controlled. This paper describes the steps involved in the certification of an organic-rich soil reference material, BCR-700, for the EDTA- and acetic acid-extractable contents of some trace elements, following collaboratively tested and harmonised extraction procedures. Details are given for the preparation of the soil, homogeneity and stability testing, analytical procedures and the statistical selection of data to be included in the certification.

Arctic Digital Elevation Models (DEMs) generated by Surface Extraction from TIN-Based Searchspace Minimization (SETSM) algorithm from RPCs-based Imagery

NASA Astrophysics Data System (ADS)

Noh, M. J.; Howat, I. M.; Porter, C. C.; Willis, M. J.; Morin, P. J.

2016-12-01

The Arctic is undergoing rapid change associated with climate warming. Digital Elevation Models (DEMs) provide critical information for change measurement and infrastructure planning in this vulnerable region, yet the existing quality and coverage of DEMs in the Arctic is poor. Low contrast and repeatedly-textured surfaces, such as snow and glacial ice and mountain shadows, all common in the Arctic, challenge existing stereo-photogrammetric techniques. Submeter resolution, stereoscopic satellite imagery with high geometric and radiometric quality, and wide spatial coverage are becoming increasingly accessible to the scientific community. To utilize these imagery for extracting DEMs at a large scale over glaciated and high latitude regions we developed the Surface Extraction from TIN-based Searchspace Minimization (SETSM) algorithm. SETSM is fully automatic (i.e. no search parameter settings are needed) and uses only the satellite rational polynomial coefficients (RPCs). Using SETSM, we have generated a large number of DEMs (> 100,000 scene pair) from WorldView, GeoEye and QuickBird stereo images collected by DigitalGlobe Inc. and archived by the Polar Geospatial Center (PGC) at the University of Minnesota through an academic licensing program maintained by the US National Geospatial-Intelligence Agency (NGA). SETSM is the primary DEM generation software for the US National Science Foundation's ArcticDEM program, with the objective of generating high resolution (2-8m) topography for the entire Arctic landmass, including seamless DEM mosaics and repeat DEM strips for change detection. ArcticDEM is collaboration between multiple US universities, governmental agencies and private companies, as well as international partners assisting with quality control and registration. ArcticDEM is being produced using the petascale Blue Waters supercomputer at the National Center for Supercomputer Applications at the University of Illinois. In this paper, we introduce the SETSM algorithm and the processing system used for the ArcticDEM project, as well as provide notable examples of ArcticDEM products.

Multi-response optimisation of ultrasound-assisted extraction for recovery of flavonoids from red grape skins using response surface methodology.

PubMed

Tomaz, Ivana; Maslov, Luna; Stupić, Domagoj; Preiner, Darko; Ašperger, Danijela; Karoglan Kontić, Jasminka

2016-01-01

For the characterisation of grape cultivars, the profile and content of flavonoids are important because these compounds impact grape and wine quality. To determine the correct profile and content of flavonoids, the use of robust, sensitive and reliable methods is necessary. The object of this research is to develop a new ultrasound-assisted extraction (UAE) method for the recovery of flavonoids from grape skins using response surface methodology. Optimisation of UAE was performed using a complementary study combining a Box-Behnken experimental design with qualitative analysis by high-performance liquid chromatography. Optimal extraction conditions were obtained using the extraction solvent composed of acetonitrile:water:formic acid (26:73:1, v/v/v) at an extraction temperature of 50 °C, an extraction time of 15 min in a single-extraction step and with a solid-to-solvent ratio of 1:80 g/mL. The calculated relative standard deviations for the optimal extraction method were very low, measuring less than 5%. This study demonstrates that numerous factors have strong effects on the extraction efficiency, including the type of organic modifier and its percentage in the extraction solvent, the number of extraction steps, the solid-to-solvent ratio, the extraction time and temperature and, finally, the particular nature of analyte and their position within the grape skin cell. Copyright © 2015 John Wiley & Sons, Ltd.

Improvement of efficiency of oil extraction from wild apricot kernels by using enzymes.

PubMed

Bisht, Tejpal Singh; Sharma, Satish Kumar; Sati, Ramesh Chandra; Rao, Virendra Kumar; Yadav, Vijay Kumar; Dixit, Anil Kumar; Sharma, Ashok Kumar; Chopra, Chandra Shekhar

2015-03-01

An experiment was conducted to evaluate and standardize the protocol for enhancing recovery of oil and quality from cold pressed wild apricot kernels by using various enzymes. Wild apricot kernels were ground into powder in a grinder. Different lots of 3 kg powdered kernel were prepared and treated with different concentrations of enzyme solutions viz. Pectazyme (Pectinase), Mashzyme (Cellulase) and Pectazyme + Mashzyme. Kernel powder mixed with enzyme solutions were kept for 2 h at 50(±2) °C temperature for enzymatic treatment before its use for oil extraction through oil expeller. Results indicate that use of enzymes resulted in enhancement of oil recovery by 9.00-14.22 %. Maximum oil recovery was observed at 0.3-0.4 % enzyme concentration for both the enzymes individually, as well as in combination. All the three enzymatic treatments resulted in increasing oil yield. However, with 0.3 % (Pectazyme + Mashzyme) combination, maximum oil recovery of 47.33 % could be observed against were 33.11 % in control. The oil content left (wasted) in the cake and residue were reduced from 11.67 and 11.60 % to 7.31 and 2.72 % respectively, thus showing a high increase in efficiency of oil recovery from wild apricot kernels. Quality characteristics indicate that the oil quality was not adversely affected by enzymatic treatment. It was concluded treatment of powdered wild apricot kernels with 0.3 % (Pectazyme + Mashzyme) combination was highly effective in increasing oil recovery by 14.22 % without adversely affecting the quality and thus may be commercially used by the industry for reducing wastage of highly precious oil in the cake.

VizieR Online Data Catalog: Fundamental parameters of Kepler stars (Silva Aguirre+, 2015)

NASA Astrophysics Data System (ADS)

Silva Aguirre, V.; Davies, G. R.; Basu, S.; Christensen-Dalsgaard, J.; Creevey, O.; Metcalfe, T. S.; Bedding, T. R.; Casagrande, L.; Handberg, R.; Lund, M. N.; Nissen, P. E.; Chaplin, W. J.; Huber, D.; Serenelli, A. M.; Stello, D.; van Eylen, V.; Campante, T. L.; Elsworth, Y.; Gilliland, R. L.; Hekker, S.; Karoff, C.; Kawaler, S. D.; Kjeldsen, H.; Lundkvist, M. S.

2016-02-01

Our sample has been extracted from the 77 exoplanet host stars presented in Huber et al. (2013, Cat. J/ApJ/767/127). We have made use of the full time-base of observations from the Kepler satellite to uniformly determine precise fundamental stellar parameters, including ages, for a sample of exoplanet host stars where high-quality asteroseismic data were available. We devised a Bayesian procedure flexible in its input and applied it to different grids of models to study systematics from input physics and extract statistically robust properties for all stars. (4 data files).

The effect of pigment matrix, temperature and amount of carrier on the yield and final color properties of spray dried purple corn (Zea mays L.) cob anthocyanin powders.

PubMed

Lao, Fei; Giusti, M Monica

2017-07-15

Spray drying is an economic technique to produce anthocyanin-based colorants. High pigments yields with minimum color degradation are desirable to maximize quality and profits. This study evaluated the impacts of purple corncob (PCC) anthocyanin extraction matrices (hot water, 40% ethanol, C18 purified), drying inlet temperature (130, 150, 170°C) and amount of carrier (2%, 5%, 10% maltodextrin) on the yields and quality of PCC anthocyanin powders. Monomeric and polymeric anthocyanins, color properties (CIELch, haze), and pigments composition before and after spray drying were determined. The yield and final color quality of spray dried PCC anthocyanins were affected (p<0.05) by all parameters evaluated. The pigment matrix, inlet temperature, and carrier amount had biggest impacts on product water solubility, pigments degradation and yield, respectively. The optimal combination of hot water extracts spray dried with 5% maltodextrin at 150°C gave the highest pigment yield (∼90%) with good solubility with the least color loss. Copyright © 2017 Elsevier Ltd. All rights reserved.

CTEPP STANDARD OPERATING PROCEDURE FOR DETECTION AND QUANTIFICATION OF TARGET ANALYTES BY GAS CHROMATOGRAPHY/MASS SPECTROMETRY (GC/MS) (SOP-5.24)

EPA Science Inventory

This standard operating procedure describes the method used for the determination of target analytes in sample extracts and related quality assurance/quality control sample extracts generated in the CTEPP study.

Production of Magnesium and Aluminum-Magnesium Alloys from Recycled Secondary Aluminum Scrap Melts

NASA Astrophysics Data System (ADS)

Gesing, Adam J.; Das, Subodh K.; Loutfy, Raouf O.

2016-02-01

An experimental proof of concept was demonstrated for a patent-pending and trademark-pending RE12™ process for extracting a desired amount of Mg from recycled scrap secondary Al melts. Mg was extracted by electrorefining, producing a Mg product suitable as a Mg alloying hardener additive to primary-grade Al alloys. This efficient electrorefining process operates at high current efficiency, high Mg recovery and low energy consumption. The Mg electrorefining product can meet all the impurity specifications with subsequent melt treatment for removing alkali contaminants. All technical results obtained in the RE12™ project indicate that the electrorefining process for extraction of Mg from Al melt is technically feasible. A techno-economic analysis indicates high potential profitability for applications in Al foundry alloys as well as beverage—can and automotive—sheet alloys. The combination of technical feasibility and potential market profitability completes a successful proof of concept. This economical, environmentally-friendly and chlorine-free RE12™ process could be disruptive and transformational for the Mg production industry by enabling the recycling of 30,000 tonnes of primary-quality Mg annually.

Evaluation of Three Protein-Extraction Methods for Proteome Analysis of Maize Leaf Midrib, a Compound Tissue Rich in Sclerenchyma Cells.

PubMed

Wang, Ning; Wu, Xiaolin; Ku, Lixia; Chen, Yanhui; Wang, Wei

2016-01-01

Leaf morphology is closely related to the growth and development of maize (Zea mays L.) plants and final kernel production. As an important part of the maize leaf, the midrib holds leaf blades in the aerial position for maximum sunlight capture. Leaf midribs of adult plants contain substantial sclerenchyma cells with heavily thickened and lignified secondary walls and have a high amount of phenolics, making protein extraction and proteome analysis difficult in leaf midrib tissue. In the present study, three protein-extraction methods that are commonly used in plant proteomics, i.e., phenol extraction, TCA/acetone extraction, and TCA/acetone/phenol extraction, were qualitatively and quantitatively evaluated based on 2DE maps and MS/MS analysis using the midribs of the 10th newly expanded leaves of maize plants. Microscopy revealed the existence of substantial amounts of sclerenchyma underneath maize midrib epidermises (particularly abaxial epidermises). The spot-number order obtained via 2DE mapping was as follows: phenol extraction (655) > TCA/acetone extraction (589) > TCA/acetone/phenol extraction (545). MS/MS analysis identified a total of 17 spots that exhibited 2-fold changes in abundance among the three methods (using phenol extraction as a control). Sixteen of the proteins identified were hydrophilic, with GRAVY values ranging from -0.026 to -0.487. For all three methods, we were able to obtain high-quality protein samples and good 2DE maps for the maize leaf midrib. However, phenol extraction produced a better 2DE map with greater resolution between spots, and TCA/acetone extraction produced higher protein yields. Thus, this paper includes a discussion regarding the possible reasons for differential protein extraction among the three methods. This study provides useful information that can be used to select suitable protein extraction methods for the proteome analysis of recalcitrant plant tissues that are rich in sclerenchyma cells.

Studies on rye (Secale cereale L.) lines exhibiting a range of extract viscosities. 2. Rheological and baking characteristics of rye and rye/wheat blends and feeding value for chicks of wholemeals and breads.

PubMed

Ragaee, S M; Campbell, G L; Scoles, G J; McLeod, J G; Tyler, R T

2001-05-01

Five rye lines exhibiting a wide range of extract viscosities were evaluated for the rheological and baking properties of their flours, individually and in blends with hard red spring wheat flour. Commercial cultivars of rye and triticale were included in the study as controls. Extract viscosities of rye flours were higher than those of corresponding wholemeals, indicating shifting of water-extractable arabinoxylan into flour during roller milling. Falling numbers of the rye flours correlated positively with their extract viscosities in the presence (r = 0.73, p < 0.05) or absence (r = 0.65, p < 0.05) of an enzyme inhibitor. Farinograms revealed the weakness of rye and triticale flours compared to wheat flour. Extract viscosities of rye flours were negatively correlated (r = -0.65, p < 0.05) with mixing tolerance index and positively correlated (r = 0.64, p < 0.05) with dough stability, suggesting a positive impact of extract viscosity on dough strength. Extract viscosity was negatively correlated (r = -0.74, p < 0.05) with loaf volume and specific volume (r = -0.73, p < 0.05) and positively correlated (r = 0.73, p < 0.05) with loaf weight of rye/wheat bread. Overall, the results indicated that 30% of flour from high or low extract viscosity rye could be incorporated into rye/wheat breads without seriously compromising bread quality. Inclusion of rye, particularly high extract viscosity rye, in chick diets seriously impeded growth performance and feed efficiency. Part of the arabinoxylan survived bread-making and exerted an effect on chicks, although substantially lower digesta viscosities were observed in chicks fed rye bread diets than in those fed rye wholemeals.

The use of FTA cards for preserving unfixed cytological material for high-throughput molecular analysis.

PubMed

Saieg, Mauro Ajaj; Geddie, William R; Boerner, Scott L; Liu, Ni; Tsao, Ming; Zhang, Tong; Kamel-Reid, Suzanne; da Cunha Santos, Gilda

2012-06-25

Novel high-throughput molecular technologies have made the collection and storage of cells and small tissue specimens a critical issue. The FTA card provides an alternative to cryopreservation for biobanking fresh unfixed cells. The current study compared the quality and integrity of the DNA obtained from 2 types of FTA cards (Classic and Elute) using 2 different extraction protocols ("Classic" and "Elute") and assessed the feasibility of performing multiplex mutational screening using fine-needle aspiration (FNA) biopsy samples. Residual material from 42 FNA biopsies was collected in the cards (21 Classic and 21 Elute cards). DNA was extracted using the Classic protocol for Classic cards and both protocols for Elute cards. Polymerase chain reaction for p53 (1.5 kilobase) and CARD11 (500 base pair) was performed to assess DNA integrity. Successful p53 amplification was achieved in 95.2% of the samples from the Classic cards and in 80.9% of the samples from the Elute cards using the Classic protocol and 28.5% using the Elute protocol (P = .001). All samples (both cards) could be amplified for CARD11. There was no significant difference in the DNA concentration or 260/280 purity ratio when the 2 types of cards were compared. Five samples were also successfully analyzed by multiplex MassARRAY spectrometry, with a mutation in KRAS found in 1 case. High molecular weight DNA was extracted from the cards in sufficient amounts and quality to perform high-throughput multiplex mutation assays. The results of the current study also suggest that FTA Classic cards preserve better DNA integrity for molecular applications compared with the FTA Elute cards. Copyright © 2012 American Cancer Society.

Sliding Window-Based Region of Interest Extraction for Finger Vein Images

PubMed Central

Yang, Lu; Yang, Gongping; Yin, Yilong; Xiao, Rongyang

2013-01-01

Region of Interest (ROI) extraction is a crucial step in an automatic finger vein recognition system. The aim of ROI extraction is to decide which part of the image is suitable for finger vein feature extraction. This paper proposes a finger vein ROI extraction method which is robust to finger displacement and rotation. First, we determine the middle line of the finger, which will be used to correct the image skew. Then, a sliding window is used to detect the phalangeal joints and further to ascertain the height of ROI. Last, for the corrective image with certain height, we will obtain the ROI by using the internal tangents of finger edges as the left and right boundary. The experimental results show that the proposed method can extract ROI more accurately and effectively compared with other methods, and thus improve the performance of finger vein identification system. Besides, to acquire the high quality finger vein image during the capture process, we propose eight criteria for finger vein capture from different aspects and these criteria should be helpful to some extent for finger vein capture. PMID:23507824

Green synthesis of silver nanoparticles using flower extract of Malva sylvestris and investigation of their antibacterial activity.

PubMed

Mahmoodi Esfanddarani, Hassan; Abbasi Kajani, Abolghasem; Bordbar, Abdol-Khalegh

2018-06-01

High-quality colloidal silver nanoparticles (AgNP) were synthesised via a green approach by using hydroalcoholic extracts of Malva sylvestris . Silver nitrate was used as a substrate ion while the plant extract successfully played the role of reducing and stabilising agents. The synthesised nanoparticles were carefully characterised by using transmission electron microscopy, atomic-force microscopy, energy dispersive X-ray spectroscopy, Fourier transform infrared spectroscopy and UV-vis spectroscopy. The maximum absorption wavelengths of the colloidal solutions synthesised using 70 and 96% ethanol and 100% methanol, as extraction solvents, were 430, 485 and 504 nm, respectively. Interestingly, the size distribution of nanoparticles depended on the used solvent. The best particle size distribution belonged to the nanoparticles synthesised by 70% ethanol extract, which was 20-40 nm. The antibacterial activity of the synthesised nanoparticles was studied on Escherichia coli , Staphylococcus aureus and Streptococcus pyogenes using disk diffusion, minimum inhibitory concentrations and minimum bactericidal concentrations assays. The best antibacterial activity obtained for the AgNPs produced by using 96% ethanolic extract.

Methodological quality of systematic reviews on influenza vaccination.

PubMed

Remschmidt, Cornelius; Wichmann, Ole; Harder, Thomas

2014-03-26

There is a growing body of evidence on the risks and benefits of influenza vaccination in various target groups. Systematic reviews are of particular importance for policy decisions. However, their methodological quality can vary considerably. To investigate the methodological quality of systematic reviews on influenza vaccination (efficacy, effectiveness, safety) and to identify influencing factors. A systematic literature search on systematic reviews on influenza vaccination was performed, using MEDLINE, EMBASE and three additional databases (1990-2013). Review characteristics were extracted and the methodological quality of the reviews was evaluated using the assessment of multiple systematic reviews (AMSTAR) tool. U-test, Kruskal-Wallis test, chi-square test, and multivariable linear regression analysis were used to assess the influence of review characteristics on AMSTAR-score. Fourty-six systematic reviews fulfilled the inclusion criteria. Average methodological quality was high (median AMSTAR-score: 8), but variability was large (AMSTAR range: 0-11). Quality did not differ significantly according to vaccination target group. Cochrane reviews had higher methodological quality than non-Cochrane reviews (p=0.001). Detailed analysis showed that this was due to better study selection and data extraction, inclusion of unpublished studies, and better reporting of study characteristics (all p<0.05). In the adjusted analysis, no other factor, including industry sponsorship or journal impact factor had an influence on AMSTAR score. Systematic reviews on influenza vaccination showed large differences regarding their methodological quality. Reviews conducted by the Cochrane collaboration were of higher quality than others. When using systematic reviews to guide the development of vaccination recommendations, the methodological quality of a review in addition to its content should be considered. Copyright © 2014 Elsevier Ltd. All rights reserved.

A service for the application of data quality information to NASA earth science satellite records

NASA Astrophysics Data System (ADS)

Armstrong, E. M.; Xing, Z.; Fry, C.; Khalsa, S. J. S.; Huang, T.; Chen, G.; Chin, T. M.; Alarcon, C.

2016-12-01

A recurring demand in working with satellite-based earth science data records is the need to apply data quality information. Such quality information is often contained within the data files as an array of "flags", but can also be represented by more complex quality descriptions such as combinations of bit flags, or even other ancillary variables that can be applied as thresholds to the geophysical variable of interest. For example, with Level 2 granules from the Group for High Resolution Sea Surface Temperature (GHRSST) project up to 6 independent variables could be used to screen the sea surface temperature measurements on a pixel-by-pixel basis. Quality screening of Level 3 data from the Soil Moisture Active Passive (SMAP) instrument can be become even more complex, involving 161 unique bit states or conditions a user can screen for. The application of quality information is often a laborious process for the user until they understand the implications of all the flags and bit conditions, and requires iterative approaches using custom software. The Virtual Quality Screening Service, a NASA ACCESS project, is addressing these issues and concerns. The project has developed an infrastructure to expose, apply, and extract quality screening information building off known and proven NASA components for data extraction and subset-by-value, data discovery, and exposure to the user of granule-based quality information. Further sharing of results through well-defined URLs and web service specifications has also been implemented. The presentation will focus on overall description of the technologies and informatics principals employed by the project. Examples of implementations of the end-to-end web service for quality screening with GHRSST and SMAP granules will be demonstrated.

Data extraction from electronic health records (EHRs) for quality measurement of the physical therapy process: comparison between EHR data and survey data.

PubMed

Scholte, Marijn; van Dulmen, Simone A; Neeleman-Van der Steen, Catherina W M; van der Wees, Philip J; Nijhuis-van der Sanden, Maria W G; Braspenning, Jozé

2016-11-08

With the emergence of the electronic health records (EHRs) as a pervasive healthcare information technology, new opportunities and challenges for use of clinical data for quality measurements arise with respect to data quality, data availability and comparability. The objective of this study is to test whether data extracted from electronic health records (EHRs) was of comparable quality as survey data for the calculation of quality indicators. Data from surveys describing patient cases and filled out by physiotherapists in 2009-2010 were used to calculate scores on eight quality indicators (QIs) to measure the quality of physiotherapy care. In 2011, data was extracted directly from EHRs. The data collection methods were evaluated for comparability. EHR data was compared to survey data on completeness and correctness. Five of the eight QIs could be extracted from the EHRs. Three were omitted from the indicator set, as they proved too difficult to be extracted from the EHRs. Another QI proved incomparable due to errors in the extraction software of some of the EHRs. Three out of four comparable QIs performed better (p < 0.001) in EHR data on completeness. EHR data also proved to be correct; the relative change in indicator scores between EHR and survey data were small (<5 %) in three out of four QIs. Data quality of EHRs was sufficient to be used for the calculation of QIs, although comparability to survey data was problematic. Standardization is needed, not only to be able to compare different data collection methods properly, but also to compare between practices with different EHRs. EHRs have the option to administrate narrative data, but natural language processing tools are needed to quantify these text boxes. Such development, can narrow the comparability gap between scoring QIs based on EHR data and based on survey data. EHRs have the potential to provide real time feedback to professionals and quality measurements for research, but more effort is needed to create unambiguous and uniform information and to unlock written text in a standardized manner.

Critical points of DNA quantification by real-time PCR – effects of DNA extraction method and sample matrix on quantification of genetically modified organisms

PubMed Central

Cankar, Katarina; Štebih, Dejan; Dreo, Tanja; Žel, Jana; Gruden, Kristina

2006-01-01

Background Real-time PCR is the technique of choice for nucleic acid quantification. In the field of detection of genetically modified organisms (GMOs) quantification of biotech products may be required to fulfil legislative requirements. However, successful quantification depends crucially on the quality of the sample DNA analyzed. Methods for GMO detection are generally validated on certified reference materials that are in the form of powdered grain material, while detection in routine laboratories must be performed on a wide variety of sample matrixes. Due to food processing, the DNA in sample matrixes can be present in low amounts and also degraded. In addition, molecules of plant origin or from other sources that affect PCR amplification of samples will influence the reliability of the quantification. Further, the wide variety of sample matrixes presents a challenge for detection laboratories. The extraction method must ensure high yield and quality of the DNA obtained and must be carefully selected, since even components of DNA extraction solutions can influence PCR reactions. GMO quantification is based on a standard curve, therefore similarity of PCR efficiency for the sample and standard reference material is a prerequisite for exact quantification. Little information on the performance of real-time PCR on samples of different matrixes is available. Results Five commonly used DNA extraction techniques were compared and their suitability for quantitative analysis was assessed. The effect of sample matrix on nucleic acid quantification was assessed by comparing 4 maize and 4 soybean matrixes. In addition 205 maize and soybean samples from routine analysis were analyzed for PCR efficiency to assess variability of PCR performance within each sample matrix. Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was chosen as the primary criterion by which to evaluate the quality and performance on different matrixes and extraction techniques. The effect of PCR efficiency on the resulting GMO content is demonstrated. Conclusion The crucial influence of extraction technique and sample matrix properties on the results of GMO quantification is demonstrated. Appropriate extraction techniques for each matrix need to be determined to achieve accurate DNA quantification. Nevertheless, as it is shown that in the area of food and feed testing matrix with certain specificities is impossible to define strict quality controls need to be introduced to monitor PCR. The results of our study are also applicable to other fields of quantitative testing by real-time PCR. PMID:16907967

Low temperature synthesis of hierarchical TiO 2 nanostructures for high performance perovskite solar cells by pulsed laser deposition

DOE PAGES

Yang, Bin; Mahjouri-Samani, Masoud; Rouleau, Christopher M.; ...

2016-06-10

A promising way to advance perovskite solar cells is to improve the quality of the electron transport material e.g., titanium dioxide (TiO 2) in a direction that increases electron transport and extraction. Although dense TiO 2 films are easily grown in solution, efficient electron extraction suffers due to a lack of interfacial contact area with the perovskite. Conversely, mesoporous films do offer high surface-area-to-volume ratios, thereby promoting efficient electron extraction, but their morphology is relatively difficult to control via conventional solution synthesis methods. Here, a pulsed laser deposition method was used to assemble TiO 2 nanoparticles into TiO 2 hierarchicalmore » nanoarchitectures having the anatase crystal structure, and prototype solar cells employing these structures yielded power conversion efficiencies of ~ 14%. Our approach demonstrates a way to grow high aspect-ratio TiO 2 nanostructures for improved interfacial contact between TiO 2 and perovskite materials, leading to high electron-hole pair separation and electron extraction efficiencies for superior photovoltaic performance. In addition, compared to conventional solution-processed TiO 2 films that require 500 °C to obtain a good crystallinity, our relatively low temperature (300 °C) TiO 2 processing method may promote reduced energy-consumption during device fabrication as well as enable compatibility with various flexible polymer substrates.« less

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar

PubMed Central

Leite, D.C.A.; Balieiro, F.C.; Pires, C.A.; Madari, B.E.; Rosado, A.S.; Coutinho, H.L.C.; Peixoto, R.S.

2014-01-01

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples. PMID:24948928

Comparison of DNA extraction protocols for microbial communities from soil treated with biochar.

PubMed

Leite, D C A; Balieiro, F C; Pires, C A; Madari, B E; Rosado, A S; Coutinho, H L C; Peixoto, R S

2014-01-01

Many studies have evaluated the effects of biochar application on soil structure and plant growth. However, there are very few studies describing the effect of biochar on native soil microbial communities. Microbial analysis of environmental samples requires accurate and reproducible methods for the extraction of DNA from samples. Because of the variety among microbial species and the strong adsorption of the phosphate backbone of the DNA molecule to biochar, extracting and purifying high quality microbial DNA from biochar-amended soil is not a trivial process and can be considerably more difficult than the extraction of DNA from other environmental samples. The aim of this study was to compare the relative efficacies of three commercial DNA extraction kits, the FastDNA® SPIN Kit for Soil (FD kit), the PowerSoil® DNA Isolation Kit (PS kit) and the ZR Soil Microbe DNA Kit Miniprep™ (ZR kit), for extracting microbial genomic DNA from sand treated with different types of biochar. The methods were evaluated by comparing the DNA yields and purity and by analysing the bacterial and fungal community profiles generated by PCR-DGGE. Our results showed that the PCR-DGGE profiles for bacterial and fungal communities were highly affected by the purity and yield of the different DNA extracts. Among the tested kits, the PS kit was the most efficient with respect to the amount and purity of recovered DNA and considering the complexity of the generated DGGE microbial fingerprint from the sand-biochar samples.

[Identification of special quality eggs with NIR spectroscopy technology based on symbol entropy feature extraction method].

PubMed

Zhao, Yong; Hong, Wen-Xue

2011-11-01

Fast, nondestructive and accurate identification of special quality eggs is an urgent problem. The present paper proposed a new feature extraction method based on symbol entropy to identify near infrared spectroscopy of special quality eggs. The authors selected normal eggs, free range eggs, selenium-enriched eggs and zinc-enriched eggs as research objects and measured the near-infrared diffuse reflectance spectra in the range of 12 000-4 000 cm(-1). Raw spectra were symbolically represented with aggregation approximation algorithm and symbolic entropy was extracted as feature vector. An error-correcting output codes multiclass support vector machine classifier was designed to identify the spectrum. Symbolic entropy feature is robust when parameter changed and the highest recognition rate reaches up to 100%. The results show that the identification method of special quality eggs using near-infrared is feasible and the symbol entropy can be used as a new feature extraction method of near-infrared spectra.

Combined Effect of Kimchi Powder and Onion Peel Extract on Quality Characteristics of Emulsion Sausages Prepared with Irradiated Pork.

PubMed

Lee, Soo-Yoen; Kim, Hyun-Wook; Hwang, Ko-Eun; Song, Dong-Heon; Choi, Min-Sung; Ham, Youn-Kyung; Choi, Yun-Sang; Lee, Ju-Woon; Lee, Si-Kyung; Kim, Cheon-Jei

2015-01-01

This study was conducted to investigate the effects of kimchi powder and onion peel extract on the quality characteristics of emulsion sausage manufactured with irradiated pork. The emulsion sausages were formulated with 2% kimchi powder and/or 0.05% onion peel extract. The changes in pH value of all treatments were similar, depending on storage periods. The addition of kimchi powder increased the redness and yellowness of the emulsion sausage. The addition of onion peel extract decreased the thiobarbituric acid reactive substances value of the emulsion sausages prepared with irradiated pork. The volatile basic nitrogen value of the emulsion sausage prepared with kimchi powder was the highest, whereas that of the emulsion sausage prepared with onion peel extract was the lowest. The treatment without kimchi powder or onion peel extract and the treatments prepared with onion peel extract showed lower microbial populations than the other treatment. Sensory evaluations indicated that a higher acceptability was attained when kimchi powder was added to the emulsion sausages manufactured with irradiated pork. In conclusion, our results suggest that combined use of kimchi powder and onion peel extract could improve quality characteristics and shelf stability of the emulsion sausage formulated with irradiated pork during chilled storage.

Combined Effect of Kimchi Powder and Onion Peel Extract on Quality Characteristics of Emulsion Sausages Prepared with Irradiated Pork

PubMed Central

Choi, Yun-Sang; Lee, Ju-Woon; Lee, Si-Kyung

2015-01-01

This study was conducted to investigate the effects of kimchi powder and onion peel extract on the quality characteristics of emulsion sausage manufactured with irradiated pork. The emulsion sausages were formulated with 2% kimchi powder and/or 0.05% onion peel extract. The changes in pH value of all treatments were similar, depending on storage periods. The addition of kimchi powder increased the redness and yellowness of the emulsion sausage. The addition of onion peel extract decreased the thiobarbituric acid reactive substances value of the emulsion sausages prepared with irradiated pork. The volatile basic nitrogen value of the emulsion sausage prepared with kimchi powder was the highest, whereas that of the emulsion sausage prepared with onion peel extract was the lowest. The treatment without kimchi powder or onion peel extract and the treatments prepared with onion peel extract showed lower microbial populations than the other treatment. Sensory evaluations indicated that a higher acceptability was attained when kimchi powder was added to the emulsion sausages manufactured with irradiated pork. In conclusion, our results suggest that combined use of kimchi powder and onion peel extract could improve quality characteristics and shelf stability of the emulsion sausage formulated with irradiated pork during chilled storage. PMID:26761840

SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects

PubMed Central

2014-01-01

Background Light microscopic analysis of diatom frustules is widely used both in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. In these applications, usually large numbers of frustules need to be identified and/or measured. Although there is a need for automation in these applications, and image processing and analysis methods supporting these tasks have previously been developed, they did not become widespread in diatom analysis. While methodological reports for a wide variety of methods for image segmentation, diatom identification and feature extraction are available, no single implementation combining a subset of these into a readily applicable workflow accessible to diatomists exists. Results The newly developed tool SHERPA offers a versatile image processing workflow focused on the identification and measurement of object outlines, handling all steps from image segmentation over object identification to feature extraction, and providing interactive functions for reviewing and revising results. Special attention was given to ease of use, applicability to a broad range of data and problems, and supporting high throughput analyses with minimal manual intervention. Conclusions Tested with several diatom datasets from different sources and of various compositions, SHERPA proved its ability to successfully analyze large amounts of diatom micrographs depicting a broad range of species. SHERPA is unique in combining the following features: application of multiple segmentation methods and selection of the one giving the best result for each individual object; identification of shapes of interest based on outline matching against a template library; quality scoring and ranking of resulting outlines supporting quick quality checking; extraction of a wide range of outline shape descriptors widely used in diatom studies and elsewhere; minimizing the need for, but enabling manual quality control and corrections. Although primarily developed for analyzing images of diatom valves originating from automated microscopy, SHERPA can also be useful for other object detection, segmentation and outline-based identification problems. PMID:24964954

SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects.

PubMed

Kloster, Michael; Kauer, Gerhard; Beszteri, Bánk

2014-06-25

Light microscopic analysis of diatom frustules is widely used both in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. In these applications, usually large numbers of frustules need to be identified and/or measured. Although there is a need for automation in these applications, and image processing and analysis methods supporting these tasks have previously been developed, they did not become widespread in diatom analysis. While methodological reports for a wide variety of methods for image segmentation, diatom identification and feature extraction are available, no single implementation combining a subset of these into a readily applicable workflow accessible to diatomists exists. The newly developed tool SHERPA offers a versatile image processing workflow focused on the identification and measurement of object outlines, handling all steps from image segmentation over object identification to feature extraction, and providing interactive functions for reviewing and revising results. Special attention was given to ease of use, applicability to a broad range of data and problems, and supporting high throughput analyses with minimal manual intervention. Tested with several diatom datasets from different sources and of various compositions, SHERPA proved its ability to successfully analyze large amounts of diatom micrographs depicting a broad range of species. SHERPA is unique in combining the following features: application of multiple segmentation methods and selection of the one giving the best result for each individual object; identification of shapes of interest based on outline matching against a template library; quality scoring and ranking of resulting outlines supporting quick quality checking; extraction of a wide range of outline shape descriptors widely used in diatom studies and elsewhere; minimizing the need for, but enabling manual quality control and corrections. Although primarily developed for analyzing images of diatom valves originating from automated microscopy, SHERPA can also be useful for other object detection, segmentation and outline-based identification problems.

The Effect of LAB as Probiotic Starter Culture and Green Tea Extract Addition on Dry Fermented Pork Loins Quality.

PubMed

Neffe-Skocińska, Katarzyna; Jaworska, Danuta; Kołożyn-Krajewska, Danuta; Dolatowski, Zbigniew; Jachacz-Jówko, Luiza

2015-01-01

The objective of this study was to evaluate the microbiological, physicochemical, and sensory quality of dry fermented pork loin produced with the addition of Lb. rhamnosus LOCK900 probiotic strain, 0.2% glucose, and 1.5% green tea extract. Three loins were prepared: control sample (P0: no additives), sample supplemented with glucose and probiotic strain (P1), and sample with glucose, green tea extract, and probiotic (P2). The samples were analyzed after 21 days of ripening and 180 days of storage. The results indicated that the highest count of LAB was observed both in the samples: with probiotic and with probiotic and green tea extract (7.00 log cfu/g after ripening; 6.00 log cfu/g after storage). The oxidation-reduction potential values were lower in the probiotic loin samples. Probiotic and green tea extract have not caused color changes of study loins during storage. The study demonstrated that an addition of probiotic and green tea extract to dry fermented loins is possible and had no impact on sensory quality after product storage.

The Effect of LAB as Probiotic Starter Culture and Green Tea Extract Addition on Dry Fermented Pork Loins Quality

PubMed Central

Jaworska, Danuta; Kołożyn-Krajewska, Danuta; Dolatowski, Zbigniew; Jachacz-Jówko, Luiza

2015-01-01

The objective of this study was to evaluate the microbiological, physicochemical, and sensory quality of dry fermented pork loin produced with the addition of Lb. rhamnosus LOCK900 probiotic strain, 0.2% glucose, and 1.5% green tea extract. Three loins were prepared: control sample (P0: no additives), sample supplemented with glucose and probiotic strain (P1), and sample with glucose, green tea extract, and probiotic (P2). The samples were analyzed after 21 days of ripening and 180 days of storage. The results indicated that the highest count of LAB was observed both in the samples: with probiotic and with probiotic and green tea extract (7.00 log cfu/g after ripening; 6.00 log cfu/g after storage). The oxidation-reduction potential values were lower in the probiotic loin samples. Probiotic and green tea extract have not caused color changes of study loins during storage. The study demonstrated that an addition of probiotic and green tea extract to dry fermented loins is possible and had no impact on sensory quality after product storage. PMID:25961018

Application of RT-PCR in formalin-fixed and paraffin-embedded lung cancer tissues.

PubMed

Zhang, Fan; Wang, Zhuo-min; Liu, Hong-yu; Bai, Yun; Wei, Sen; Li, Ying; Wang, Min; Chen, Jun; Zhou, Qing-hua

2010-01-01

To analyze gene expression in formalin-fixed, paraffin-embedded lung cancer tissues using modified method. Total RNA from frozen tissues was extracted using TRIZOL reagent. RNA was extracted from formalin-fixed, paraffin-embedded tissues by digestion with proteinase K before the acid-phenol:chloroform extraction and carrier precipitation. We modified this method by using a higher concentration of proteinase K and a longer digestion time, optimized to 16 hours. RT-PCR and real-time RT-PCR were used to check reproducibility and the concordance between frozen and paraffin-embedded samples. The results showed that the RNA extracted from the paraffin-embedded lung tissues had high quality with the most fragment length between 28S and 18S bands (about 1000 to 2000 bases). The housekeeping gene GUSB exhibited low variation of expression in frozen and paraffin-embedded lung tissues, whereas PGK1 had the lowest variation in lymphoma tissues. Furthermore, real-time PCR analysis of the expression of known prognostic genes in non-small cell lung carcinoma (NSCLC) demonstrated an extremely high correlation (r>0.880) between the paired frozen and formalin-fixed, paraffin-embedded specimens. This improved method of RNA extraction is suitable for real-time quantitative RT-PCR, and may be used for global gene expression profiling of paraffin-embedded tissues.

The Risk of Bias in Randomized Trials in General Dentistry Journals.

PubMed

Hinton, Stephanie; Beyari, Mohammed M; Madden, Kim; Lamfon, Hanadi A

2015-01-01

The use of a randomized controlled trial (RCT) research design is considered the gold standard for conducting evidence-based clinical research. In this present study, we aimed to assess the quality of RCTs in dentistry and create a general foundation for evidence-based dentistry on which to perform subsequent RCTs. We conducted a systematic assessment of bias of RCTs in seven general dentistry journals published between January 2011 and March 2012. We extracted study characteristics in duplicate and assessed each trial's quality using the Cochrane Risk of Bias tool. We compared risk of bias across studies graphically. Among 1,755 studies across seven journals, we identified 67 RCTs. Many included studies were conducted in Europe (39%), with an average sample size of 358 participants. These studies included 52% female participants and the maximum follow-up period was 13 years. Overall, we found a high percentage of unclear risk of bias among included RCTs, indicating poor quality of reporting within the included studies. An overall high proportion of trials with an "unclear risk of bias" suggests the need for better quality of reporting in dentistry. As such, key concepts in dental research and future trials should focus on high-quality reporting.

The influence of DNA degradation in formalin-fixed, paraffin-embedded (FFPE) tissue on locus-specific methylation assessment by MS-HRM.

PubMed

Daugaard, Iben; Kjeldsen, Tina E; Hager, Henrik; Hansen, Lise Lotte; Wojdacz, Tomasz K

2015-12-01

Readily accessible formalin-fixed paraffin embedded (FFPE) tissues are a highly valuable source of genetic material for molecular analyses in both research and in vitro diagnostics but frequently genetic material in those samples is highly degraded. With locus-specific methylation changes being widely investigated for use as biomarkers in various aspects of clinical disease management, we aimed to evaluate to what extent standard laboratory procedures can approximate the quality of the DNA extracted from FFPE samples prior to methylation analyses. DNA quality in 107 FFPE non-small cell lung cancer (NSCLC) samples was evaluated using spectrophotometry and gel electrophoresis. Subsequently, the quality assessment results were correlated with the results of locus specific methylation assessment with methylation sensitive high resolution melting (MS-HRM). The correlation of template quality with PCR amplification performance and HRM based methylation detection indicated a significant influence of DNA quality on PCR amplification but not on methylation assessment. In conclusion, standard laboratory procedures fairly well approximate DNA degradation of FFPE samples and DNA degradation does not seem to considerably affect locus-specific methylation assessment by MS-HRM. Copyright © 2015 Elsevier Inc. All rights reserved.

A Microcontroller Operated Device for the Generation of Liquid Extracts from Conventional Cigarette Smoke and Electronic Cigarette Aerosol.

PubMed

Anderson, Chastain A; Bokota, Rachael E; Majeste, Andrew E; Murfee, Walter L; Wang, Shusheng

2018-01-18

Electronic cigarettes are the most popular tobacco product among middle and high schoolers and are the most popular alternative tobacco product among adults. High quality, reproducible research on the consequences of electronic cigarette use is essential for understanding emerging public health concerns and crafting evidence based regulatory policy. While a growing number of papers discuss electronic cigarettes, there is little consistency in methods across groups and very little consensus on results. Here, we describe a programmable laboratory device that can be used to create extracts of conventional cigarette smoke and electronic cigarette aerosol. This protocol details instructions for the assembly and operation of said device, and demonstrates the use of the generated extract in two sample applications: an in vitro cell viability assay and gas-chromatography mass-spectrometry. This method provides a tool for making direct comparisons between conventional cigarettes and electronic cigarettes, and is an accessible entry point into electronic cigarette research.

BreathSens: A Continuous On-Bed Respiratory Monitoring System With Torso Localization Using an Unobtrusive Pressure Sensing Array.

PubMed

Liu, Jason J; Huang, Ming-Chun; Xu, Wenyao; Zhang, Xiaoyi; Stevens, Luke; Alshurafa, Nabil; Sarrafzadeh, Majid

2015-09-01

The ability to continuously monitor respiration rates of patients in homecare or in clinics is an important goal. Past research showed that monitoring patient breathing can lower the associated mortality rates for long-term bedridden patients. Nowadays, in-bed sensors consisting of pressure sensitive arrays are unobtrusive and are suitable for deployment in a wide range of settings. Such systems aim to extract respiratory signals from time-series pressure sequences. However, variance of movements, such as unpredictable extremities activities, affect the quality of the extracted respiratory signals. BreathSens, a high-density pressure sensing system made of e-Textile, profiles the underbody pressure distribution and localizes torso area based on the high-resolution pressure images. With a robust bodyparts localization algorithm, respiratory signals extracted from the localized torso area are insensitive to arbitrary extremities movements. In a study of 12 subjects, BreathSens demonstrated its respiratory monitoring capability with variations of sleep postures, locations, and commonly tilted clinical bed conditions.

Renewable platform chemicals from directional microwave-assisted liquefaction coupling stepwise extraction of waste biomass.

PubMed

Feng, Junfeng; Hse, Chungyun; Yang, Zhongzhi; Wang, Kui; Jiang, Jianchun; Xu, Junming

2017-11-01

Directional microwave-assisted liquefaction and stepwise extraction are introduced for producing platform chemicals: aromatics and monosaccharides. When sulfuric acid was used as a catalyst, a 45% monosaccharides yield and a 29% aromatics yield were obtained from bamboo with 0.3g catalyst per 18g methanol and 2g bamboo at 160°C with 10min. Approximately 78-86wt% of the six biomass materials were converted into liquid products. After the stepwise extraction and precipitation process, the yields of monosaccharide derivatives and three phenolic compound fractions were 39-45% and 28-32%, respectively. Monosaccharides from holocellulose collected with a high purity of methyl glycosides were higher than 90%. Aromatic derivatives with different weight-molecular distributions were separated into three fractions with more than 80% phenolics. As their similar chemical properties within each fraction, platform chemicals have great commercial potential for producing high-quality chemicals and biofuels using mild upgrading conditions. Copyright © 2017. Published by Elsevier Ltd.

Effect of dietary plant extract on meat quality and sensory parameters of meat from Equidae.

PubMed

Rossi, Raffaella; Ratti, Sabrina; Pastorelli, Grazia; Maghin, Federica; Martemucci, Giovanni; Casamassima, Donato; D'Alessandro, Angela Gabriella; Corino, Carlo

2017-11-01

Plant extracts as Lippia spp. have been proven antioxidant properties. Recent studies have been shown that dietary supplementation with plant extracts is able to enhance meat quality parameters. Studies regarding meat quality in Equidae are limited. The effect of dietary plant extract (PE), containing verbascoside, on meat quality, oxidative stability and sensory parameters of Longissimus Lumborum (LL) muscle in Equidae was studied. Dietary treatment did not affect (P > 0.05) pH, colour indices and chemical parameters of muscle in both donkey and horse. Dietary PE improved (P < 0.01) oxidative stability in donkey muscle during refrigerated storage. Sensory characteristics of LL muscle were positively affected (P < 0.05) by dietary PE in both donkey and horse. In particular, colour, taste and texture were enhanced in LL muscle from animals fed PE. Oxidative stability was lower (P < 0.05) in LL muscle of horse than that of donkey. Dietary plant extract, containing verbascoside, can be considered as a natural source of antioxidants, and is also able to improve oxidative stability of donkey meat and to affect the sensory attributes of Equidae meat. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

A Systematic Review of the Level of Evidence in Economic Evaluations of Medical Devices: The Example of Vertebroplasty and Kyphoplasty

PubMed Central

van den Brink, Hélène; Pineau, Judith; Prognon, Patrice; Borget, Isabelle

2015-01-01

Context Economic evaluations are far less frequently reported for medical devices than for drugs. In addition, little is known about the quality of existing economic evaluations, particularly for innovative devices, such as those used in vertebroplasty and kyphoplasty. Objective To assess the level of evidence provided by the available economic evaluations for vertebroplasty and kyphoplasty. Data Sources A systematic review of articles in English or French listed in the MEDLINE, PASCAL, COCHRANE and National Health Service Economic Evaluation databases, with limits on publication date (up to the date of the review, March 2014). Study Selection We included only economic evaluations of vertebroplasty or kyphoplasty. Editorial and methodological articles were excluded. Data Extraction Data were extracted from articles by two authors working independently and using two analysis grids to measure the quality of economic evaluations. Data Synthesis Twenty-one studies met our inclusion criteria. All were published between 2008 and 2014. Eighteen (86%) were full economic evaluations. Cost-effectiveness analysis (CEA) was the most frequent type of economic evaluation, and was present in 11 (52%) studies. Only three CEAs complied fully with the British Medical Journal checklist. The quality of the data sources used in the 21 studies was high, but the CEAs conforming to methodological guidelines did not use high-quality data sources for all components of the analysis. Conclusions This systematic review shows that the level of evidence in economic evaluations of vertebroplasty and kyphoplasty is low, despite the recent publication of a large number of studies. This finding highlights the challenges to be faced to improve the quality of economic evaluations of medical devices. PMID:26661078

A new morphology algorithm for shoreline extraction from DEM data

NASA Astrophysics Data System (ADS)

Yousef, Amr H.; Iftekharuddin, Khan; Karim, Mohammad

2013-03-01

Digital elevation models (DEMs) are a digital representation of elevations at regularly spaced points. They provide an accurate tool to extract the shoreline profiles. One of the emerging sources of creating them is light detection and ranging (LiDAR) that can capture a highly dense cloud points with high resolution that can reach 15 cm and 100 cm in the vertical and horizontal directions respectively in short periods of time. In this paper we present a multi-step morphological algorithm to extract shorelines locations from the DEM data and a predefined tidal datum. Unlike similar approaches, it utilizes Lowess nonparametric regression to estimate the missing values within the DEM file. Also, it will detect and eliminate the outliers and errors that result from waves, ships, etc by means of anomality test with neighborhood constrains. Because, there might be some significant broken regions such as branches and islands, it utilizes a constrained morphological open and close to reduce these artifacts that can affect the extracted shorelines. In addition, it eliminates docks, bridges and fishing piers along the extracted shorelines by means of Hough transform. Based on a specific tidal datum, the algorithm will segment the DEM data into water and land objects. Without sacrificing the accuracy and the spatial details of the extracted boundaries, the algorithm should smooth and extract the shoreline profiles by tracing the boundary pixels between the land and the water segments. For given tidal values, we qualitatively assess the visual quality of the extracted shorelines by superimposing them on the available aerial photographs.

Rapid and sensitive determination of major polyphenolic components in Euphoria longana Lam. seeds using matrix solid-phase dispersion extraction and UHPLC with hybrid linear ion trap triple quadrupole mass spectrometry.

PubMed

Rathore, Atul S; Sathiyanarayanan, L; Deshpande, Shreekant; Mahadik, Kakasaheb R

2016-11-01

A rapid and sensitive method for the extraction and determination of four major polyphenolic components in Euphoria longana Lam. seeds is presented for the first time based on matrix solid-phase dispersion extraction followed by ultra high performance liquid chromatography with hybrid triple quadrupole linear ion trap mass spectrometry. Matrix solid-phase dispersion method was designed for the extraction of Euphoria longana seed constituents and compared with microwave-assisted extraction and ultrasonic-assisted extraction methods. An Ultra high performance liquid chromatography with hybrid triple quadrupole linear ion-trap mass spectrometry method was developed for quantitative analysis in multiple-reaction monitoring mode in negative electrospray ionization. The chromatographic separation was accomplished using an ACQUITY UPLC BEH C 18 (2.1 mm × 50 mm, 1.7 μm) column with gradient elution of 0.1% aqueous formic acid and 0.1% formic acid in acetonitrile. The developed method was validated with acceptable linearity (r 2 > 0.999), precision (RSD ≤ 2.22%) and recovery (RSD ≤ 2.35%). The results indicated that matrix solid-phase dispersion produced comparable extraction efficiency compared with other methods nevertheless was more convenient and time-saving with reduced requirements on sample and solvent volumes. The proposed method is rapid and sensitive in providing a promising alternative for extraction and comprehensive determination of active components for quality control of Euphoria longana products. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SOLID PHASE EXTRACTION AND HIGH PERFORMANCE LIQUID CHROMATOGRAPHY WITH PHOTODIODE ARRAY DETECTION OF CHEMICAL INDICATORS OF HUMAN FECAL CONTAMINATION IN WATER

EPA Science Inventory

Faster and more sensitive analysis of water that is contaminated by human fecal matter is very important for health. The current microbiological methods to assess water quality do not meet this need. Alternate non-microbial human fecal indicators have been proposed by various r...

SEM vouchers and genomic data from an individual specimen: maximizing the utility of delicate and rare specimens

USDA-ARS?s Scientific Manuscript database

Specimen vouchering is a critical aspect of systematics, especially in genetic studies where the identity of a DNA sample needs to be assured. It can be difficult to obtain a high quality voucher after DNA extraction when dealing with tiny and delicate invertebrates that often do not survive the ext...

Detection of viable Cyptosporidium parvum in soil by reverse transcription real time PCR targeting hsp70 mRNA

EPA Science Inventory

Extraction of high-quality mRNA from Cryptosporidium parvum is a key step in PCR detection of viable oocysts in environmental samples. Current methods for monitoring oocysts are limited to water samples; therefore, the goal of this study was to develop a rapid and sensitive proce...

Rye and Wheat Bran Extracts Isolated with Pressurized Solvents Increase Oxidative Stability and Antioxidant Potential of Beef Meat Hamburgers.

PubMed

Šulniūtė, Vaida; Jaime, Isabel; Rovira, Jordi; Venskutonis, Petras Rimantas

2016-02-01

Rye and wheat bran extracts containing phenolic compounds and demonstrating high DPPH• (2,2-diphenyl-1-picrylhydrazyl), ABTS(•+) (2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) scavenging and oxygen radical absorbance capacities (ORAC) were tested in beef hamburgers as possible functional ingredients. Bran extracts significantly increased the indicators of antioxidant potential of meat products and their global antioxidant response (GAR) during physiological in vitro digestion. The extracts also inhibited the formation of oxidation products, hexanal and malondialdehyde, of hamburgers during their storage; however, they did not have significant effect on the growth of microorganisms. Hamburgers with 0.8% wheat bran extract demonstrated the highest antioxidant potential. Some effects of bran extracts on other quality characteristics such as pH, color, formation of metmyoglobin were also observed, however, these effects did not have negative influence on the overall sensory evaluation score of hamburgers. Consequently, the use of bran extracts in meat products may be considered as promising means of increasing oxidative product stability and enriching with functional ingredients which might possess health benefits. © 2016 Institute of Food Technologists®

HPLC-PDA analysis and anti-inflammatory effects of Mori Cortex Radicis.

PubMed

Seo, Chang-Seob; Lim, Hye-Sun; Jeong, Soo-Jin; Ha, Hyekyung; Shin, Hyeun-Kyoo

2013-10-01

Mori Cortex Radicis (MCR, Moraceae) is used traditionally in the treatment ofjaundice, hematemesis, edema, and pollakisuria in Korea. In this study, the antiinflammatory effects of MCR extract were investigated using RAW 264.7 cells. The simultaneous analysis of five components present (neochlorogenic acid, chlorogenic acid, cryptochlorogenic acid, caffeic acid, and p-coumaric acid) in the MCR extract was performed using high-performance liquid chromatography (HPLC) coupled with photodiode array (PDA) detection. We determined the effects of MCR extract and its components on the production of nitric oxide (NO), prostaglandin E2 (PGE2), and mRNA expression of cyclooxygenase-2 (COX-2) in RAW 264.7 cells. MCR extract suppressed the production of NO and PGE2 in RAW 264.7 cells in a dose-dependent manner. None of the five components of the MCR extract had any influence on the production of NO. However, caffeic acid and p-coumaric acid inhibited the production of PGE2 and mRNA expression of COX-2 in RAW 264.7 cells. Our results suggest that MCR extract may offer potential as a therapeutic agent for the treatment of inflammation. The method we have established will help to improve the quality control of MCR extracts.

Comparison of commercial DNA extraction kits for isolation and purification of bacterial and eukaryotic DNA from PAH-contaminated soils.

PubMed

Mahmoudi, Nagissa; Slater, Greg F; Fulthorpe, Roberta R

2011-08-01

Molecular characterization of the microbial populations of soils and sediments contaminated with polycyclic aromatic hydrocarbons (PAHs) is often a first step in assessing intrinsic biodegradation potential. However, soils are problematic for molecular analysis owing to the presence of organic matter, such as humic acids. Furthermore, the presence of contaminants, such as PAHs, can cause further challenges to DNA extraction, quantification, and amplification. The goal of our study was to compare the effectiveness of four commercial soil DNA extraction kits (UltraClean Soil DNA Isolation kit, PowerSoil DNA Isolation kit, PowerMax Soil DNA Isolation kit, and FastDNA SPIN kit) to extract pure, high-quality bacterial and eukaryotic DNA from PAH-contaminated soils. Six different contaminated soils were used to determine if there were any biases among the kits due to soil properties or level of contamination. Extracted DNA was used as a template for bacterial 16S rDNA and eukaryotic 18S rDNA amplifications, and PCR products were subsequently analyzed using denaturing gel gradient electrophoresis (DGGE). We found that the FastDNA SPIN kit provided significantly higher DNA yields for all soils; however, it also resulted in the highest levels of humic acid contamination. Soil texture and organic carbon content of the soil did not affect the DNA yield of any kit. Moreover, a liquid-liquid extraction of the DNA extracts found no residual PAHs, indicating that all kits were effective at removing contaminants in the extraction process. Although the PowerSoil DNA Isolation kit gave relatively low DNA yields, it provided the highest quality DNA based on successful amplification of both bacterial and eukaryotic DNA for all six soils. DGGE fingerprints among the kits were dramatically different for both bacterial and eukaryotic DNA. The PowerSoil DNA Isolation kit revealed multiple bands for each soil and provided the most consistent DGGE profiles among replicates for both bacterial and eukaryotic DNA.

Systematic review of recent dementia practice guidelines.

PubMed

Ngo, Jennifer; Holroyd-Leduc, Jayna M

2015-01-01

dementia is a highly prevalent acquired cognitive disorder that interferes with activities of daily living, relationships and quality of life. Recognition and effective management strategies are necessary to provide comprehensive care for these patients and their families. High-quality clinical practice guidelines can improve the quality and consistency of care in all aspects of dementia diagnosis and management by clarifying interventions supported by sound evidence and by alerting clinicians to interventions without proven benefit. we aimed to offer a synthesis of existing practice recommendations for the diagnosis and management of dementia, based upon moderate-to-high quality dementia guidelines. we performed a systematic search in EMBASE and MEDLINE as well as the grey literature for guidelines produced between 2008 and 2013. thirty-nine retrieved practice guidelines were included for quality appraisal by the Appraisal of Guidelines Research and Evaluation II (AGREE-II) tool, performed by two independent reviewers. From the 12 moderate-to-high quality guidelines included, specific practice recommendations for the diagnosis and/or management of any aspect of dementia were extracted for comparison based upon the level of evidence and strength of recommendation. there was a general agreement between guidelines for many practice recommendations. However, direct comparisons between guidelines were challenging due to variations in grading schemes. © The Author 2014. Published by Oxford University Press on behalf of the British Geriatrics Society. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Protective effects of ethanol extracts of Artemisia asiatica Nakai ex Pamp. on ageing-induced deterioration in mouse oocyte quality.

PubMed

Jeon, Hyuk-Joon; You, Seung Yeop; Kim, Dong Hyun; Jeon, Hong Bae; Oh, Jeong Su

2017-08-01

Following ovulation, oocytes undergo a time-dependent deterioration in quality referred to as post-ovulatory ageing. Although various factors influence the post-ovulatory ageing of oocytes, oxidative stress is a key factor involved in deterioration of oocyte quality. Artemisia asiatica Nakai ex Pamp. has been widely used in East Asia as a food ingredient and traditional medicine for the treatment of inflammation, cancer, and microbial infections. Recent studies have shown that A. asiatica exhibits antioxidative effects. In this study, we investigated whether A. asiatica has the potential to attenuate deterioration in oocyte quality during post-ovulatory ageing. Freshly ovulated mouse oocytes were cultured with 0, 50, 100 or 200 μg/ml ethanol extracts of A. asiatica Nakai ex Pamp. After culture for up to 24 h, various ageing-induced oocyte abnormalities, including morphological changes, reactive oxygen species (ROS) accumulation, apoptosis, chromosome and spindle defects, and mitochondrial aggregation were determined. Treatment of oocytes with A. asiatica extracts reduced ageing-induced morphological changes. Moreover, A. asiatica extracts decreased ROS generation and the onset of apoptosis by preventing elevation of the Bax/Bcl-2 expression ratio during post-ovulatory ageing. Furthermore, A. asiatica extracts attenuated the ageing-induced abnormalities including spindle defects, chromosome misalignment and mitochondrial aggregation. Our results demonstrate that A. asiatica can relieve deterioration in oocyte quality and delay the onset of apoptosis during post-ovulatory ageing.

Blood cell mRNAs and microRNAs: optimized protocols for extraction and preservation.

PubMed

Eikmans, Michael; Rekers, Niels V; Anholts, Jacqueline D H; Heidt, Sebastiaan; Claas, Frans H J

2013-03-14

Assessing messenger RNA (mRNA) and microRNA levels in peripheral blood cells may complement conventional parameters in clinical practice. Working with small, precious samples requires optimal RNA yields and minimal RNA degradation. Several procedures for RNA extraction and complementary DNA (cDNA) synthesis were compared for their efficiency. The effect on RNA quality of freeze-thawing peripheral blood cells and storage in preserving reagents was investigated. In terms of RNA yield and convenience, quality quantitative polymerase chain reaction signals per nanogram of total RNA and using NucleoSpin and mirVana columns is preferable. The SuperScript III protocol results in the highest cDNA yields. During conventional procedures of storing peripheral blood cells at -180°C and thawing them thereafter, RNA integrity is maintained. TRIzol preserves RNA in cells stored at -20°C. Detection of mRNA levels significantly decreases in degraded RNA samples, whereas microRNA molecules remain relatively stable. When standardized to reference targets, mRNA transcripts and microRNAs can be reliably quantified in moderately degraded (quality index 4-7) and severely degraded (quality index <4) RNA samples, respectively. We describe a strategy for obtaining high-quality and quantity RNA from fresh and stored cells from blood. The results serve as a guideline for sensitive mRNA and microRNA expression assessment in clinical material.

Effect of Plant Age on the Quantity and Quality of Proteins Extracted from Sugar Beet (Beta vulgaris L.) Leaves.

PubMed

Kiskini, Alexandra; Vissers, Anne; Vincken, Jean-Paul; Gruppen, Harry; Wierenga, Peter Alexander

2016-11-09

Effects of the developmental stage (e.g., young, mature, or senescent) of leaves on their chemical composition have been described in the literature. This study focuses on the variation in chemical composition and quantity and quality of proteins extracted from leaves due to variation in plant age (i.e., harvesting time), using leaves from sugar beets grown in a field (Rhino, Arrival) and in a greenhouse (Isabella). Within the same variety (Rhino, field; Arrival, field; Isabella, greenhouse) the protein content was similar for leaves from young and old plants (22 ± 1, 16 ± 1, and 10 ± 3% w/w db, respectively). Variation in final protein isolation yield was mostly due to variation in nitrogen extractability (28-56%), although no consistent correlation with plant age was found. A significant effect of plant age was observed on the quality (color) of the extracted protein, that is, brown (indicative of polyphenol oxidase activity) and yellow for extracts from old and young plants, respectively.

Camera pose refinement by matching uncertain 3D building models with thermal infrared image sequences for high quality texture extraction

NASA Astrophysics Data System (ADS)

Iwaszczuk, Dorota; Stilla, Uwe

2017-10-01

Thermal infrared (TIR) images are often used to picture damaged and weak spots in the insulation of the building hull, which is widely used in thermal inspections of buildings. Such inspection in large-scale areas can be carried out by combining TIR imagery and 3D building models. This combination can be achieved via texture mapping. Automation of texture mapping avoids time consuming imaging and manually analyzing each face independently. It also provides a spatial reference for façade structures extracted in the thermal textures. In order to capture all faces, including the roofs, façades, and façades in the inner courtyard, an oblique looking camera mounted on a flying platform is used. Direct geo-referencing is usually not sufficient for precise texture extraction. In addition, 3D building models have also uncertain geometry. In this paper, therefore, methodology for co-registration of uncertain 3D building models with airborne oblique view images is presented. For this purpose, a line-based model-to-image matching is developed, in which the uncertainties of the 3D building model, as well as of the image features are considered. Matched linear features are used for the refinement of the exterior orientation parameters of the camera in order to ensure optimal co-registration. Moreover, this study investigates whether line tracking through the image sequence supports the matching. The accuracy of the extraction and the quality of the textures are assessed. For this purpose, appropriate quality measures are developed. The tests showed good results on co-registration, particularly in cases where tracking between the neighboring frames had been applied.

RNA-seq transcriptome analysis of formalin fixed, paraffin-embedded canine meningioma

PubMed Central

Grenier, Jennifer K.; Foureman, Polly A.; Sloma, Erica A.

2017-01-01

Meningiomas are the most commonly reported primary intracranial tumor in dogs and humans and between the two species there are similarities in histology and biologic behavior. Due to these similarities, dogs have been proposed as models for meningioma pathobiology. However, little is known about specific pathways and individual genes that are involved in the development and progression of canine meningioma. In addition, studies are lacking that utilize RNAseq to characterize gene expression in clinical cases of canine meningioma. The primary objective of this study was to develop a technique for which high quality RNA can be extracted from formalin-fixed, paraffin embedded tissue and then used for transcriptome analysis to determine patterns of gene expression. RNA was extracted from thirteen canine meningiomas–eleven from formalin fixed and two flash-frozen. These represented six grade I and seven grade II meningiomas based on the World Health Organization classification system for human meningioma. RNA was also extracted from fresh frozen leptomeninges from three control dogs for comparison. RNAseq libraries made from formalin fixed tissue were of sufficient quality to successfully identify 125 significantly differentially expressed genes, the majority of which were related to oncogenic processes. Twelve genes (AQP1, BMPER, FBLN2, FRZB, MEDAG, MYC, PAMR1, PDGFRL, PDPN, PECAM1, PERP, ZC2HC1C) were validated using qPCR. Among the differentially expressed genes were oncogenes, tumor suppressors, transcription factors, VEGF-related genes, and members of the WNT pathway. Our work demonstrates that RNA of sufficient quality can be extracted from FFPE canine meningioma samples to provide biologically relevant transcriptome analyses using a next-generation sequencing technique, such as RNA-seq. PMID:29073243

Quality Matters: Systematic Analysis of Endpoints Related to “Cellular Life” in Vitro Data of Radiofrequency Electromagnetic Field Exposure

PubMed Central

Simkó, Myrtill; Remondini, Daniel; Zeni, Olga; Scarfi, Maria Rosaria

2016-01-01

Possible hazardous effects of radiofrequency electromagnetic fields (RF-EMF) at low exposure levels are controversially discussed due to inconsistent study findings. Therefore, the main focus of the present study is to detect if any statistical association exists between RF-EMF and cellular responses, considering cell proliferation and apoptosis endpoints separately and with both combined as a group of “cellular life” to increase the statistical power of the analysis. We searched for publications regarding RF-EMF in vitro studies in the PubMed database for the period 1995–2014 and extracted the data to the relevant parameters, such as cell culture type, frequency, exposure duration, SAR, and five exposure-related quality criteria. These parameters were used for an association study with the experimental outcome in terms of the defined endpoints. We identified 104 published articles, from which 483 different experiments were extracted and analyzed. Cellular responses after exposure to RF-EMF were significantly associated to cell lines rather than to primary cells. No other experimental parameter was significantly associated with cellular responses. A highly significant negative association with exposure condition-quality and cellular responses was detected, showing that the more the quality criteria requirements were satisfied, the smaller the number of detected cellular responses. According to our knowledge, this is the first systematic analysis of specific RF-EMF bio-effects in association to exposure quality, highlighting the need for more stringent quality procedures for the exposure conditions. PMID:27420084

A no-reference video quality assessment metric based on ROI

NASA Astrophysics Data System (ADS)

Jia, Lixiu; Zhong, Xuefei; Tu, Yan; Niu, Wenjuan

2015-01-01

A no reference video quality assessment metric based on the region of interest (ROI) was proposed in this paper. In the metric, objective video quality was evaluated by integrating the quality of two compressed artifacts, i.e. blurring distortion and blocking distortion. The Gaussian kernel function was used to extract the human density maps of the H.264 coding videos from the subjective eye tracking data. An objective bottom-up ROI extraction model based on magnitude discrepancy of discrete wavelet transform between two consecutive frames, center weighted color opponent model, luminance contrast model and frequency saliency model based on spectral residual was built. Then only the objective saliency maps were used to compute the objective blurring and blocking quality. The results indicate that the objective ROI extraction metric has a higher the area under the curve (AUC) value. Comparing with the conventional video quality assessment metrics which measured all the video quality frames, the metric proposed in this paper not only decreased the computation complexity, but improved the correlation between subjective mean opinion score (MOS) and objective scores.

Determination of caffeoylquinic acids in feed and related products by focused ultrasound solid-liquid extraction and ultra-high performance liquid chromatography-mass spectrometry.

PubMed

Tena, M T; Martínez-Moral, M P; Cardozo, P W

2015-06-26

A method to determine caffeoylquinic acids (CQAs) in three sources (herbal extract, feed additive and finished feed) using for the first time focused ultrasound solid-liquid extraction (FUSLE) followed by ultra-high performance liquid chromatography (UPLC) coupled to quadrupole-time of flight mass spectrometry is presented. Pressurized liquid extraction (PLE) was also tested as extraction technique but it was discarded because cynarin was not stable under temperature values used in PLE. The separation of the CQAs isomers was carried out in only seven minutes. FUSLE variables such as extraction solvent, power and time were optimized by a central composite design. Under optimal conditions, FUSLE extraction was performed with 8mL of an 83:17 methanol-water mixture for 30s at a power of 60%. Only two extraction steps were found necessary to recover analytes quantitatively. Sensitivity, linearity, accuracy and precision were established. Matrix effect was studied for each type of sample. It was not detected for mono-CQAs, whereas the cynarin signal was strongly decreased due to ionization suppression in presence of matrix components; so the quantification by standard addition was mandatory for the determination of di-caffeoylquinic acids. Finally, the method was applied to the analysis of herbal extracts, feed additives and finished feed. In all samples, chlorogenic acid was the predominant CQA, followed by criptochlorogenic acid, neochlorogenic acid and cynarin. The method allows an efficient determination of chlorogenic acid with good recovery rates. Therefore, it may be used for screening of raw material and for process and quality control in feed manufacture. Copyright © 2015 Elsevier B.V. All rights reserved.

HPLC Quantification of astaxanthin and canthaxanthin in Salmonidae eggs.

PubMed

Tzanova, Milena; Argirova, Mariana; Atanasov, Vasil

2017-04-01

Astaxanthin and canthaxanthin are naturally occurring antioxidants referred to as xanthophylls. They are used as food additives in fish farms to improve the organoleptic qualities of salmonid products and to prevent reproductive diseases. This study reports the development and single-laboratory validation of a rapid method for quantification of astaxanthin and canthaxanthin in eggs of rainbow trout (Oncorhynchus mykiss) and brook trout (Salvelinus fontinalis М.). An advantage of the proposed method is the perfect combination of selective extraction of the xanthophylls and analysis of the extract by high-performance liquid chromatography and photodiode array detection. The method validation was carried out in terms of linearity, accuracy, precision, recovery and limits of detection and quantification. The method was applied for simultaneous quantification of the two xanthophylls in eggs of rainbow trout and brook trout after their selective extraction. The results show that astaxanthin accumulations in salmonid fish eggs are larger than those of canthaxanthin. As the levels of these two xanthophylls affect fish fertility, this method can be used to improve the nutritional quality and to minimize the occurrence of the M74 syndrome in fish populations. Copyright © 2016 John Wiley & Sons, Ltd.

Wire bonding quality monitoring via refining process of electrical signal from ultrasonic generator

NASA Astrophysics Data System (ADS)

Feng, Wuwei; Meng, Qingfeng; Xie, Youbo; Fan, Hong

2011-04-01

In this paper, a technique for on-line quality detection of ultrasonic wire bonding is developed. The electrical signals from the ultrasonic generator supply, namely, voltage and current, are picked up by a measuring circuit and transformed into digital signals by a data acquisition system. A new feature extraction method is presented to characterize the transient property of the electrical signals and further evaluate the bond quality. The method includes three steps. First, the captured voltage and current are filtered by digital bandpass filter banks to obtain the corresponding subband signals such as fundamental signal, second harmonic, and third harmonic. Second, each subband envelope is obtained using the Hilbert transform for further feature extraction. Third, the subband envelopes are, respectively, separated into three phases, namely, envelope rising, stable, and damping phases, to extract the tiny waveform changes. The different waveform features are extracted from each phase of these subband envelopes. The principal components analysis (PCA) method is used for the feature selection in order to remove the relevant information and reduce the dimension of original feature variables. Using the selected features as inputs, an artificial neural network (ANN) is constructed to identify the complex bond fault pattern. By analyzing experimental data with the proposed feature extraction method and neural network, the results demonstrate the advantages of the proposed feature extraction method and the constructed artificial neural network in detecting and identifying bond quality.

Effect of various stabilizing agents on Imperata cylindrica grass pollen allergen extract.

PubMed

Bijli, K M; Singh, B P; Sridhara, S; Gaur, S N; Arora, N

2003-01-01

Allergen extracts are unstable, heat labile or susceptible to proteases. Stability of allergen extracts is important for proper diagnosis and therapy of allergic disorders. The present study was undertaken to determine the preservation and stabilization conditions of Imperata cylindrica (Ic) grass pollen extract. The Ic extract was kept with 0.1 mepsilon-aminocaproic acid (EACA), 0.75 m sucrose, 5% glycerol, 0.03% human serum albumin (HSA) or 0.4% phenol for different time periods. The extracts were stored for 3, 6 and 12 months each at 4 degrees C, 4 degrees C with daily exposure to room temperature (RT) for 1 h, and RT. The quality of extracts was analysed by SDS-PAGE, Western blot, ELISA, ELISA inhibition and skin test. Extracts kept with EACA and sucrose retained most of the protein bands followed by glycerol as determined by SDS-PAGE and Western blot during all storage periods and conditions in comparison with standard extracts. The extracts kept with HSA, phenol and without preservative (WP) showed protein degradation below 33 kDa after 3 months storage at all conditions. However, a 67-kDa allergen was stable in these extracts. EACA extract required 75 to 120 ng of protein for 50% inhibition in IgE binding under different conditions, whereas standard extract required 70 ng for the same. ELISA also demonstrated high allergenic reactivity of EACA extract. ID test on allergy patients with EACA extract demonstrated same allergenic potency as that of standard extract. EACA is the best preservative/stabilizing agent of Ic pollen extract, followed by sucrose and glycerol. Ic extract kept with phenol, HSA and without preservative showed degradation within 3 months. EACA preserved extract is equally potent as that of standard extract up to 1 year's storage.

Effect of the type of brewing water on the chemical composition, sensory quality and antioxidant capacity of Chinese teas.

PubMed

Xu, Yong-Quan; Zou, Chun; Gao, Ying; Chen, Jian-Xin; Wang, Fang; Chen, Gen-Sheng; Yin, Jun-Feng

2017-12-01

The physicochemical characteristics, sensory quality, and antioxidant activity of tea infusions prepared with purified water (PW), mineral water (MW), mountain spring water (MSW), and tap water (TW) from Hangzhou were investigated. The results showed that the taste quality, catechin concentration, and antioxidant capacity of green, oolong, and black tea infusions prepared using MW and TW were significantly lower than those prepared using PW. Extraction of catechins and caffeine was reduced with high-conductivity water, while high pH influenced the stability of catechins. PW and MSW were more suitable for brewing green and oolong teas, while MSW, with low pH and moderate ion concentration, was the most suitable water for brewing black tea. Lowering the pH of mineral water partially improved the taste quality and increased the concentration of catechins in the infusions. These results aid selection of the most appropriate water for brewing Chinese teas. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optimization of Shea (Vitellaria paradoxa) butter quality using screw expeller extraction.

PubMed

Gezahegn, Yonas A; Emire, Shimelis A; Asfaw, Sisay F

2016-11-01

The quality of Shea butter is highly affected by processing factors. Hence, the aim of this work was to evaluate the effects of conditioning duration (CD), moisture content (MC), and die temperature (DT) of screw expeller on Shea butter quality. A combination of 3 3 full factorial design and response surface methodology was used for this investigation. Response variables were refractive index, acid value, and peroxide value. The model enabled to identify the optimum operating settings (CD = 28-30 min, MC = 3-5 g/100 g, and DT = 65-70°C) for maximize refractive index and minimum acid value. For minimum peroxide value 0 min CD, 10 g/100 g MC, and 30°C were discovered. In all-over optimization, optimal values of 30 min CD, 9.7 g/100 g MC, and 70°C DT were found. Hence, the processing factors must be at their optimal values to achieve high butter quality and consistence.

Quantitation of tamsulosin in human plasma by liquid chromatography-electrospray ionization mass spectrometry.

PubMed

Din, Li; Li, Limin; Tao, Ping; Yang, Jin; Zhang, Zhengxing

2002-02-05

A highly sensitive method for quantitation of tamsulosin in human plasma using 1-(2,6-dimethyl-3-hydroxylphenoxy)-2-(3,4-methoxyphenylethylamino)-propane hydrochloride as the internal standard (I.S.) was established using liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS). After alkalization with saturated sodium bicarbonate, plasma were extracted by ethyl acetate and separated by HPLC on a C18 reversed-phase column using a mobile phase of methanol-water-acetic acid-triethylamine (620:380:1.5:1.5, v/v). Analytes were quantitated using positive electrospray ionization in a quadrupole spectrometer. LC-ESI-MS was performed in the selected ion monitoring (SIM) mode using target ions at m/z 228 for tamsulosin and m/z 222 for the I.S. Calibration curves, which were linear over the range 0.2-30 ng/ml, were analyzed contemporaneously with each batch of samples, along with low (0.5 ng/ml), medium (3 ng/ml) and high (30 ng/ml) quality control samples. The intra- and inter-assay variability ranged from 2.14 to 8.87% for the low, medium and high quality control samples. The extraction recovery of tamsulosin from plasma was in the range of 84.2-94.5%. The method has been used successfully to study tamsulosin pharmacokinetics in adult humans.

Extracting transient Rayleigh wave and its application in detecting quality of highway roadbed

USGS Publications Warehouse

Liu, J.; Xia, J.; Luo, Y.; Li, X.; Xu, S.; ,

2004-01-01

This paper first explains the tau-p mapping method of extracting Rayleigh waves (LR waves) from field shot gathers. It also explains a mathematical model of physical character parameters of quality of high-grade roads. This paper then discusses an algorithm of computing dispersion curves using adjacent channels. Shear velocity and physical character parameters are obtained by inversion of dispersion curves. The algorithm using adjacent channels to calculating dispersion curves eliminates average effects that exist by using multi-channels to obtain dispersion curves so that it improves longitudinal and transverse resolution of LR waves and precision of non-invasive detection, and also broadens its application fields. By analysis of modeling results of detached computation of the ground roll and real examples of detecting density and pressure strength of a high-grade roadbed, and by comparison of shallow seismic image method with borehole cores, we concluded that: 1 the abnormal scale and configuration obtained by LR waves are mostly the same as the result of shallow seismic image method; 2 an average relative error of density obtained from LR waves inversion is 1.6% comparing with borehole coring; 3 transient LR waves in detecting density and pressure strength of a high-grade roadbed is feasible and effective.

Isocratic non-aqueous reversed-phase high-performance liquid chromatographic separation of capsanthin and capsorubin in red peppers (Capsicum annuum L.), paprika and oleoresin.

PubMed

Weissenberg, M; Schaeffler, I; Menagem, E; Barzilai, M; Levy, A

1997-01-03

A simple, rapid high-performance liquid chromatography method has been devised in order to separate and quantify the xanthophylls capsorubin and capasanthin present in red pepper (Capsicum annuum L.) fruits and preparations made from them (paprika and oleoresin). A reversed-phase isocratic non-aqueous system allows the separation of xanthophylls within a few minutes, with detection at 450 nm, using methyl red as internal standard to locate the various carotenoids and xanthophylls found in plant extracts. The selection of extraction solvents, mild saponification conditions, and chromatographic features is evaluated and discussed. The method is proposed for rapid screening of large plant populations, plant selection, as well as for paprika products and oleoresin, and also for nutrition and quality control studies.

'First 1000 days' health interventions in low- and middle-income countries: alignment of South African policies with high-quality evidence.

PubMed

English, René; Peer, Nazia; Honikman, Simone; Tugendhaft, Aviva; Hofman, Karen J

2017-01-01

In South Africa (SA), despite adoption of international strategies and approaches, maternal, neonatal and child (MNC) morbidity and mortality rates have not sufficiently declined. To conduct an umbrella review (UR) that identifies interventions in low- and middle-income countries, with a high-quality evidence base, that improve MNC morbidity and mortality outcomes within the first 1000 days of life; and to assess the incorporation of the evidence into local strategies, guidelines and documents. We included publications about women and children in the first 1000 days of life; healthcare professionals and community members. Comparators were those who did not receive the intervention. Interventions were pharmacological and non-pharmacological. Outcomes were MNC morbidity and mortality. Authors conducted English language electronic and manual searches (2000-2013). The quality of systematic reviews and meta-analyses (SRs/MAs) were reviewed. Interventions were ranked according to level of evidence; and then aligned with SA strategies, policies and guidelines. A tool to extract data was developed and used by two authors who independently extracted data. Summary measures from MAs or summaries of SRs were reviewed and the specificities of the various interventions listed. A search of all local high-level documents was done and these were assessed to determine the specificities of the recommendations and their alignment to the evidence. In total, 19 interventions presented in 32 SRs were identified. Overall, SA's policymakers have sufficiently included high-quality evidence-based interventions into local policies. However, optimal period of birth spacing (two to five years) is not explicitly promoted nor was ante- and postnatal depression adequately incorporated. Antenatal care visits should be increased from four to about eight according to the evidence. Incorporation of existing evidence into policies can be strengthened in SA. The UR methods are useful to inform policymaking and identify research gaps. RESPONSIBLE EDITOR Nawi Ng, Umeå University, Sweden.

‘First 1000 days’ health interventions in low- and middle-income countries: alignment of South African policies with high-quality evidence

PubMed Central

English, René; Peer, Nazia; Honikman, Simone; Tugendhaft, Aviva; Hofman, Karen J

2017-01-01

ABSTRACT Background: In South Africa (SA), despite adoption of international strategies and approaches, maternal, neonatal and child (MNC) morbidity and mortality rates have not sufficiently declined. Objectives: To conduct an umbrella review (UR) that identifies interventions in low- and middle-income countries, with a high-quality evidence base, that improve MNC morbidity and mortality outcomes within the first 1000 days of life; and to assess the incorporation of the evidence into local strategies, guidelines and documents. Methods: We included publications about women and children in the first 1000 days of life; healthcare professionals and community members. Comparators were those who did not receive the intervention. Interventions were pharmacological and non-pharmacological. Outcomes were MNC morbidity and mortality. Authors conducted English language electronic and manual searches (2000–2013). The quality of systematic reviews and meta-analyses (SRs/MAs) were reviewed. Interventions were ranked according to level of evidence; and then aligned with SA strategies, policies and guidelines. A tool to extract data was developed and used by two authors who independently extracted data. Summary measures from MAs or summaries of SRs were reviewed and the specificities of the various interventions listed. A search of all local high-level documents was done and these were assessed to determine the specificities of the recommendations and their alignment to the evidence. Results: In total, 19 interventions presented in 32 SRs were identified. Overall, SA’s policymakers have sufficiently included high-quality evidence-based interventions into local policies. However, optimal period of birth spacing (two to five years) is not explicitly promoted nor was ante- and postnatal depression adequately incorporated. Antenatal care visits should be increased from four to about eight according to the evidence. Conclusion: Incorporation of existing evidence into policies can be strengthened in SA. The UR methods are useful to inform policymaking and identify research gaps. RESPONSIBLE EDITOR Nawi Ng, Umeå University, Sweden PMID:28715934

Differentiating the Spatiotemporal Distribution of Natural and Anthropogenic Processes on River Water-Quality Variation Using a Self-Organizing Map With Factor Analysis.

PubMed

Wang, Yeuh-Bin; Liu, Chen-Wuing; Lee, Jin-Jing

2015-08-01

To elucidate the historical improvement and advanced measure of river water quality in the Taipei metropolitan area, this study applied the self-organizing map (SOM) technique with factor analysis (FA) to differentiate the spatiotemporal distribution of natural and anthropogenic processes on river water-quality variation spanning two decades. The SOM clustered river water quality into five groups: very low pollution, low pollution, moderate pollution, high pollution, and very high pollution. FA was then used to extract four latent factors that dominated water quality from 1991 to 2011 including three anthropogenic process factors (organic, industrial, and copper pollution) and one natural process factor [suspended solids (SS) pollution]. The SOM revealed that the water quality improved substantially over time. However, the downstream river water quality was still classified as high pollution because of an increase in anthropogenic activity. FA showed the spatiotemporal pattern of each factor score decreasing over time, but the organic pollution factor downstream of the Tamsui River, as well as the SS factor scores in the upstream major tributary (the Dahan Stream), remained within the high pollution level. Therefore, we suggest that public sewage-treatment plants should be upgraded from their current secondary biological processing to advanced treatment processing. The conservation of water and soil must also be reinforced to decrease the SS loading of the Dahan Stream from natural erosion processes in the future.

Determination of four major saponins in the seeds of Aesculus chinensis Bunge using accelerated solvent extraction followed by high-performance liquid chromatography and electrospray-time of flight mass spectrometry.

PubMed

Chen, Junhui; Li, Wenlong; Yang, Baijuan; Guo, Xiuchun; Lee, Frank Sen-Chun; Wang, Xiaoru

2007-07-23

A new method based on accelerated solvent extraction (ASE) followed by a reliable high-performance liquid chromatography-diode array detector (HPLC-DAD) and positive ion electrospray-time of flight mass spectrometry (ESI-TOF/MS) analysis has been developed for the characterization and quantification of four major saponins in extracts of the seeds of Aesculus chinensis Bunge (semen aesculi). The saponins escin Ia, escin Ib, isoescin Ia and isoescin Ib were extracted from seeds of A. chinesis Bunge via ASE, and the operational parameters of ASE were optimized, such as extraction solvent, extraction temperature, static extraction time and extraction cycles. The optimized procedure employed 70% MeOH as extraction solvent, 120 degrees C of extraction temperature, 7 min of static extraction time, 60% flush volume and the extraction recoveries of the four compounds were nearly to 100% for two cycles. The HPLC conditions are as follows: SinoChrom ODS BP C18 (4.6 mm x 200 mm, 5 microm) column, acetonitrile and 0.10% phosphoric acid solution as mobile phase, flow rate is 1.0 mL min(-1), detection length of UV is 203 nm, injection volume is 10 microL. The results indicated that the developed HPLC method is simple, sensitive and reliable for the determination of four major saponins in seeds of A. chinesis Bunge with a good linearity (r2 > 0.9994), precision (relative standard deviation (R.S.D.) < 1.5%) and the recovery ranges of 95.2-97.3%. The limits of detection (LOD) of the four compounds were in the range of 0.40-0.75 microg mL(-1). This assay can be readily utilized as a quality control method for semen aesculi and other related medicinal plants.

Effect of room temperature transport vials on DNA quality and phylogenetic composition of faecal microbiota of elderly adults and infants.

PubMed

Hill, Cian J; Brown, Jillian R M; Lynch, Denise B; Jeffery, Ian B; Ryan, C Anthony; Ross, R Paul; Stanton, Catherine; O'Toole, Paul W

2016-05-10

Alterations in intestinal microbiota have been correlated with a growing number of diseases. Investigating the faecal microbiota is widely used as a non-invasive and ethically simple proxy for intestinal biopsies. There is an urgent need for collection and transport media that would allow faecal sampling at distance from the processing laboratory, obviating the need for same-day DNA extraction recommended by previous studies of freezing and processing methods for stool. We compared the faecal bacterial DNA quality and apparent phylogenetic composition derived using a commercial kit for stool storage and transport (DNA Genotek OMNIgene GUT) with that of freshly extracted samples, 22 from infants and 20 from older adults. Use of the storage vials increased the quality of extracted bacterial DNA by reduction of DNA shearing. When infant and elderly datasets were examined separately, no differences in microbiota composition were observed due to storage. When the two datasets were combined, there was a difference according to a Wilcoxon test in the relative proportions of Faecalibacterium, Sporobacter, Clostridium XVIII, and Clostridium XlVa after 1 week's storage compared to immediately extracted samples. After 2 weeks' storage, Bacteroides abundance was also significantly different, showing an apparent increase from week 1 to week 2. The microbiota composition of infant samples was more affected than that of elderly samples by storage, with significantly higher Spearman distances between paired freshly extracted and stored samples (p < 0.001). When the microbiota profiles were analysed at the operational taxonomic unit (OTU) level, three infant datasets in the study did not cluster together, while only one elderly dataset did not. The lower microbiota diversity of the infant gut microbiota compared to the elderly gut microbiota (p < 0.001) means that any alteration in the infant datasets has a proportionally larger effect. The commercial storage vials appear to be suitable for high diversity microbiota samples, but may be less appropriate for lower diversity samples. Differences between fresh and stored samples mean that where storage is unavoidable, a consistent storage regime should be used. We would recommend extraction ideally within the first week of storage.

An improved dehazing algorithm of aerial high-definition image

NASA Astrophysics Data System (ADS)

Jiang, Wentao; Ji, Ming; Huang, Xiying; Wang, Chao; Yang, Yizhou; Li, Tao; Wang, Jiaoying; Zhang, Ying

2016-01-01

For unmanned aerial vehicle(UAV) images, the sensor can not get high quality images due to fog and haze weather. To solve this problem, An improved dehazing algorithm of aerial high-definition image is proposed. Based on the model of dark channel prior, the new algorithm firstly extracts the edges from crude estimated transmission map and expands the extracted edges. Then according to the expended edges, the algorithm sets a threshold value to divide the crude estimated transmission map into different areas and makes different guided filter on the different areas compute the optimized transmission map. The experimental results demonstrate that the performance of the proposed algorithm is substantially the same as the one based on dark channel prior and guided filter. The average computation time of the new algorithm is around 40% of the one as well as the detection ability of UAV image is improved effectively in fog and haze weather.

Comparison of Moringa Oleifera seeds oil characterization produced chemically and mechanically

NASA Astrophysics Data System (ADS)

Eman, N. A.; Muhamad, K. N. S.

2016-06-01

It is established that virtually every part of the Moringa oleifera tree (leaves, stem, bark, root, flowers, seeds, and seeds oil) are beneficial in some way with great benefits to human being. The tree is rich in proteins, vitamins, minerals. All Moringa oleifera food products have a very high nutritional value. They are eaten directly as food, as supplements, and as seasonings as well as fodder for animals. The purpose of this research is to investigate the effect of seeds particle size on oil extraction using chemical method (solvent extraction). Also, to compare Moringa oleifera seeds oil properties which are produced chemically (solvent extraction) and mechanically (mechanical press). The Moringa oleifera seeds were grinded, sieved, and the oil was extracted using soxhlet extraction technique with n-Hexane using three different size of sample (2mm, 1mm, and 500μm). The average oil yield was 36.1%, 40.80%, and 41.5% for 2mm, 1mm, and 500μm particle size, respectively. The properties of Moringa oleifera seeds oil were: density of 873 kg/m3, and 880 kg/m3, kinematic viscosity of 42.2mm2/s and 9.12mm2/s for the mechanical and chemical method, respectively. pH, cloud point and pour point were same for oil produced with both methods which is 6, 18°C and 12°C, respectively. For the fatty acids, the oleic acid is present with high percentage of 75.39%, and 73.60% from chemical and mechanical method, respectively. Other fatty acids are present as well in both samples which are (Gadoleic acid, Behenic acid, Palmitic acid) which are with lower percentage of 2.54%, 5.83%, and 5.73%, respectively in chemical method oil, while they present as 2.40%, 6.73%, and 6.04%, respectively in mechanical method oil. In conclusion, the results showed that both methods can produce oil with high quality. Moringa oleifera seeds oil appear to be an acceptable good source for oil rich in oleic acid which is equal to olive oil quality, that can be consumed in Malaysia where the olive oil is imported with high prices. In the same time cultivation of Moringa oleifera tree is considered to be a new source of income for the country and give more job opportunities.

Image quality improvement in cone-beam CT using the super-resolution technique.

PubMed

Oyama, Asuka; Kumagai, Shinobu; Arai, Norikazu; Takata, Takeshi; Saikawa, Yusuke; Shiraishi, Kenshiro; Kobayashi, Takenori; Kotoku, Jun'ichi

2018-04-05

This study was conducted to improve cone-beam computed tomography (CBCT) image quality using the super-resolution technique, a method of inferring a high-resolution image from a low-resolution image. This technique is used with two matrices, so-called dictionaries, constructed respectively from high-resolution and low-resolution image bases. For this study, a CBCT image, as a low-resolution image, is represented as a linear combination of atoms, the image bases in the low-resolution dictionary. The corresponding super-resolution image was inferred by multiplying the coefficients and the high-resolution dictionary atoms extracted from planning CT images. To evaluate the proposed method, we computed the root mean square error (RMSE) and structural similarity (SSIM). The resulting RMSE and SSIM between the super-resolution images and the planning CT images were, respectively, as much as 0.81 and 1.29 times better than those obtained without using the super-resolution technique. We used super-resolution technique to improve the CBCT image quality.

GoGene: gene annotation in the fast lane.

PubMed

Plake, Conrad; Royer, Loic; Winnenburg, Rainer; Hakenberg, Jörg; Schroeder, Michael

2009-07-01

High-throughput screens such as microarrays and RNAi screens produce huge amounts of data. They typically result in hundreds of genes, which are often further explored and clustered via enriched GeneOntology terms. The strength of such analyses is that they build on high-quality manual annotations provided with the GeneOntology. However, the weakness is that annotations are restricted to process, function and location and that they do not cover all known genes in model organisms. GoGene addresses this weakness by complementing high-quality manual annotation with high-throughput text mining extracting co-occurrences of genes and ontology terms from literature. GoGene contains over 4,000,000 associations between genes and gene-related terms for 10 model organisms extracted from more than 18,000,000 PubMed entries. It does not cover only process, function and location of genes, but also biomedical categories such as diseases, compounds, techniques and mutations. By bringing it all together, GoGene provides the most recent and most complete facts about genes and can rank them according to novelty and importance. GoGene accepts keywords, gene lists, gene sequences and protein sequences as input and supports search for genes in PubMed, EntrezGene and via BLAST. Since all associations of genes to terms are supported by evidence in the literature, the results are transparent and can be verified by the user. GoGene is available at http://gopubmed.org/gogene.

Thermal stability of liquid antioxidative extracts from pomegranate peel.

PubMed

Qu, Wenjuan; Li, Pingping; Hong, Jihua; Liu, Zhiling; Chen, Yufang; Breksa, Andrew P; Pan, Zhongli

2014-03-30

Liquid extracts from pomegranate peel have the potential for use as natural antioxidant products. This study investigates the quality changes of liquid extracts before and after thermal treatment during sterilization and storage. Liquid pomegranate peel extracts were prepared, sterilized under ultra-high temperature (UHT) at 121 °C for 10 s and then stored at three temperatures (4, 25 and 37 °C) for up to 180 days. The industrial, color, UV-visible spectrum profile and antioxidant (phenolics) characteristics were measured. Thermal sterilization treatment had no negative effects on the industrial, color, spectral and antioxidant characteristics of the extracts. After 180 days, the extracts stored at 4 °C retained 67% of the initial total soluble phenolic content and 58% of the original scavenging activity. The major antioxidant components in the extracts (stored at 4 °C for 180 days) were gallic acid, punicalagin A, punicalagin B and ellagic acid having concentrations of 19.3, 197.2, 221.1 and 92.4 mg L⁻¹, respectively. The results show that liquid pomegranate peel extracts had acceptable thermal stability after sterilization and storage. The recommended storage condition of this product was low temperature. © 2013 Society of Chemical Industry.

Case-based learning in education of Traditional Chinese Medicine: a systematic review.

PubMed

Chen, Ji; Li, Ying; Tang, Yong; Zeng, Fang; Wu, Xi; Liang, Fanrong

2013-10-01

To assess the effect of case-based learning (CBL) in the education of Traditional Chinese Medicine (TCM). The studies concerning TCM courses designed with CBL were included by searching the databases of EBSCO, Pubmed, Science Citation Index, China National Knowledge Infrastructure, Chongqing VIP database. The valid data was extracted in accordance with the included criteria. The quality of the studies was assessed with Gemma Flores-Masteo. A total of 22 articles were retrieved that met the selection criteria: one was of high quality; two were of low quality; the rest were categorized as moderate quality. The majority of the studies demonstrated the better effect produced by CBL, while a few studies showed no difference, compared with the didactic format. All included studies confirmed the favorable effect on learners' attitude, skills and ability. CBL showed the desirable results in achieving the goal of learning. Compared to didactic approach, it played a more active role in promoting students' competency. Since the quality of the articles on which the study was based was not so high, the findings still need further research to become substantiated.

AN EVALUATION OF SAMPLE DISPERSION MEDIAS USED WITH ACCELERATED SOLVENT EXTRACTION FOR THE EXTRACTION AND RECOVERY OF ARSENICALS FROM LFB AND DORM-2

EPA Science Inventory

An accelerated solvent extraction (ASE) device was evaluated as a semi-automated means for extracting arsenicals from quality control (QC) samples and DORM-2 [standard reference material (SRM)]. Unlike conventional extraction procedures, the ASE requires that the sample be dispe...

Effects of lipid extraction on nutritive composition of winged bean (Psophocarpus tetragonolobus), rubber seed (Hevea brasiliensis), and tropical almond (Terminalia catappa).

PubMed

Jayanegara, Anuraga; Harahap, Rakhmad P; Rozi, Richard F; Nahrowi

2018-04-01

This experiment aimed to evaluate the nutritive composition and in vitro rumen fermentability and digestibility of intact and lipid-extracted winged bean, rubber seed, and tropical almond. Soybean, winged bean, rubber seed, and tropical almond were subjected to lipid extraction and chemical composition determination. Lipid extraction was performed through solvent extraction by Soxhlet procedure. Non-extracted and extracted samples of these materials were evaluated for in vitro rumen fermentation and digestibility assay using rumen: Buffer mixture. Parameters measured were gas production kinetics, total volatile fatty acid (VFA) concentration, ammonia, in vitro dry matter (IVDMD) and in vitro organic matter digestibility (IVOMD). Data were analyzed by analysis of variance and Duncan's multiple range test. Soybean, winged bean, rubber seed, and tropical almond contained high amounts of ether extract, i.e., above 20% DM. Crude protein contents of soybean, winged bean, rubber seed, and tropical almond increased by 17.7, 4.7, 55.2, and 126.5% after lipid extraction, respectively. In vitro gas production of intact winged bean was the highest among other materials at various time point intervals (p<0.05), followed by soybean > rubber seed > tropical almond. Extraction of lipid increased in vitro gas production, total VFA concentration, IVDMD, and IVOMD of soybean, winged bean, rubber seed, and tropical almond (p<0.05). After lipid extraction, all feed materials had similar IVDMD and IVOMD values. Lipid extraction improved the nutritional quality of winged bean, rubber seed, and tropical almond.

Effects of dietary marigold extract supplementation on growth performance, pigmentation, antioxidant capacity and meat quality in broiler chickens.

PubMed

Wang, Shuhao; Zhang, Lin; Li, Jiaolong; Cong, Jiahui; Gao, Feng; Zhou, Guanghong

2017-01-01

This experiment was conducted to investigate the effects of dietary supplementation with marigold extract on growth performance, pigmentation, antioxidant capacity and meat quality in broiler chickens. A total of 320 one-day-old Arbor Acres chickens were randomly divided into 5 groups with 8 replicates of 8 chickens each. The chickens of control group were fed with basal diet and other experimental groups were fed with basal diet supplemented with 0.075%, 0.15%, 0.30%, and 0.60% marigold extract respectively (the corresponding concentrations of lutein were 15, 30, 60, and 120 mg/kg). The results showed that marigold extract supplementation increased the yellowness values of shank, beak, skin and muscle and the redness (a*) value of thigh muscle (linear, p<0.01). Marigold extract supplementation significantly increased the total antioxidant capacity, and the activities of superoxide dismutase in liver and thigh muscle (linear, p<0.01) and significantly decreased the malondialdehyde contents of liver and thigh muscle (linear, p<0.01). Marigold extract supplementation significantly decreased the drip loss and shear force of thigh muscles (linear, p<0.01). There was no significant effect on growth performance with marigold extract supplementation. In conclusion, dietary supplementation of marigold extract significantly increased the yellowness values of carcass, antioxidant capacity and meat quality in broiler chickens.

Effects of dietary marigold extract supplementation on growth performance, pigmentation, antioxidant capacity and meat quality in broiler chickens

PubMed Central

Wang, Shuhao; Zhang, Lin; Li, Jiaolong; Cong, Jiahui; Gao, Feng; Zhou, Guanghong

2017-01-01

Objective This experiment was conducted to investigate the effects of dietary supplementation with marigold extract on growth performance, pigmentation, antioxidant capacity and meat quality in broiler chickens. Methods A total of 320 one-day-old Arbor Acres chickens were randomly divided into 5 groups with 8 replicates of 8 chickens each. The chickens of control group were fed with basal diet and other experimental groups were fed with basal diet supplemented with 0.075%, 0.15%, 0.30%, and 0.60% marigold extract respectively (the corresponding concentrations of lutein were 15, 30, 60, and 120 mg/kg). Results The results showed that marigold extract supplementation increased the yellowness values of shank, beak, skin and muscle and the redness (a*) value of thigh muscle (linear, p<0.01). Marigold extract supplementation significantly increased the total antioxidant capacity, and the activities of superoxide dismutase in liver and thigh muscle (linear, p<0.01) and significantly decreased the malondialdehyde contents of liver and thigh muscle (linear, p<0.01). Marigold extract supplementation significantly decreased the drip loss and shear force of thigh muscles (linear, p<0.01). There was no significant effect on growth performance with marigold extract supplementation. Conclusion In conclusion, dietary supplementation of marigold extract significantly increased the yellowness values of carcass, antioxidant capacity and meat quality in broiler chickens. PMID:27282969

Optimization of the incubation time and temperature for spermatozoa extraction in freshwater crayfish Pontastacus leptodactylus (Eschscholtz, 1823).

PubMed

Farhadi, Ardavan; Harlıoğlu, Muzaffer Mustafa; Gür, Seyfettin; Acısu, Tutku Can

2018-06-01

Determination and control of spermatozoa quality in crustacean aquaculture is an important issue for successful and controlled reproduction. Investigation of spermatozoa number in spermatophores is a basic and common parameter for determining the reproductive quality in farmed decapods. In the present study, spermatozoa extraction from spermatophores located in the ductus deferens was conducted in Pontastacus leptodactylus using different incubation times and temperatures. The results indicate that the duration of incubation and temperature affected (P < 0.05) spermatozoa extraction. Greater temperatures (40 and 75 °C) resulted in a reduction (P < 0.05) in number of extracted spermatozoa. In contrast, more spermatozoa were extracted when the 4 and 23 °C temperatures were imposed. After 4 h of incubation, the number of extracted spermatozoa were greatest in number at 23 °C. In conclusion, the greater numbers of crayfish spermatozoa can be obtained when the ductus deferens containing spermatophores is incubated at 23 °C for 4 h as compared with other temperatures and incubation durations. The results of present study are useful for assessing spermatozoa quality in aquaculture as well as the extraction of spermatozoa for research purposes. Copyright © 2018 Elsevier B.V. All rights reserved.

Optimization of microwave assisted extraction of essential oils from Iranian Rosmarinus officinalis L. using RSM.

PubMed

Akhbari, Maryam; Masoum, Saeed; Aghababaei, Fahimeh; Hamedi, Sepideh

2018-06-01

In this study, the efficiencies of conventional hydro-distillation and novel microwave hydro-distillation methods in extraction of essential oil from Rosemary officinalis leaves have been compared. In order to attain the best yield and also highest quality of the essential oil in the microwave assisted method, the optimal values of operating parameters such as extraction time, microwave irradiation power and water volume to plant mass ratio were investigated using central composite design under response surface methodology. Optimal conditions for obtaining the maximum extraction yield in the microwave assisted method were predicted as follows: extraction time of 85 min, microwave power of 888 W, and water volume to plant mass ratio of 0.5 ml/g. The extraction yield at these predicted conditions was computed as 0.7756%. The qualities of the obtained essential oils under designed experiments were optimized based on total contents of four major compounds (α-pinene, 1,8-cineole, camphor and verbenone) which determined by gas chromatography equipped with mass spectroscopy (GC-MS). The highest essential oil quality (55.87%) was obtained at extraction time of 68 min; microwave irradiation power of 700 W; and water volume to plant mass ratio of zero.

Effect of mechanical extraction parameters on the yield and quality of tobacco (Nicotiana tabacum L.) seed oil.

PubMed

Sannino, M; Del Piano, L; Abet, Massimo; Baiano, S; Crimaldi, M; Modestia, F; Raimo, F; Ricciardiello, G; Faugno, S

2017-11-01

The aim of this study was to investigate how the combination of extraction parameters, such as extraction temperature seeds preheating and screw rotation speed, influenced the yield and chemical quality of tobacco seed oil (TSO). For its peculiar properties, TSO can be used for several purposes, as raw material in the manufacturing of soap, paints, resins, lubricants, biofuels and also as edible oil. TSO was obtained using a mechanical screw press and the quality of the oil was evaluated by monitoring the free fatty acids (FFA), the peroxide value (PV), the spectroscopic indices K 232 , K 270 and ΔK and the fatty acid composition. The maximum extraction yield, expressed as percent of oil mechanically extracted respect to the oil content in the seeds, determined by solvent extraction, was obtained with the combination of the highest extraction temperature, the slowest screw rotation speed and seeds preheating. Under these conditions yield was 80.28 ± 0.33% (w/w), 25% higher than the lowest yield obtained among investigated conditions. The extraction temperature and seed preheating showed a significant effect on FFA, on spectroscopic indices K 232 , K 270 and ΔK values. The average values of these parameters slightly increased rising the temperature and in presence of preheating, the screw rotation speed did not affect the chemical characteristic tested. In the extraction conditions investigated no significant changes in PV and fatty acids composition of oil were observed.

Systematic review of scope and quality of electronic patient record data in primary care

PubMed Central

Thiru, Krish; Hassey, Alan; Sullivan, Frank

2003-01-01

Objective To systematically review measures of data quality in electronic patient records (EPRs) in primary care. Design Systematic review of English language publications, 1980-2001. Data sources Bibliographic searches of medical databases, specialist medical informatics databases, conference proceedings, and institutional contacts. Study selection Studies selected according to a predefined framework for categorising review papers. Data extraction Reference standards and measurements used to judge quality. Results Bibliographic searches identified 4589 publications. After primary exclusions 174 articles were classified, 52 of which met the inclusion criteria for review. Selected studies were primarily descriptive surveys. Variability in methods prevented meta-analysis of results. Forty eight publications were concerned with diagnostic data, 37 studies measured data quality, and 15 scoped EPR quality. Reliability of data was assessed with rate comparison. Measures of sensitivity were highly dependent on the element of EPR data being investigated, while the positive predictive value was consistently high, indicating good validity. Prescribing data were generally of better quality than diagnostic or lifestyle data. Conclusion The lack of standardised methods for assessment of quality of data in electronic patient records makes it difficult to compare results between studies. Studies should present data quality measures with clear numerators, denominators, and confidence intervals. Ambiguous terms such as “accuracy” should be avoided unless precisely defined. PMID:12750210

Fuzzy Logic-based expert system for evaluating cake quality of freeze-dried formulations.

PubMed

Trnka, Hjalte; Wu, Jian X; Van De Weert, Marco; Grohganz, Holger; Rantanen, Jukka

2013-12-01

Freeze-drying of peptide and protein-based pharmaceuticals is an increasingly important field of research. The diverse nature of these compounds, limited understanding of excipient functionality, and difficult-to-analyze quality attributes together with the increasing importance of the biosimilarity concept complicate the development phase of safe and cost-effective drug products. To streamline the development phase and to make high-throughput formulation screening possible, efficient solutions for analyzing critical quality attributes such as cake quality with minimal material consumption are needed. The aim of this study was to develop a fuzzy logic system based on image analysis (IA) for analyzing cake quality. Freeze-dried samples with different visual quality attributes were prepared in well plates. Imaging solutions together with image analytical routines were developed for extracting critical visual features such as the degree of cake collapse, glassiness, and color uniformity. On the basis of the IA outputs, a fuzzy logic system for analysis of these freeze-dried cakes was constructed. After this development phase, the system was tested with a new screening well plate. The developed fuzzy logic-based system was found to give comparable quality scores with visual evaluation, making high-throughput classification of cake quality possible. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association.

Isolation of DNA from small amounts of elephant ivory: Sampling the cementum with total demineralization extraction.

PubMed

Winters, M; Torkelson, A; Booth, R; Mailand, C; Hoareau, Y; Tucker, S; Wasser, S K

2018-07-01

Genotyping ivory samples can determine the geographic origin of poached ivory as well as the legality of ivory being sold in ivory markets. We conducted a series of experiments to determine where the DNA is most concentrated in ivory samples and how best to increase DNA yield from groups of samples likely to vary in DNA concentration. We examined variation in DNA amplification success from: the layer(s) of the tusk (cementum and/or dentine) being extracted, demineralization temperature and time, and the concentration of eluates. Since demineralization of the pulverized sample produces a pellet and supernatant, we also assessed DNA amplification success from the pellet, the supernatant, their combination, as well as variation in the respective amounts used for extraction. Our results show that the outer cementum layer of the tusk contains the highest concentration of DNA and should be separated and used exclusively as the source material of ivory processed for extraction, when available. Utilizing the combined demineralized lysate improves extraction efficiency, as does increasing demineralization time to 3 or more days, conducted at 4°C. The most significant improvements occurred for low template DNA ivory samples followed by medium quality samples. Amplification success of high quality samples was not affected by these changes. Application of this optimized method to 3068 ivory samples resulted in 81.2% of samples being confirmed for both alleles at a minimum of 10 out of 16 microsatellite loci, which is our threshold for inclusion in DNA assignment analyses. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Phytochemical composition and antioxidant capacity of Cordia dichotoma seeds.

PubMed

Tian, Shuge; Liu, Feng; Zhang, Xuejia; Upur, Halmuart

2014-09-01

This study aims to determine the phytochemical composition and antioxidant activity of air-dried Cordia dichotoma seeds. Total polyphenolic content was analyzed via the Folin-Ciocalteu method. Total triterpenoid content and amino acids was analyzed colorimetrically. The rosmarinic acid content was examined using high-performance liquid chromatography tandem mass spectrometry. The ethanolic extracts contained polyphenolic compounds (1.0%), triterpenoids (0.075%), amino acids (1.39%), and rosmarinic acid (0.0028%). The results from this study indicate that C. dichotoma seeds are a rich source of polyphenolic compounds and amino acids, which can be used for quality assessment. The ethanolic extract of C. dichotoma seeds has good antioxidant capacity.

An improvement of vehicle detection under shadow regions in satellite imagery

NASA Astrophysics Data System (ADS)

Karim, Shahid; Zhang, Ye; Ali, Saad; Asif, Muhammad Rizwan

2018-04-01

The processing of satellite imagery is dependent upon the quality of imagery. Due to low resolution, it is difficult to extract accurate information according to the requirements of applications. For the purpose of vehicle detection under shadow regions, we have used HOG for feature extraction, SVM is used for classification and HOG is discerned worthwhile tool for complex environments. Shadow images have been scrutinized and found very complex for detection as observed very low detection rates therefore our dedication is towards enhancement of detection rate under shadow regions by implementing appropriate preprocessing. Vehicles are precisely detected under non-shadow regions with high detection rate than shadow regions.