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.

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.

Simultaneous analysis of carotenoids and tocopherols in botanical species using one step solid-liquid extraction followed by high performance liquid chromatography.

PubMed

Valdivielso, Izaskun; Bustamante, María Ángeles; Ruiz de Gordoa, Juan Carlos; Nájera, Ana Isabel; de Renobales, Mertxe; Barron, Luis Javier R

2015-04-15

Carotenoids and tocopherols from botanical species abundant in Atlantic mountain grasslands were simultaneously extracted using one-step solid-liquid phase. A single n-hexane/2-propanol extract containing both types of compounds was injected twice under two different sets of HPLC conditions to separate the tocopherols by normal-phase chromatography and carotenoids by reverse-phase mode. The method allowed reproducible quantification in plant samples of very low amounts of α-, β-, γ- and δ-tocopherols (LOD from 0.0379 to 0.0720 μg g(-1) DM) and over 15 different xanthophylls and carotene isomers. The simplified one-step extraction without saponification significantly increased the recovery of tocopherols and carotenoids, thereby enabling the determination of α-tocopherol acetate in plant samples. The two different sets of chromatographic analysis provided near baseline separation of individual compounds without interference from other lipid compounds extracted from plants, and a very sensitive and accurate detection of tocopherols and carotenoids. The detection of minor individual components in botanical species from grasslands is nowadays of high interest in searching for biomarkers for foods derived from grazing animals. Copyright © 2014 Elsevier Ltd. All rights reserved.

Combining cationic and anionic mixed-mode sorbents in a single cartridge to extract basic and acidic pharmaceuticals simultaneously from environmental waters.

PubMed

Salas, Daniela; Borrull, Francesc; Fontanals, Núria; Marcé, Rosa Maria

2018-01-01

The aim of the present study is to broaden the applications of mixed-mode ion-exchange solid-phase extraction sorbents to extract both basic and acidic compounds simultaneously by combining the sorbents in a single cartridge and developing a simplified extraction procedure. Four different cartridges containing negative and positive charges in the same configuration were evaluated and compared to extract a group of basic, neutral, and acidic pharmaceuticals selected as model compounds. After a thorough optimization of the extraction conditions, the four different cartridges showed to be capable of retaining basic and acidic pharmaceuticals simultaneously through ionic interactions, allowing the introduction of a washing step with 15 mL methanol to eliminate interferences retained by hydrophobic interactions. Using the best combined cartridge, a method was developed, validated, and further applied to environmental waters to demonstrate that the method is promising for the extraction of basic and acidic compounds from very complex samples.

A MISO-ARX-Based Method for Single-Trial Evoked Potential Extraction.

PubMed

Yu, Nannan; Wu, Lingling; Zou, Dexuan; Chen, Ying; Lu, Hanbing

2017-01-01

In this paper, we propose a novel method for solving the single-trial evoked potential (EP) estimation problem. In this method, the single-trial EP is considered as a complex containing many components, which may originate from different functional brain sites; these components can be distinguished according to their respective latencies and amplitudes and are extracted simultaneously by multiple-input single-output autoregressive modeling with exogenous input (MISO-ARX). The extraction process is performed in three stages: first, we use a reference EP as a template and decompose it into a set of components, which serve as subtemplates for the remaining steps. Then, a dictionary is constructed with these subtemplates, and EPs are preliminarily extracted by sparse coding in order to roughly estimate the latency of each component. Finally, the single-trial measurement is parametrically modeled by MISO-ARX while characterizing spontaneous electroencephalographic activity as an autoregression model driven by white noise and with each component of the EP modeled by autoregressive-moving-average filtering of the subtemplates. Once optimized, all components of the EP can be extracted. Compared with ARX, our method has greater tracking capabilities of specific components of the EP complex as each component is modeled individually in MISO-ARX. We provide exhaustive experimental results to show the effectiveness and feasibility of our method.

Selective Extraction of Rare Earth Elements from Permanent Magnet Scraps with Membrane Solvent Extraction.

PubMed

Kim, Daejin; Powell, Lawrence E; Delmau, Lætitia H; Peterson, Eric S; Herchenroeder, Jim; Bhave, Ramesh R

2015-08-18

The rare earth elements (REEs) such as neodymium, praseodymium, and dysprosium were successfully recovered from commercial NdFeB magnets and industrial scrap magnets via membrane assisted solvent extraction (MSX). A hollow fiber membrane system was evaluated to extract REEs in a single step with the feed and strip solutions circulating continuously through the MSX system. The effects of several experimental variables on REE extraction such as flow rate, concentration of REEs in the feed solution, membrane configuration, and composition of acids were investigated with the MSX system. A multimembrane module configuration with REEs dissolved in aqueous nitric acid solutions showed high selectivity for REE extraction with no coextraction of non-REEs, whereas the use of aqueous hydrochloric acid solution resulted in coextraction of non-REEs due to the formation of chloroanions of non-REEs. The REE oxides were recovered from the strip solution through precipitation, drying, and annealing steps. The resulting REE oxides were characterized with XRD, SEM-EDX, and ICP-OES, demonstrating that the membrane assisted solvent extraction is capable of selectively recovering pure REEs from the industrial scrap magnets.

Single-step preparation of selected biological fluids for the high performance liquid chromatographic analysis of fat-soluble vitamins and antioxidants.

PubMed

Lazzarino, Giacomo; Longo, Salvatore; Amorini, Angela Maria; Di Pietro, Valentina; D'Urso, Serafina; Lazzarino, Giuseppe; Belli, Antonio; Tavazzi, Barbara

2017-12-08

Fat-soluble vitamins and antioxidants are of relevance in health and disease. Current methods to extract these compounds from biological fluids mainly need use of multi-steps and multi organic solvents. They are time-consuming and difficult to apply to treat simultaneously large sample number. We here describe a single-step, one solvent extraction of fat-soluble vitamins and antioxidants from biological fluids, and the chromatographic separation of all-trans-retinoic acid, 25-hydroxycholecalciferol, all-trans-retinol, astaxanthin, lutein, zeaxanthin, trans-β-apo-8'-carotenal, γ-tocopherol, β-cryptoxanthin, α-tocopherol, phylloquinone, lycopene, α-carotene, β-carotene and coenzyme Q 10 . Extraction is obtained by adding one volume of biological fluid to two acetonitrile volumes, vortexing for 60s and incubating for 60min at 37°C under agitation. HPLC separation occurs in 30min using Hypersil C18, 100×4.6mm, 5μm particle size column, gradient from 70% methanol+30% H 2 O to 100% acetonitrile, flow rate of 1.0ml/min and 37°C column temperature. Compounds are revealed using highly sensitive UV-VIS diode array detector. The HPLC method suitability was assessed in terms of sensitivity, reproducibility and recovery. Using the present extraction and chromatographic conditions we obtained values of the fat-soluble vitamins and antioxidants in serum from 50 healthy controls similar to those found in literature. Additionally, the profile of these compounds was also measured in seminal plasma from 20 healthy fertile donors. Results indicate that this simple, rapid and low cost sample processing is suitable to extract fat-soluble vitamins and antioxidants from biological fluids and can be applied in clinical and nutritional studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Inferring subunit stoichiometry from single molecule photobleaching

PubMed Central

2013-01-01

Single molecule photobleaching is a powerful tool for determining the stoichiometry of protein complexes. By attaching fluorophores to proteins of interest, the number of associated subunits in a complex can be deduced by imaging single molecules and counting fluorophore photobleaching steps. Because some bleaching steps might be unobserved, the ensemble of steps will be binomially distributed. In this work, it is shown that inferring the true composition of a complex from such data is nontrivial because binomially distributed observations present an ill-posed inference problem. That is, a unique and optimal estimate of the relevant parameters cannot be extracted from the observations. Because of this, a method has not been firmly established to quantify confidence when using this technique. This paper presents a general inference model for interpreting such data and provides methods for accurately estimating parameter confidence. The formalization and methods presented here provide a rigorous analytical basis for this pervasive experimental tool. PMID:23712552

In situ Transesterification of Microalgal Oil to Produce Algal Biodiesel

DOT National Transportation Integrated Search

2012-06-01

This research was to process whole microalgae cells for biodiesel production without first extracting lipids. The ultimate : goal is develop a novel process for algal biodiesel production directly from microalgae cells in a single step, i.e., in situ...

Comparison of the DNA extraction methods for polymerase chain reaction amplification from formalin-fixed and paraffin-embedded tissues.

PubMed

Sato, Y; Sugie, R; Tsuchiya, B; Kameya, T; Natori, M; Mukai, K

2001-12-01

To obtain an adequate quality and quantity of DNA from formalin-fixed and paraffin-embedded tissue, six different DNA extraction methods were compared. Four methods used deparaffinization by xylene followed by proteinase K digestion and phenol-chloroform extraction. The temperature of the different steps was changed to obtain higher yields and improved quality of extracted DNA. The remaining two methods used microwave heating for deparaffinization. The best DNA extraction method consisted of deparaffinization by microwave irradiation, protein digestion with proteinase K at 48 degrees C overnight, and no further purification steps. By this method, the highest DNA yield was obtained and the amplification of a 989-base pair beta-globin gene fragment was achieved. Furthermore, DNA extracted by means of this procedure from five gastric carcinomas was successfully used for single strand conformation polymorphism and direct sequencing assays of the beta-catenin gene. Because the microwave-based DNA extraction method presented here is simple, has a lower contamination risk, and results in a higher yield of DNA compared with the ordinary organic chemical reagent-based extraction method, it is considered applicable to various clinical and basic fields.

Comparison of Single and Multi-Scale Method for Leaf and Wood Points Classification from Terrestrial Laser Scanning Data

NASA Astrophysics Data System (ADS)

Wei, Hongqiang; Zhou, Guiyun; Zhou, Junjie

2018-04-01

The classification of leaf and wood points is an essential preprocessing step for extracting inventory measurements and canopy characterization of trees from the terrestrial laser scanning (TLS) data. The geometry-based approach is one of the widely used classification method. In the geometry-based method, it is common practice to extract salient features at one single scale before the features are used for classification. It remains unclear how different scale(s) used affect the classification accuracy and efficiency. To assess the scale effect on the classification accuracy and efficiency, we extracted the single-scale and multi-scale salient features from the point clouds of two oak trees of different sizes and conducted the classification on leaf and wood. Our experimental results show that the balanced accuracy of the multi-scale method is higher than the average balanced accuracy of the single-scale method by about 10 % for both trees. The average speed-up ratio of single scale classifiers over multi-scale classifier for each tree is higher than 30.

Automated sample preparation using membrane microtiter extraction for bioanalytical mass spectrometry.

PubMed

Janiszewski, J; Schneider, P; Hoffmaster, K; Swyden, M; Wells, D; Fouda, H

1997-01-01

The development and application of membrane solid phase extraction (SPE) in 96-well microtiter plate format is described for the automated analysis of drugs in biological fluids. The small bed volume of the membrane allows elution of the analyte in a very small solvent volume, permitting direct HPLC injection and negating the need for the time consuming solvent evaporation step. A programmable liquid handling station (Quadra 96) was modified to automate all SPE steps. To avoid drying of the SPE bed and to enhance the analytical precision a novel protocol for performing the condition, load and wash steps in rapid succession was utilized. A block of 96 samples can now be extracted in 10 min., about 30 times faster than manual solvent extraction or single cartridge SPE methods. This processing speed complements the high-throughput speed of contemporary high performance liquid chromatography mass spectrometry (HPLC/MS) analysis. The quantitative analysis of a test analyte (Ziprasidone) in plasma demonstrates the utility and throughput of membrane SPE in combination with HPLC/MS. The results obtained with the current automated procedure compare favorably with those obtained using solvent and traditional solid phase extraction methods. The method has been used for the analysis of numerous drug prototypes in biological fluids to support drug discovery efforts.

Drop-on-Demand Single Cell Isolation and Total RNA Analysis

PubMed Central

Moon, Sangjun; Kim, Yun-Gon; Dong, Lingsheng; Lombardi, Michael; Haeggstrom, Edward; Jensen, Roderick V.; Hsiao, Li-Li; Demirci, Utkan

2011-01-01

Technologies that rapidly isolate viable single cells from heterogeneous solutions have significantly contributed to the field of medical genomics. Challenges remain both to enable efficient extraction, isolation and patterning of single cells from heterogeneous solutions as well as to keep them alive during the process due to a limited degree of control over single cell manipulation. Here, we present a microdroplet based method to isolate and pattern single cells from heterogeneous cell suspensions (10% target cell mixture), preserve viability of the extracted cells (97.0±0.8%), and obtain genomic information from isolated cells compared to the non-patterned controls. The cell encapsulation process is both experimentally and theoretically analyzed. Using the isolated cells, we identified 11 stem cell markers among 1000 genes and compare to the controls. This automated platform enabling high-throughput cell manipulation for subsequent genomic analysis employs fewer handling steps compared to existing methods. PMID:21412416

Soil pretreatment and fast cell lysis for direct polymerase chain reaction from forest soils for terminal restriction fragment length polymorphism analysis of fungal communities

Treesearch

Fei Cheng; Lin Hou; Keith Woeste; Zhengchun Shang; Xiaobang Peng; Peng Zhao; Shuoxin Zhang

2016-01-01

Humic substances in soil DNA samples can influence the assessment of microbial diversity and community composition. Using multiple steps during or after cell lysis adds expenses, is time-consuming, and causes DNA loss. A pretreatment of soil samples and a single step DNA extraction may improve experimental results. In order to optimize a protocol for obtaining high...

Sequence-specific sepsis-related DNA capture and fluorescent labeling in monoliths prepared by single-step photopolymerization in microfluidic devices.

PubMed

Knob, Radim; Hanson, Robert L; Tateoka, Olivia B; Wood, Ryan L; Guerrero-Arguero, Israel; Robison, Richard A; Pitt, William G; Woolley, Adam T

2018-05-21

Fast determination of antibiotic resistance is crucial in selecting appropriate treatment for sepsis patients, but current methods based on culture are time consuming. We are developing a microfluidic platform with a monolithic column modified with oligonucleotides designed for sequence-specific capture of target DNA related to the Klebsiella pneumoniae carbapenemase (KPC) gene. We developed a novel single-step monolith fabrication method with an acrydite-modified capture oligonucleotide in the polymerization mixture, enabling fast monolith preparation in a microfluidic channel using UV photopolymerization. These prepared columns had a threefold higher capacity compared to monoliths prepared in a multistep process involving Schiff-base DNA attachment. Conditions for denaturing, capture and fluorescence labeling using hybridization probes were optimized with synthetic 90-mer oligonucleotides. These procedures were applied for extraction of a PCR amplicon from the KPC antibiotic resistance gene in bacterial lysate obtained from a blood sample spiked with E. coli. The results showed similar eluted peak areas for KPC amplicon extracted from either hybridization buffer or bacterial lysate. Selective extraction of the KPC DNA was verified by real time PCR on eluted fractions. These results show great promise for application in an integrated microfluidic diagnostic system that combines upstream blood sample preparation and downstream single-molecule counting detection. Copyright © 2018 Elsevier B.V. All rights reserved.

Daily rainfall forecasting for one year in a single run using Singular Spectrum Analysis

NASA Astrophysics Data System (ADS)

Unnikrishnan, Poornima; Jothiprakash, V.

2018-06-01

Effective modelling and prediction of smaller time step rainfall is reported to be very difficult owing to its highly erratic nature. Accurate forecast of daily rainfall for longer duration (multi time step) may be exceptionally helpful in the efficient planning and management of water resources systems. Identification of inherent patterns in a rainfall time series is also important for an effective water resources planning and management system. In the present study, Singular Spectrum Analysis (SSA) is utilized to forecast the daily rainfall time series pertaining to Koyna watershed in Maharashtra, India, for 365 days after extracting various components of the rainfall time series such as trend, periodic component, noise and cyclic component. In order to forecast the time series for longer time step (365 days-one window length), the signal and noise components of the time series are forecasted separately and then added together. The results of the study show that the method of SSA could extract the various components of the time series effectively and could also forecast the daily rainfall time series for longer duration such as one year in a single run with reasonable accuracy.

Selective Extraction of Rare Earth Elements from Permanent Magnet Scraps with Membrane Solvent Extraction

DOE PAGES

Kim, Daejin; Powell, Lawrence E.; Delmau, Lætitia H.; ...

2015-06-24

In this paper, the rare earth elements (REEs) such as neodymium, praseodymium, and dysprosium were successfully recovered from commercial NdFeB magnets and industrial scrap magnets via membrane assisted solvent extraction (MSX). A hollow fiber membrane system was evaluated to extract REEs in a single step with the feed and strip solutions circulating continuously through the MSX system. The effects of several experimental variables on REE extraction such as flow rate, concentration of REEs in the feed solution, membrane configuration, and composition of acids were investigated with the MSX system. A multimembrane module configuration with REEs dissolved in aqueous nitric acidmore » solutions showed high selectivity for REE extraction with no coextraction of non-REEs, whereas the use of aqueous hydrochloric acid solution resulted in coextraction of non-REEs due to the formation of chloroanions of non-REEs. The REE oxides were recovered from the strip solution through precipitation, drying, and annealing steps. Finally, the resulting REE oxides were characterized with XRD, SEM-EDX, and ICP-OES, demonstrating that the membrane assisted solvent extraction is capable of selectively recovering pure REEs from the industrial scrap magnets.« less

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.

Ultrasonication followed by single-drop microextraction combined with GC/MS for rapid determination of organochlorine pesticides from fish.

PubMed

Shrivas, Kamlesh; Wu, Hui-Fen

2008-02-01

A novel, rapid and simple sample pretreatment technique termed ultrasonication followed by single-drop micro-extraction (U-SDME) has been developed and combined with GC/MS for the determination of organochlorine pesticides (OCPs) in fish. In the present work, the lengthy procedures generally used in the conventional methods like, Soxhlet extraction, supercritical fluid extraction, pressurized liquid extraction and microwave assisted solvent extraction for extraction of OCPs from fish tissues are minimized by the use of two simple extraction procedures. Firstly, OCPs from fish were extracted in organic solvent with ultrasonication and then subsequently preconcentrated by single-drop micro-extraction (SDME). Extraction parameters of ultrasonication and SDME were optimized in spiked sample solution in order to obtain efficient extraction of OCPs from fish tissues. The calibration curves for OCPs were found to be linear between 10-1000 ng/g with correlation of estimations in the range 0.990-0.994. The recoveries obtained in blank fish tissues were ranged from 82.1 to 95.3%. The LOD and RSD for determination of OCPs in fish were 0.5 ng/g and 9.4-10.0%, respectively. The proposed method was applied for the determination of bioconcentration factor in fish after exposure to different concentrations of OCPs in cultured water. The present method avoids the co-extraction of lipids, long extraction steps (>12 h) and large amount of organic solvent for the separation of OCPs. The main advantages of the present method are rapid, selective, sensitive and low cost for the determination of OCPs in fish.

Combined non-parametric and parametric approach for identification of time-variant systems

NASA Astrophysics Data System (ADS)

Dziedziech, Kajetan; Czop, Piotr; Staszewski, Wieslaw J.; Uhl, Tadeusz

2018-03-01

Identification of systems, structures and machines with variable physical parameters is a challenging task especially when time-varying vibration modes are involved. The paper proposes a new combined, two-step - i.e. non-parametric and parametric - modelling approach in order to determine time-varying vibration modes based on input-output measurements. Single-degree-of-freedom (SDOF) vibration modes from multi-degree-of-freedom (MDOF) non-parametric system representation are extracted in the first step with the use of time-frequency wavelet-based filters. The second step involves time-varying parametric representation of extracted modes with the use of recursive linear autoregressive-moving-average with exogenous inputs (ARMAX) models. The combined approach is demonstrated using system identification analysis based on the experimental mass-varying MDOF frame-like structure subjected to random excitation. The results show that the proposed combined method correctly captures the dynamics of the analysed structure, using minimum a priori information on the model.

Simultaneous dispersive liquid-liquid microextraction derivatisation and gas chromatography mass spectrometry analysis of subcritical water extracts of sweet and sour cherry stems.

PubMed

Švarc-Gajić, Jaroslava; Clavijo, Sabrina; Suárez, Ruth; Cvetanović, Aleksandra; Cerdà, Víctor

2018-03-01

Cherry stems have been used in traditional medicine mostly for the treatment of urinary tract infections. Extraction with subcritical water, according to its selectivity, efficiency and other aspects, differs substantially from conventional extraction techniques. The complexity of plant subcritical water extracts is due to the ability of subcritical water to extract different chemical classes of different physico-chemical properties and polarities in a single run. In this paper, dispersive liquid-liquid microextraction (DLLME) with simultaneous derivatisation was optimised for the analysis of complex subcritical water extracts of cherry stems to allow simple and rapid preparation prior to gas chromatography-mass spectrometry (GC-MS). After defining optimal extracting and dispersive solvents, the optimised method was used for the identification of compounds belonging to different chemical classes in a single analytical run. The developed sample preparation protocol enabled simultaneous extraction and derivatisation, as well as convenient coupling with GC-MS analysis, reducing the analysis time and number of steps. The applied analytical protocol allowed simple and rapid chemical screening of subcritical water extracts and was used for the comparison of subcritical water extracts of sweet and sour cherry stems. Graphical abstract DLLME GC MS analysis of cherry stem extracts obtained by subcritical water.

Single Layer Permittivity Extraction from Multilayered Biaxial Anisotropic Media Using a Rectangular Waveguide

DTIC Science & Technology

Electromagnetic characterization of layered biaxial media is a critical step in the design of modern low observable (LO) coatings, and with the...the flexibility they provide for control over magnitude, phase, and polarization of the material systems response to interrogating electromagnetic (EM

Comparison of in situ DGT measurement with ex situ methods for predicting cadmium bioavailability in soils with combined pollution to biotas.

PubMed

Wang, Peifang; Liu, Cui; Yao, Yu; Wang, Chao; Wang, Teng; Yuan, Ye; Hou, Jun

2017-05-01

To assess the capabilities of the different techniques in predicting Cadmium (Cd) bioavailability in Cd-contaminated soils with the addition of Zn, one in situ technique (diffusive gradients in thin films; DGT) was compared with soil solution concentration and four widely used single-step extraction methods (acetic acid, EDTA, sodium acetate and CaCl 2 ). Wheat and maize were selected as tested species. The results demonstrated that single Cd-polluted soils inhibited the growth of wheat and maize significantly compared with control plants; the shoot and root biomasses of the plants both dropped significantly (P < 0.05). The addition of Zn exhibited a strong antagonism to the physiological toxicity induced by Cd. The Pearson correlation coefficient presented positive correlations (P < 0.01, R > 0.9) between Cd concentrations in two plants and Cd bioavailability indicated by each method in soils. Consequently, the results indicated that the DGT technique could be regarded as a good predictor of Cd bioavailability to plants, comparable to soil solution concentration and the four single-step extraction methods. Because the DGT technique can offer in situ data, it is expected to be widely used in more areas.

Reducing Time and Increasing Sensitivity in Sample Preparation for Adherent Mammalian Cell Metabolomics

PubMed Central

Lorenz, Matthew A.; Burant, Charles F.; Kennedy, Robert T.

2011-01-01

A simple, fast, and reproducible sample preparation procedure was developed for relative quantification of metabolites in adherent mammalian cells using the clonal β-cell line INS-1 as a model sample. The method was developed by evaluating the effect of different sample preparation procedures on high performance liquid chromatography- mass spectrometry quantification of 27 metabolites involved in glycolysis and the tricarboxylic acid cycle on a directed basis as well as for all detectable chromatographic features on an undirected basis. We demonstrate that a rapid water rinse step prior to quenching of metabolism reduces components that suppress electrospray ionization thereby increasing signal for 26 of 27 targeted metabolites and increasing total number of detected features from 237 to 452 with no detectable change of metabolite content. A novel quenching technique is employed which involves addition of liquid nitrogen directly to the culture dish and allows for samples to be stored at −80 °C for at least 7 d before extraction. Separation of quenching and extraction steps provides the benefit of increased experimental convenience and sample stability while maintaining metabolite content similar to techniques that employ simultaneous quenching and extraction with cold organic solvent. The extraction solvent 9:1 methanol: chloroform was found to provide superior performance over acetonitrile, ethanol, and methanol with respect to metabolite recovery and extract stability. Maximal recovery was achieved using a single rapid (~1 min) extraction step. The utility of this rapid preparation method (~5 min) was demonstrated through precise metabolite measurements (11% average relative standard deviation without internal standards) associated with step changes in glucose concentration that evoke insulin secretion in the clonal β-cell line INS-1. PMID:21456517

Investigation of different ethylenediamine-N,N'-disuccinic acid-enhanced washing configurations for remediation of a Cu-contaminated soil: process kinetics and efficiency comparison between single-stage and multi-stage configurations.

PubMed

Ferraro, Alberto; Fabbricino, Massimiliano; van Hullebusch, Eric D; Esposito, Giovanni

2017-09-01

A comparison of Cu extraction yields for three different ethylenediamine-N,N'-disuccinic acid (EDDS)-enhanced washing configurations was performed on a Cu-contaminated soil. Batch experiments were used to simulate a single-stage continuous stirred tank reactor (CSTR) and a multi-stage (side feeding and counter-current) reactor. Single-stage CSTR conditions were simulated for various EDDS:(Cu + Cd + Pb + Co + Ni + Zn) molar ratio (EDDS:M ratio) (from 1 to 30) and liquid to soil (L/S) ratio (from 15 to 45). The highest Cu extraction yield (≃56%) was achieved with EDDS:M = 30. In contrast, a Cu extraction yield decrease was observed with increasing L/S ratio with highest extracted Cu achievement (≃48%) for L/S = 15. Side feeding configuration was tested in four experimental conditions through different fractionation mode of EDDS dose and treatment time at each washing step. Results from the four tests showed all enhanced Cu extraction (maximum values from ≃43 to ≃51%) achieved at lower treatment time and lower EDDS:M molar ratio compared to CSTR configuration with L/S = 25 and EDDS:M = 10. The counter-current washing was carried out through two washing flows achieving a process performance enhancement with 27% increase of extracted Cu compared to single-stage CSTR configuration. Higher Cu extraction percentage (36.8%) was observed in the first washing phase than in the second one (24.7%).

Comparative Study of Green Sub- and Supercritical Processes to Obtain Carnosic Acid and Carnosol-Enriched Rosemary Extracts with in Vitro Anti-Proliferative Activity on Colon Cancer Cells

PubMed Central

Sánchez-Camargo, Andrea del Pilar; García-Cañas, Virginia; Herrero, Miguel; Cifuentes, Alejandro; Ibáñez, Elena

2016-01-01

In the present work, four green processes have been compared to evaluate their potential to obtain rosemary extracts with in vitro anti-proliferative activity against two colon cancer cell lines (HT-29 and HCT116). The processes, carried out under optimal conditions, were: (1) pressurized liquid extraction (PLE, using an hydroalcoholic mixture as solvent) at lab-scale; (2) Single-step supercritical fluid extraction (SFE) at pilot scale; (3) Intensified two-step sequential SFE at pilot scale; (4) Integrated PLE plus supercritical antisolvent fractionation (SAF) at pilot scale. Although higher extraction yields were achieved by using PLE (38.46% dry weight), this extract provided the lowest anti-proliferative activity with no observed cytotoxic effects at the assayed concentrations. On the other hand, extracts obtained using the PLE + SAF process provided the most active rosemary extracts against both colon cancer cell lines, with LC50 ranging from 11.2 to 12.4 µg/mL and from 21.8 to 31.9 µg/mL for HCT116 and HT-29, respectively. In general, active rosemary extracts were characterized by containing carnosic acid (CA) and carnosol (CS) at concentrations above 263.7 and 33.9 mg/g extract, respectively. Some distinct compounds have been identified in the SAF extracts (rosmaridiphenol and safficinolide), suggesting their possible role as additional contributors to the observed strong anti-proliferative activity of CA and CS in SAF extracts. PMID:27941607

Comparative Study of Green Sub- and Supercritical Processes to Obtain Carnosic Acid and Carnosol-Enriched Rosemary Extracts with in Vitro Anti-Proliferative Activity on Colon Cancer Cells.

PubMed

Sánchez-Camargo, Andrea Del Pilar; García-Cañas, Virginia; Herrero, Miguel; Cifuentes, Alejandro; Ibáñez, Elena

2016-12-07

In the present work, four green processes have been compared to evaluate their potential to obtain rosemary extracts with in vitro anti-proliferative activity against two colon cancer cell lines (HT-29 and HCT116). The processes, carried out under optimal conditions, were: (1) pressurized liquid extraction (PLE, using an hydroalcoholic mixture as solvent) at lab-scale; (2) Single-step supercritical fluid extraction (SFE) at pilot scale; (3) Intensified two-step sequential SFE at pilot scale; (4) Integrated PLE plus supercritical antisolvent fractionation (SAF) at pilot scale. Although higher extraction yields were achieved by using PLE (38.46% dry weight), this extract provided the lowest anti-proliferative activity with no observed cytotoxic effects at the assayed concentrations. On the other hand, extracts obtained using the PLE + SAF process provided the most active rosemary extracts against both colon cancer cell lines, with LC 50 ranging from 11.2 to 12.4 µg/mL and from 21.8 to 31.9 µg/mL for HCT116 and HT-29, respectively. In general, active rosemary extracts were characterized by containing carnosic acid (CA) and carnosol (CS) at concentrations above 263.7 and 33.9 mg/g extract, respectively. Some distinct compounds have been identified in the SAF extracts (rosmaridiphenol and safficinolide), suggesting their possible role as additional contributors to the observed strong anti-proliferative activity of CA and CS in SAF extracts.

Supercritical CO2 assisted process for the production of high-purity and sterile nano-hydroxyapatite/chitosan hybrid scaffolds.

PubMed

Ruphuy, G; Souto-Lopes, M; Paiva, D; Costa, P; Rodrigues, A E; Monteiro, F J; Salgado, C L; Fernandes, M H; Lopes, J C; Dias, M M; Barreiro, M F

2018-04-01

Hybrid scaffolds composed of hydroxyapatite (HAp), in particular in its nanometric form (n-HAp), and chitosan (CS) are promising materials for non-load-bearing bone graft applications. The main constraints of their production concern the successful implementation of the final purification/neutralization and sterilization steps. Often, the used purification strategies can compromise scaffold structural features, and conventional sterilization techniques can result in material's thermal degradation and/or contamination with toxic residues. In this context, this work presents a process to produce n-HAp/CS scaffolds mimicking bone composition and structure, where an innovative single step based on supercritical CO 2 extraction was used for both purification and sterilization. A removal of 80% of the residual acetic acid was obtained (T = 75°C, p = 8.0 MPa, 2 extraction cycles of 2 h) giving rise to scaffolds exhibiting adequate interconnected porous structure, fast swelling and storage modulus compatible with non-load-bearing applications. Moreover, the obtained scaffolds showed cytocompatibility and osteoconductivity without further need of disinfection/sterilization procedures. Among the main advantages, the proposed process comprises only three steps (n-HAp/CS dispersion preparation; freeze-drying; and supercritical CO 2 extraction), and the supercritical CO 2 extraction show clear advantages over currently used procedures based on neutralization steps. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 965-975, 2018. © 2017 Wiley Periodicals, Inc.

Isolation and Characterization of Anthocyanins from Hibiscus sabdariffa Flowers.

PubMed

Grajeda-Iglesias, Claudia; Figueroa-Espinoza, Maria C; Barouh, Nathalie; Baréa, Bruno; Fernandes, Ana; de Freitas, Victor; Salas, Erika

2016-07-22

The intense red-colored Hibiscus sabdariffa flowers are an inexpensive source of anthocyanins with potential to be used as natural, innocuous, and health-beneficial colorants. An anthocyanin-rich extract from hibiscus flowers was obtained by ultrasound-assisted extraction. By a single-step process fractionation using a Sep-Pak C18 cartridge, the main hibiscus anthocyanins, delphinidin-3-O-sambubioside (Dp-samb) and cyanidin-3-O-sambubioside (Cy-samb), were separated and then characterized via NMR and HPLC-ESIMS data. Since Dp-samb was the most abundant anthocyanin identified in the extract, its colorant properties were studied by the pH jumps method, which allowed the calculation of the single acid-base equilibrium (pK'a 2.92), the acidity (pKa 3.70), and the hydration constants (pKh 3.02). Moreover, by using size-exclusion chromatography, new cyanidin-derived anthocyanins (with three or more sugar units) were successfully identified and reported for the first time in the hibiscus extract.

Comparing the Behavior of Polarimetric SAR Imagery (TerraSAR-X and Radarsat-2) for Automated Sea Ice Classification

NASA Astrophysics Data System (ADS)

Ressel, Rudolf; Singha, Suman; Lehner, Susanne

2016-08-01

Arctic Sea ice monitoring has attracted increasing attention over the last few decades. Besides the scientific interest in sea ice, the operational aspect of ice charting is becoming more important due to growing navigational possibilities in an increasingly ice free Arctic. For this purpose, satellite borne SAR imagery has become an invaluable tool. In past, mostly single polarimetric datasets were investigated with supervised or unsupervised classification schemes for sea ice investigation. Despite proven sea ice classification achievements on single polarimetric data, a fully automatic, general purpose classifier for single-pol data has not been established due to large variation of sea ice manifestations and incidence angle impact. Recently, through the advent of polarimetric SAR sensors, polarimetric features have moved into the focus of ice classification research. The higher information content four polarimetric channels promises to offer greater insight into sea ice scattering mechanism and overcome some of the shortcomings of single- polarimetric classifiers. Two spatially and temporally coincident pairs of fully polarimetric acquisitions from the TerraSAR-X/TanDEM-X and RADARSAT-2 satellites are investigated. Proposed supervised classification algorithm consists of two steps: The first step comprises a feature extraction, the results of which are ingested into a neural network classifier in the second step. Based on the common coherency and covariance matrix, we extract a number of features and analyze the relevance and redundancy by means of mutual information for the purpose of sea ice classification. Coherency matrix based features which require an eigendecomposition are found to be either of low relevance or redundant to other covariance matrix based features. Among the most useful features for classification are matrix invariant based features (Geometric Intensity, Scattering Diversity, Surface Scattering Fraction).

Self-driven filter-based blood plasma separator microfluidic chip for point-of-care testing.

PubMed

Madadi, Hojjat; Casals-Terré, Jasmina; Mohammadi, Mahdi

2015-05-22

There is currently a growing need for lab-on-a-chip devices for use in clinical analysis and diagnostics, especially in the area of patient care. The first step in most blood assays is plasma extraction from whole blood. This paper presents a novel, self-driven blood plasma separation microfluidic chip, which can extract more than 0.1 μl plasma from a single droplet of undiluted fresh human blood (~5 μl). This volume of blood plasma is extracted from whole blood with high purity (more than 98%) in a reasonable time frame (3 to 5 min), and without the need for any external force. This would be the first step towards the realization of a single-use, self-blood test that does not require any external force or power source to deliver and analyze a fresh whole-blood sample, in contrast to the existing time-consuming conventional blood analysis. The prototypes are manufactured in polydimethylsiloxane that has been modified with a strong nonionic surfactant (Silwet L-77) to achieve hydrophilic behavior. The main advantage of this microfluidic chip design is the clogging delay in the filtration area, which results in an increased amount of extracted plasma (0.1 μl). Moreover, the plasma can be collected in one or more 10 μm-deep channels to facilitate the detection and readout of multiple blood assays. This high volume of extracted plasma is achieved thanks to a novel design that combines maximum pumping efficiency without disturbing the red blood cells' trajectory through the use of different hydrodynamic principles, such as a constriction effect and a symmetrical filtration mode. To demonstrate the microfluidic chip's functionality, we designed and fabricated a novel hybrid microdevice that exhibits the benefits of both microfluidics and lateral flow immunochromatographic tests. The performance of the presented hybrid microdevice is validated using rapid detection of thyroid stimulating hormone within a single droplet of whole blood.

Kruskal-Wallis-based computationally efficient feature selection for face recognition.

PubMed

Ali Khan, Sajid; Hussain, Ayyaz; Basit, Abdul; Akram, Sheeraz

2014-01-01

Face recognition in today's technological world, and face recognition applications attain much more importance. Most of the existing work used frontal face images to classify face image. However these techniques fail when applied on real world face images. The proposed technique effectively extracts the prominent facial features. Most of the features are redundant and do not contribute to representing face. In order to eliminate those redundant features, computationally efficient algorithm is used to select the more discriminative face features. Extracted features are then passed to classification step. In the classification step, different classifiers are ensemble to enhance the recognition accuracy rate as single classifier is unable to achieve the high accuracy. Experiments are performed on standard face database images and results are compared with existing techniques.

Clean-up of aqueous acetone vegetable extracts by solid-matrix partition for pyrethroid residue determination by gas chromatography-electron-capture detection.

PubMed

Di Muccio, A; Barbini, D A; Generali, T; Pelosi, P; Ausili, A; Vergori, F; Camoni, I

1997-03-21

Disposable, ready-to-use cartridges filled with macroporous diatomaceous material are used to carry out a partition clean-up that, in a single step, is capable of transferring pesticide residues from aqueous acetone extracts into light petroleum-dichloromethane (75:25, v/v). This procedure takes the place of some functions (such as separatory-funnel partition, drying over anhydrous sodium sulphate and partial adsorption clean-up) usually performed by separate steps in classical schemes. Fourteen pyrethroid pesticides, including tefluthrin, tetramethrin, cyphenothrin, cyfluthrin, flucythrinate, tau-fluvalinate, deltamethrin, bioallethrin, fenpropathrin, lambda-cyhalothrin, permethrin, alpha-cypermethrin, esfenvalerate and tralomethrin were determined using the described procedure with satisfactory recoveries for most of them, at spiking levels ranging from 0.08 to 0.82 mg/kg for the different compounds. Crops subjected to the described procedure included strawberry, apple, and orange gave extracts containing a mass of co-extractives that was between 5 and 30 mg. Compared with classical schemes, the described procedure is simple, less labour intensive, allows parallel handling of several extracts and does not require the preparation and maintenance of equipment. Troublesome emulsions such as those frequently observed in separation funnel partitioning do not occur.

Rapid, single-step most-probable-number method for enumerating fecal coliforms in effluents from sewage treatment plants

NASA Technical Reports Server (NTRS)

Munoz, E. F.; Silverman, M. P.

1979-01-01

A single-step most-probable-number method for determining the number of fecal coliform bacteria present in sewage treatment plant effluents is discussed. A single growth medium based on that of Reasoner et al. (1976) and consisting of 5.0 gr. proteose peptone, 3.0 gr. yeast extract, 10.0 gr. lactose, 7.5 gr. NaCl, 0.2 gr. sodium lauryl sulfate, and 0.1 gr. sodium desoxycholate per liter is used. The pH is adjusted to 6.5, and samples are incubated at 44.5 deg C. Bacterial growth is detected either by measuring the increase with time in the electrical impedance ratio between the innoculated sample vial and an uninnoculated reference vial or by visual examination for turbidity. Results obtained by the single-step method for chlorinated and unchlorinated effluent samples are in excellent agreement with those obtained by the standard method. It is suggested that in automated treatment plants impedance ratio data could be automatically matched by computer programs with the appropriate dilution factors and most probable number tables already in the computer memory, with the corresponding result displayed as fecal coliforms per 100 ml of effluent.

Time dependent calibration of a sediment extraction scheme.

PubMed

Roychoudhury, Alakendra N

2006-04-01

Sediment extraction methods to quantify metal concentration in aquatic sediments usually present limitations in accuracy and reproducibility because metal concentration in the supernatant is controlled to a large extent by the physico-chemical properties of the sediment that result in a complex interplay between the solid and the solution phase. It is suggested here that standardization of sediment extraction methods using pure mineral phases or reference material is futile and instead the extraction processes should be calibrated using site-specific sediments before their application. For calibration, time dependent release of metals should be observed for each leachate to ascertain the appropriate time for a given extraction step. Although such an approach is tedious and time consuming, using iron extraction as an example, it is shown here that apart from quantitative data such an approach provides additional information on factors that play an intricate role in metal dynamics in the environment. Single step ascorbate, HCl, oxalate and dithionite extractions were used for targeting specific iron phases from saltmarsh sediments and their response was observed over time in order to calibrate the extraction times for each extractant later to be used in a sequential extraction. For surficial sediments, an extraction time of 24 h, 1 h, 2 h and 3 h was ascertained for ascorbate, HCl, oxalate and dithionite extractions, respectively. Fluctuations in iron concentration in the supernatant over time were ubiquitous. The adsorption-desorption behavior is possibly controlled by the sediment organic matter, formation or consumption of active exchange sites during extraction and the crystallinity of iron mineral phase present in the sediments.

An improved protocol for DNA extraction from alkaline soil and sediment samples for constructing metagenomic libraries.

PubMed

Verma, Digvijay; Satyanarayana, T

2011-09-01

An improved single-step protocol has been developed for extracting pure community humic substance-free DNA from alkaline soils and sediments. The method is based on direct cell lysis in the presence of powdered activated charcoal and polyvinylpolypyrrolidone followed by precipitation with polyethyleneglycol and isopropanol. The strategy allows simultaneous isolation and purification of DNA while minimizing the loss of DNA with respect to other available protocols for metagenomic DNA extraction. Moreover, the purity levels are significant, which are difficult to attain with any of the methods reported in the literature for DNA extraction from soils. The DNA thus extracted was free from humic substances and, therefore, could be processed for restriction digestion, PCR amplification as well as for the construction of metagenomic libraries.

Quantification and characterisation of fatty acid methyl esters in microalgae: Comparison of pretreatment and purification methods.

PubMed

Lage, Sandra; Gentili, Francesco G

2018-06-01

A systematic qualitative and quantitative analysis of fatty acid methyl esters (FAMEs) is crucial for microalgae species selection for biodiesel production. The aim of this study is to identify the best method to assess microalgae FAMEs composition and content. A single-step method, was tested with and without purification steps-that is, separation of lipid classes by thin-layer chromatography (TLC) or solid-phase extraction (SPE). The efficiency of a direct transesterification method was also evaluated. Additionally, the yield of the FAMEs and the profiles of the microalgae samples with different pretreatments (boiled in isopropanol, freezing, oven-dried and freeze-dried) were compared. The application of a purification step after lipid extraction proved to be essential for an accurate FAMEs characterisation. The purification methods, which included TLC and SPE, provided superior results compared to not purifying the samples. Freeze-dried microalgae produced the lowest FAMEs yield. However, FAMEs profiles were generally equivalent among the pretreatments. Copyright © 2018 Elsevier Ltd. All rights reserved.

Technical difficulties and solutions of direct transesterification process of microbial oil for biodiesel synthesis.

PubMed

Yousuf, Abu; Khan, Maksudur Rahman; Islam, M Amirul; Wahid, Zularisam Ab; Pirozzi, Domenico

2017-01-01

Microbial oils are considered as alternative to vegetable oils or animal fats as biodiesel feedstock. Microalgae and oleaginous yeast are the main candidates of microbial oil producers' community. However, biodiesel synthesis from these sources is associated with high cost and process complexity. The traditional transesterification method includes several steps such as biomass drying, cell disruption, oil extraction and solvent recovery. Therefore, direct transesterification or in situ transesterification, which combines all the steps in a single reactor, has been suggested to make the process cost effective. Nevertheless, the process is not applicable for large-scale biodiesel production having some difficulties such as high water content of biomass that makes the reaction rate slower and hurdles of cell disruption makes the efficiency of oil extraction lower. Additionally, it requires high heating energy in the solvent extraction and recovery stage. To resolve these difficulties, this review suggests the application of antimicrobial peptides and high electric fields to foster the microbial cell wall disruption.

Single-nucleus Hi-C of mammalian oocytes and zygotes.

PubMed

Gassler, Johanna; Flyamer, Ilya M; Tachibana, Kikuë

2018-01-01

The 3D folding of the genome is linked to essential nuclear processes including gene expression, DNA repair, and replication. Chromatin conformation capture assays such as Hi-C are providing unprecedented insights into higher-order chromatin structure. Bulk Hi-C of millions of cells enables detection of average chromatin features at high resolution but is challenging to apply to rare cell types. This chapter describes our recently developed single-nucleus Hi-C (snHi-C) approach for detection of chromatin contacts in single nuclei of murine oocytes and one-cell embryos (zygotes). The step-by-step protocol includes isolation of these cells, extraction of nuclei, fixation, restriction digestion, ligation, and whole genome amplification. Contacts obtained by snHi-C allow detection of chromatin features including loops, topologically associating domains, and compartments when averaged over the genome. The combination of snHi-C with other single-cell techniques in these and other rare cell types will likely provide a comprehensive picture of how chromatin architecture shapes cell identity. © 2018 Elsevier Inc. All rights reserved.

Hydrometallurgical Separation of Niobium and Tantalum: A Fundamental Approach

NASA Astrophysics Data System (ADS)

Nete, Motlalepula; Purcell, Walter; Nel, Johann T.

2016-02-01

A mixture of pure Ta2O5 and Nb2O5 was dissolved using two different fluxes, namely NH4F·HF and Na2HPO4/NaH2PO4·H2O. Selective precipitation and ion exchange were used as separation techniques. Selective precipitation using p-phenylediamine in a fluoride matrix resulted in the isolation of 73(3)% tantalum accompanied by 23(5)% niobium. A separation factor of 11(4) was obtained. A single solvent extraction step using methyl-isobutyl ketone at a 4 M H2SO4 yielded excellent Ta and Nb separation in the fluoride solution with 80% of the Ta and only 2% Nb recovered in the organic layer. A two-step extraction recovered 100% Ta at 0.5-4 M H2SO4 with a separation factor of ~2000. A study of the extraction mechanism indicated that the stability of the protonated compounds such as H2TaF7/H2NbOF5 is in the extraction and separation determining steps in this process. A K' (double de-protonated constant) of approximately 0.2 was calculated for H2TaF7. Only 91.7% Nb and 73.4% Ta were recovered from anion separation using strong Amberlite resin and 96.1% Nb and 52.3% using the weak Dowex Marathon resin from fluoride dissolution.

Texture-based segmentation and analysis of emphysema depicted on CT images

NASA Astrophysics Data System (ADS)

Tan, Jun; Zheng, Bin; Wang, Xingwei; Lederman, Dror; Pu, Jiantao; Sciurba, Frank C.; Gur, David; Leader, J. Ken

2011-03-01

In this study we present a texture-based method of emphysema segmentation depicted on CT examination consisting of two steps. Step 1, a fractal dimension based texture feature extraction is used to initially detect base regions of emphysema. A threshold is applied to the texture result image to obtain initial base regions. Step 2, the base regions are evaluated pixel-by-pixel using a method that considers the variance change incurred by adding a pixel to the base in an effort to refine the boundary of the base regions. Visual inspection revealed a reasonable segmentation of the emphysema regions. There was a strong correlation between lung function (FEV1%, FEV1/FVC, and DLCO%) and fraction of emphysema computed using the texture based method, which were -0.433, -.629, and -0.527, respectively. The texture-based method produced more homogeneous emphysematous regions compared to simple thresholding, especially for large bulla, which can appear as speckled regions in the threshold approach. In the texture-based method, single isolated pixels may be considered as emphysema only if neighboring pixels meet certain criteria, which support the idea that single isolated pixels may not be sufficient evidence that emphysema is present. One of the strength of our complex texture-based approach to emphysema segmentation is that it goes beyond existing approaches that typically extract a single or groups texture features and individually analyze the features. We focus on first identifying potential regions of emphysema and then refining the boundary of the detected regions based on texture patterns.

Two-step passivation for enhanced InGaN/GaN light emitting diodes with step graded electron injectors

NASA Astrophysics Data System (ADS)

Sheremet, V.; Genç, M.; Gheshlaghi, N.; Elçi, M.; Sheremet, N.; Aydınlı, A.; Altuntaş, I.; Ding, K.; Avrutin, V.; Özgür, Ü.; Morkoç, H.

2018-01-01

Enhancement of InGaN/GaN based light emitting diode performance with step graded electron injectors through a two-step passivation is reported. Perimeter passivation of LED dies with SiO2 immediately following ICP mesa etch in addition to conventional Si3N4 dielectric surface passivation leads to decrease in the reverse bias leakage current by a factor of two as well as a decrease in the shunt current under forward bias by an order of magnitude. Mitigation of the leakage currents owing to the two-step passivation leads to significant increase in the radiant intensity of LEDs by more than a factor of two compared to the conventional single step surface passivation. Further, micro-dome patterned surface of Si3N4 passivation layer allow enhanced light extraction from LEDs.

Separation of Be and Al for AMS using single-step column chromatography

NASA Astrophysics Data System (ADS)

Binnie, Steven A.; Dunai, Tibor J.; Voronina, Elena; Goral, Tomasz; Heinze, Stefan; Dewald, Alfred

2015-10-01

With the aim of simplifying AMS target preparation procedures for TCN measurements we tested a new extraction chromatography approach which couples an anion exchange resin (WBEC) to a chelating resin (Beryllium resin) to separate Be and Al from dissolved quartz samples. Results show that WBEC-Beryllium resin stacks can be used to provide high purity Be and Al separations using a combination of hydrochloric/oxalic and nitric acid elutions. 10Be and 26Al concentrations from quartz samples prepared using more standard procedures are compared with results from replicate samples prepared using the coupled WBEC-Beryllium resin approach and show good agreement. The new column procedure is performed in a single step, reducing sample preparation times relative to more traditional methods of TCN target production.

A deep learning pipeline for Indian dance style classification

NASA Astrophysics Data System (ADS)

Dewan, Swati; Agarwal, Shubham; Singh, Navjyoti

2018-04-01

In this paper, we address the problem of dance style classification to classify Indian dance or any dance in general. We propose a 3-step deep learning pipeline. First, we extract 14 essential joint locations of the dancer from each video frame, this helps us to derive any body region location within the frame, we use this in the second step which forms the main part of our pipeline. Here, we divide the dancer into regions of important motion in each video frame. We then extract patches centered at these regions. Main discriminative motion is captured in these patches. We stack the features from all such patches of a frame into a single vector and form our hierarchical dance pose descriptor. Finally, in the third step, we build a high level representation of the dance video using the hierarchical descriptors and train it using a Recurrent Neural Network (RNN) for classification. Our novelty also lies in the way we use multiple representations for a single video. This helps us to: (1) Overcome the RNN limitation of learning small sequences over big sequences such as dance; (2) Extract more data from the available dataset for effective deep learning by training multiple representations. Our contributions in this paper are three-folds: (1) We provide a deep learning pipeline for classification of any form of dance; (2) We prove that a segmented representation of a dance video works well with sequence learning techniques for recognition purposes; (3) We extend and refine the ICD dataset and provide a new dataset for evaluation of dance. Our model performs comparable or better in some cases than the state-of-the-art on action recognition benchmarks.

Simultaneous determination of azathioprine and 6-mercaptopurine by high-performance liquid chromatography.

PubMed

Van Os, E C; McKinney, J A; Zins, B J; Mays, D C; Schriver, Z H; Sandborn, W J; Lipsky, J J

1996-04-26

A specific, sensitive, single-step solid-phase extraction and reversed-phase high-performance liquid chromatographic method for the simultaneous determination of plasma 6-mercaptopurine and azathioprine concentrations is reported. Following solid-phase extraction, analytes are separated on a C18 column with mobile phase consisting of 0.8% acetonitrile in 1 mM triethylamine, pH 3.2, run on a gradient system. Quantitation limits were 5 ng/ml and 2 ng/ml for azathioprine and 6-mercaptopurine, respectively. Peak heights correlated linearly to known extracted standards for 6-mercaptopurine and azathioprine (r = 0.999) over a range of 2-200 ng/ml. No chromatographic interferences were detected.

A rapid and simple method for estimating sulfate reduction activity and quantifying inorganic sulfides

USGS Publications Warehouse

Ulrich, G.A.; Krumholz, L.R.; Suflita, J.M.

1997-01-01

A simplified passive extraction procedure for quantifying reduced inorganic sulfur compounds from sediments and water is presented. This method may also be used for the estimation of sulfate reduction rates. Efficient extraction of FeS, FeS(inf2), and S(sup2-) was obtained with this procedure; however, the efficiency for S(sup0) depended on the form that was tested. Passive extraction can be used with samples containing up to 20 mg of reduced sulfur. We demonstrated the utility of this technique in a determination of both sulfate reduction rates and reduced inorganic sulfur pools in marine and freshwater sediments. A side-by-side comparison of the passive extraction method with the established single-step distillation technique yielded comparable results with a fraction of the effort.

Gold Nanorod-based Photo-PCR System for One-Step, Rapid Detection of Bacteria

PubMed Central

Kim, Jinjoo; Kim, Hansol; Park, Ji Ho; Jon, Sangyong

2017-01-01

The polymerase chain reaction (PCR) has been an essential tool for diagnosis of infectious diseases, but conventional PCR still has some limitations with respect to applications to point-of-care (POC) diagnostic systems that require rapid detection and miniaturization. Here we report a light-based PCR method, termed as photo-PCR, which enables rapid detection of bacteria in a single step. In the photo-PCR system, poly(enthylene glycol)-modified gold nanorods (PEG-GNRs), used as a heat generator, are added into the PCR mixture, which is subsequently periodically irradiated with a 808-nm laser to create thermal cycling. Photo-PCR was able to significantly reduce overall thermal cycling time by integrating bacterial cell lysis and DNA amplification into a single step. Furthermore, when combined with KAPA2G fast polymerase and cooling system, the entire process of bacterial genomic DNA extraction and amplification was further shortened, highlighting the potential of photo-PCR for use in a portable, POC diagnostic system. PMID:29071186

Single-Camera-Based Method for Step Length Symmetry Measurement in Unconstrained Elderly Home Monitoring.

PubMed

Cai, Xi; Han, Guang; Song, Xin; Wang, Jinkuan

2017-11-01

single-camera-based gait monitoring is unobtrusive, inexpensive, and easy-to-use to monitor daily gait of seniors in their homes. However, most studies require subjects to walk perpendicularly to camera's optical axis or along some specified routes, which limits its application in elderly home monitoring. To build unconstrained monitoring environments, we propose a method to measure step length symmetry ratio (a useful gait parameter representing gait symmetry without significant relationship with age) from unconstrained straight walking using a single camera, without strict restrictions on walking directions or routes. according to projective geometry theory, we first develop a calculation formula of step length ratio for the case of unconstrained straight-line walking. Then, to adapt to general cases, we propose to modify noncollinear footprints, and accordingly provide general procedure for step length ratio extraction from unconstrained straight walking. Our method achieves a mean absolute percentage error (MAPE) of 1.9547% for 15 subjects' normal and abnormal side-view gaits, and also obtains satisfactory MAPEs for non-side-view gaits (2.4026% for 45°-view gaits and 3.9721% for 30°-view gaits). The performance is much better than a well-established monocular gait measurement system suitable only for side-view gaits with a MAPE of 3.5538%. Independently of walking directions, our method can accurately estimate step length ratios from unconstrained straight walking. This demonstrates our method is applicable for elders' daily gait monitoring to provide valuable information for elderly health care, such as abnormal gait recognition, fall risk assessment, etc. single-camera-based gait monitoring is unobtrusive, inexpensive, and easy-to-use to monitor daily gait of seniors in their homes. However, most studies require subjects to walk perpendicularly to camera's optical axis or along some specified routes, which limits its application in elderly home monitoring. To build unconstrained monitoring environments, we propose a method to measure step length symmetry ratio (a useful gait parameter representing gait symmetry without significant relationship with age) from unconstrained straight walking using a single camera, without strict restrictions on walking directions or routes. according to projective geometry theory, we first develop a calculation formula of step length ratio for the case of unconstrained straight-line walking. Then, to adapt to general cases, we propose to modify noncollinear footprints, and accordingly provide general procedure for step length ratio extraction from unconstrained straight walking. Our method achieves a mean absolute percentage error (MAPE) of 1.9547% for 15 subjects' normal and abnormal side-view gaits, and also obtains satisfactory MAPEs for non-side-view gaits (2.4026% for 45°-view gaits and 3.9721% for 30°-view gaits). The performance is much better than a well-established monocular gait measurement system suitable only for side-view gaits with a MAPE of 3.5538%. Independently of walking directions, our method can accurately estimate step length ratios from unconstrained straight walking. This demonstrates our method is applicable for elders' daily gait monitoring to provide valuable information for elderly health care, such as abnormal gait recognition, fall risk assessment, etc.

Fast kinetics of chromatin assembly revealed by single-molecule videomicroscopy and scanning force microscopy

PubMed Central

Ladoux, Benoit; Quivy, Jean-Pierre; Doyle, Patrick; Roure, Olivia du; Almouzni, Geneviève; Viovy, Jean-Louis

2000-01-01

Fluorescence videomicroscopy and scanning force microscopy were used to follow, in real time, chromatin assembly on individual DNA molecules immersed in cell-free systems competent for physiological chromatin assembly. Within a few seconds, molecules are already compacted into a form exhibiting strong similarities to native chromatin fibers. In these extracts, the compaction rate is more than 100 times faster than expected from standard biochemical assays. Our data provide definite information on the forces involved (a few piconewtons) and on the reaction path. DNA compaction as a function of time revealed unique features of the assembly reaction in these extracts. They imply a sequential process with at least three steps, involving DNA wrapping as the final event. An absolute and quantitative measure of the kinetic parameters of the early steps in chromatin assembly under physiological conditions could thus be obtained. PMID:11114182

Laboratory procedures to generate viral metagenomes.

PubMed

Thurber, Rebecca V; Haynes, Matthew; Breitbart, Mya; Wegley, Linda; Rohwer, Forest

2009-01-01

This collection of laboratory protocols describes the steps to collect viruses from various samples with the specific aim of generating viral metagenome sequence libraries (viromes). Viral metagenomics, the study of uncultured viral nucleic acid sequences from different biomes, relies on several concentration, purification, extraction, sequencing and heuristic bioinformatic methods. No single technique can provide an all-inclusive approach, and therefore the protocols presented here will be discussed in terms of hypothetical projects. However, care must be taken to individualize each step depending on the source and type of viral-particles. This protocol is a description of the processes we have successfully used to: (i) concentrate viral particles from various types of samples, (ii) eliminate contaminating cells and free nucleic acids and (iii) extract, amplify and purify viral nucleic acids. Overall, a sample can be processed to isolate viral nucleic acids suitable for high-throughput sequencing in approximately 1 week.

Back-extraction of trace elements from organometallic-halide extracts for determination by flameless atomic absorption spectrometry

USGS Publications Warehouse

Clark, J.R.; Viets, J.G.

1981-01-01

The Methyl isobutyl ketone-Amine synerGistic Iodkte Complex (MAGIC) extraction system offers the advantage that a large number of trace elements can be rapidly determined with a single sample preparation procedure. However, many of the elements extracted by the MAGIC system form volatile organometallic halide salts when the organic extract is heated in the graphite furnace. High concentrations of some elements such as Cu and Zn extracted by the system from anomalous geological samples produce serious interferences when certain other elements are determined by flameless atomic absorption. Stripping systems have been developed using solutions of HNO3, H2SO4, and CH3COOH individually or combined with H2O2 in order to circumvent these problems. With these systems most of the elements in the organic extract can be sequentially stripped into an aqueous phase. Organometallic volatilization and the most serious interelement interferences, therefore, can be eliminated by stripping with various combinations of reagents in a series of steps.

Synthesis, characterization and catalytic activity of silver nanoparticles using Tribulus terrestris leaf extract.

PubMed

Ashokkumar, S; Ravi, S; Kathiravan, V; Velmurugan, S

2014-01-01

Biomediated silver nanoparticles were synthesized with the aid of an eco-friendly biomaterial, namely, aqueous Tribulus terrestris extract. Silver nanoparticles were synthesized using a rapid, single step, and completely green biosynthetic method employing aqueous T. terrestris leaf extracts as both the reducing and capping agent. Silver ions were rapidly reduced by aqueous T. terrestris leaf extracts, leading to the formation of highly crystalline silver nanoparticles. An attempt has been made and formation of the silver nanoparticles was verified by surface plasmon spectra using an UV-vis (Ultra violet), spectrophotometer. Morphology and crystalline structure of the prepared silver nanoparticles were characterized by TEM (Transmission Electron Microscope) and XRD (X-ray Diffraction), techniques, respectively. FT-IR (Fourier Transform Infrared), analysis suggests that the obtained silver nanoparticles might be stabilized through the interactions of carboxylic groups, carbonyl groups and the flavonoids present in the T. terrestris extract. Copyright © 2013 Elsevier B.V. All rights reserved.

Parallel RNA extraction using magnetic beads and a droplet array.

PubMed

Shi, Xu; Chen, Chun-Hong; Gao, Weimin; Chao, Shih-Hui; Meldrum, Deirdre R

2015-02-21

Nucleic acid extraction is a necessary step for most genomic/transcriptomic analyses, but it often requires complicated mechanisms to be integrated into a lab-on-a-chip device. Here, we present a simple, effective configuration for rapidly obtaining purified RNA from low concentration cell medium. This Total RNA Extraction Droplet Array (TREDA) utilizes an array of surface-adhering droplets to facilitate the transportation of magnetic purification beads seamlessly through individual buffer solutions without solid structures. The fabrication of TREDA chips is rapid and does not require a microfabrication facility or expertise. The process takes less than 5 minutes. When purifying mRNA from bulk marine diatom samples, its repeatability and extraction efficiency are comparable to conventional tube-based operations. We demonstrate that TREDA can extract the total mRNA of about 10 marine diatom cells, indicating that the sensitivity of TREDA approaches single-digit cell numbers.

Parallel RNA extraction using magnetic beads and a droplet array

PubMed Central

Shi, Xu; Chen, Chun-Hong; Gao, Weimin; Meldrum, Deirdre R.

2015-01-01

Nucleic acid extraction is a necessary step for most genomic/transcriptomic analyses, but it often requires complicated mechanisms to be integrated into a lab-on-a-chip device. Here, we present a simple, effective configuration for rapidly obtaining purified RNA from low concentration cell medium. This Total RNA Extraction Droplet Array (TREDA) utilizes an array of surface-adhering droplets to facilitate the transportation of magnetic purification beads seamlessly through individual buffer solutions without solid structures. The fabrication of TREDA chips is rapid and does not require a microfabrication facility or expertise. The process takes less than 5 minutes. When purifying mRNA from bulk marine diatom samples, its repeatability and extraction efficiency are comparable to conventional tube-based operations. We demonstrate that TREDA can extract the total mRNA of about 10 marine diatom cells, indicating that the sensitivity of TREDA approaches single-digit cell numbers. PMID:25519439

Final state interactions and the extraction of neutron single spin asymmetries from semi-inclusive deep-inelastic scattering by a transversely polarized 3He target

NASA Astrophysics Data System (ADS)

Del Dotto, A.; Kaptari, L. P.; Pace, E.; Salmè, G.; Scopetta, S.

2017-12-01

The semi-inclusive deep-inelastic electron scattering off transversely polarized 3He, i.e., the process e +3He ⃗→e'+h +X , with h being a detected fast hadron, is studied beyond the plane-wave impulse approximation. To this end, a distorted spin-dependent spectral function of a nucleon inside an A =3 nucleus is actually evaluated through a generalized eikonal approximation, in order to take into account the final state interactions between the hadronizing system and the (A -1 ) nucleon spectator one. Our realistic description of both nuclear target and final state is a substantial step forward for achieving a reliable extraction of the Sivers and Collins single spin asymmetries of the free neutron. To illustrate how and to what extent the model dependence due to the treatment of the nuclear effects is under control, we apply our approach to the extraction procedure of the neutron single spin asymmetries from those measured for 3He for values of the kinematical variables relevant both for forthcoming experiments at Jefferson Laboratory and, with an exploratory purpose, for the future Electron Ion Collider.

Symposium on the reprocessing of irradiated fuels. Book 2, Session IV

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

None

1958-12-31

Book two of this conference has a single-focused session IV entitled Nonaqueous Processing, with 8 papers. The session deals with fluoride volatility processes and pyrometallurgical or pyrochemical processes. The latter involves either an oxide drossing or molten metal extraction or fused salt extraction technique and results in only partial decontamination. Fluoride volatility processes appear to be especially favorable for recovery of enriched uranium and decontamination factors of 10/sup 7/ to 10/sup 8/ would be achieved by simpler means than those employed in solvent extraction. Data from lab research on the BrF/sub 3/ process and the ClF/sub 3/ process are givenmore » and discussed and pilot plant experience is described, all in connection with natural uranium or slightly enriched uranium processing. Fluoride volatility processes for enriched or high alloy fuels are described step by step. The economic and engineering considerations of both types of nonaqueous processing are treated separately and as fully as present knowledge allows. A comprehensive review of the chemistry of pyrometallurgical processes is included.« less

Extraction, detection, and quantification of flavano-ellagitannins and ethylvescalagin in a Bordeaux red wine aged in oak barrels.

PubMed

Saucier, Cedric; Jourdes, Michael; Glories, Yves; Quideau, Stephane

2006-09-20

An extraction procedure and an analytical method have been developed to detect and quantify for the first time a series of ellagitannin derivatives formed in wine during aging in oak barrels. The method involves a preliminary purification step on XAD7 HP resin followed by a second purification step on TSK 40 HW gel. The resulting extract is analyzed for compound identification and quantitative determination by high-performance liquid chromatography-electrospray ionization-mass spectrometry in single ion recording mode. Reference compounds, which are accessible through hemisynthesis from the oak C-glycosidic ellagitannin vescalagin, were used to build calibration curves, and chlorogenic acid was selected as an internal standard. This method enabled us to estimate the content of four flavano-ellagitannins and that of another newly identified wine polyphenol, beta-1-O-ethylvescalagin, in a Bordeaux red wine aged for 18 months in oak barrels. All five ellagitannin derivatives are derived from the nucleophilic substitution reaction of vescalagin with the grape flavan-3-ols catechin and epicatechin or ethanol.

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

Damian, Luminita, E-mail: luminitadamian@microcal.eu.com; Universite de Toulouse, UPS, IPBS, F-31077 Toulouse; IUB, School of Engineering and Science, D-28727 Bremen

Is single-strand DNA translatable? Since the 60s, the question still remains whether or not DNA could be directly translated into protein. Some discrepancies in the results were reported about functional translation of single-strand DNA but all results converged on a similar behavior of RNA and ssDNA in the initiation step. Isothermal Titration Calorimetry method was used to determine thermodynamic constants of interaction between single-strand DNA and S30 extract of Escherichia coli. Our results showed that the binding was not affected by the nature of the template tested and the dissociation constants were in the same range when ssDNA (K{sub d}more » = 3.62 {+-} 2.1 x 10{sup -8} M) or the RNA corresponding sequence (K{sub d} = 2.7 {+-} 0.82 x 10{sup -8} M) bearing SD/ATG sequences were used. The binding specificity was confirmed by antibiotic interferences which block the initiation complex formation. These results suggest that the limiting step in translation of ssDNA is the elongation process.« less

Simultaneous Measurement of Thermal Conductivity and Specific Heat in a Single TDTR Experiment

NASA Astrophysics Data System (ADS)

Sun, Fangyuan; Wang, Xinwei; Yang, Ming; Chen, Zhe; Zhang, Hang; Tang, Dawei

2018-01-01

Time-domain thermoreflectance (TDTR) technique is a powerful thermal property measurement method, especially for nano-structures and material interfaces. Thermal properties can be obtained by fitting TDTR experimental data with a proper thermal transport model. In a single TDTR experiment, thermal properties with different sensitivity trends can be extracted simultaneously. However, thermal conductivity and volumetric heat capacity usually have similar trends in sensitivity for most materials; it is difficult to measure them simultaneously. In this work, we present a two-step data fitting method to measure the thermal conductivity and volumetric heat capacity simultaneously from a set of TDTR experimental data at single modulation frequency. This method takes full advantage of the information carried by both amplitude and phase signals; it is a more convenient and effective solution compared with the frequency-domain thermoreflectance method. The relative error is lower than 5 % for most cases. A silicon wafer sample was measured by TDTR method to verify the two-step fitting method.

Concurrent extraction and reaction for the production of biodiesel from wet microalgae.

PubMed

Im, Hanjin; Lee, HanSol; Park, Min S; Yang, Ji-Won; Lee, Jae W

2014-01-01

This work addresses a reliable in situ transesterification process which integrates lipid extraction from wet microalgae, and its conversion to biodiesel, with a yield higher than 90 wt.%. This process enables single-step production of biodiesel from microalgae by mixing wet microalgal cells with solvent, methanol, and acid catalyst; and then heating them in one pot. The effects of reaction parameters such as reaction temperature, wet cell weight, reaction time, and catalyst volume on the conversion yield are investigated. This simultaneous extraction and transesterification of wet microalgae may enable a significant reduction in energy consumption by eliminating the drying process of algal cells and realize the economic production of biodiesel using wet microalgae. Copyright © 2013 Elsevier Ltd. All rights reserved.

Ionic-liquid-impregnated resin for the microwave-assisted solid-liquid extraction of triazine herbicides in honey.

PubMed

Wu, Lijie; Song, Ying; Hu, Mingzhu; Yu, Cui; Zhang, Hanqi; Yu, Aimin; Ma, Qiang; Wang, Ziming

2015-09-01

Microwave-assisted ionic-liquid-impregnated resin solid-liquid extraction was developed for the extraction of triazine herbicides, including cyanazine, metribuzin, desmetryn, secbumeton, terbumeton, terbuthylazine, dimethametryn, and dipropetryn in honey samples. The ionic-liquid-impregnated resin was prepared by immobilizing 1-hexyl-3-methylimidazolium hexafluorophosphate in the microspores of resin. The resin was used as the extraction adsorbent. The extraction and enrichment of analytes were performed in a single step. The extraction time can be shortened greatly with the help of microwave. The effects of experimental parameters including type of resin, type of ionic liquid, mass ratio of resin to ionic liquid, extraction time, amount of the impregnated resin, extraction temperature, salt concentration, and desorption conditions on the extraction efficiency, were investigated. A Box-Behnken design was applied to the selection of the experimental parameters. The recoveries were in the range of 80.1 to 103.4% and the relative standard deviations were lower than 6.8%. The present method was applied to the analysis of honey samples. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Antiviral activity of an extract of Cordia salicifolia on herpes simplex virus type 1.

PubMed

Hayashi, K; Hayashi, T; Morita, N; Niwayama, S

1990-10-01

A partially purified extract (COL 1-6) from whole plant of Cordia salicifolia showed an inhibitory effect on herpes simplex virus type 1 (HSV-1). The activity of COL 1-6 on different steps of HSV-1 replication in HeLa cells was investigated. Under single-cycle replication conditions, COL 1-6 exerted a greater than 99.9% inhibition in virus yield when added to the cells 3 h or 1.5 h before infection, and even when added 8 h after infection the extract still caused a greater than 99% inhibition. The extract has been shown to have a direct virucidal activity. And also, analysis of early events following infection showed that COL 1-6 affected viral penetration in HeLa cells but did not interfere with adsorption to the cells.

The utilization of modified BCR three-step sequential extraction procedure for the fractionation of Cd, Cr, Cu, Ni, Pb and Zn in soil reference materials of different origins.

PubMed

Zemberyová, Mária; Barteková, Jana; Hagarová, Ingrid

2006-12-15

A modified three-step sequential extraction procedure for the fractionation of heavy metals, proposed by the Commission of the European Communities Bureau of Reference (BCR) has been applied to the Slovak reference materials of soils (soil orthic luvisols, soil rendzina and soil eutric cambisol), which represent pedologically different types of soils in Slovakia. Analyses were carried out by flame or electrothermal atomic absorption spectrometry (FAAS or ETAAS). The fractions extracted were: exchangeable (extraction step 1), reducible-iron/manganese oxides (extraction step 2), oxidizable-organic matter and sulfides (extraction step 3). The sum of the element contents in the three fractions plus aqua-regia extractable content of the residue was compared to the aqua-regia extractable content of the elements in the origin soils. The accuracy obtained by comparing the determined contents of the elements with certified values, using BCR CRM 701, certified for the extractable contents (mass fractions) of Cd, Cr, Cu, Ni, Pb and Zn in sediment following a modified BCR-three step sequential extraction procedure, was found to be satisfactory.

In-situ determination of metallic variation and multi-association in single particles by combining synchrotron microprobe, sequential chemical extraction and multivariate statistical analysis.

PubMed

Zhu, Yu-Min; Zhang, Hua; Fan, Shi-Suo; Wang, Si-Jia; Xia, Yi; Shao, Li-Ming; He, Pin-Jing

2014-07-15

Due to the heterogeneity of metal distribution, it is challenging to identify the speciation, source and fate of metals in solid samples at micro scales. To overcome these challenges single particles of air pollution control residues were detected in situ by synchrotron microprobe after each step of chemical extraction and analyzed by multivariate statistical analysis. Results showed that Pb, Cu and Zn co-existed as acid soluble fractions during chemical extraction, regardless of their individual distribution as chlorides or oxides in the raw particles. Besides the forms of Fe2O3, MnO2 and FeCr2O4, Fe, Mn, Cr and Ni were closely associated with each other, mainly as reducible fractions. In addition, the two groups of metals had interrelations with the Si-containing insoluble matrix. The binding could not be directly detected by micro-X-ray diffraction (μ-XRD) and XRD, suggesting their partial existence as amorphous forms or in the solid solution. The combined method on single particles can effectively determine metallic multi-associations and various extraction behaviors that could not be identified by XRD, μ-XRD or X-ray absorption spectroscopy. The results are useful for further source identification and migration tracing of heavy metals. Copyright © 2014 Elsevier B.V. All rights reserved.

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.

Extractability and Bioavailability of Pb and As in Historically Contaminated Orchard Soil: Effects of Compost Amendments

PubMed Central

Fleming, Margaret; Yiping, Tai; Ping, Zhuang; McBride, Murray B.

2015-01-01

The availability of Pb and As in an historically contaminated orchard soil, after amendment with compost and aging in the field, was determined by single-step chemical extraction with 1.0 M ammonium acetate at pH 4.8, sequential extraction using the modified BCR test, and a redworm bioassay in the laboratory. The efficiency of soil Pb extraction by ammonium acetate was greater at higher total soil Pb but was reduced by compost amendment. Conversely, the extraction efficiency of total soil As increased with compost amendment, but was not sensitive to total soil As. The redworm bioassay indicated Pb (but not As) bioavailability to be reduced by soil amendment with compost, a result consistent with the ammonium acetate extraction test but not reflected in modified BCR test. Electron microprobe studies of the orchard soil revealed Pb and As to be spatially associated in discrete particles along with phosphorus and iron. PMID:23474982

Universal nucleic acids sample preparation method for cells, spores and their mixture

DOEpatents

Bavykin, Sergei [Darien, IL

2011-01-18

The present invention relates to a method for extracting nucleic acids from biological samples. More specifically the invention relates to a universal method for extracting nucleic acids from unidentified biological samples. An advantage of the presently invented method is its ability to effectively and efficiently extract nucleic acids from a variety of different cell types including but not limited to prokaryotic or eukaryotic cells and/or recalcitrant organisms (i.e. spores). Unlike prior art methods which are focused on extracting nucleic acids from vegetative cell or spores, the present invention effectively extracts nucleic acids from spores, multiple cell types or mixtures thereof using a single method. Important that the invented method has demonstrated an ability to extract nucleic acids from spores and vegetative bacterial cells with similar levels effectiveness. The invented method employs a multi-step protocol which erodes the cell structure of the biological sample, isolates, labels, fragments nucleic acids and purifies labeled samples from the excess of dye.

A green deep eutectic solvent-based aqueous two-phase system for protein extracting.

PubMed

Xu, Kaijia; Wang, Yuzhi; Huang, Yanhua; Li, Na; Wen, Qian

2015-03-15

As a new type of green solvent, deep eutectic solvent (DES) has been applied for the extraction of proteins with an aqueous two-phase system (ATPS) in this work. Four kinds of choline chloride (ChCl)-based DESs were synthesized to extract bovine serum albumin (BSA), and ChCl-glycerol was selected as the suitable extraction solvent. Single factor experiments have been done to investigate the effects of the extraction process, including the amount of DES, the concentration of salt, the mass of protein, the shaking time, the temperature and PH value. Experimental results show 98.16% of the BSA could be extracted into the DES-rich phase in a single-step extraction under the optimized conditions. A high extraction efficiency of 94.36% was achieved, while the conditions were applied to the extraction of trypsin (Try). Precision, repeatability and stability experiments were studied and the relative standard deviations (RSD) of the extraction efficiency were 0.4246% (n=3), 1.6057% (n=3) and 1.6132% (n=3), respectively. Conformation of BSA was not changed during the extraction process according to the investigation of UV-vis spectra, FT-IR spectra and CD spectra of BSA. The conductivity, dynamic light scattering (DLS) and transmission electron microscopy (TEM) were used to explore the mechanism of the extraction. It turned out that the formation of DES-protein aggregates play a significant role in the separation process. All the results suggest that ChCl-based DES-ATPS are supposed to have the potential to provide new possibilities in the separation of proteins. Copyright © 2015 Elsevier B.V. All rights reserved.

Chemical mimicking of bio-assisted aluminium extraction by Aspergillus niger's exometabolites.

PubMed

Boriová, Katarína; Urík, Martin; Bujdoš, Marek; Pifková, Ivana; Matúš, Peter

2016-11-01

Presence of microorganisms in soils strongly affects mobility of metals. This fact is often excluded when mobile metal fraction in soil is studied using extraction procedures. Thus, the first objective of this paper was to evaluate strain Aspergillus niger's exometabolites contribution on aluminium mobilization. Fungal exudates collected in various time intervals during cultivation were analyzed and used for two-step bio-assisted extraction of alumina and gibbsite. Oxalic, citric and gluconic acids were identified in collected culture media with concentrations up to 68.4, 2.0 and 16.5 mmol L -1 , respectively. These exometabolites proved to be the most efficient agents in mobile aluminium fraction extraction with aluminium extraction efficiency reaching almost 2.2%. However, fungal cultivation is time demanding process. Therefore, the second objective was to simplify acquisition of equally efficient extracting agent by chemically mimicking composition of main organic acid components of fungal exudates. This was successfully achieved with organic acids mixture prepared according to medium composition collected on the 12th day of Aspergillus niger cultivation. This mixture extracted similar amounts of aluminium from alumina compared to culture medium. The aluminium extraction efficiency from gibbsite by organic acids mixture was lesser than 0.09% which is most likely because of more rigid mineral structure of gibbsite compared to alumina. The prepared organic acid mixture was then successfully applied for aluminium extraction from soil samples and compared to standard single step extraction techniques. This showed there is at least 2.9 times higher content of mobile aluminium fraction in soils than it was previously considered, if contribution of microbial metabolites is considered in extraction procedures. Thus, our contribution highlights the significance of fungal metabolites in aluminium extraction from environmental samples, but it also simplifies the extraction procedure inspired by bio-assisted extraction of aluminium by common soil fungus A. niger. Copyright © 2016 Elsevier Ltd. All rights reserved.

Development of two-step process for enhanced biorecovery of Cu-Zn-Ni from computer printed circuit boards.

PubMed

Shah, Monal B; Tipre, Devayani R; Purohit, Mamta S; Dave, Shailesh R

2015-08-01

Metal pollution due to the huge electronic waste (E-waste) accumulation is widespread across the globe. Extraction of copper, zinc and nickel from computer printed circuit boards (c-PCB) with a two-step bleaching process using ferric sulphate generated by Leptospirillum ferriphilum dominated consortium and the factors influencing the process were investigated in the present study. The studied factors with 10 g/L pulp density showed that pH 2.0 was optimum which resulted in 87.50-97.80% Cu-Zn-Ni extraction. Pre-treatment of PCB powder with acidified distilled water and NaCl solution showed 3.80-7.98% increase in metal extraction corresponding to 94.08% Cu, 99.80% Zn and 97.99% Ni extraction. Particle size of 75 μm for Cu and Zn while 1680 μm for Ni showed 2-folds increase in metal extraction, giving 97.35-99.80% Cu-Zn-Ni extraction in 2-6 days of reaction time. Whereas; 2.76-3.12 folds increase in Cu and Zn extraction was observed with the addition of 0.1% chelating agents. When the studies were carried out with high pulp density, ferric iron concentration of 16.57 g/L was found to be optimum for metal extraction from 75 g/L c-PCB and c-PCB addition in multiple installments resulted in 8.81-26.35% increase in metal extraction compared to single addition. The studied factors can be implemented for the scale-up aimed at faster recovery of multimetals from E-waste and thereby providing a secondary source of metal in an eco-friendly manner. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Nonlinear Analyte Concentration Gradients for One-Step Kinetic Analysis Employing Optical Microring Resonators

PubMed Central

Marty, Michael T.; Kuhnline Sloan, Courtney D.; Bailey, Ryan C.; Sligar, Stephen G.

2012-01-01

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics. PMID:22686186

Nonlinear analyte concentration gradients for one-step kinetic analysis employing optical microring resonators.

PubMed

Marty, Michael T; Sloan, Courtney D Kuhnline; Bailey, Ryan C; Sligar, Stephen G

2012-07-03

Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes, and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics.

Improving Signal-to-Noise Ratio in Scanning Transmission Electron Microscopy Energy-Dispersive X-Ray (STEM-EDX) Spectrum Images Using Single-Atomic-Column Cross-Correlation Averaging.

PubMed

Jeong, Jong Seok; Mkhoyan, K Andre

2016-06-01

Acquiring an atomic-resolution compositional map of crystalline specimens has become routine practice, thus opening possibilities for extracting subatomic information from such maps. A key challenge for achieving subatomic precision is the improvement of signal-to-noise ratio (SNR) of compositional maps. Here, we report a simple and reliable solution for achieving high-SNR energy-dispersive X-ray (EDX) spectroscopy spectrum images for individual atomic columns. The method is based on standard cross-correlation aided by averaging of single-column EDX maps with modifications in the reference image. It produces EDX maps with minimal specimen drift, beam drift, and scan distortions. Step-by-step procedures to determine a self-consistent reference map with a discussion on the reliability, stability, and limitations of the method are presented here.

Validation of a One-Step Method for Extracting Fatty Acids from Salmon, Chicken and Beef Samples.

PubMed

Zhang, Zhichao; Richardson, Christine E; Hennebelle, Marie; Taha, Ameer Y

2017-10-01

Fatty acid extraction methods are time-consuming and expensive because they involve multiple steps and copious amounts of extraction solvents. In an effort to streamline the fatty acid extraction process, this study compared the standard Folch lipid extraction method to a one-step method involving a column that selectively elutes the lipid phase. The methods were tested on raw beef, salmon, and chicken. Compared to the standard Folch method, the one-step extraction process generally yielded statistically insignificant differences in chicken and salmon fatty acid concentrations, percent composition and weight percent. Initial testing showed that beef stearic, oleic and total fatty acid concentrations were significantly lower by 9-11% with the one-step method as compared to the Folch method, but retesting on a different batch of samples showed a significant 4-8% increase in several omega-3 and omega-6 fatty acid concentrations with the one-step method relative to the Folch. Overall, the findings reflect the utility of a one-step extraction method for routine and rapid monitoring of fatty acids in chicken and salmon. Inconsistencies in beef concentrations, although minor (within 11%), may be due to matrix effects. A one-step fatty acid extraction method has broad applications for rapidly and routinely monitoring fatty acids in the food supply and formulating controlled dietary interventions. © 2017 Institute of Food Technologists®.

Magnetic molecularly imprinted polymers based on silica modified by deep eutectic solvents for the rapid simultaneous magnetic-based solid-phase extraction of Salvia miltiorrhiza bunge, Glycine max (Linn.) Merr and green tea.

PubMed

Li, Guizhen; Wang, Xiaoqin; Row, Kyung Ho

2018-04-01

Novel magnetic molecularly imprinted polymers (MMIPs) with multiple-template based on silica were modified by four types of deep eutectic solvents (DESs) for the rapid simultaneous magnetic solid-phase extraction (MSPE) of tanshinone Ⅰ, tanshinone ⅡA, and cryptotanshinone from Salvia miltiorrhiza bunge; glycitein, genistein, and daidzein from Glycine max (Linn.) Merr; and epicatechin, epigallocatechin gallate, and epicatechin gallate from green tea, respectively. The synthesized materials were characterized by Fourier transform infrared spectroscopy and field emission scanning electron microscopy. Single factor experiments were to explore the relationship between the extraction efficiency and four factors (the sample solution pH, amount of DESs for modification, amount of adsorbent, and extraction time). It was showed that the DES4-MMIPs have better extraction ability than the MMIPs without DESs and the other three DESs-modified MMIPs. The best extraction recoveries with DES4-MMIP were tanshinone Ⅰ (85.57%), tanshinone ⅡA (80.58%), cryptotanshinone (92.12%), glycitein (81.65%), genistein (87.72%), daidzein (92.24%), epicatechin (86.43%), epigallocatechin gallate (80.92%), and epicatechin gallate (93.64%), respectively. The novel multiple-template MMIPs materials modified by DES for the rapid simultaneous MSPE of active compounds were proved to reduce the experimental steps than single-template technique, and increase the extraction efficiency. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fully integrated lab-on-a-disc for nucleic acid analysis of food-borne pathogens.

PubMed

Kim, Tae-Hyeong; Park, Juhee; Kim, Chi-Ju; Cho, Yoon-Kyoung

2014-04-15

This paper describes a micro total analysis system for molecular analysis of Salmonella, a major food-borne pathogen. We developed a centrifugal microfluidic device, which integrated the three main steps of pathogen detection, DNA extraction, isothermal recombinase polymerase amplification (RPA), and detection, onto a single disc. A single laser diode was utilized for wireless control of valve actuation, cell lysis, and noncontact heating in the isothermal amplification step, thereby yielding a compact and miniaturized system. To achieve high detection sensitivity, rare cells in large volumes of phosphate-buffered saline (PBS) and milk samples were enriched before loading onto the disc by using antibody-coated magnetic beads. The entire procedure, from DNA extraction through to detection, was completed within 30 min in a fully automated fashion. The final detection was carried out using lateral flow strips by direct visual observation; detection limit was 10 cfu/mL and 10(2) cfu/mL in PBS and milk, respectively. Our device allows rapid molecular diagnostic analysis and does not require specially trained personnel or expensive equipment. Thus, we expect that it would have an array of potential applications, including in the detection of food-borne pathogens, environmental monitoring, and molecular diagnostics in resource-limited settings.

Downstream processing of antibodies: single-stage versus multi-stage aqueous two-phase extraction.

PubMed

Rosa, P A J; Azevedo, A M; Ferreira, I F; Sommerfeld, S; Bäcker, W; Aires-Barros, M R

2009-12-11

Single-stage and multi-stage strategies have been evaluated and compared for the purification of human antibodies using liquid-liquid extraction in aqueous two-phase systems (ATPSs) composed of polyethylene glycol 3350 (PEG 3350), dextran, and triethylene glycol diglutaric acid (TEG-COOH). The performance of single-stage extraction systems was firstly investigated by studying the effect of pH, TEG-COOH concentration and volume ratio on the partitioning of the different components of a Chinese hamster ovary (CHO) cells supernatant. It was observed that lower pH values and high TEG-COOH concentrations favoured the selective extraction of human immunoglobulin G (IgG) to the PEG-rich phase. Higher recovery yields, purities and percentage of contaminants removal were always achieved in the presence of the ligand, TEG-COOH. The extraction of IgG could be enhanced using higher volume ratios, however with a significant decrease in both purity and percentage of contaminants removal. The best single-stage extraction conditions were achieved for an ATPS containing 1.3% (w/w) TEG-COOH with a volume ratio of 2.2, which allowed the recovery of 96% of IgG in the PEG-rich phase with a final IgG concentration of 0.21mg/mL, a protein purity of 87% and a total purity of 43%. In order to enhance simultaneously both recovery yield and purity, a four stage cross-current operation was simulated and the corresponding liquid-liquid equilibrium (LLE) data determined. A predicted optimised scheme of a counter-current multi-stage aqueous two-phase extraction was hence described. IgG can be purified in the PEG-rich top phase with a final recovery yield of 95%, a final concentration of 1.04mg/mL and a protein purity of 93%, if a PEG/dextran ATPS containing 1.3% (w/w) TEG-COOH, 5 stages and volume ratio of 0.4 are used. Moreover, according to the LLE data of all CHO cells supernatant components, it was possible to observe that most of the cells supernatant contaminants can be removed during this extraction step leading to a final total purity of about 85%.

Study Approach of Antioxidant Properties in Foods: Update and Considerations.

PubMed

Durazzo, Alessandra

2017-02-28

The assessment of interactions between natural antioxidants and other food matrix components represents the main step in the investigation of total antioxidant properties, in terms of potential health benefits. The diversity of chemical structures of natural compounds, besides their possible interactions, as well as the biological role and different modes of action makes it difficult to assess a single and reliable procedure for the evaluation of antioxidant activity. Today, much attention is given to the distinction between extractable and non-extractable antioxidants as a key tool in the description of the nutritional and healthy properties of food matrices. The starting point for the investigation of antioxidant effects of food extracts is the analysis of antioxidant properties of pure compounds and their interactions. Another complementary approach could be represented by the study of how different biologically active compound-rich extracts contribute to the total antioxidant capacity.

Detection of lysergic acid diethylamide (LSD) in urine by gas chromatography-ion trap tandem mass spectrometry.

PubMed

Sklerov, J H; Kalasinsky, K S; Ehorn, C A

1999-10-01

A confirmatory method for the detection and quantitation of lysergic acid diethylamide (LSD) is presented. The method employs gas chromatography-tandem mass spectrometry (GC-MS-MS) using an internal ionization ion trap detector for sensitive MS-MS-in-time measurements of LSD extracted from urine. Following a single-step solid-phase extraction of 5 mL of urine, underivatized LSD can be measured with limits of quantitation and detection of 80 and 20 pg/mL, respectively. Temperature-programmed on-column injections of urine extracts were linear over the concentration range 20-2000 pg/mL (r2 = 0.999). Intraday and interday coefficients of variation were < 6% and < 13%, respectively. This procedure has been applied to quality-control specimens and LSD-positive samples in this laboratory. Comparisons with alternate GC-MS methods and extraction procedures are discussed.

Study Approach of Antioxidant Properties in Foods: Update and Considerations

PubMed Central

Durazzo, Alessandra

2017-01-01

The assessment of interactions between natural antioxidants and other food matrix components represents the main step in the investigation of total antioxidant properties, in terms of potential health benefits. The diversity of chemical structures of natural compounds, besides their possible interactions, as well as the biological role and different modes of action makes it difficult to assess a single and reliable procedure for the evaluation of antioxidant activity. Today, much attention is given to the distinction between extractable and non-extractable antioxidants as a key tool in the description of the nutritional and healthy properties of food matrices. The starting point for the investigation of antioxidant effects of food extracts is the analysis of antioxidant properties of pure compounds and their interactions. Another complementary approach could be represented by the study of how different biologically active compound-rich extracts contribute to the total antioxidant capacity. PMID:28264480

Comparison of the Anti-Adhesion Activity of Three Different Cranberry Extracts on Uropathogenic P-fimbriated Escherichia coli: a Randomized, Double-blind, Placebo Controlled, Ex Vivo, Acute Study.

PubMed

Howell, Amy; Souza, Dan; Roller, Marc; Fromentin, Emilie

2015-07-01

Research suggests that cranberry (Vaccinium macrocarpon) helps maintain urinary tract health. Bacterial adhesion to the uroepithelium is the initial step in the progression to development of a urinary tract infection. The bacterial anti-adhesion activity of cranberry proanthocyanidins (PACs) has been demonstrated in vitro. Three different cranberry extracts were developed containing a standardized level of 36 mg of PACs. This randomized, double-blind, placebo controlled, ex vivo, acute study was designed to compare the anti-adhesion activity exhibited by human urine following consumption of three different cranberry extracts on uropathogenic P-fimbriated Escherichia coli in healthy men and women. All three cranberry extracts significantly increased anti-adhesion activity in urine. from 6 to 12 hours after intake of a single dose standardized to deliver 36 mg of PACs (as measured by the BL-DMAC method), versus placebo.

Comparative pharmacokinetics study of orientin in rat plasma by UHPLC-MS/MS after intravenous administration of single orientin and Trollius chinensis Bunge extract.

PubMed

Zhao, Nan; Sun, Qi; Song, Yang; Wang, Lin; Zhang, Tingjian; Meng, Fanhao

2018-04-01

Orientin showed a broad array of biological activities, and it is the major bioactive compound in the Trollius chinensis Bunge. The aim of this study was to investigate the comparative pharmacokinetics of orientin after intravenous administration of single orientin and T. chinensis Bunge extract. Sample preparation involved a simple one-step deproteinization procedure with acetonitrile. Chromatographic separation was achieved on a Waters BEH C 18 column with a mobile phase consisting of acetonitrile and water containing 0.1% formic acid in an isocratic elution way. The detection was accomplished in multiple reaction monitoring mode with positive electrospray ionization. The pharmacokinetic properties of orientin were compared after intravenous administrations of pure orientin and T. chinensis Bunge extract to rats with approximately the same dosage of 10 mg/kg. The results of the study indicate that the pharmacokinetics of orientin in rat plasma show significant differences between two groups. This is useful for the clinical uses of therapeutic dosing of orientin and T. chinensis Bunge. Copyright © 2017 John Wiley & Sons, Ltd.

Determination of Total Biotin by Liquid Chromatography Coupled with Immunoaffinity Column Cleanup Extraction: Multilaboratory Testing, Final Action 2016.02.

PubMed

Joseph, George; Devi, Ranjani; Marley, Elaine C; Leeman, David

2018-05-01

Single- and multilaboratory testing data have provided systematic scientific evidence that a simple, selective, accurate, and precise method can be used as a potential candidate reference method for dispute resolution in determining total biotin in all forms of infant, adult, and/or pediatric formula. Using LC coupled with immunoaffinity column cleanup extraction, the method fully meets the intended purpose and applicability statement in AOAC Standard Method Performance Requirement 2014.005. The method was applied to a cross-section of infant formula and adult nutritional matrixes, and acceptable precision and accuracy were established. The analytical platform is inexpensive, and the method can be used in almost any laboratory worldwide with basic facilities. The immunoaffinity column cleanup extraction is the key step to successful analysis.

A fatal intoxication following the ingestion of 5-methoxy-N,N-dimethyltryptamine in an ayahuasca preparation.

PubMed

Sklerov, Jason; Levine, Barry; Moore, Karla A; King, Theodore; Fowler, David

2005-01-01

A case of a 25-year-old white male who was found dead the morning after consuming herbal extracts containing beta-carbolines and hallucinogenic tryptamines is presented. No anatomic cause of death was found at autopsy. Toxicologic analysis of the heart blood identified N,N-dimethyltryptamine (0.02 mg/L), 5-methoxy-N,N-dimethyltryptamine (1.88 mg/L), tetrahydroharmine (0.38 mg/L), harmaline (0.07 mg/L), and harmine (0.17 mg/L). All substances were extracted by a single-step n-butyl chloride extraction following alkalinization with borate buffer. Detection and quantitation was performed using liquid chromatography-electrospray mass spectrometry. The medical examiner ruled that the cause of death was hallucinogenic amine intoxication, and the manner of death was undetermined.

Single hair analysis of small molecules using MALDI-triple quadrupole MS imaging and LC-MS/MS: investigations on opportunities and pitfalls.

PubMed

Poetzsch, Michael; Steuer, Andrea E; Roemmelt, Andreas T; Baumgartner, Markus R; Kraemer, Thomas

2014-12-02

Single hair analysis normally requires extensive sample preparation microscale protocols including time-consuming steps like segmentation and extraction. Matrix assisted laser desorption and ionization mass spectrometric imaging (MALDI-MSI) was shown to be an alternative tool in single hair analysis, but still, questions remain. Therefore, an investigation of MALDI-MSI in single hair analysis concerning the extraction process, usage of internal standard (IS), and influences on the ionization processes were systematically investigated to enable the reliable application to hair analysis. Furthermore, single dose detection, quantitative correlation to a single hair, and hair strand LC-MS/MS results were performed, and the performance was compared to LC-MS/MS single hair monitoring. The MALDI process was shown to be independent from natural hair color and not influenced by the presence of melanin. Ionization was shown to be reproducible along and in between different hair samples. MALDI image intensities in single hair and hair snippets showed good semiquantitative correlation to zolpidem hair concentrations obtained from validated routine LC-MS/MS methods. MALDI-MSI is superior to LC-MS/MS analysis when a fast, easy, and cheap sample preparation is necessary, whereas LC-MS/MS showed higher sensitivity with the ability of single dose detection for zolpidem. MALDI-MSI and LC-MS/MS segmental single hair analysis showed good correlation, and both are suitable for consumption monitoring of drugs of abuse with a high time resolution.

Droplet Microfluidics for Compartmentalized Cell Lysis and Extension of DNA from Single-Cells

NASA Astrophysics Data System (ADS)

Zimny, Philip; Juncker, David; Reisner, Walter

Current single cell DNA analysis methods suffer from (i) bias introduced by the need for molecular amplification and (ii) limited ability to sequence repetitive elements, resulting in (iii) an inability to obtain information regarding long range genomic features. Recent efforts to circumvent these limitations rely on techniques for sensing single molecules of DNA extracted from single-cells. Here we demonstrate a droplet microfluidic approach for encapsulation and biochemical processing of single-cells inside alginate microparticles. In our approach, single-cells are first packaged inside the alginate microparticles followed by cell lysis, DNA purification, and labeling steps performed off-chip inside this microparticle system. The alginate microparticles are then introduced inside a micro/nanofluidic system where the alginate is broken down via a chelating buffer, releasing long DNA molecules which are then extended inside nanofluidic channels for analysis via standard mapping protocols.

The influence of Brazilian plant extracts on Streptococcus mutans biofilm.

PubMed

Barnabé, Michele; Saraceni, Cíntia Helena Coury; Dutra-Correa, Maristela; Suffredini, Ivana Barbosa

2014-01-01

Nineteen plant extracts obtained from plants from the Brazilian Amazon showed activity against planktonic Streptococcus mutans, an important bacterium involved in the first steps of biofilm formation and the subsequent initiation of several oral diseases. Our goal was to verify whether plant extracts that showed activity against planktonic S. mutans could prevent the organization of or even disrupt a single-species biofilm made by the same bacteria. Plant extracts were tested on a single-bacteria biofilm prepared using the Zürich method. Each plant extract was tested at a concentration 5 times higher than its minimum inhibitory concentration (MIC). Discs of hydroxyapatite were submersed overnight in brain-heart infusion broth enriched with saccharose 5%, which provided sufficient time for biofilm formation. The discs were then submersed in extract solutions for one minute, three times per day, for two subsequent days. The discs were then washed with saline three times, at ten seconds each, after each treatment. Supports were allowed to remain in the enriched medium for one additional night. At the end of the process, the bacteria were removed from the discs by vortexing and were counted. Only two of 19 plant extracts showed activity in the present assay: EB1779, obtained from Dioscorea altissima, and EB1673, obtained from Annona hypoglauca. Although the antibacterial activity of the plant extracts was first observed against planktonic S. mutans, influence over biofilm formation was not necessarily observed in the biofilm model. The present results motivate us to find new natural products to be used in dentistry.

The influence of Brazilian plant extracts on Streptococcus mutans biofilm

PubMed Central

BARNABÉ, Michele; SARACENI, Cíntia Helena Coury; DUTRA-CORREA, Maristela; SUFFREDINI, Ivana Barbosa

2014-01-01

Nineteen plant extracts obtained from plants from the Brazilian Amazon showed activity against planktonic Streptococcus mutans, an important bacterium involved in the first steps of biofilm formation and the subsequent initiation of several oral diseases. Objective Our goal was to verify whether plant extracts that showed activity against planktonic S. mutans could prevent the organization of or even disrupt a single-species biofilm made by the same bacteria. Material and Methods Plant extracts were tested on a single-bacteria biofilm prepared using the Zürich method. Each plant extract was tested at a concentration 5 times higher than its minimum inhibitory concentration (MIC). Discs of hydroxyapatite were submersed overnight in brain-heart infusion broth enriched with saccharose 5%, which provided sufficient time for biofilm formation. The discs were then submersed in extract solutions for one minute, three times per day, for two subsequent days. The discs were then washed with saline three times, at ten seconds each, after each treatment. Supports were allowed to remain in the enriched medium for one additional night. At the end of the process, the bacteria were removed from the discs by vortexing and were counted. Results Only two of 19 plant extracts showed activity in the present assay: EB1779, obtained from Dioscorea altissima, and EB1673, obtained from Annona hypoglauca. Although the antibacterial activity of the plant extracts was first observed against planktonic S. mutans, influence over biofilm formation was not necessarily observed in the biofilm model. The present results motivate us to find new natural products to be used in dentistry. PMID:25466471

Isolation of proteolytic bacteria from mealworm (Tenebrio molitor) exoskeletons to produce chitinous material.

PubMed

da Silva, Fernanda Kerche Paes; Brück, Dieter W; Brück, Wolfram M

2017-09-15

The use of insects as a source of protein is becoming an important factor for feeding an increasing population. After protein extraction for food use, the insect exoskeleton may offer the possibility for the production of added value products. Here, the aim was to isolate bacteria from the surface of farmed mealworms (Tenebrio molitor Linnaeus, 1758) for the production of chitinous material from insect exoskeletons using microbial fermentation. Isolates were screened for proteases and acid production that may aid deproteination and demineralisation of insects through fermentation to produce chitin. Selected isolates were used single-step (isolated bacteria only) or two-step fermentations with Lactobacillus plantarum (DSM 20174). Two-step fermentations with isolates from mealworm exoskeletons resulted in a demineralisation of 97.9 and 98.5% from deproteinated mealworm fractions. Attenuated total reflectance-Fourier- transform infrared spectroscopy analysis showed that crude chitin was produced. However, further optimisation is needed before the process can be upscaled. This is, to our knowledge, the first report using microbial fermentation for the extraction of chitin from insects. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

A novel framework for feature extraction in multi-sensor action potential sorting.

PubMed

Wu, Shun-Chi; Swindlehurst, A Lee; Nenadic, Zoran

2015-09-30

Extracellular recordings of multi-unit neural activity have become indispensable in neuroscience research. The analysis of the recordings begins with the detection of the action potentials (APs), followed by a classification step where each AP is associated with a given neural source. A feature extraction step is required prior to classification in order to reduce the dimensionality of the data and the impact of noise, allowing source clustering algorithms to work more efficiently. In this paper, we propose a novel framework for multi-sensor AP feature extraction based on the so-called Matched Subspace Detector (MSD), which is shown to be a natural generalization of standard single-sensor algorithms. Clustering using both simulated data and real AP recordings taken in the locust antennal lobe demonstrates that the proposed approach yields features that are discriminatory and lead to promising results. Unlike existing methods, the proposed algorithm finds joint spatio-temporal feature vectors that match the dominant subspace observed in the two-dimensional data without needs for a forward propagation model and AP templates. The proposed MSD approach provides more discriminatory features for unsupervised AP sorting applications. Copyright © 2015 Elsevier B.V. All rights reserved.

Extraction of chitin from red crab shell waste by cofermentation with Lactobacillus paracasei subsp. tolerans KCTC-3074 and Serratia marcescens FS-3.

PubMed

Jung, W J; Jo, G H; Kuk, J H; Kim, K Y; Park, R D

2006-06-01

For one-step extraction of chitin from red crab shell waste, cofermentation with Lactobacillus paracasei subsp. tolerans KCTC-3074, a lactic-acid-producing bacterium, and Serratia marcescens FS-3, a protease-producing bacterium, was conducted. Fermentation with single strain (L. 3074 or FS-3) was also conducted. At day 7, the pH in L. 3074, FS-3, and L. 3074+FS-3 (1:1) treatment decreased from 6.90 to 3.30, 5.88, and 3.48, respectively. Ash content in the residue after fermentation treatment of crab shells in L. 3074 and L. 3074+FS-3 (1:1) treatment drastically decreased from 41.2% to 3.19 and 1.15%, respectively. In L. 3074+FS-3 (1:1) cofermentation, the level of demineralization was the highest value of 97.2%, but the level of deproteinization in the cofermentation was 52.6% at day 7. Protein content in the treatment of FS-3 alone reduced from 22.4 to 3.62%. These results indicate that cofermentation of the shells using the two strains is efficient and applicable for the one-step extraction of crude chitin from red crab shell waste.

Matching Aerial Images to 3D Building Models Using Context-Based Geometric Hashing

PubMed Central

Jung, Jaewook; Sohn, Gunho; Bang, Kiin; Wichmann, Andreas; Armenakis, Costas; Kada, Martin

2016-01-01

A city is a dynamic entity, which environment is continuously changing over time. Accordingly, its virtual city models also need to be regularly updated to support accurate model-based decisions for various applications, including urban planning, emergency response and autonomous navigation. A concept of continuous city modeling is to progressively reconstruct city models by accommodating their changes recognized in spatio-temporal domain, while preserving unchanged structures. A first critical step for continuous city modeling is to coherently register remotely sensed data taken at different epochs with existing building models. This paper presents a new model-to-image registration method using a context-based geometric hashing (CGH) method to align a single image with existing 3D building models. This model-to-image registration process consists of three steps: (1) feature extraction; (2) similarity measure; and matching, and (3) estimating exterior orientation parameters (EOPs) of a single image. For feature extraction, we propose two types of matching cues: edged corner features representing the saliency of building corner points with associated edges, and contextual relations among the edged corner features within an individual roof. A set of matched corners are found with given proximity measure through geometric hashing, and optimal matches are then finally determined by maximizing the matching cost encoding contextual similarity between matching candidates. Final matched corners are used for adjusting EOPs of the single airborne image by the least square method based on collinearity equations. The result shows that acceptable accuracy of EOPs of a single image can be achievable using the proposed registration approach as an alternative to a labor-intensive manual registration process. PMID:27338410

Production of three types of krill oils from krill meal by a three-step solvent extraction procedure.

PubMed

Xie, Dan; Mu, Hongyan; Tang, Tianpei; Wang, Xiaosan; Wei, Wei; Jin, Jun; Wang, Xingguo; Jin, Qingzhe

2018-05-15

In this study, a three-step extraction method (separately use acetone, hexane, and ethanol as extraction solvent in each step) was conducted to selectively extract three types of krill oils with different compositions. The lipid yields were 5.08% in step 1, 4.80% in step 2, and 9.11% in step 3, with a total of 18.99%. The krill oil extracted with acetone in step 1 (A-KO) contained the lowest contents of phospholipids (PL) (2.32%) and n-3 polyunsaturated fatty acids (PUFA) (16.63%), but the highest levels of minor components (505.00 mg/kg of astaxanthin, 29.39 mg/100 g of tocopherols, 34.32 mg/100 g of vitamin A and 27.95 mg/g of cholesterol). By contrast, despite having traces of minor components, the krill oil extracted using ethanol in step 3 (E-KO) was the most abundant in PL (59.52%) and n-3 PUFA (41.74%). The krill oil extracted using hexane in step 2 (H-KO) expressed medium contents of all the testing indices. The oils showed significant differences in the antioxidant capacity (E-KO > H-KO > A-KO) which exhibited positive correlation with the PL content. These results could be used for further development of a wide range of krill oil products with tailor-made functions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Advanced Extraction of Spatial Information from High Resolution Satellite Data

NASA Astrophysics Data System (ADS)

Pour, T.; Burian, J.; Miřijovský, J.

2016-06-01

In this paper authors processed five satellite image of five different Middle-European cities taken by five different sensors. The aim of the paper was to find methods and approaches leading to evaluation and spatial data extraction from areas of interest. For this reason, data were firstly pre-processed using image fusion, mosaicking and segmentation processes. Results going into the next step were two polygon layers; first one representing single objects and the second one representing city blocks. In the second step, polygon layers were classified and exported into Esri shapefile format. Classification was partly hierarchical expert based and partly based on the tool SEaTH used for separability distinction and thresholding. Final results along with visual previews were attached to the original thesis. Results are evaluated visually and statistically in the last part of the paper. In the discussion author described difficulties of working with data of large size, taken by different sensors and different also thematically.

Software Technology for Adaptable Reliable Systems (STARS) Workshop March 24-27 1986.

DTIC Science & Technology

1986-03-01

syntax is aug- monitor program behavior. Trace and mented to accept design notes in arbitrary single-step facilities will provide the capability ... capabilities of these worksta- inrs tions make them a logical choice for hosting The final component of Vise is the a visual development environment. We...the following When the user picks the desired action, capabilities : graphical program display and linguistic analysis is used to extract informa

A simple rapid process for semi-automated brain extraction from magnetic resonance images of the whole mouse head.

PubMed

Delora, Adam; Gonzales, Aaron; Medina, Christopher S; Mitchell, Adam; Mohed, Abdul Faheem; Jacobs, Russell E; Bearer, Elaine L

2016-01-15

Magnetic resonance imaging (MRI) is a well-developed technique in neuroscience. Limitations in applying MRI to rodent models of neuropsychiatric disorders include the large number of animals required to achieve statistical significance, and the paucity of automation tools for the critical early step in processing, brain extraction, which prepares brain images for alignment and voxel-wise statistics. This novel timesaving automation of template-based brain extraction ("skull-stripping") is capable of quickly and reliably extracting the brain from large numbers of whole head images in a single step. The method is simple to install and requires minimal user interaction. This method is equally applicable to different types of MR images. Results were evaluated with Dice and Jacquard similarity indices and compared in 3D surface projections with other stripping approaches. Statistical comparisons demonstrate that individual variation of brain volumes are preserved. A downloadable software package not otherwise available for extraction of brains from whole head images is included here. This software tool increases speed, can be used with an atlas or a template from within the dataset, and produces masks that need little further refinement. Our new automation can be applied to any MR dataset, since the starting point is a template mask generated specifically for that dataset. The method reliably and rapidly extracts brain images from whole head images, rendering them useable for subsequent analytical processing. This software tool will accelerate the exploitation of mouse models for the investigation of human brain disorders by MRI. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Isotalo, Aarno

A method referred to as tally nuclides is presented for accurately and efficiently calculating the time-step averages and integrals of any quantities that are weighted sums of atomic densities with constant weights during the step. The method allows all such quantities to be calculated simultaneously as a part of a single depletion solution with existing depletion algorithms. Some examples of the results that can be extracted include step-average atomic densities and macroscopic reaction rates, the total number of fissions during the step, and the amount of energy released during the step. Furthermore, the method should be applicable with several depletionmore » algorithms, and the integrals or averages should be calculated with an accuracy comparable to that reached by the selected algorithm for end-of-step atomic densities. The accuracy of the method is demonstrated in depletion calculations using the Chebyshev rational approximation method. Here, we demonstrate how the ability to calculate energy release in depletion calculations can be used to determine the accuracy of the normalization in a constant-power burnup calculation during the calculation without a need for a reference solution.« less

Calculating Time-Integral Quantities in Depletion Calculations

DOE PAGES

Isotalo, Aarno

2016-06-02

A method referred to as tally nuclides is presented for accurately and efficiently calculating the time-step averages and integrals of any quantities that are weighted sums of atomic densities with constant weights during the step. The method allows all such quantities to be calculated simultaneously as a part of a single depletion solution with existing depletion algorithms. Some examples of the results that can be extracted include step-average atomic densities and macroscopic reaction rates, the total number of fissions during the step, and the amount of energy released during the step. Furthermore, the method should be applicable with several depletionmore » algorithms, and the integrals or averages should be calculated with an accuracy comparable to that reached by the selected algorithm for end-of-step atomic densities. The accuracy of the method is demonstrated in depletion calculations using the Chebyshev rational approximation method. Here, we demonstrate how the ability to calculate energy release in depletion calculations can be used to determine the accuracy of the normalization in a constant-power burnup calculation during the calculation without a need for a reference solution.« less

Interactive Exploration and Analysis of Large-Scale Simulations Using Topology-Based Data Segmentation.

PubMed

Bremer, Peer-Timo; Weber, Gunther; Tierny, Julien; Pascucci, Valerio; Day, Marcus S; Bell, John B

2011-09-01

Large-scale simulations are increasingly being used to study complex scientific and engineering phenomena. As a result, advanced visualization and data analysis are also becoming an integral part of the scientific process. Often, a key step in extracting insight from these large simulations involves the definition, extraction, and evaluation of features in the space and time coordinates of the solution. However, in many applications, these features involve a range of parameters and decisions that will affect the quality and direction of the analysis. Examples include particular level sets of a specific scalar field, or local inequalities between derived quantities. A critical step in the analysis is to understand how these arbitrary parameters/decisions impact the statistical properties of the features, since such a characterization will help to evaluate the conclusions of the analysis as a whole. We present a new topological framework that in a single-pass extracts and encodes entire families of possible features definitions as well as their statistical properties. For each time step we construct a hierarchical merge tree a highly compact, yet flexible feature representation. While this data structure is more than two orders of magnitude smaller than the raw simulation data it allows us to extract a set of features for any given parameter selection in a postprocessing step. Furthermore, we augment the trees with additional attributes making it possible to gather a large number of useful global, local, as well as conditional statistic that would otherwise be extremely difficult to compile. We also use this representation to create tracking graphs that describe the temporal evolution of the features over time. Our system provides a linked-view interface to explore the time-evolution of the graph interactively alongside the segmentation, thus making it possible to perform extensive data analysis in a very efficient manner. We demonstrate our framework by extracting and analyzing burning cells from a large-scale turbulent combustion simulation. In particular, we show how the statistical analysis enabled by our techniques provides new insight into the combustion process.

Extraction behaviour and mechanism of Pt(iv) and Pd(ii) by liquid-liquid extraction with an ionic liquid [HBBIm]Br.

PubMed

Liu, Wenhui; Wang, Qi; Zheng, Yan; Wang, Shubin; Yan, Yan; Yang, Yanzhao

2017-06-06

In this study, a method of one-step separation and recycling of high purity Pd(ii) and Pt(iv) using an ionic liquid, 1-butyl-3-benzimidazolium bromate ([HBBIm]Br), was investigated. The effects of [HBBIm]Br concentration, initial metal concentration, and loading capacity of [HBBIm]Br were examined in detail. It was observed that [HBBIm]Br was a very effective extractant for selectively extracting Pd(ii) and precipitating Pt(iv). Through selectively extracting Pd(ii) and precipitating Pt(iv), each metal with high purity was separately obtained from mixed Pd(ii) and Pt(iv) multi-metal solution. The method of one-step separation of Pd(ii) and Pt(iv) is simple and convenient. The anion exchange mechanism between [HBBIm]Br and Pt(iv) was proven through Job's method and FTIR and 1 H NMR spectroscopies. The coordination mechanism between [HBBIm]Br and Pd(ii) was demonstrated via single X-ray diffraction and was found to be robust and distinct, as supported by the ab initio quantum-chemical studies. The crystals of the [PdBr 2 ·2BBIm] complex were formed first. Moreover, the influence of the concentrations of hydrochloric acid, sodium chloride, and sodium nitrate on the precipitation of Pt(iv) and extraction of Pd(ii) was studied herein. It was found that only the concentration of H + could inhibit the separation of Pt(iv) because H + could attract the anion PtCl 6 2- ; thus, the exchange (anion exchange mechanism) between the anions PtCl 6 2- and Br - was prevented. However, both the concentration of H + and Cl - can obviously inhibit the extraction of Pd(ii) because H + and Cl - are the reaction products and increasing their concentration can inhibit the progress of the reaction (coordination mechanism).

In vitro evaluation of endodontic posts.

PubMed

Drummond, J L

2000-05-01

To compare stainless steel posts and three different fibrous posts with respect to pullout (shear) strength from extracted third molars embedded in denture acrylic. Post space was prepared and the posts cemented with a resin cement according to manufacturer's instructions. Single step and multi-step dentin bonding systems were also evaluated. The testing was in tension at a loading rate of 2 mm/min. The statistical analysis indicated no significant difference in the pullout (shear) strength between any of the post groups tested. Also evaluated was the flexure strength of the fibrous posts before and after thermal cycling. Statistical analysis indicated a significant decrease in flexure strength for the respective fibrous posts following thermal cycling.

Investigation of cloud point extraction for the analysis of metallic nanoparticles in a soil matrix

PubMed Central

Hadri, Hind El; Hackley, Vincent A.

2017-01-01

The characterization of manufactured nanoparticles (MNPs) in environmental samples is necessary to assess their behavior, fate and potential toxicity. Several techniques are available, but the limit of detection (LOD) is often too high for environmentally relevant concentrations. Therefore, pre-concentration of MNPs is an important component in the sample preparation step, in order to apply analytical tools with a LOD higher than the ng kg−1 level. The objective of this study was to explore cloud point extraction (CPE) as a viable method to pre-concentrate gold nanoparticles (AuNPs), as a model MNP, spiked into a soil extract matrix. To that end, different extraction conditions and surface coatings were evaluated in a simple matrix. The CPE method was then applied to soil extract samples spiked with AuNPs. Total gold, determined by inductively coupled plasma mass spectrometry (ICP-MS) following acid digestion, yielded a recovery greater than 90 %. The first known application of single particle ICP-MS and asymmetric flow field-flow fractionation to evaluate the preservation of the AuNP physical state following CPE extraction is demonstrated. PMID:28507763

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.

Single-Molecule Sensing with Nanopore Confinement: From Chemical Reactions to Biological Interactions.

PubMed

Lin, Yao; Ying, Yi-Lun; Gao, Rui; Long, Yi-Tao

2018-03-25

The nanopore can generate an electrochemical confinement for single-molecule sensing that help understand the fundamental chemical principle in nanoscale dimensions. By observing the generated ionic current, individual bond-making and bond-breaking steps, single biomolecule dynamic conformational changes and electron transfer processes that occur within pore can be monitored with high temporal and current resolution. These single-molecule studies in nanopore confinement are revealing information about the fundamental chemical and biological processes that cannot be extracted from ensemble measurements. In this Concept article, we introduce and discuss the electrochemical confinement effects on single-molecule covalent reactions, conformational dynamics of individual molecules and host-guest interactions in protein nanopores. Then, we extend the concept of nanopore confinement effects to confine electrochemical redox reactions in solid-state nanopores for developing new sensing mechanisms. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Use of partial dissolution techniques in geochemical exploration

USGS Publications Warehouse

Chao, T.T.

1984-01-01

Application of partial dissolution techniques to geochemical exploration has advanced from an early empirical approach to an approach based on sound geochemical principles. This advance assures a prominent future position for the use of these techniques in geochemical exploration for concealed mineral deposits. Partial dissolution techniques are classified as single dissolution or sequential multiple dissolution depending on the number of steps taken in the procedure, or as "nonselective" extraction and as "selective" extraction in terms of the relative specificity of the extraction. The choice of dissolution techniques for use in geochemical exploration is dictated by the geology of the area, the type and degree of weathering, and the expected chemical forms of the ore and of the pathfinding elements. Case histories have illustrated many instances where partial dissolution techniques exhibit advantages over conventional methods of chemical analysis used in geochemical exploration. ?? 1984.

Automatic tissue characterization from ultrasound imagery

NASA Astrophysics Data System (ADS)

Kadah, Yasser M.; Farag, Aly A.; Youssef, Abou-Bakr M.; Badawi, Ahmed M.

1993-08-01

In this work, feature extraction algorithms are proposed to extract the tissue characterization parameters from liver images. Then the resulting parameter set is further processed to obtain the minimum number of parameters representing the most discriminating pattern space for classification. This preprocessing step was applied to over 120 pathology-investigated cases to obtain the learning data for designing the classifier. The extracted features are divided into independent training and test sets and are used to construct both statistical and neural classifiers. The optimal criteria for these classifiers are set to have minimum error, ease of implementation and learning, and the flexibility for future modifications. Various algorithms for implementing various classification techniques are presented and tested on the data. The best performance was obtained using a single layer tensor model functional link network. Also, the voting k-nearest neighbor classifier provided comparably good diagnostic rates.

Pretreatment methods to improve nerve immunostaining in corneas from long-term fixed embryonic quail eyes

NASA Technical Reports Server (NTRS)

Barrett, J. E.; Wells, D. C.; Conrad, G. W.

1999-01-01

Pretreatment methods were used to improve neurofilament immunostaining in corneas from embryonic day 16 Japanese quail corneas that had been stored in fixative solution for several months. A sequential combination of the following three pretreatments: brief microwave heating in saline, followed by extraction with sodium dodecyl sulfate (SDS) at 37 degrees C, followed by digestion with hyaluronidase at 37 degrees C, produced significantly increased antibody staining of corneal neurofilament proteins, compared with embryonic corneas subjected to no prior pretreatments or to single or two-step protocols. After applying the sequence of all three pretreatments, darkest nerve staining and increased numbers of fine branches were observed, together with lower background staining. Thus, the result of applying the three-step pretreatment sequence is better than that of applying any of its component single pretreatments or even combinations of any two of them. These findings therefore suggest that each of these three pretreatments causes a unique effect, beneficial to immunostaining of neurofilament proteins, and that their individual effects are independent and additive. In addition to embryonic corneas, the three-step procedure also may be useful for immunostaining of nerves in other very delicate, highly-hydrated tissues containing an abundance of extracellular matrix.

Experimental and modeling study on relation of pedestrian step length and frequency under different headways

NASA Astrophysics Data System (ADS)

Zeng, Guang; Cao, Shuchao; Liu, Chi; Song, Weiguo

2018-06-01

It is important to study pedestrian stepping behavior and characteristics for facility design and pedestrian flow study due to pedestrians' bipedal movement. In this paper, data of steps are extracted based on trajectories of pedestrians from a single-file experiment. It is found that step length and step frequency will decrease 75% and 33%, respectively, when global density increases from 0.46 ped/m to 2.28 ped/m. With the increment of headway, they will first increase and then remain constant when the headway is beyond 1.16 m and 0.91 m, respectively. Step length and frequency under different headways can be described well by normal distributions. Meanwhile, relationships between step length and frequency under different headways exist. Step frequency decreases with the increment of step length. However, the decrease tendencies depend on headways as a whole. And there are two decrease tendencies: when the headway is between about 0.6 m and 1.0 m, the decrease rate of the step frequency will increase with the increment of step length; while it will decrease when the headway is beyond about 1.0 m and below about 0.6 m. A model is built based on the experiment results. In fundamental diagrams, the results of simulation agree well with those of experiment. The study can be helpful for understanding pedestrian stepping behavior and designing public facilities.

Measurement of intrahepatic pressure during radiofrequency ablation in porcine liver.

PubMed

Kawamoto, Chiaki; Yamauchi, Atsushi; Baba, Yoko; Kaneko, Keiko; Yakabi, Koji

2010-04-01

To identify the most effective procedures to avoid increased intrahepatic pressure during radiofrequency ablation, we evaluated different ablation methods. Laparotomy was performed in 19 pigs. Intrahepatic pressure was monitored using an invasive blood pressure monitor. Radiofrequency ablation was performed as follows: single-step standard ablation; single-step at 30 W; single-step at 70 W; 4-step at 30 W; 8-step at 30 W; 8-step at 70 W; and cooled-tip. The array was fully deployed in single-step methods. In the multi-step methods, the array was gradually deployed in four or eight steps. With the cooled-tip, ablation was performed by increasing output by 10 W/min, starting at 40 W. Intrahepatic pressure was as follows: single-step standard ablation, 154.5 +/- 30.9 mmHg; single-step at 30 W, 34.2 +/- 20.0 mmHg; single-step at 70 W, 46.7 +/- 24.3 mmHg; 4-step at 30 W, 42.3 +/- 17.9 mmHg; 8-step at 30 W, 24.1 +/- 18.2 mmHg; 8-step at 70 W, 47.5 +/- 31.5 mmHg; and cooled-tip, 114.5 +/- 16.6 mmHg. The radiofrequency ablation-induced area was spherical with single-step standard ablation, 4-step at 30 W, and 8-step at 30 W. Conversely, the ablated area was irregular with single-step at 30 W, single-step at 70 W, and 8-step at 70 W. The ablation time was significantly shorter for the multi-step method than for the single-step method. Increased intrahepatic pressure could be controlled using multi-step methods. From the shapes of the ablation area, 30-W 8-step expansions appear to be most suitable for radiofrequency ablation.

Rapid analysis of the essential oil components of dried Zanthoxylum bungeanum Maxim by Fe2O3-magnetic-microsphere-assisted microwave distillation and simultaneous headspace single-drop microextraction followed by GC-MS.

PubMed

Ye, Qing

2013-06-01

In this work, microwave distillation assisted by Fe2 O3 magnetic microspheres (FMMS) and headspace single-drop microextraction were combined, and developed for determination of essential oil compounds in dried Zanthoxylum bungeanum Maxim (ZBM). The FMMS were used as microwave absorption solid medium for dry distillation of dried ZBM. Using the proposed method, isolation, extraction, and concentration of essential oil compounds can be carried out in a single step. The experimental parameters including extraction solvent, solvent volume, microwave power, irradiation time, and the amount of added FMMS, were studied. The optimal analytical conditions were: 2.0 μL decane as the extraction solvent, microwave power of 300 W, irradiation time of 2 min, and the addition of 0.1 g FMMS to ZBM. The method precision was from 4 to 10%. A total of 52 compounds were identified by the proposed method. The conventional steam distillation method was also used for the analysis of essential oil in dried ZBM and only 31 compounds were identified by steam distillation method. It was found that the proposed method is a simple, rapid, reliable, and solvent-free technique for the determination of volatile compounds in Chinese herbs. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

New nucleic acid testing devices to diagnose infectious diseases in resource-limited settings.

PubMed

Maffert, P; Reverchon, S; Nasser, W; Rozand, C; Abaibou, H

2017-10-01

Point-of-care diagnosis based on nucleic acid testing aims to incorporate all the analytical steps, from sample preparation to nucleic acid amplification and detection, in a single device. This device needs to provide a low-cost, robust, sensitive, specific, and easily readable analysis. Microfluidics has great potential for handling small volumes of fluids on a single platform. Microfluidic technology has recently been applied to paper, which is already used in low-cost lateral flow tests. Nucleic acid extraction from a biological specimen usually requires cell filtration and lysis on specific membranes, while affinity matrices, such as chitosan or polydiacetylene, are well suited to concentrating nucleic acids for subsequent amplification. Access to electricity is often difficult in resource-limited areas, so the amplification step needs to be equipment-free. Consequently, the reaction has to be isothermal to alleviate the need for a thermocycler. LAMP, NASBA, HDA, and RPA are examples of the technologies available. Nucleic acid detection techniques are currently based on fluorescence, colorimetry, or chemiluminescence. For point-of-care diagnostics, the results should be readable with the naked eye. Nowadays, interpretation and communication of results to health professionals could rely on a smartphone, used as a telemedicine device. The major challenge of creating an "all-in-one" diagnostic test involves the design of an optimal solution and a sequence for each analytical step, as well as combining the execution of all these steps on a single device. This review provides an overview of available materials and technologies which seem to be adapted to point-of-care nucleic acid-based diagnosis, in low-resource areas.

Macro-fingerprint analysis-through-separation of licorice based on FT-IR and 2DCOS-IR

NASA Astrophysics Data System (ADS)

Wang, Yang; Wang, Ping; Xu, Changhua; Yang, Yan; Li, Jin; Chen, Tao; Li, Zheng; Cui, Weili; Zhou, Qun; Sun, Suqin; Li, Huifen

2014-07-01

In this paper, a step-by-step analysis-through-separation method under the navigation of multi-step IR macro-fingerprint (FT-IR integrated with second derivative IR (SD-IR) and 2DCOS-IR) was developed for comprehensively characterizing the hierarchical chemical fingerprints of licorice from entirety to single active components. Subsequently, the chemical profile variation rules of three parts (flavonoids, saponins and saccharides) in the separation process were holistically revealed and the number of matching peaks and correlation coefficients with standards of pure compounds was increasing along the extracting directions. The findings were supported by UPLC results and a verification experiment of aqueous separation process. It has been demonstrated that the developed multi-step IR macro-fingerprint analysis-through-separation approach could be a rapid, effective and integrated method not only for objectively providing comprehensive chemical characterization of licorice and all its separated parts, but also for rapidly revealing the global enrichment trend of the active components in licorice separation process.

Automated identification and geometrical features extraction of individual trees from Mobile Laser Scanning data in Budapest

NASA Astrophysics Data System (ADS)

Koma, Zsófia; Székely, Balázs; Folly-Ritvay, Zoltán; Skobrák, Ferenc; Koenig, Kristina; Höfle, Bernhard

2016-04-01

Mobile Laser Scanning (MLS) is an evolving operational measurement technique for urban environment providing large amounts of high resolution information about trees, street features, pole-like objects on the street sides or near to motorways. In this study we investigate a robust segmentation method to extract the individual trees automatically in order to build an object-based tree database system. We focused on the large urban parks in Budapest (Margitsziget and Városliget; KARESZ project) which contained large diversity of different kind of tree species. The MLS data contained high density point cloud data with 1-8 cm mean absolute accuracy 80-100 meter distance from streets. The robust segmentation method contained following steps: The ground points are determined first. As a second step cylinders are fitted in vertical slice 1-1.5 meter relative height above ground, which is used to determine the potential location of each single trees trunk and cylinder-like object. Finally, residual values are calculated as deviation of each point from a vertically expanded fitted cylinder; these residual values are used to separate cylinder-like object from individual trees. After successful parameterization, the model parameters and the corresponding residual values of the fitted object are extracted and imported into the tree database. Additionally, geometric features are calculated for each segmented individual tree like crown base, crown width, crown length, diameter of trunk, volume of the individual trees. In case of incompletely scanned trees, the extraction of geometric features is based on fitted circles. The result of the study is a tree database containing detailed information about urban trees, which can be a valuable dataset for ecologist, city planners, planting and mapping purposes. Furthermore, the established database will be the initial point for classification trees into single species. MLS data used in this project had been measured in the framework of KARESZ project for whole Budapest. BSz contributed as an Alexander von Humboldt Research Fellow.

Single-step biosynthesis and characterization of silver nanoparticles using Zornia diphylla leaves: A potent eco-friendly tool against malaria and arbovirus vectors.

PubMed

Govindarajan, Marimuthu; Rajeswary, Mohan; Muthukumaran, Udaiyan; Hoti, S L; Khater, Hanem F; Benelli, Giovanni

2016-08-01

Mosquitoes (Diptera: Culicidae) are vectors of important pathogens and parasites, including malaria, dengue, chikungunya, Japanese encephalitis, lymphatic filariasis and Zika virus. The application of synthetic insecticides causes development of resistance, biological magnification of toxic substances through the food chain, and adverse effects on the environment and human health. In this scenario, eco-friendly control tools of mosquito vectors are a priority. Here single-step fabrication of silver nanoparticles (AgNP) using a cheap aqueous leaf extract of Zornia diphylla as reducing and capping agent pf Ag(+) ions has been carried out. Biosynthesized AgNP were characterized by UV-visible spectrophotometry, Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy-dispersive spectroscopy (EDX) and X-ray diffraction analysis (XRD). The acute toxicity of Z. diphylla leaf extract and biosynthesized AgNP was evaluated against larvae of the malaria vector Anopheles subpictus, the dengue vector Aedes albopictus and the Japanese encephalitis vector Culex tritaeniorhynchus. Both the Z. diphylla leaf extract and Ag NP showed dose dependent larvicidal effect against all tested mosquito species. Compared to the leaf aqueous extract, biosynthesized Ag NP showed higher toxicity against An. subpictus, Ae. albopictus, and Cx. tritaeniorhynchus with LC50 values of 12.53, 13.42 and 14.61μg/ml, respectively. Biosynthesized Ag NP were found safer to non-target organisms Chironomus circumdatus, Anisops bouvieri and Gambusia affinis, with the respective LC50 values ranging from 613.11 to 6903.93μg/ml, if compared to target mosquitoes. Overall, our results highlight that Z. diphylla-fabricated Ag NP are a promising and eco-friendly tool against larval populations of mosquito vectors of medical and veterinary importance, with negligible toxicity against other non-target organisms. Copyright © 2016 Elsevier B.V. All rights reserved.

Improving the two-step remediation process for CCA-treated wood. Part I, Evaluating oxalic acid extraction

Treesearch

Carol Clausen

2004-01-01

In this study, three possible improvements to a remediation process for chromated-copper-arsenate (CCA) treated wood were evaluated. The process involves two steps: oxalic acid extraction of wood fiber followed by bacterial culture with Bacillus licheniformis CC01. The three potential improvements to the oxalic acid extraction step were (1) reusing oxalic acid for...

Helium, neon, and argon composition of the solar wind as recorded in gold and other Genesis collector materials

NASA Astrophysics Data System (ADS)

Pepin, Robert O.; Schlutter, Dennis J.; Becker, Richard H.; Reisenfeld, Daniel B.

2012-07-01

We report compositions and fluxes of light noble gases in the solar wind (SW), extracted by stepped pyrolysis and amalgamation from gold collector materials carried on the Genesis Solar Wind Sample Return Mission. Results are compared with data from other laboratories on SW-He, Ne and Ar distributions implanted in Genesis aluminum, carbon, and silicon collectors and extracted by laser ablation. Corrections for mass-dependent losses (“backscatter”) of impinging SW ions due to scattering from the collector material are substantially larger for gold than for these lower atomic weight targets. We assess such losses by SRIM simulation calculations of SW backscatter from gold which are applied to the measurements to recover the composition of the incident SW. Averaged results of integrated stepped pyrolysis and single-step amalgamation measurements, with 1σ errors, are as follows: for SW-Ne and Ar isotope ratios (3He/4He was not measured), 20Ne/22Ne = 14.001 ± 0.042, 21Ne/22Ne = 0.03361 ± 0.00018, 36Ar/38Ar = 5.501 ± 0.014; for SW element ratios, 4He/20Ne = 641 ± 15, 20Ne/36Ar = 51.6 ± 0.5; and for SW fluxes in atoms cm-2 s-1 at the Genesis L1 station, 4He = 1.14 ± 0.04 × 107, 20Ne = 1.80 ± 0.06 × 104, 36Ar = 3.58 ± 0.11 × 102. Except for the 21Ne/22Ne and 20Ne/36Ar ratios, these values are in reasonable accord (within ∼1-3σ) with measurements on different collector materials reported by one or both of two other Genesis noble gas research groups. We further find, in three stepped pyrolysis experiments on gold foil, that He, Ne and Ar are released at increasing temperatures without elemental fractionation, in contrast to a pyrolytic extraction of a single non-gold collector (Al) where the release patterns point to mass-dependent thermal diffusion. The pyrolyzed gold foils exhibit enhancements, relative to sample totals, in 20Ne/22Ne and 21Ne/22Ne ratios evolved at low temperatures. The absence of elemental fractionation in pyrolytic release from gold implies that these isotope ratio enhancements, involving much smaller mass differences, do not result from preferential diffusive release of the lighter Ne isotopes. This effect, not predicted by SRIM calculations, has also been observed in stepped acid-etch releases from a different Genesis collector material in another laboratory.

Applications of Evolutionary Algorithms to Electromagnetic Materials Characterization and Design Problems

NASA Astrophysics Data System (ADS)

Frasch, Jonathan Lemoine

Determining the electrical permittivity and magnetic permeability of materials is an important task in electromagnetics research. The method using reflection and transmission scattering parameters to determine these constants has been widely employed for many years, ever since the work of Nicolson, Ross, and Weir in the 1970's. For general materials that are homogeneous, linear, and isotropic, the method they developed (the NRW method) works very well and provides an analytical solution. For materials which possess a metal backing or are applied as a coating to a metal surface, it can be difficult or even impossible to obtain a transmission measurement, especially when the coating is thin. In such a circumstance, it is common to resort to a method which uses two reflection type measurements. There are several such methods for free-space measurements, using multiple angles or polarizations for example. For waveguide measurements, obtaining two independent sources of information from which to extract two complex parameters can be a challenge. This dissertation covers three different topics. Two of these involve different techniques to characterize conductor-backed materials, and the third proposes a method for designing synthetic validation standards for use with standard NRW measurements. All three of these topics utilize modal expansions of electric and magnetic fields to analyze propagation in stepped rectangular waveguides. Two of the projects utilize evolutionary algorithms (EA) to design waveguide structures. These algorithms were developed specifically for these projects and utilize fairly recent innovations within the optimization community. The first characterization technique uses two different versions of a single vertical step in the waveguide. Samples to be tested lie inside the steps with the conductor reflection plane behind them. If the two reflection measurements are truly independent it should be possible to recover the values of two complex parameters, but success of the technique ultimately depends upon how independent the measurements actually are. Next, a method is demonstrated for developing synthetic verification standards. These standards are created from combinations of vertical steps formed from a single piece of metal or metal coated plastic. These fully insertable structures mimic some of the measurement characteristics of typical lab specimens and thus provide a useful tool for verifying the proper calibration and function of the experimental setup used for NRW characterization. These standards are designed with the use an EA, which compares possible designs based on the quality of the match with target parameter values. Several examples have been fabricated and tested, and the design specifications and results are presented. Finally, a second characterization technique is considered. This method uses multiple vertical steps to construct an error reducing structure within the waveguide, which allows parameters to be reliably extracted using both reflection and transmission measurements. These structures are designed with an EA, measuring fitness by the reduction of error in the extracted parameters. An additional EA is used to assist in the extraction of the material parameters supplying better initial guesses to a secant method solver. This hybrid approach greatly increases the stability of the solver and increases the speed of parameter extractions. Several designs have been identified and are analyzed.

Rapid habitability assessment of Mars samples by pyrolysis-FTIR

NASA Astrophysics Data System (ADS)

Gordon, Peter R.; Sephton, Mark A.

2016-02-01

Pyrolysis Fourier transform infrared spectroscopy (pyrolysis FTIR) is a potential sample selection method for Mars Sample Return missions. FTIR spectroscopy can be performed on solid and liquid samples but also on gases following preliminary thermal extraction, pyrolysis or gasification steps. The detection of hydrocarbon and non-hydrocarbon gases can reveal information on sample mineralogy and past habitability of the environment in which the sample was created. The absorption of IR radiation at specific wavenumbers by organic functional groups can indicate the presence and type of any organic matter present. Here we assess the utility of pyrolysis-FTIR to release water, carbon dioxide, sulfur dioxide and organic matter from Mars relevant materials to enable a rapid habitability assessment of target rocks for sample return. For our assessment a range of minerals were analyzed by attenuated total reflectance FTIR. Subsequently, the mineral samples were subjected to single step pyrolysis and multi step pyrolysis and the products characterised by gas phase FTIR. Data from both single step and multi step pyrolysis-FTIR provide the ability to identify minerals that reflect habitable environments through their water and carbon dioxide responses. Multi step pyrolysis-FTIR can be used to gain more detailed information on the sources of the liberated water and carbon dioxide owing to the characteristic decomposition temperatures of different mineral phases. Habitation can be suggested when pyrolysis-FTIR indicates the presence of organic matter within the sample. Pyrolysis-FTIR, therefore, represents an effective method to assess whether Mars Sample Return target rocks represent habitable conditions and potential records of habitation and can play an important role in sample triage operations.

Research of infrared laser based pavement imaging and crack detection

NASA Astrophysics Data System (ADS)

Hong, Hanyu; Wang, Shu; Zhang, Xiuhua; Jing, Genqiang

2013-08-01

Road crack detection is seriously affected by many factors in actual applications, such as some shadows, road signs, oil stains, high frequency noise and so on. Due to these factors, the current crack detection methods can not distinguish the cracks in complex scenes. In order to solve this problem, a novel method based on infrared laser pavement imaging is proposed. Firstly, single sensor laser pavement imaging system is adopted to obtain pavement images, high power laser line projector is well used to resist various shadows. Secondly, the crack extraction algorithm which has merged multiple features intelligently is proposed to extract crack information. In this step, the non-negative feature and contrast feature are used to extract the basic crack information, and circular projection based on linearity feature is applied to enhance the crack area and eliminate noise. A series of experiments have been performed to test the proposed method, which shows that the proposed automatic extraction method is effective and advanced.

High hydrostatic pressure processing: a method having high success potential in pollen protein extraction

NASA Astrophysics Data System (ADS)

Murat Altuner, Ergin; Çeter, Talip; Alpas, Hami

2012-06-01

Even a single peptide that is present in the pollen wall and cytoplasm could cause pollen allergy. To produce skin-prick test kits, the first step is the extraction of these molecules. In this study, Cedrus atlantica pollens were subjected to 220 and 330 MPa for 10 and 30 min in order to extract these molecules. After high hydrostatic pressure processing (HHPP), the total amounts of proteins (TAPs) are measured and compared with the results of the conventional extraction method (CEM). As a result, the TAPs extracted by HHPP is 18.0210 μ g/mL at 220 MPa for 10 min, 22.5770 μ g/mL at 220 MPa for 30 min, 23.3810 μ g/mL at 330 MPa for 10 min and 25.9270 μ g/mL at 330 MPa for 30 min, while this is 1.9460 μ g/mL in 24 h by the CEM. In addition to these results, visual pollen deformation and eruption, pollen wall and surface damage have also been observed.

Development of multiplex PCR assay for authentication of Cornu Cervi Pantotrichum in traditional Chinese medicine based on cytochrome b and C oxidase subunit 1 genes.

PubMed

Gao, Lijun; Xia, Wei; Ai, Jinxia; Li, Mingcheng; Yuan, Guanxin; Niu, Jiamu; Fu, Guilian; Zhang, Lihua

2016-07-01

This study describes a method for discriminating the true Cervus antlers from its counterfeits using multiplex PCR. Bioinformatics were carried out to design the specific alleles primers for mitochondrial (mt) cytochrome b (Cyt b) and cytochrome C oxidase subunit 1 (Cox 1) genes. The mt DNA and genomic DNA were extracted from Cervi Cornu Pantotrichum through the modified alkaline and the salt-extracting method in addition to its counterfeits, respectively. Sufficient DNA templates were extracted from all samples used in two methods, and joint fragments of 354 bp and 543 bp that were specifically amplified from both of true Cervus antlers served as a standard control. The data revealed that the multiplex PCR-based assays using two primer sets can be used for forensic and quantitative identification of original Cervus deer products from counterfeit antlers in a single step.

Speed-dependent Voigt lineshape parameter database from dual frequency comb measurements up to 1305 K. Part I: Pure H2O absorption, 6801-7188 cm-1

NASA Astrophysics Data System (ADS)

Schroeder, Paul J.; Cich, Matthew J.; Yang, Jinyu; Giorgetta, Fabrizio R.; Swann, William C.; Coddington, Ian; Newbury, Nathan R.; Drouin, Brian J.; Rieker, Gregory B.

2018-05-01

We measure speed-dependent Voigt lineshape parameters with temperature-dependence exponents for several hundred spectroscopic features of pure water spanning 6801-7188 cm-1. The parameters are extracted from broad bandwidth, high-resolution dual frequency comb absorption spectra with multispectrum fitting techniques. The data encompass 25 spectra ranging from 296 K to 1305 K and 1 to 17 Torr of pure water vapor. We present the extracted parameters, compare them to published data, and present speed-dependence, self-shift, and self-broadening temperature-dependent parameters for the first time. Lineshape data is extracted using a quadratic speed-dependent Voigt profile and a single self-broadening power law temperature-dependence exponent over the entire temperature range. The results represent an important step toward a new high-temperature database using advanced lineshape profiles.

Development of two step liquid-liquid extraction tandem UHPLC-MS/MS method for the simultaneous determination of Ginkgo flavonoids, terpene lactones and nimodipine in rat plasma: Application to the pharmacokinetic study of the combination of Ginkgo biloba dispersible tablets and Nimodipine tablets.

PubMed

Xiao, Jie; Wang, Tianyang; Li, Pei; Liu, Ran; Li, Qing; Bi, Kaishun

2016-08-15

A sensitive, reliable and accurate UHPLC-MS/MS method has been firstly established and validated for the simultaneous quantification of ginkgo flavonoids, terpene lactones and nimodipine in rat plasma after oral administration of Ginkgo biloba dispersible tablets, Nimodipine tablets and the combination of the both, respectively. The plasma samples were extracted by two step liquid-liquid extraction, nimodipine was extracted by hexane-ether (3:1, v/v) at the first step, after that ginkgo flavonoids and terpene lactones were extracted by ethyl acetate. Then the analytes were successfully separated by running gradient elution with the mobile phase consisting of 0.1% formic acid in water and methanol at a flow rate of 0.6mL/min. The detection of the analytes was performed on a UHPLC-MS/MS system with turbo ion spray source in the negative ion and multiple reaction monitoring (MRM) mode. The calibration curves for the determination of all the analytes showed good linearity (R(2)>0.99), and the lower limits of quantification were 0.50-4.00ng/mL. Intra-day and inter-day precisions were in the range of 3.6%-9.2% and 3.2%-13.1% for all the analytes. The mean extraction recoveries of the analytes were within 69.82%-103.5% and the matrix were within 82.8%-110.0%. The validated method had been successfully applied to compare the pharmacokinetic parameters of ginkgo flavonoids, terpene lactones and nimodipine in rat plasma after oral administration of Ginkgo biloba dispersible tablets, Nimodipine tablets with the combination of the both. There were no statistically significant differences on the pharmacokinetic behaviors of all the analytes between the combined and single administration groups. Results showed that the combination of the two agents may avoid dosage adjustments in clinic and the combination is more convenient as well as efficient on different pathogenesis of cerebral ischemia. Copyright © 2016 Elsevier B.V. All rights reserved.

Natural colorants: Pigment stability and extraction yield enhancement via utilization of appropriate pretreatment and extraction methods.

PubMed

Ngamwonglumlert, Luxsika; Devahastin, Sakamon; Chiewchan, Naphaporn

2017-10-13

Natural colorants from plant-based materials have gained increasing popularity due to health consciousness of consumers. Among the many steps involved in the production of natural colorants, pigment extraction is one of the most important. Soxhlet extraction, maceration, and hydrodistillation are conventional methods that have been widely used in industry and laboratory for such a purpose. Recently, various non-conventional methods, such as supercritical fluid extraction, pressurized liquid extraction, microwave-assisted extraction, ultrasound-assisted extraction, pulsed-electric field extraction, and enzyme-assisted extraction have emerged as alternatives to conventional methods due to the advantages of the former in terms of smaller solvent consumption, shorter extraction time, and more environment-friendliness. Prior to the extraction step, pretreatment of plant materials to enhance the stability of natural pigments is another important step that must be carefully taken care of. In this paper, a comprehensive review of appropriate pretreatment and extraction methods for chlorophylls, carotenoids, betalains, and anthocyanins, which are major classes of plant pigments, is provided by using pigment stability and extraction yield as assessment criteria.

One-step zymogram method for the simultaneous detection of cellulase/xylanase activity and molecular weight estimation of the enzyme.

PubMed

Cano-Ramírez, Claudia; Santiago-Hernández, Alejandro; Rivera-Orduña, Flor Nohemí; Pineda-Mendoza, Rosa María; Zúñiga, Gerardo; Hidalgo-Lara, María Eugenia

2017-02-01

Here, we describe a zymographic method for the simultaneous detection of enzymatic activity and molecular weight (MW) estimation, following a single electrophoresis step. This involved separating cellulase and xylanase activities from bacteria and fungi, obtained from different sources, such as commercial extracts, crude extract and purified proteins, under denaturing conditions, by 10% polyacrylamide gel electrophoresis, using polyacrylamide gels copolymerized with 1% (w/v) carboxymethylcellulose or beechwood xylan as substrates. Then, enzymes were refolded by treatment with 2.5% Triton X-100 in an appropriate buffer for each enzymatic activity, and visualized by Coomassie blue staining for MW estimation. Finally, Congo red staining revealed bio-active cellulase and xylanase bands after electrophoretic separation of the proteins in the preparations. This method may provide a useful additional tool for screening of particular cellulase and xylanase producers, identification and MW estimation of polypeptides that manifest these activities, and for monitoring and control of fungal and bacterial cellulase and xylanase production. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Separation of time scales in one-dimensional directed nucleation-growth processes

NASA Astrophysics Data System (ADS)

Pierobon, Paolo; Miné-Hattab, Judith; Cappello, Giovanni; Viovy, Jean-Louis; Lagomarsino, Marco Cosentino

2010-12-01

Proteins involved in homologous recombination such as RecA and hRad51 polymerize on single- and double-stranded DNA according to a nucleation-growth kinetics, which can be monitored by single-molecule in vitro assays. The basic models currently used to extract biochemical rates rely on ensemble averages and are typically based on an underlying process of bidirectional polymerization, in contrast with the often observed anisotropic polymerization of similar proteins. For these reasons, if one considers single-molecule experiments, the available models are useful to understand observations only in some regimes. In particular, recent experiments have highlighted a steplike polymerization kinetics. The classical model of one-dimensional nucleation growth, the Kolmogorov-Avrami-Mehl-Johnson (KAMJ) model, predicts the correct polymerization kinetics only in some regimes and fails to predict the steplike behavior. This work illustrates by simulations and analytical arguments the limitation of applicability of the KAMJ description and proposes a minimal model for the statistics of the steps based on the so-called stick-breaking stochastic process. We argue that this insight might be useful to extract information on the time and length scales involved in the polymerization kinetics.

Carboxylated graphene oxide/polyvinyl chloride as solid-phase extraction sorbent combined with ion chromatography for the determination of sulfonamides in cosmetics.

PubMed

Zhong, Zhixiong; Li, Gongke; Luo, Zhibin; Liu, Zhe; Shao, Yijuan; He, Wanwen; Deng, Jianchao; Luo, Xingling

2015-08-12

A carboxylated graphene oxide/polyvinyl chloride (CGO/PVC) material was prepared as a sorbent for the selective extraction of sulphonamides from complex sample. After being dispersed in buffer solution, sample was transferred into the prefabricated solid-phase extraction (SPE) column, which integrated extraction and cleanup into one single-step. A multi-response optimization based on the Box-Behnken design was used to optimize factors affecting extraction efficiency. Compared with the commonly commercial sorbents including MCX, WCX and C18, CGO/PVC hybrid material had higher extraction selectivity and capacity to sulphonamides. The limits of detection and quantification for seven target compounds were in the range of 3.4-7.1 μg/L and 11.4-23.7 μg/L, respectively. The self-assembly SPE cartridge was successfully used to enrich seven analytes in anti-acne cosmetics prior to ion chromatography detection with good recoveries of 87.8-102.0% and relative standard deviations of 1.2-6.4%, implying that this method was suitable for routine analysis of cosmetics. Copyright © 2015 Elsevier B.V. All rights reserved.

Screening of cyanobacterial extracts for synthesis of silver nanoparticles.

PubMed

Husain, Shaheen; Sardar, Meryam; Fatma, Tasneem

2015-08-01

Improvement of reliable and eco-friendly process for synthesis of metallic nanoparticles is a significant step in the field of application nanotechnology. One approach that shows vast potential is based on the biosynthesis of nanoparticles using micro-organisms. In this study, biosynthesis of silver nanoparticles (AgNP) using 30 cyanobacteria were investigated. Cyanobacterial aqueous extracts were subjected to AgNP synthesis at 30 °C. Scanning of these aqueous extracts containing AgNP in UV-Visible range showed single peak. The λ max for different extracts varied and ranged between 440 and 490 nm that correspond to the "plasmon absorbance" of AgNP. Micrographs from scanning electron microscope of AgNP from cyanobacterial extracts showed that though synthesis of nanoparticles occurred in all strains but their reaction time, shape and size varied. Majority of the nanoparticles were spherical. Time taken for induction of nanoparticles synthesis by cyanobacterial extracts ranged from 30 to 360 h and their size from 38 to 88 nm. In terms of size Cylindrospermum stagnale NCCU-104 was the best organism with 38 and 40 nm. But in terms of time Microcheate sp. NCCU-342 was the best organism as it took 30 h for AgNP synthesis.

Effective alkaline metal-catalyzed oxidative delignification of hybrid poplar

DOE PAGES

Bhalla, Aditya; Bansal, Namita; Stoklosa, Ryan J.; ...

2016-02-09

Background: Strategies to improve copper-catalyzed alkaline hydrogen peroxide (Cu-AHP) pretreatment of hybrid poplar were investigated. These improvements included a combination of increasing hydrolysis yields, while simultaneously decreasing process inputs through (i) more efficient utilization of H 2O 2 and (ii) the addition of an alkaline extraction step prior to the metal-catalyzed AHP pretreatment. We hypothesized that utilizing this improved process could substantially lower the chemical inputs needed during pretreatment. Results: Hybrid poplar was pretreated utilizing a modified process in which an alkaline extraction step was incorporated prior to the Cu-AHP treatment step and H 2O 2 was added batch-wise overmore » the course of 10 h. Our results revealed that the alkaline pre-extraction step improved both lignin and xylan solubilization, which ultimately led to improved glucose (86 %) and xylose (95 %) yields following enzymatic hydrolysis. An increase in the lignin solubilization was also observed with fed-batch H 2O 2 addition relative to batch-only addition, which again resulted in increased glucose and xylose yields (77 and 93 % versus 63 and 74 %, respectively). Importantly, combining these strategies led to significantly improved sugar yields (96 % glucose and 94 % xylose) following enzymatic hydrolysis. In addition, we found that we could substantially lower the chemical inputs (enzyme, H 2O 2, and catalyst), while still maintaining high product yields utilizing the improved Cu-AHP process. This pretreatment also provided a relatively pure lignin stream consisting of ≥90 % Klason lignin and only 3 % xylan and 2 % ash following precipitation. Two-dimensional heteronuclear single-quantum coherence (2D HSQC) NMR and size-exclusion chromatography demonstrated that the solubilized lignin was high molecular weight (Mw ≈ 22,000 Da) and only slightly oxidized relative to lignin from untreated poplar. In conclusion: This study demonstrated that the fed-batch, two-stage Cu-AHP pretreatment process was effective in pretreating hybrid poplar for its conversion into fermentable sugars. Results showed sugar yields near the theoretical maximum were achieved from enzymatically hydrolyzed hybrid poplar by incorporating an alkaline extraction step prior to pretreatment and by efficiently utilizing H 2O 2 during the Cu-AHP process. Significantly, this study reports high sugar yields from woody biomass treated with an AHP pretreatment under mild reaction conditions.« less

Systematic assessment of different solvents for the extraction of drugs of abuse and pharmaceuticals from an authentic hair pool.

PubMed

Madry, Milena M; Kraemer, Thomas; Baumgartner, Markus R

2018-01-01

Hair analysis has been established as a prevalent tool for retrospective drug monitoring. In this study, different extraction solvents for the determination of drugs of abuse and pharmaceuticals in hair were evaluated for their efficiency. A pool of authentic hair from drug users was used for extraction experiments. Hair was pulverized and extracted in triplicate with seven different solvents in a one- or two-step extraction. Three one- (methanol, acetonitrile, and acetonitrile/water) and four two-step extractions (methanol two-fold, methanol and methanol/acetonitrile/formate buffer, methanol and methanol/formate buffer, and methanol and methanol/hydrochloric acid) were tested under accurately equal experimental conditions. The extracts were directly analyzed by liquid chromatography-tandem mass spectrometry for opiates/opioids, stimulants, ketamine, selected benzodiazepines, antidepressants, antipsychotics, and antihistamines using deuterated internal standards. For most analytes, a two-step extraction with methanol did not significantly improve the yield compared to a one-step extraction with methanol. Extraction with acetonitrile alone was least efficient for most analytes. Extraction yields of acetonitrile/water, methanol and methanol/acetonitrile/formate buffer, and methanol and methanol/formate buffer were significantly higher compared to methanol. Highest efficiencies were obtained by a two-step extraction with methanol and methanol/hydrochloric acid, particularly for morphine, 6-monoacetylmorphine, codeine, 6-acetylcodeine, MDMA, zopiclone, zolpidem, amitriptyline, nortriptyline, citalopram, and doxylamine. For some analytes (e.g., tramadol, fluoxetine, sertraline), all extraction solvents, except for acetonitrile, were comparably efficient. There was no significant correlation between extraction efficiency with an acidic solvent and the pka or log P of the analyte. However, there was a significant trend for the extraction efficiency with acetonitrile to the log P of the analyte. The study demonstrates that the choice of extraction solvent has a strong impact on hair analysis outcomes. Therefore, validation protocols should include the evaluation of extraction efficiency of drugs by using authentic rather than spiked hair. Different extraction procedures may contribute to the scatter of quantitative results in inter-laboratory comparisons. Harmonization of extraction protocols is recommended, when interpretation is based on same cut-off levels. Copyright © 2017 Elsevier B.V. All rights reserved.

Experimental design for extraction and quantification of phenolic compounds and organic acids in white "Vinho Verde" grapes.

PubMed

Dopico-García, M S; Valentão, P; Guerra, L; Andrade, P B; Seabra, R M

2007-01-30

An experimental design was applied for the optimization of extraction and clean-up processes of phenolic compounds and organic acids from white "Vinho Verde" grapes. The developed analytical method consisted in two steps: first a solid-liquid extraction of both phenolic compounds and organic acids and then a clean-up step using solid-phase extraction (SPE). Afterwards, phenolic compounds and organic acids were determined by high-performance liquid chromatography (HPLC) coupled to a diode array detector (DAD) and HPLC-UV, respectively. Plackett-Burman design was carried out to select the significant experimental parameters affecting both the extraction and the clean-up steps. The identified and quantified phenolic compounds were: quercetin-3-O-glucoside, quercetin-3-O-rutinoside, kaempferol-3-O-rutinoside, isorhamnetin-3-O-glucoside, quercetin, kaempferol and epicatechin. The determined organic acids were oxalic, citric, tartaric, malic, shikimic and fumaric acids. The obtained results showed that the most important variables were the temperature (40 degrees C) and the solvent (acid water at pH 2 with 5% methanol) for the extraction step and the type of sorbent (C18 non end-capped) for the clean-up step.

A rapid and sensitive LC-MS/MS assay for the determination of saxagliptin and its active metabolite 5-hydroxy saxagliptin in human plasma and its application to a pharmacokinetic study.

PubMed

Batta, N; Pilli, N R; Derangula, V R; Vurimindi, H B; Damaramadugu, R; Yejella, R P

2015-03-01

The authors proposed a simple, rapid and sensitive liquid chromatography-tandem mass spectrometric (LC-MS/MS) assay method for the simultaneous determination of saxagliptin and its active metabolite 5-hydroxy saxagliptin in human plasma. The developed method was fully validated as per the US FDA guidelines. The method utilized stable labeled isotopes saxagliptin-15 N d2 (IS1) and 5-hydroxy saxagliptin-15 N-d2 (IS2) as internal standards for the quantification of saxagliptin and 5-hydroxy saxagliptin, respectively. Analytes and the internal standards were extracted from human plasma by a single step solid-phase extraction technique without drying, evaporation and reconstitution steps. The optimized mobile phase was composed of 0.1% acetic acid in 5 mM ammonium acetate and acetonitrile (30:70, v/v) and delivered at a flow rate of 0.85 mL/min. The method exhibits the linear calibration range of 0.05-100 ng/mL for both the analytes. The precision and accuracy results for both the analytes were well within the acceptance limits. The different stability experiments conducted in aqueous samples and in matrix samples are meeting the acceptance criteria. The chromatographic run time was set at 1.8 min; hence more than 400 samples can be analyzed in a single day. © Georg Thieme Verlag KG Stuttgart · New York.

Optical and electrical characterizations of a single step ion beam milling mesa devices of chloride passivated PbS colloidal quantum dots based film

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

Hechster, Elad, E-mail: elad.hechster@gmail.com; Sarusi, Gabby; Shapiro, Arthur

Colloidal Quantum Dots (CQDs) are of increasing interest, thanks to their quantum size effect that gives rise to their usage in various applications, such as biological tagging, solar cells and as the sensitizing layer of night vision devices. Here, we analyze the optical absorbance of chloride passivated PbS CQDs as well as revealing a correlation between their photoluminescence and sizes distribution, using theoretical models and experimental results from the literature. Next, we calculate the CQDs resistivity as a film. Although resistivity can be calculated from sheet resistance measurement using four point probes, such measurement is usually carried-out on the layer’smore » surface that in most cases has dangling bonds and surface states, which might affect the charges flow and modify the resistivity. Therefore; our approach, which was applied in this work, is to extract the actual resistivity from measurements that are performed along the film’s thickness (z-direction). For this intent, we fabricated gold capped PbS mesas devices using a single step Ion Beam Milling (IBM) process where we milled the gold and the PbS film continually, and then measured the vertical resistance. Knowing the mesas’ dimensions, we calculate the resistivity. To the best of our knowledge, no previous work has extracted, vertically, the resistivity of chloride passivated PbS CQDs using the above method.« less

Single-step affinity and cost-effective purification of recombinant proteins using the Sepharose-binding lectin-tag from the mushroom Laetiporus sulphureus as fusion partner.

PubMed

Li, Xiao-Jing; Liu, Jin-Ling; Gao, Dong-Sheng; Wan, Wen-Yan; Yang, Xia; Li, Yong-Tao; Chang, Hong-Tao; Chen, Lu; Wang, Chuan-Qing; Zhao, Jun

2016-03-01

Previous research showed that a lectin from the mushroom Laetiporus sulphureus, designed LSL, bound to Sepharose and could be eluted by lactose. In this study, by taking advantage of the strong affinity of LSL-tag for Sepharose, we developed a single-step purification method for LSL-tagged fusion proteins. We utilized unmodified Sepharose-4B as a specific adsorbent and 0.2 M lactose solution as an elution buffer. Fusion proteins of LSL-tag and porcine circovirus capsid protein, designated LSL-Cap was recovered with purity of 90 ± 4%, and yield of 87 ± 3% from crude extract of recombinant Escherichia coli. To enable the remove of LSL-tag, tobacco etch virus (TEV) protease recognition sequence was placed downstream of LSL-tag in the expression vector, and LSL-tagged TEV protease, designated LSL-TEV, was also expressed in E. coli., and was recovered with purity of 82 ± 5%, and yield of 85 ± 2% from crude extract of recombinant E. coli. After digestion of LSL-tagged recombinant proteins with LSL-TEV, the LSL tag and LSL-TEV can be easily removed by passing the digested products through the Sepharose column. It is of worthy noting that the Sepharose can be reused after washing with PBS. The LSL affinity purification method enables rapid and inexpensive purification of LSL-tagged fusion proteins and scale-up production of native proteins. Copyright © 2015 Elsevier Inc. All rights reserved.

Considering dominance in reduced single-step genomic evaluations.

PubMed

Ertl, J; Edel, C; Pimentel, E C G; Emmerling, R; Götz, K-U

2018-06-01

Single-step models including dominance can be an enormous computational task and can even be prohibitive for practical application. In this study, we try to answer the question whether a reduced single-step model is able to estimate breeding values of bulls and breeding values, dominance deviations and total genetic values of cows with acceptable quality. Genetic values and phenotypes were simulated (500 repetitions) for a small Fleckvieh pedigree consisting of 371 bulls (180 thereof genotyped) and 553 cows (40 thereof genotyped). This pedigree was virtually extended for 2,407 non-genotyped daughters. Genetic values were estimated with the single-step model and with different reduced single-step models. Including more relatives of genotyped cows in the reduced single-step model resulted in a better agreement of results with the single-step model. Accuracies of genetic values were largest with single-step and smallest with reduced single-step when only the cows genotyped were modelled. The results indicate that a reduced single-step model is suitable to estimate breeding values of bulls and breeding values, dominance deviations and total genetic values of cows with acceptable quality. © 2018 Blackwell Verlag GmbH.

Immunocontraceptive activity guided fractionation and characterization of active constituents of neem (Azadirachta indica) seed extracts.

PubMed

Garg, S; Talwar, G P; Upadhyay, S N

1998-04-01

A novel approach for immunocontraception by intervention of local cell mediated immunity in the reproductive system by using single intrauterine application of neem oil has been described earlier. The reversible block in fertility was reported to last for 107-180 days in female Wistar rats (Upadhyay et al., 1990. Antifertility effects of neem oil by single intrauterine administration: A novel method of contraception. Proceedings Of The Royal Society Of London B 242, 175-180) and 7-11 months in monkeys (Upadhyay et al., 1994. Long term contraceptive effects of intrauterine neem treatment (IUNT) in bonnet monkeys: An alternative to intrauterine contraceptive devices. Contraception 49, 161-167). The present study, describes the identification and characterization of the biologically active fraction from neem seeds (Azadirachta indica A. Juss. Family Meliaceae), responsible for the above activity in adult female Wistar rats. Initial studies with the mechanically extracted oil and solvent extracts of neem seeds have revealed that the antifertility activity was present in constituents of low to intermediate polarity. A hexane extract of neem seeds was reported to be biologically active (Garg et al., 1994. Comparison of extraction procedures on the immunocontraceptive activity of neem seed extracts. Journal of Ethnopharmacology 22, 87-92). Subsequently, hexane extract was sequentially fractionated through the last active fraction using various separation techniques and tested for antifertility activity at each step. Preparative HPLC was used for isolating individual components of the active fraction in quantities, sufficient for characterization. An analytical HPLC method was developed for standardization of the fraction. The active fraction was identified to be a mixture of six components, which comprises of saturated, mono and di-unsaturated free fatty acids and their methyl esters. Dose response study was performed with the last active fractions. The antifertility activity with the active fraction was reversible in nature and it was completely active until 5% concentration. There was no systemic toxic effect following the administration of the active fraction. This study, for the first time, proposes an active fraction from neem seeds, responsible for long term and reversible blocking of fertility after a single intrauterine administration with high efficacy.

Rule-based Approach on Extraction of Malay Compound Nouns in Standard Malay Document

NASA Astrophysics Data System (ADS)

Abu Bakar, Zamri; Kamal Ismail, Normaly; Rawi, Mohd Izani Mohamed

2017-08-01

Malay compound noun is defined as a form of words that exists when two or more words are combined into a single syntax and it gives a specific meaning. Compound noun acts as one unit and it is spelled separately unless an established compound noun is written closely from two words. The basic characteristics of compound noun can be seen in the Malay sentences which are the frequency of that word in the text itself. Thus, this extraction of compound nouns is significant for the following research which is text summarization, grammar checker, sentiments analysis, machine translation and word categorization. There are many research efforts that have been proposed in extracting Malay compound noun using linguistic approaches. Most of the existing methods were done on the extraction of bi-gram noun+noun compound. However, the result still produces some problems as to give a better result. This paper explores a linguistic method for extracting compound Noun from stand Malay corpus. A standard dataset are used to provide a common platform for evaluating research on the recognition of compound Nouns in Malay sentences. Therefore, an improvement for the effectiveness of the compound noun extraction is needed because the result can be compromised. Thus, this study proposed a modification of linguistic approach in order to enhance the extraction of compound nouns processing. Several pre-processing steps are involved including normalization, tokenization and tagging. The first step that uses the linguistic approach in this study is Part-of-Speech (POS) tagging. Finally, we describe several rules-based and modify the rules to get the most relevant relation between the first word and the second word in order to assist us in solving of the problems. The effectiveness of the relations used in our study can be measured using recall, precision and F1-score techniques. The comparison of the baseline values is very essential because it can provide whether there has been an improvement in the result.

Whole head quantitative susceptibility mapping using a least-norm direct dipole inversion method.

PubMed

Sun, Hongfu; Ma, Yuhan; MacDonald, M Ethan; Pike, G Bruce

2018-06-15

A new dipole field inversion method for whole head quantitative susceptibility mapping (QSM) is proposed. Instead of performing background field removal and local field inversion sequentially, the proposed method performs dipole field inversion directly on the total field map in a single step. To aid this under-determined and ill-posed inversion process and obtain robust QSM images, Tikhonov regularization is implemented to seek the local susceptibility solution with the least-norm (LN) using the L-curve criterion. The proposed LN-QSM does not require brain edge erosion, thereby preserving the cerebral cortex in the final images. This should improve its applicability for QSM-based cortical grey matter measurement, functional imaging and venography of full brain. Furthermore, LN-QSM also enables susceptibility mapping of the entire head without the need for brain extraction, which makes QSM reconstruction more automated and less dependent on intermediate pre-processing methods and their associated parameters. It is shown that the proposed LN-QSM method reduced errors in a numerical phantom simulation, improved accuracy in a gadolinium phantom experiment, and suppressed artefacts in nine subjects, as compared to two-step and other single-step QSM methods. Measurements of deep grey matter and skull susceptibilities from LN-QSM are consistent with established reconstruction methods. Copyright © 2018 Elsevier Inc. All rights reserved.

Estimation of Cadmium uptake by tobacco plants from laboratory leaching tests.

PubMed

Marković, Jelena P; Jović, Mihajlo D; Smičiklas, Ivana D; Šljivić-Ivanović, Marija Z; Smiljanić, Slavko N; Onjia, Antonije E; Popović, Aleksandar R

2018-03-21

The objective of the present study was to determine the impact of cadmium (Cd) concentration in the soil on its uptake by tobacco plants, and to compare the ability of diverse extraction procedures for determining Cd bioavailability and predicting soil-to-plant transfer and Cd plant concentrations. The pseudo-total digestion procedure, modified Tessier sequential extraction and six standard single-extraction tests for estimation of metal mobility and bioavailability were used for the leaching of Cd from a native soil, as well as samples artificially contaminated over a wide range of Cd concentrations. The results of various leaching tests were compared between each other, as well as with the amounts of Cd taken up by tobacco plants in pot experiments. In the native soil sample, most of the Cd was found in fractions not readily available under natural conditions, but with increasing pollution level, Cd amounts in readily available forms increased. With increasing concentrations of Cd in the soil, the quantity of pollutant taken up in tobacco also increased, while the transfer factor (TF) decreased. Linear and non-linear empirical models were developed for predicting the uptake of Cd by tobacco plants based on the results of selected leaching tests. The non-linear equations for ISO 14870 (diethylenetriaminepentaacetic acid extraction - DTPA), ISO/TS 21268-2 (CaCl 2 leaching procedure), US EPA 1311 (toxicity characteristic leaching procedure - TCLP) single step extractions, and the sum of the first two fractions of the sequential extraction, exhibited the best correlation with the experimentally determined concentrations of Cd in plants over the entire range of pollutant concentrations. This approach can improve and facilitate the assessment of human exposure to Cd by tobacco smoking, but may also have wider applicability in predicting soil-to-plant transfer.

Compact mass spectrometer for plasma discharge ion analysis

DOEpatents

Tuszewski, M.G.

1997-07-22

A mass spectrometer and methods are disclosed for mass spectrometry which are useful in characterizing a plasma. This mass spectrometer for determining type and quantity of ions present in a plasma is simple, compact, and inexpensive. It accomplishes mass analysis in a single step, rather than the usual two-step process comprised of ion extraction followed by mass filtering. Ions are captured by a measuring element placed in a plasma and accelerated by a known applied voltage. Captured ions are bent into near-circular orbits by a magnetic field such that they strike a collector, producing an electric current. Ion orbits vary with applied voltage and proton mass ratio of the ions, so that ion species may be identified. Current flow provides an indication of quantity of ions striking the collector. 7 figs.

Compact mass spectrometer for plasma discharge ion analysis

DOEpatents

Tuszewski, Michel G.

1997-01-01

A mass spectrometer and methods for mass spectrometry which are useful in characterizing a plasma. This mass spectrometer for determining type and quantity of ions present in a plasma is simple, compact, and inexpensive. It accomplishes mass analysis in a single step, rather than the usual two-step process comprised of ion extraction followed by mass filtering. Ions are captured by a measuring element placed in a plasma and accelerated by a known applied voltage. Captured ions are bent into near-circular orbits by a magnetic field such that they strike a collector, producing an electric current. Ion orbits vary with applied voltage and proton mass ratio of the ions, so that ion species may be identified. Current flow provides an indication of quantity of ions striking the collector.

Extracting built-up areas from TerraSAR-X data using object-oriented classification method

NASA Astrophysics Data System (ADS)

Wang, SuYun; Sun, Z. C.

2017-02-01

Based on single-polarized TerraSAR-X, the approach generates homogeneous segments on an arbitrary number of scale levels by applying a region-growing algorithm which takes the intensity of backscatter and shape-related properties into account. The object-oriented procedure consists of three main steps: firstly, the analysis of the local speckle behavior in the SAR intensity data, leading to the generation of a texture image; secondly, a segmentation based on the intensity image; thirdly, the classification of each segment using the derived texture file and intensity information in order to identify and extract build-up areas. In our research, the distribution of BAs in Dongying City is derived from single-polarized TSX SM image (acquired on 17th June 2013) with average ground resolution of 3m using our proposed approach. By cross-validating the random selected validation points with geo-referenced field sites, Quick Bird high-resolution imagery, confusion matrices with statistical indicators are calculated and used for assessing the classification results. The results demonstrate that an overall accuracy 92.89 and a kappa coefficient of 0.85 could be achieved. We have shown that connect texture information with the analysis of the local speckle divergence, combining texture and intensity of construction extraction is feasible, efficient and rapid.

One-Step Extraction and Hydrolysis of Flavonoid Glycosides in Rape Bee Pollen Based on Soxhlet-Assisted Matrix Solid Phase Dispersion.

PubMed

Tu, Xijuan; Ma, Shuangqin; Gao, Zhaosheng; Wang, Jing; Huang, Shaokang; Chen, Wenbin

2017-11-01

Flavonoids are frequently found as glycosylated derivatives in plant materials. To determine contents of flavonoid aglycones in these matrices, procedures for the extraction and hydrolysis of flavonoid glycosides are required. The current sample preparation method is both labour and time consuming. Develop a modified matrix solid phase dispersion (MSPD) procedure as an alternative methodology for the one-step extraction and hydrolysis of flavonoid glycosides. HPLC-DAD was applied for demonstrating the one-step extraction and hydrolysis of flavonoids in rape bee pollen. The obtained contents of flavonoid aglycones (quercetin, kaempferol, isorhamnetin) were used for the optimisation and validation of the method. The extraction and hydrolysis were accomplished in one step. The procedure completes in 2 h with silica gel as dispersant, a 1:2 ratio of sample to dispersant, and 60% aqueous ethanol with 0.3 M hydrochloric acid as the extraction solution. The relative standard deviations (RSDs) of repeatability were less than 5%, and the recoveries at two fortified levels were between 88.3 and 104.8%. The proposed methodology is simple and highly efficient, with good repeatability and recovery. Compared with currently available methods, the present work has advantages of using less time and labour, higher extraction efficiency, and less consumption of the acid catalyst. This method may have applications for the one-step extraction and hydrolysis of bioactive compounds from plant materials. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Synthesis of silver nanoparticles using reducing agents obtained from natural sources (Rumex hymenosepalus extracts)

PubMed Central

2013-01-01

We have synthesized silver nanoparticles from silver nitrate solutions using extracts of Rumex hymenosepalus, a plant widely found in a large region in North America, as reducing agent. This plant is known to be rich in antioxidant molecules which we use as reducing agents. Silver nanoparticles grow in a single-step method, at room temperature, and with no addition of external energy. The nanoparticles have been characterized by ultraviolet-visible spectroscopy and transmission electron microscopy, as a function of the ratio of silver ions to reducing agent molecules. The nanoparticle diameters are in the range of 2 to 40 nm. High-resolution transmission electron microscopy and fast Fourier transform analysis show that two kinds of crystal structures are obtained: face-centered cubic and hexagonal. PMID:23841946

Successive DNA extractions improve characterization of soil microbial communities

PubMed Central

de Hollander, Mattias; Smidt, Hauke; van Veen, Johannes A.

2017-01-01

Currently, characterization of soil microbial communities relies heavily on the use of molecular approaches. Independently of the approach used, soil DNA extraction is a crucial step, and success of downstream procedures will depend on how well DNA extraction was performed. Often, studies describing and comparing soil microbial communities are based on a single DNA extraction, which may not lead to a representative recovery of DNA from all organisms present in the soil. The use of successive DNA extractions might improve soil microbial characterization, but the benefit of this approach has only been limitedly studied. To determine whether successive DNA extractions of the same soil sample would lead to different observations in terms of microbial abundance and community composition, we performed three successive extractions, with two widely used commercial kits, on a range of clay and sandy soils. Successive extractions increased DNA yield considerably (1–374%), as well as total bacterial and fungal abundances in most of the soil samples. Analysis of the 16S and 18S ribosomal RNA genes using 454-pyrosequencing, revealed that microbial community composition (taxonomic groups) observed in the successive DNA extractions were similar. However, successive DNA extractions did reveal several additional microbial groups. For some soil samples, shifts in microbial community composition were observed, mainly due to shifts in relative abundance of a number of microbial groups. Our results highlight that performing successive DNA extractions optimize DNA yield, and can lead to a better picture of overall community composition. PMID:28168105

Novel approach to microwave-assisted extraction and micro-solid-phase extraction from soil using graphite fibers as sorbent.

PubMed

Xu, Li; Lee, Hian Kee

2008-05-30

A single-step extraction-cleanup procedure involving microwave-assisted extraction (MAE) and micro-solid-phase extraction (micro-SPE) has been developed for the analysis of polycyclic aromatic hydrocarbons (PAHs) from soil samples. Micro-SPE is a relatively new extraction procedure that makes use of a sorbent enclosed within a sealed polypropylene membrane envelope. In the present work, for the first time, graphite fiber was used as a sorbent material for extraction. MAE-micro-SPE was used to cleanup sediment samples and to extract and preconcentrate five PAHs in sediment samples prepared as slurries with addition of water. The best extraction conditions comprised of microwave heating at 50 degrees C for a duration of 20 min, and an elution (desorption) time of 5 min using acetonitrile with sonication. Using gas chromatography (GC)-flame ionization detection (FID), the limits of detection (LODs) of the PAHs ranged between 2.2 and 3.6 ng/g. With GC-mass spectrometry (MS), LODs were between 0.0017 and 0.0057 ng/g. The linear ranges were between 0.1 and 50 or 100 microg/g for GC-FID analysis, and 1 and 500 or 1000 ng/g for GC-MS analysis. Granular activated carbon was also used for the micro-SPE device but was found to be not as efficient in the PAH extraction. The MAE-micro-SPE method was successfully used for the extraction of PAHs in river and marine sediments, demonstrating its applicability to real environmental solid matrixes.

Loop-mediated isothermal amplification assay for detection and discrimination of Toxocara canis and Toxocara cati eggs directly from sand samples.

PubMed

Macuhova, K; Kumagai, T; Akao, N; Ohta, N

2010-12-01

We developed a novel and simple method, using loop-mediated isothermal amplification (LAMP), for the detection and discrimination of Toxocara canis and Toxocara cati eggs. The new method employs 4 steps: (1) concentration of Toxocara eggs in a small amount of sand; (2) dissolution of the proteinaceous membrane of eggs and simultaneously separation of them from the sand using NaClO treatment; (3) extraction of DNA using NaOH treatment; and (4) detection of T. canis / T. cati DNA using a LAMP assay. All these steps are fast, easy to perform, and do not require expensive equipment or reagents. The novel method was tested both experimentally and in a field study. In the laboratory, we could reliably detect as few as 3 T. canis eggs in artificially contaminated sand, if the experiment was repeated twice. In the field trial, we were able to detect T. cati DNA from 4 natural sandpits having moderate to heavy contamination, although not in a single lightly contaminated sandpit. All of the examined sandpits were found to be contaminated with eggs of T. cati, but none appeared to contain T. canis. Our new method could extract DNA from T. canis and T. cati eggs directly from sand samples as well as detect and distinguish these 2 species in a few easy steps, with markedly reduced time and expense.

Preparative separation of bioactive compounds from essential oil of Flaveria bidentis (L.) Kuntze using steam distillation extraction and one step high-speed counter-current chromatography.

PubMed

Wei, Yun; Du, Jilin; Lu, Yuanyuan

2012-10-01

In order to utilize and control the invasive weed, bioactive compounds from essential oil of Flaveria bidentis (L.) Kuntze were studied. Steam distillation extraction and one step high-speed counter-current chromatography were applied to separate and purify the caryophyllene oxide, 7,11-dimethyl-3-methylene-1,6,10-dodecatriene, and caryophyllene from essential oil of Flaveria bidentis (L.) Kuntze. The two-phase solvent system containing n-hexane/acetonitrile/ethanol (5:4:3, v/v/v) was selected for the one step separation mode according to the partition coefficient values (K) of the target compounds and the separation factor (α). The purity of each isolated fraction after a single high-speed counter-current chromatography run was determined by high performance liquid chromatography. A 3.2 mg of caryophyllene oxide at a purity of 92.6%, 10.4 mg of 7,11-dimethyl-3-methylene-1,6,10-dodecatriene at a purity of 99.1% and 5.7 mg of caryophyllene at a purity of 98.8% were obtained from 200 mg essential oil of Flaveria bidentis (L.) Kuntze. The chemical structures of these components were identified by GC-MS, (1) H-NMR, and (13) C-NMR. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A new approach for bioassays based on frequency- and time-domain measurements of magnetic nanoparticles.

PubMed

Oisjöen, Fredrik; Schneiderman, Justin F; Astalan, Andrea Prieto; Kalabukhov, Alexey; Johansson, Christer; Winkler, Dag

2010-01-15

We demonstrate a one-step wash-free bioassay measurement system capable of tracking biochemical binding events. Our approach combines the high resolution of frequency- and high speed of time-domain measurements in a single device in combination with a fast one-step bioassay. The one-step nature of our magnetic nanoparticle (MNP) based assay reduces the time between sample extraction and quantitative results while mitigating the risks of contamination related to washing steps. Our method also enables tracking of binding events, providing the possibility of, for example, investigation of how chemical/biological environments affect the rate of a binding process or study of the action of certain drugs. We detect specific biological binding events occurring on the surfaces of fluid-suspended MNPs that modify their magnetic relaxation behavior. Herein, we extrapolate a modest sensitivity to analyte of 100 ng/ml with the present setup using our rapid one-step bioassay. More importantly, we determine the size-distributions of the MNP systems with theoretical fits to our data obtained from the two complementary measurement modalities and demonstrate quantitative agreement between them. Copyright 2009 Elsevier B.V. All rights reserved.

Optimized production of vanillin from green vanilla pods by enzyme-assisted extraction combined with pre-freezing and thawing.

PubMed

Zhang, Yanjun; Mo, Limei; Chen, Feng; Lu, Minquan; Dong, Wenjiang; Wang, Qinghuang; Xu, Fei; Gu, Fenglin

2014-02-19

Production of vanillin from natural green vanilla pods was carried out by enzyme-assisted extraction combined with pre-freezing and thawing. In the first step the green vanilla pods were pre-frozen and then thawed to destroy cellular compartmentation. In the second step pectinase from Aspergillus niger was used to hydrolyze the pectin between the glucovanillin substrate and β-glucosidase. Four main variables, including enzyme amount, reaction temperature, time and pH, which were of significance for the vanillin content were studied and a central composite design (CCD) based on the results of a single-factor tests was used. Response surface methodology based on CCD was employed to optimize the combination of enzyme amount, reaction temperature, time, and pH for maximum vanillin production. This resulted in the optimal condition in regards of the enzyme amount, reaction temperature, time, and pH at 84.2 mg, 49.5 °C, 7.1 h, and 4.2, respectively. Under the optimal condition, the experimental yield of vanillin was 4.63% ± 0.11% (dwb), which was in good agreement with the value predicted by the model. Compared to the traditional curing process (1.98%) and viscozyme extract (2.36%), the optimized method for the vanillin production significantly increased the yield by 133.85% and 96%, respectively.

Single-tube analysis of DNA methylation with silica superparamagnetic beads.

PubMed

Bailey, Vasudev J; Zhang, Yi; Keeley, Brian P; Yin, Chao; Pelosky, Kristen L; Brock, Malcolm; Baylin, Stephen B; Herman, James G; Wang, Tza-Huei

2010-06-01

DNA promoter methylation is a signature for the silencing of tumor suppressor genes. Most widely used methods to detect DNA methylation involve 3 separate, independent processes: DNA extraction, bisulfite conversion, and methylation detection via a PCR method, such as methylation-specific PCR (MSP). This method includes many disconnected steps with associated losses of material, potentially reducing the analytical sensitivity required for analysis of challenging clinical samples. Methylation on beads (MOB) is a new technique that integrates DNA extraction, bisulfite conversion, and PCR in a single tube via the use of silica superparamagnetic beads (SSBs) as a common DNA carrier for facilitating cell debris removal and buffer exchange throughout the entire process. In addition, PCR buffer is used to directly elute bisulfite-treated DNA from SSBs for subsequent target amplifications. The diagnostic sensitivity of MOB was evaluated by methylation analysis of the CDKN2A [cyclin-dependent kinase inhibitor 2A (melanoma, p16, inhibits CDK4); also known as p16(INK4a)] promoter in serum DNA of lung cancer patients and compared with that of conventional methods. Methylation analysis consisting of DNA extraction followed by bisulfite conversion and MSP was successfully carried out within 9 h in a single tube. The median pre-PCR DNA yield was 6.61-fold higher with the MOB technique than with conventional techniques. Furthermore, MOB increased the diagnostic sensitivity in our analysis of the CDKN2A promoter in patient serum by successfully detecting methylation in 74% of cancer patients, vs the 45% detection rate obtained with conventional techniques. The MOB technique successfully combined 3 processes into a single tube, thereby allowing ease in handling and an increased detection throughput. The increased pre-PCR yield in MOB allowed efficient, diagnostically sensitive methylation detection.

Preparative isolation, fast centrifugal partition chromatography purification and biological activity of cajaflavanone from Derris ferruginea stems.

PubMed

Morel, Sylvie; Landreau, Anne; Nguyen, Van Hung; Derbré, Séverine; Grellier, Philippe; Pape, Patrice Le; Pagniez, Fabrice; Litaudon, Marc; Richomme, Pascal

2012-01-01

The Derris genus is known to contain flavonoid derivatives, including prenylated flavanones and isoflavonoids such as rotenoids, which are generally associated with significant biological activity. To develop an efficient preparative isolation procedure for bioactive cajaflavanone. Fast centrifugal partition chromatography (FCPC) was optimised to purify cajaflavanone from Derris ferruginea stems in a single step as compared to fractionation from the cyclohexane extract by successive conventional solid-liquid chromatography procedures. The purification yield, purity, time and solvent consumption per procedure are described. The anti-fungal, anti-bacterial, anti-leishmanial, anti-plasmodial, anti-oxidant activities and the inhibition of advanced glycation end-products (AGEs) by cajaflavanone accumulation are described. FCPC enabled cajaflavanone purification in a single separation step, yielding sufficient quantities to perform in vitro biological screening. Interestingly, cajaflavanone had an inhibitory effect on the formation of AGEs, without displaying any in vitro anti-oxidant activity. A simple and efficient procedure, in comparison with other preparative methods, for bioactive cajaflavone purification has been developed using FCPC. Copyright © 2011 John Wiley & Sons, Ltd.

Coexpression of β-D-galactosidase and L-arabinose isomerase in the production of D-tagatose: a functional sweetener.

PubMed

Zhan, Yijing; Xu, Zheng; Li, Sha; Liu, Xiaoliu; Xu, Lu; Feng, Xiaohai; Xu, Hong

2014-03-19

The functional sweetener, d-tagatose, is commonly transformed from galactose by l-arabinose isomerase. To make use of a much cheaper starting material, lactose, hydrolization, and isomerization are required to take place collaboratively. Therefore, a single-step method involving β-d-galactosidase was explored for d-tagatose production. The two vital genes, β-d-galactosidase gene (lacZ) and l-arabinose isomerase mutant gene (araA') were extracted separately from Escherichia coli strains and incorporated into E. coli simultaneously. This gave us E. coli-ZY, a recombinant producing strain capable of coexpressing the two key enzymes. The resulted cells exhibited maximum d-tagatose producing activity at 34 °C and pH 6.5 and in the presence of borate, 10 mM Fe(2+), and 1 mM Mn(2+). Further monitoring showed that the recombinant cells could hydrolyze more than 95% lactose and convert 43% d-galactose into d-tagatose. This research has verified the feasibility of single-step d-tagatose fermentation, thereby laying down the foundation for industrial usage of lactose.

Structural Studies of Silver Nanoparticles Obtained Through Single-Step Green Synthesis

NASA Astrophysics Data System (ADS)

Prasad Peddi, Siva; Abdallah Sadeh, Bilal

2015-10-01

Green synthesis of silver Nanoparticles (AGNP's) has been the most prominent among the metallic nanoparticles for research for over a decade and half now due to both the simplicity of preparation and the applicability of biological species with extensive applications in medicine and biotechnology to reduce and trap the particles. The current article uses Eclipta Prostrata leaf extract as the biological species to cap the AGNP's through a single step process. The characterization data obtained was used for the analysis of the sample structure. The article emphasizes the disquisition of their shape and size of the lattice parameters and proposes a general scheme and a mathematical model for the analysis of their dependence. The data of the synthesized AGNP's has been used to advantage through the introduction of a structural shape factor for the crystalline nanoparticles. The properties of the structure of the AGNP's proposed and evaluated through a theoretical model was undeviating with the experimental consequences. This modus operandi gives scope for the structural studies of ultrafine particles prepared using biological methods.

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.

Evaluation of a modified QuEChERS extraction of multiple classes of pesticides from a rice paddy soil by LC-APCI-MS/MS.

PubMed

Caldas, Sergiane S; Bolzan, Cátia M; Cerqueira, Maristela B; Tomasini, Débora; Furlong, Eliana B; Fagundes, Carlos; Primel, Ednei G

2011-11-23

A new method for the determination of clomazone, fipronil, tebuconazole, propiconazole, and azoxystrobin in samples of rice paddy soil is presented. The extraction of the pesticides from soil samples was performed by using a modified quick, easy, cheap, effective, rugged, and safe (QuEChERS) method. Some extraction conditions such as salt addition, sample acidification, use of buffer, and cleanup step were evaluated. The optimized method dealt with a single extraction of the compounds under study with acidified acetonitrile, followed by the addition of MgSO(4) and NaCl prior to the final determination by liquid chromatography-atmospheric chemical pressure ionization-tandem mass spectrometry. Validation studies were carried out in soil samples. Recoveries of the spiked samples ranged between 70.3 and 120% with relative standard deviation lower than 18.2%. The limits of quantification were between 10 and 50 μg kg(-1). The method was applied to the analysis of real samples of soils where rice is cultivated.

Development of a reliable extraction and quantification method for glucosinolates in Moringa oleifera.

PubMed

Förster, Nadja; Ulrichs, Christian; Schreiner, Monika; Müller, Carsten T; Mewis, Inga

2015-01-01

Glucosinolates are the characteristic secondary metabolites of plants in the order Brassicales. To date the common DIN extraction 'desulfo glucosinolates' method remains the common procedure for determination and quantification of glucosinolates. However, the desulfation step in the extraction of glucosinolates from Moringa oleifera leaves resulted in complete conversion and degradation of the naturally occurring glucosinolates in this plant. Therefore, a method for extraction of intact Moringa glucosinolates was developed and no conversion and degradation of the different rhamnopyranosyloxy-benzyl glucosinolates was found. Buffered eluents (0.1 M ammonium acetate) were necessary to stabilize 4-α-rhamnopyranosyloxy-benzyl glucosinolate (Rhamno-Benzyl-GS) and acetyl-4-α-rhamnopyranosyloxy-benzyl glucosinolate isomers (Ac-Isomers-GS) during HPLC analysis. Due to the instability of intact Moringa glucosinolates at room temperature and during the purification process of single glucosinolates, influences of different storage (room temperature, frozen, thawing and refreezing) and buffer conditions on glucosinolate conversion were analysed. Conversion and degradations processes were especially determined for the Ac-Isomers-GS III. Copyright © 2014 Elsevier Ltd. All rights reserved.

Green Synthesis of Silver Nanoparticles by using Eucalyptus Globulus Leaf Extract

NASA Astrophysics Data System (ADS)

Balamurugan, Madheswaran; Saravanan, Shanmugam

2017-12-01

A single step eco-friendly, energy efficient and economically scalable green method was employed to synthesize silver nanoparticles. In this work, the synthesis of silver nanoparticles using Eucalyptus globulus leaf extract as reducing and capping agent along with water as solvent at normal room temperature is described. Silver nanoparticles were prepared from aqueous silver nitrate solution by adding the leaf extract. The prepared nanoparticles were characterized by using UV-visible Spectrophotometer, X-ray diffractometer, High Resolution Transmission Electron Microscope (HR-TEM) and Fourier Transform Infrared Spectroscope (FTIS). X-ray diffraction studies brought to light the crystalline nature and the face centered cubic structure of the silver nanoparticles. Using HR-TEM. the nano sizes and morphology of the particles were studied. The mean sizes of the prepared silver nanoparticles ranged from 30 to 36 nm. The density of the particles was tuned by varying the molar ratio of silver nitrate. FTIS studies showed the functional group of organic molecules which were located on the surface of the silver nanoparticles. Originating from the leaf extracts, these organic molecules reduced and capped the particles.

An insight into the determination of trace levels of benzodiazepines in biometric systems: Use of crab shell powder as an environmentally friendly biosorbent.

PubMed

Samadi, Fatemeh; Sarafraz-Yazdi, Ali; Es'haghi, Zarrin

2018-05-30

A vortex assisted dispersive solid phase extraction approach (VADSPE) based on crab shell powder as biodegradable and biocompatible μ-sorbent was developed for simultaneous analysis of three benzodiazepines (BZPs): Oxazepam, Flurazepamand Diazepam, in biological matrixes included blood, nail, hair and urine samples. The effective parameters in VADSPE process, including the volume of uptake solvent, the dosage of sorbent, extraction time and back extraction time, were optimized using response surface methodology(RSM) based on central composite design(CCD). The suggested technique allows successful trapping of BZPs in a single-step extraction. Under the optimized extraction conditions, the proposed approach was exhibited low limits of detection (0.003-1.2 μg·mL -1 ), an acceptable linearity (0.04-20 μg·mL -1 ). Method performance was assessed by recovery experiments at spiking levels of 10 μg·mL -1 (n = 5) for BZPs in blood, nail, hair and urine samples. Relative recoveries were determined by HPLC, which were between 36%and 95.6%. Copyright © 2018. Published by Elsevier B.V.

Decomposition and extraction: a new framework for visual classification.

PubMed

Fang, Yuqiang; Chen, Qiang; Sun, Lin; Dai, Bin; Yan, Shuicheng

2014-08-01

In this paper, we present a novel framework for visual classification based on hierarchical image decomposition and hybrid midlevel feature extraction. Unlike most midlevel feature learning methods, which focus on the process of coding or pooling, we emphasize that the mechanism of image composition also strongly influences the feature extraction. To effectively explore the image content for the feature extraction, we model a multiplicity feature representation mechanism through meaningful hierarchical image decomposition followed by a fusion step. In particularly, we first propose a new hierarchical image decomposition approach in which each image is decomposed into a series of hierarchical semantical components, i.e, the structure and texture images. Then, different feature extraction schemes can be adopted to match the decomposed structure and texture processes in a dissociative manner. Here, two schemes are explored to produce property related feature representations. One is based on a single-stage network over hand-crafted features and the other is based on a multistage network, which can learn features from raw pixels automatically. Finally, those multiple midlevel features are incorporated by solving a multiple kernel learning task. Extensive experiments are conducted on several challenging data sets for visual classification, and experimental results demonstrate the effectiveness of the proposed method.

Determination of parabens and endocrine-disrupting alkylphenols in soil by gas chromatography-mass spectrometry following matrix solid-phase dispersion or in-column microwave-assisted extraction: a comparative study.

PubMed

Pérez, R A; Albero, B; Miguel, E; Sánchez-Brunete, C

2012-03-01

Two rapid methods were evaluated for the simultaneous extraction of seven parabens and two alkylphenols from soil based on matrix solid-phase dispersion (MSPD) and microwave-assisted extraction (MAE). Soil extracts were derivatized with N,O-bis(trimethylsilyl)trifluoroacetamide and analyzed by gas chromatography with mass spectrometry. Extraction and clean-up of samples were carried out by both methods in a single step. A glass sample holder, inside the microwave cell, was used in MAE to allow the simultaneous extraction and clean-up of samples and shorten the MAE procedure. The detection limits achieved by MSPD were lower than those obtained by MAE because the presence of matrix interferences increased with this extraction method. The extraction yields obtained by MSPD and MAE for three different types of soils were compared. Both procedures showed good recoveries and sensitivity for the determination of parabens and alkylphenols in two of the soils assayed, however, only MSPD yielded good recoveries with the other soil. Finally, MSPD was applied to the analysis of soils collected in different sites of Spain. In most of the samples analyzed, methylparaben and butylparaben were detected at levels ranging from 1.21 to 8.04 ng g(-1) dry weight and 0.48 to 1.02 ng g(-1) dry weight, respectively.

Photovoltaic energy technologies: Health and environmental effects document

NASA Astrophysics Data System (ADS)

Moskowitz, P. D.; Hamilton, L. D.; Morris, S. C.; Rowe, M. D.

1980-09-01

The potential health and environmental consequences of producing electricity by photovoltaic energy systems was analyzed. Potential health and environmental risks are identified in representative fuel and material supply cycles including extraction, processing, refining, fabrication, installation, operation, and isposal for four photovoltaic energy systems (silicon N/P single crystal, silicon metal/insulator/semiconductor (MIS) cell, cadmium sulfide/copper sulfide backwall cell, and gallium arsenide heterojunction cell) delivering equal amounts of useful energy. Each step of the fuel and material supply cycles, materials demands, byproducts, public health, occupational health, and environmental hazards is identified.

Humus-assisted cleaning of heavy metal contaminated soils

NASA Astrophysics Data System (ADS)

Borggaard, Ole K.; Rasmussen, Signe B.

2016-04-01

Contamination of soils with non-degradable heavy metals (HMs) because of human acticities is globally a serious problem threatening human health and ecosystem functioning. To avoid negative effects, HMs must be removed either on-site by plant uptake (phytoremediation) or off-site by extraction (soil washing). In both strategies, HM solubility must be augmented by means of a strong ligand (complexant). Often polycarboxylates such as EDTA and NTA are used but these ligands are toxic, synthetic (non-natural) and may promote HM leaching. Instead naturally occurring soluble humic substances (HS) were tested as means for cleaning HM contaminated soils; HS samples from beech and spruce litter, compost percolate and processed cow slurry were tested. Various long-term HM contaminated soils were extracted with solutions of EDTA, NTA or HS at different pH by single-step and multiple-step extraction mode. The results showed that each of the three complexant types increased HM solubility but the pH-dependent HM extraction efficiency decreased in the order: EDTA ≈ NTA > HS. However, the naturally occurring HS seems suitable for cleaning As, Cd, Cu and Zn contaminated soils both in relation to phytoremediation of moderately contaminated soils and washing of strongly contaminated soils. On the other hand, HS was found unsuited as cleaning agent for Pb polluted calcareous soils. If future field experiments confirm these laboratory results, we have a new cheap and environmentally friendly method for solving a great pollution problem, i.e. cleaning of heavy metal contaminated soils. In addition, humic substances possess additional benefits such as improving soil structure and stimulating microbial activity.

Lipid extraction methods from microalgal biomass harvested by two different paths: screening studies toward biodiesel production.

PubMed

Ríos, Sergio D; Castañeda, Joandiet; Torras, Carles; Farriol, Xavier; Salvadó, Joan

2013-04-01

Microalgae can grow rapidly and capture CO2 from the atmosphere to convert it into complex organic molecules such as lipids (biodiesel feedstock). High scale economically feasible microalgae based oil depends on optimizing the entire process production. This process can be divided in three very different but directly related steps (production, concentration, lipid extraction and transesterification). The aim of this study is to identify the best method of lipid extraction to undergo the potentiality of some microalgal biomass obtained from two different harvesting paths. The first path used all physicals concentration steps, and the second path was a combination of chemical and physical concentration steps. Three microalgae species were tested: Phaeodactylum tricornutum, Nannochloropsis gaditana, and Chaetoceros calcitrans One step lipid extraction-transesterification reached the same fatty acid methyl ester yield as the Bligh and Dyer and soxhlet extraction with n-hexane methods with the corresponding time, cost and solvent saving. Copyright © 2013 Elsevier Ltd. All rights reserved.

MOCAT: A Metagenomics Assembly and Gene Prediction Toolkit

PubMed Central

Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R.; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/. PMID:23082188

Learning target masks in infrared linescan imagery

NASA Astrophysics Data System (ADS)

Fechner, Thomas; Rockinger, Oliver; Vogler, Axel; Knappe, Peter

1997-04-01

In this paper we propose a neural network based method for the automatic detection of ground targets in airborne infrared linescan imagery. Instead of using a dedicated feature extraction stage followed by a classification procedure, we propose the following three step scheme: In the first step of the recognition process, the input image is decomposed into its pyramid representation, thus obtaining a multiresolution signal representation. At the lowest three levels of the Laplacian pyramid a neural network filter of moderate size is trained to indicate the target location. The last step consists of a fusion process of the several neural network filters to obtain the final result. To perform this fusion we use a belief network to combine the various filter outputs in a statistical meaningful way. In addition, the belief network allows the integration of further knowledge about the image domain. By applying this multiresolution recognition scheme, we obtain a nearly scale- and rotational invariant target recognition with a significantly decreased false alarm rate compared with a single resolution target recognition scheme.

MOCAT: a metagenomics assembly and gene prediction toolkit.

PubMed

Kultima, Jens Roat; Sunagawa, Shinichi; Li, Junhua; Chen, Weineng; Chen, Hua; Mende, Daniel R; Arumugam, Manimozhiyan; Pan, Qi; Liu, Binghang; Qin, Junjie; Wang, Jun; Bork, Peer

2012-01-01

MOCAT is a highly configurable, modular pipeline for fast, standardized processing of single or paired-end sequencing data generated by the Illumina platform. The pipeline uses state-of-the-art programs to quality control, map, and assemble reads from metagenomic samples sequenced at a depth of several billion base pairs, and predict protein-coding genes on assembled metagenomes. Mapping against reference databases allows for read extraction or removal, as well as abundance calculations. Relevant statistics for each processing step can be summarized into multi-sheet Excel documents and queryable SQL databases. MOCAT runs on UNIX machines and integrates seamlessly with the SGE and PBS queuing systems, commonly used to process large datasets. The open source code and modular architecture allow users to modify or exchange the programs that are utilized in the various processing steps. Individual processing steps and parameters were benchmarked and tested on artificial, real, and simulated metagenomes resulting in an improvement of selected quality metrics. MOCAT can be freely downloaded at http://www.bork.embl.de/mocat/.

Using the time shift in single pushbroom datatakes to detect ships and their heading

NASA Astrophysics Data System (ADS)

Willburger, Katharina A. M.; Schwenk, Kurt

2017-10-01

The detection of ships from remote sensing data has become an essential task for maritime security. The variety of application scenarios includes piracy, illegal fishery, ocean dumping and ships carrying refugees. While techniques using data from SAR sensors for ship detection are widely common, there is only few literature discussing algorithms based on imagery of optical camera systems. A ship detection algorithm for optical pushbroom data has been developed. It takes advantage of the special detector assembly of most of those scanners, which allows apart from the detection of a ship also the calculation of its heading out of a single acquisition. The proposed algorithm for the detection of moving ships was developed with RapidEye imagery. It algorithm consists mainly of three steps: the creation of a land-watermask, the object extraction and the deeper examination of each single object. The latter step is built up by several spectral and geometric filters, making heavy use of the inter-channel displacement typical for pushbroom sensors with multiple CCD lines, finally yielding a set of ships and their direction of movement. The working principle of time-shifted pushbroom sensors and the developed algorithm is explained in detail. Furthermore, we present our first results and give an outlook to future improvements.

Rapid detection of avian influenza virus a and subtype H5N1 by single step multiplex reverse transcription-polymerase chain reaction.

PubMed

Wei, Hui-Ling; Bai, Gui-Rong; Mweene, Aaron S; Zhou, Ying-Chun; Cong, Yan-Long; Pu, Juan; Wang, Shuai; Kida, Hiroshi; Liu, Jin-Hua

2006-06-01

Outbreaks of H5N1 highly pathogenic avian influenza (HPAI) virus caused great economic losses to the poultry industry and resulted in human deaths in Thailand and Viet Nam in 2004. Rapid typing and subtyping of H5N1 viruses, especially from clinical specimens, are desirable for taking prompt control measures to prevent the spread of the disease. Here, we developed a set of oligonucleotide primers able to detect, type and subtype H5 and N1 influenza viruses in a single step multiplex reverse transcription-polymerase chain reaction (RT-PCR). RNA was extracted from allantoic fluid or from specimens with guanidinium isothiocyanate reagent. Reverse transcription and PCR were carried out with a mixture of primers specific for influenza viruses of type A, subtype H5 and N1 in a single reaction system under identical conditions. The amplified DNA fragments were analyzed by agarose gel electrophoresis. All the H5N1 viruses tested in the study and the experimental specimens presented three specific bands by the method established here. The results presented here suggest that the method described below is rapid and specific and, therefore, could be valuable in the rapid detection of H5N1 influenza viruses in clinics.

Design and optimization of reverse-transcription quantitative PCR experiments.

PubMed

Tichopad, Ales; Kitchen, Rob; Riedmaier, Irmgard; Becker, Christiane; Ståhlberg, Anders; Kubista, Mikael

2009-10-01

Quantitative PCR (qPCR) is a valuable technique for accurately and reliably profiling and quantifying gene expression. Typically, samples obtained from the organism of study have to be processed via several preparative steps before qPCR. We estimated the errors of sample withdrawal and extraction, reverse transcription (RT), and qPCR that are introduced into measurements of mRNA concentrations. We performed hierarchically arranged experiments with 3 animals, 3 samples, 3 RT reactions, and 3 qPCRs and quantified the expression of several genes in solid tissue, blood, cell culture, and single cells. A nested ANOVA design was used to model the experiments, and relative and absolute errors were calculated with this model for each processing level in the hierarchical design. We found that intersubject differences became easily confounded by sample heterogeneity for single cells and solid tissue. In cell cultures and blood, the noise from the RT and qPCR steps contributed substantially to the overall error because the sampling noise was less pronounced. We recommend the use of sample replicates preferentially to any other replicates when working with solid tissue, cell cultures, and single cells, and we recommend the use of RT replicates when working with blood. We show how an optimal sampling plan can be calculated for a limited budget. .

Determination of gold, indium, tellurium and thallium in the same sample digest of geological materials by atomic-absorption spectroscopy and two-step solvent extraction

USGS Publications Warehouse

Hubert, A.E.; Chao, T.T.

1985-01-01

A rock, soil, or stream-sediment sample is decomposed with hydrofluoric acid, aqua regia, and hydrobromic acid-bromine solution. Gold, thallium, indium and tellurium are separated and concentrated from the sample digest by a two-step MIBK extraction at two concentrations of hydrobromic add. Gold and thallium are first extracted from 0.1M hydrobromic acid medium, then indium and tellurium are extracted from 3M hydrobromic acid in the presence of ascorbic acid to eliminate iron interference. The elements are then determined by flame atomic-absorption spectrophotometry. The two-step solvent extraction can also be used in conjunction with electrothermal atomic-absorption methods to lower the detection limits for all four metals in geological materials. ?? 1985.

Improving the Accuracy of Attribute Extraction using the Relatedness between Attribute Values

NASA Astrophysics Data System (ADS)

Bollegala, Danushka; Tani, Naoki; Ishizuka, Mitsuru

Extracting attribute-values related to entities from web texts is an important step in numerous web related tasks such as information retrieval, information extraction, and entity disambiguation (namesake disambiguation). For example, for a search query that contains a personal name, we can not only return documents that contain that personal name, but if we have attribute-values such as the organization for which that person works, we can also suggest documents that contain information related to that organization, thereby improving the user's search experience. Despite numerous potential applications of attribute extraction, it remains a challenging task due to the inherent noise in web data -- often a single web page contains multiple entities and attributes. We propose a graph-based approach to select the correct attribute-values from a set of candidate attribute-values extracted for a particular entity. First, we build an undirected weighted graph in which, attribute-values are represented by nodes, and the edge that connects two nodes in the graph represents the degree of relatedness between the corresponding attribute-values. Next, we find the maximum spanning tree of this graph that connects exactly one attribute-value for each attribute-type. The proposed method outperforms previously proposed attribute extraction methods on a dataset that contains 5000 web pages.

Image segmentation and dynamic lineage analysis in single-cell fluorescence microscopy.

PubMed

Wang, Quanli; Niemi, Jarad; Tan, Chee-Meng; You, Lingchong; West, Mike

2010-01-01

An increasingly common component of studies in synthetic and systems biology is analysis of dynamics of gene expression at the single-cell level, a context that is heavily dependent on the use of time-lapse movies. Extracting quantitative data on the single-cell temporal dynamics from such movies remains a major challenge. Here, we describe novel methods for automating key steps in the analysis of single-cell, fluorescent images-segmentation and lineage reconstruction-to recognize and track individual cells over time. The automated analysis iteratively combines a set of extended morphological methods for segmentation, and uses a neighborhood-based scoring method for frame-to-frame lineage linking. Our studies with bacteria, budding yeast and human cells, demonstrate the portability and usability of these methods, whether using phase, bright field or fluorescent images. These examples also demonstrate the utility of our integrated approach in facilitating analyses of engineered and natural cellular networks in diverse settings. The automated methods are implemented in freely available, open-source software.

Parallel processing of real-time dynamic systems simulation on OSCAR (Optimally SCheduled Advanced multiprocessoR)

NASA Technical Reports Server (NTRS)

Kasahara, Hironori; Honda, Hiroki; Narita, Seinosuke

1989-01-01

Parallel processing of real-time dynamic systems simulation on a multiprocessor system named OSCAR is presented. In the simulation of dynamic systems, generally, the same calculation are repeated every time step. However, we cannot apply to Do-all or the Do-across techniques for parallel processing of the simulation since there exist data dependencies from the end of an iteration to the beginning of the next iteration and furthermore data-input and data-output are required every sampling time period. Therefore, parallelism inside the calculation required for a single time step, or a large basic block which consists of arithmetic assignment statements, must be used. In the proposed method, near fine grain tasks, each of which consists of one or more floating point operations, are generated to extract the parallelism from the calculation and assigned to processors by using optimal static scheduling at compile time in order to reduce large run time overhead caused by the use of near fine grain tasks. The practicality of the scheme is demonstrated on OSCAR (Optimally SCheduled Advanced multiprocessoR) which has been developed to extract advantageous features of static scheduling algorithms to the maximum extent.

Purification of circular DNA using benzoylated naphthoylated DEAE-cellulose.

PubMed

Gamper, H; Lehman, N; Piette, J; Hearst, J E

1985-04-01

Un-nicked circular DNA can be separated from protein, RNA, and other DNA in a simple three-step protocol consisting of exonuclease III digestion, extraction with benzoylated naphthoylated DEAE-cellulose (BND cellulose) in 1 M NaCl, and alcohol precipitation of the remaining supercoiled DNA. Exonuclease III treatment introduces single-stranded regions into contaminating linear and nicked circular DNA. This DNA, together with most RNA and protein, is adsorbed onto BND cellulose leaving form I DNA in solution. The protocol can be used to purify analytical as well as preparative amounts of supercoiled DNA. This procedure is a substitute for cesium chloride-ethidium bromide gradient ultracentrifugation and gives a comparable yield of pure form I DNA. Other classes of DNA can be isolated by changing the pretreatment step. Selective digestion of linear DNA with lambda exonuclease permits the isolation of both nicked circular and supercoiled DNA while brief heat-induced or alkali-induced denaturation leads to the recovery of rapidly reannealing DNA. In large-scale purifications, the basic protocol is usually preceded by one or more BND cellulose extractions in 1 M NaCl to remove contaminants absorbing UV or inhibiting exonuclease III.

Environmentally friendly microwave-assisted sequential extraction method followed by ICP-OES and ion-chromatographic analysis for rapid determination of sulphur forms in coal samples.

PubMed

Mketo, Nomvano; Nomngongo, Philiswa N; Ngila, J Catherine

2018-05-15

A rapid three-step sequential extraction method was developed under microwave radiation followed by inductively coupled plasma-optical emission spectroscopic (ICP-OES) and ion-chromatographic (IC) analysis for the determination of sulphur forms in coal samples. The experimental conditions of the proposed microwave-assisted sequential extraction (MW-ASE) procedure were optimized by using multivariate mathematical tools. Pareto charts generated from 2 3 full factorial design showed that, extraction time has insignificant effect on the extraction of sulphur species, therefore, all the sequential extraction steps were performed for 5 min. The optimum values according to the central composite designs and counter plots of the response surface methodology were 200 °C (microwave temperature) and 0.1 g (coal amount) for all the investigated extracting reagents (H 2 O, HCl and HNO 3 ). When the optimum conditions of the proposed MW-ASE procedure were applied in coal CRMs, SARM 18 showed more organic sulphur (72%) and the other two coal CRMs (SARMs 19 and 20) were dominated by sulphide sulphur species (52-58%). The sum of the sulphur forms from the sequential extraction steps have shown consistent agreement (95-96%) with certified total sulphur values on the coal CRM certificates. This correlation, in addition to the good precision (1.7%) achieved by the proposed procedure, suggests that the sequential extraction method is reliable, accurate and reproducible. To safe-guard the destruction of pyritic and organic sulphur forms in extraction step 1, water was used instead of HCl. Additionally, the notorious acidic mixture (HCl/HNO 3 /HF) was replaced by greener reagent (H 2 O 2 ) in the last extraction step. Therefore, the proposed MW-ASE method can be applied in routine laboratories for the determination of sulphur forms in coal and coal related matrices. Copyright © 2018 Elsevier B.V. All rights reserved.

Terpenes as green solvents for extraction of oil from microalgae.

PubMed

Dejoye Tanzi, Celine; Abert Vian, Maryline; Ginies, Christian; Elmaataoui, Mohamed; Chemat, Farid

2012-07-09

Herein is described a green and original alternative procedure for the extraction of oil from microalgae. Extractions were carried out using terpenes obtained from renewable feedstocks as alternative solvents instead of hazardous petroleum solvents such as n-hexane. The described method is achieved in two steps using Soxhlet extraction followed by the elimination of the solvent from the medium using Clevenger distillation in the second step. Oils extracted from microalgae were compared in terms of qualitative and quantitative determination. No significant difference was obtained between each extract, allowing us to conclude that the proposed method is green, clean and efficient.

Automated estimation of leaf distribution for individual trees based on TLS point clouds

NASA Astrophysics Data System (ADS)

Koma, Zsófia; Rutzinger, Martin; Bremer, Magnus

2017-04-01

Light Detection and Ranging (LiDAR) especially the ground based LiDAR (Terrestrial Laser Scanning - TLS) is an operational used and widely available measurement tool supporting forest inventory updating and research in forest ecology. High resolution point clouds from TLS already represent single leaves which can be used for a more precise estimation of Leaf Area Index (LAI) and for higher accurate biomass estimation. However, currently the methodology for extracting single leafs from the unclassified point clouds for individual trees is still missing. The aim of this study is to present a novel segmentation approach in order to extract single leaves and derive features related to leaf morphology (such as area, slope, length and width) of each single leaf from TLS point cloud data. For the study two exemplary single trees were scanned in leaf-on condition on the university campus of Innsbruck during calm wind conditions. A northern red oak (Quercus rubra) was scanned by a discrete return recording Optech ILRIS-3D TLS scanner and a tulip tree (Liliodendron tulpifera) with Riegl VZ-6000 scanner. During the scanning campaign a reference dataset was measured parallel to scanning. In this case 230 leaves were randomly collected around the lower branches of the tree and photos were taken. The developed workflow steps were the following: in the first step normal vectors and eigenvalues were calculated based on the user specified neighborhood. Then using the direction of the largest eigenvalue outliers i.e. ghost points were removed. After that region growing segmentation based on the curvature and angles between normal vectors was applied on the filtered point cloud. On each segment a RANSAC plane fitting algorithm was applied in order to extract the segment based normal vectors. Using the related features of the calculated segments the stem and branches were labeled as non-leaf and other segments were classified as leaf. The validation of the different segmentation parameters was evaluated as the following: i) the sum area of the collected leaves and the point cloud, ii) the segmented leaf length-width ratio iii) the distribution of the leaf area for the segmented and the reference-ones were compared and the ideal parameter-set was found. The results show that the leaves can be captured with the developed workflow and the slope can be determined robustly for the segmented leaves. However, area, length and width values are systematically depending on the angle and the distance from the scanner. For correction of the systematic underestimation, more systematic measurement or LiDAR simulation is required for further detailed analysis. The results of leaf segmentation algorithm show high potential in generating more precise tree models with correctly located leaves in order to extract more precise input model for biological modeling of LAI or atmospheric corrections studies. The presented workflow also can be used in monitoring the change of angle of the leaves due to sun irradiation, water balance, and day-night rhythm.

Method and apparatus for single-stepping coherence events in a multiprocessor system under software control

DOEpatents

Blumrich, Matthias A.; Salapura, Valentina

2010-11-02

An apparatus and method are disclosed for single-stepping coherence events in a multiprocessor system under software control in order to monitor the behavior of a memory coherence mechanism. Single-stepping coherence events in a multiprocessor system is made possible by adding one or more step registers. By accessing these step registers, one or more coherence requests are processed by the multiprocessor system. The step registers determine if the snoop unit will operate by proceeding in a normal execution mode, or operate in a single-step mode.

Comparison study on mechanical properties single step and three step artificial aging on duralium

NASA Astrophysics Data System (ADS)

Tsamroh, Dewi Izzatus; Puspitasari, Poppy; Andoko, Sasongko, M. Ilman N.; Yazirin, Cepi

2017-09-01

Duralium is kind of non-ferro alloy that used widely in industrial. That caused its properties such as mild, high ductility, and resistance from corrosion. This study aimed to know mechanical properties of duralium on single step and three step articial aging process. Mechanical properties that discussed in this study focused on toughness value, tensile strength, and microstructure of duralium. Toughness value of single step artificial aging was 0.082 joule/mm2, and toughness value of three step artificial aging was 0,0721 joule/mm2. Duralium tensile strength of single step artificial aging was 32.36 kgf/mm^2, and duralium tensile strength of three step artificial aging was 32,70 kgf/mm^2. Based on microstructure photo of duralium of single step artificial aging showed that precipitate (θ) was not spreading evenly indicated by black spot which increasing the toughness of material. While microstructure photo of duralium that treated by three step artificial aging showed that it had more precipitate (θ) spread evenly compared with duralium that treated by single step artificial aging.

Development and evaluation of an in-house single step loop-mediated isothermal amplification (SS-LAMP) assay for the detection of Mycobacterium tuberculosis complex in sputum samples from Moroccan patients.

PubMed

Bentaleb, El Mehdi; Abid, Mohammed; El Messaoudi, My Driss; Lakssir, Brahim; Ressami, El Mostafa; Amzazi, Saaïd; Sefrioui, Hassan; Ait Benhassou, Hassan

2016-09-27

Tuberculosis (TB) is a major global health problem and remains the leading cause of morbidity and mortality in developing countries. Routinely used TB diagnostic methods, in most endemic areas, are time-consuming, often less-sensitive, expensive and inaccessible to most patients. Therefore, there is an urgent need for the development of early, easy to use and effective diagnosis tools of TB, which can be effectively integrated into resource limited settings, to anticipate the early treatment and limit further spread of the disease. Over the last decade, Loop-mediated isothermal amplification (LAMP) assays have become a powerful tool for rapid diagnosis of infectious diseases because of the simplicity of device requirements. Indeed, LAMP is a simple, quick and cost effective Isothermal Nucleic Acid Amplification diagnostic test (INAAT) that has the potential to be used in TB endemic settings of resource-poor countries. In the present study, we have developed a simple and rapid TB molecular diagnostic test using a Single-Step Loop-mediated isothermal DNA amplification (SS-LAMP) method for the detection of Mycobacterium tuberculosis complex (MTBC) strains, with a simplified sample preparation procedure, eliminating DNA extraction prior to LAMP amplification, DNA initial denaturation and enzymatic inactivation steps during the amplification process. To perform our in-house SS-LAMP assay, a set of six specific primers was specifically designed to recognize eight distinct regions on the MTBC species-specific repetitive insertion sequence 6110 (IS6110). The amplification of the targeted DNA was carried out under isothermal conditions at 65 °C within 1 h. Our protocol was firstly optimized using 60 of confirmed MTBC isolates and a recombinant pGEMeasy-IS6110 vector for sensitivity testing. Thereafter, the assay was evaluated on liquefied sputum specimens collected from 157 Moroccan patients suspected of having TB. Our SS-LAMP developed assay was able to detect MTBC DNA directly from liquefied sputum samples without any prior DNA extraction, denaturation nor the final enzymatic inactivation step. When compared to routinely used Löwenstein Jensen (LJ) Culture method, our SS-LAMP assay is rapid and showed specificity and sensitivity of 99.14 % and 82.93 % respectively which are within the international standards. In addition, the limit of detection of our assay was found to be as little as 10 copies of bacterial DNA. To our knowledge, this is the first study using a single step LAMP (SS-LAMP) procedure as a rapid, easy to perform and cost effective testing for TB early detection. This innovative assay could be suitable for low-income countries with restricted health equipment facilities.

Displacement-dispersive liquid-liquid microextraction based on solidification of floating organic drop of trace amounts of palladium in water and road dust samples prior to graphite furnace atomic absorption spectrometry determination.

PubMed

Ghanbarian, Maryam; Afzali, Daryoush; Mostafavi, Ali; Fathirad, Fariba

2013-01-01

A new displacement-dispersive liquid-liquid microextraction method based on the solidification of floating organic drop was developed for separation and preconcentration of Pd(ll) in road dust and aqueous samples. This method involves two steps of dispersive liquid-liquid microextraction based on solidification. In Step 1, Cu ions react with diethyldithiocarbamate (DDTC) to form Cu-DDTC complex, which is extracted by dispersive liquid-liquid microextraction based on a solidification procedure using 1-undecanol (extraction solvent) and ethanol (dispersive solvent). In Step 2, the extracted complex is first dispersed using ethanol in a sample solution containing Pd ions, then a dispersive liquid-liquid microextraction based on a solidification procedure is performed creating an organic drop. In this step, Pd(ll) replaces Cu(ll) from the pre-extracted Cu-DDTC complex and goes into the extraction solvent phase. Finally, the Pd(ll)-containing drop is introduced into a graphite furnace using a microsyringe, and Pd(ll) is determined using atomic absorption spectrometry. Several factors that influence the extraction efficiency of Pd and its subsequent determination, such as extraction and dispersive solvent type and volume, pH of sample solution, centrifugation time, and concentration of DDTC, are optimized.

Environmentally-friendly lithium recycling from a spent organic li-ion battery.

PubMed

Renault, Stéven; Brandell, Daniel; Edström, Kristina

2014-10-01

A simple and straightforward method using non-polluting solvents and a single thermal treatment step at moderate temperature was investigated as an environmentally-friendly process to recycle lithium from organic electrode materials for secondary lithium batteries. This method, highly dependent on the choice of electrolyte, gives up to 99% of sustained capacity for the recycled materials used in a second life-cycle battery when compared with the original. The best results were obtained using a dimethyl carbonate/lithium bis(trifluoromethane sulfonyl) imide electrolyte that does not decompose in presence of water. The process implies a thermal decomposition step at a moderate temperature of the extracted organic material into lithium carbonate, which is then used as a lithiation agent for the preparation of fresh electrode material without loss of lithium. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid detection of fungal keratitis with DNA-stabilizing FTA filter paper.

PubMed

Menassa, Nardine; Bosshard, Philipp P; Kaufmann, Claude; Grimm, Christian; Auffarth, Gerd U; Thiel, Michael A

2010-04-01

Purpose. Polymerase chain reaction (PCR) is increasingly important for the rapid detection of fungal keratitis. However, techniques of specimen collection and DNA extraction before PCR may interfere with test sensitivity. The purpose of this study was to investigate the use of DNA-stabilizing FTA filter paper (Indicating FTA filter paper; Whatman International, Ltd., Maidstone, UK) for specimen collection without DNA extraction in a single-step, nonnested PCR for fungal keratitis. Methods. Specimens were collected from ocular surfaces with FTA filter discs, which automatically lyse collected cells and stabilize nucleic acids. Filter discs were directly used in single-step PCR reactions to detect fungal DNA. Test sensitivity was evaluated with serial dilutions of Candida albicans, Fusarium oxysporum, and Aspergillus fumigatus cultures. Test specificity was analyzed by comparing 196 and 155 healthy individuals from Switzerland and Egypt, respectively, with 15 patients with a diagnosis of microbial keratitis. Results. PCR with filter discs detected 3 C. albicans, 25 F. oxysporum, and 125 A. fumigatus organisms. In healthy volunteers, fungal PCR was positive in 1.0% and 8.4% of eyes from Switzerland and Egypt, respectively. Fungal PCR remained negative in 10 cases of culture-proven bacterial keratitis, became positive in 4 cases of fungal keratitis, but missed 1 case of culture-proven A. fumigatus keratitis. Conclusions. FTA filter paper for specimen collection together with direct PCR is a promising method of detecting fungal keratitis. The analytical sensitivity is high without the need for a semi-nested or nested second PCR, the clinical specificity is 91.7% to 99.0%, and the method is rapid and inexpensive.

Highlights of the Salt Extraction Process

NASA Astrophysics Data System (ADS)

Abbasalizadeh, Aida; Seetharaman, Seshadri; Teng, Lidong; Sridhar, Seetharaman; Grinder, Olle; Izumi, Yukari; Barati, Mansoor

2013-11-01

This article presents the salient features of a new process for the recovery of metal values from secondary sources and waste materials such as slag and flue dusts. It is also feasible in extracting metals such as nickel and cobalt from ores that normally are difficult to enrich and process metallurgically. The salt extraction process is based on extraction of the metals from the raw materials by a molten salt bath consisting of NaCl, LiCl, and KCl corresponding to the eutectic composition with AlCl3 as the chlorinating agent. The process is operated in the temperature range 973 K (700°C) to 1173 K (900°C). The process was shown to be successful in extracting Cr and Fe from electric arc furnace (EAF) slag. Electrolytic copper could be produced from copper concentrate based on chalcopyrite in a single step. Conducting the process in oxygen-free atmosphere, sulfur could be captured in the elemental form. The method proved to be successful in extracting lead from spent cathode ray tubes. In order to prevent the loss of AlCl3 in the vapor form and also chlorine gas emission at the cathode during the electrolysis, liquid aluminum was used. The process was shown to be successful in extracting Nd and Dy from magnetic scrap. The method is a highly promising process route for the recovery of strategic metals. It also has the added advantage of being environmentally friendly.

Solid-phase microextraction technology for in vitro and in vivo metabolite analysis

PubMed Central

Zhang, Qihui; Zhou, Liandi; Chen, Hua; Wang, Chong-Zhi; Xia, Zhining; Yuan, Chun-Su

2016-01-01

Analysis of endogenous metabolites in biological samples may lead to the identification of biomarkers in metabolomics studies. To achieve accurate sample analysis, a combined method of continuous quick sampling and extraction is required for online compound detection. Solid-phase microextraction (SPME) integrates sampling, extraction and concentration into a single solvent-free step for chemical analysis. SPME has a number of advantages, including simplicity, high sensitivity and a relatively non-invasive nature. In this article, we reviewed SPME technology in in vitro and in vivo analyses of metabolites after the ingestion of herbal medicines, foods and pharmaceutical agents. The metabolites of microorganisms in dietary supplements and in the gastrointestinal tract will also be examined. As a promising technology in biomedical and pharmaceutical research, SPME and its future applications will depend on advances in analytical technologies and material science. PMID:27695152

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

Rocchetti, Laura; Amato, Alessia; Fonti, Viviana

Graphical abstract: Display Omitted - Highlights: • End-of-life LCD panels represent a source of indium. • Several experimental conditions for indium leaching have been assessed. • Indium is completely extracted with 2 M sulfuric acid at 80 °C for 10 min. • Cross-current leaching improves indium extraction and operating costs are lowered. • Benefits to the environment come from reduction of CO{sub 2} emissions and reagents use. - Abstract: Indium is a critical element mainly produced as a by-product of zinc mining, and it is largely used in the production process of liquid crystal display (LCD) panels. End-of-life LCDs representmore » a possible source of indium in the field of urban mining. In the present paper, we apply, for the first time, cross-current leaching to mobilize indium from end-of-life LCD panels. We carried out a series of treatments to leach indium. The best leaching conditions for indium were 2 M sulfuric acid at 80 °C for 10 min, which allowed us to completely mobilize indium. Taking into account the low content of indium in end-of-life LCDs, of about 100 ppm, a single step of leaching is not cost-effective. We tested 6 steps of cross-current leaching: in the first step indium leaching was complete, whereas in the second step it was in the range of 85–90%, and with 6 steps it was about 50–55%. Indium concentration in the leachate was about 35 mg/L after the first step of leaching, almost 2-fold at the second step and about 3-fold at the fifth step. Then, we hypothesized to scale up the process of cross-current leaching up to 10 steps, followed by cementation with zinc to recover indium. In this simulation, the process of indium recovery was advantageous from an economic and environmental point of view. Indeed, cross-current leaching allowed to concentrate indium, save reagents, and reduce the emission of CO{sub 2} (with 10 steps we assessed that the emission of about 90 kg CO{sub 2}-Eq. could be avoided) thanks to the recovery of indium. This new strategy represents a useful approach for secondary production of indium from waste LCD panels.« less

A simple, fast, and inexpensive CTAB-PVP-silica based method for genomic DNA isolation from single, small insect larvae and pupae.

PubMed

Huanca-Mamani, W; Rivera-Cabello, D; Maita-Maita, J

2015-07-17

In this study, we report a modified CTAB-PVP method combined with silicon dioxide (silica) treatment for the extraction of high quality genomic DNA from a single larva or pupa. This method efficiently obtains DNA from small specimens, which is difficult and challenging because of the small amount of starting tissue. Maceration with liquid nitrogen, phenol treatment, and the ethanol precipitation step are eliminated using this methodology. The A260/A280 absorbance ratios of the isolated DNA were approximately 1.8, suggesting that the DNA is pure and can be used for further molecular analysis. The quality of the isolated DNA permits molecular applications and represents a fast, cheap, and effective alternative method for laboratories with low budgets.

Methods and systems for detection of radionuclides

DOEpatents

Coates, Jr., John T.; DeVol, Timothy A.

2010-05-25

Disclosed are materials and systems useful in determining the existence of radionuclides in an aqueous sample. The materials provide the dual function of both extraction and scintillation to the systems. The systems can be both portable and simple to use, and as such can beneficially be utilized to determine presence and optionally concentration of radionuclide contamination in an aqueous sample at any desired location and according to a relatively simple process without the necessity of complicated sample handling techniques. The disclosed systems include a one-step process, providing simultaneous extraction and detection capability, and a two-step process, providing a first extraction step that can be carried out in a remote field location, followed by a second detection step that can be carried out in a different location.

Combination of sorption properties of polydimethylsiloxane and solid-phase extraction sorbents in a single composite material for the passive sampling of polar and apolar pesticides in water.

PubMed

Martin, Alexis; Margoum, Christelle; Coquery, Marina; Randon, Jérôme

2016-10-01

Passive sampling techniques have been developed as an alternative method for in situ integrative monitoring of trace levels of neutral pesticides in environmental waters. The objective of this work was to develop a new receiving phase for pesticides with a wide range of polarities in a single step. We describe the development of three new composite silicone rubbers, combining polydimethylsiloxane mechanical and sorption properties with solid-phase extraction sorbents, prepared as a receiving phase for passive sampling. A composite silicone rubber composed of polydimethylsiloxane/poly(divinylbenzene-co-N-vinylpyrrolidone) was selected by batch experiments for its high sorption properties for pesticides with octanol-water partition coefficients ranging from 2.3 to 5.5. We named this composite material "Polar/Apolar Composite Silicone Rubber". A structural study by scanning electron microscopy confirmed the homogeneous dispersion of the sorbent particles and the encapsulation of particles within the polydimethylsiloxane matrix. We also demonstrate that this composite material is resistant to common solvents used for the back-extraction of analytes and has a maximal resistance temperature of 350°C. Therefore, the characteristics of the "Polar/Apolar Composite Silicone Rubber" meet most of the criteria for use as a receiving phase for the passive sampling of pesticides. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Factors affecting GEBV accuracy with single-step Bayesian models.

PubMed

Zhou, Lei; Mrode, Raphael; Zhang, Shengli; Zhang, Qin; Li, Bugao; Liu, Jian-Feng

2018-01-01

A single-step approach to obtain genomic prediction was first proposed in 2009. Many studies have investigated the components of GEBV accuracy in genomic selection. However, it is still unclear how the population structure and the relationships between training and validation populations influence GEBV accuracy in terms of single-step analysis. Here, we explored the components of GEBV accuracy in single-step Bayesian analysis with a simulation study. Three scenarios with various numbers of QTL (5, 50, and 500) were simulated. Three models were implemented to analyze the simulated data: single-step genomic best linear unbiased prediction (GBLUP; SSGBLUP), single-step BayesA (SS-BayesA), and single-step BayesB (SS-BayesB). According to our results, GEBV accuracy was influenced by the relationships between the training and validation populations more significantly for ungenotyped animals than for genotyped animals. SS-BayesA/BayesB showed an obvious advantage over SSGBLUP with the scenarios of 5 and 50 QTL. SS-BayesB model obtained the lowest accuracy with the 500 QTL in the simulation. SS-BayesA model was the most efficient and robust considering all QTL scenarios. Generally, both the relationships between training and validation populations and LD between markers and QTL contributed to GEBV accuracy in the single-step analysis, and the advantages of single-step Bayesian models were more apparent when the trait is controlled by fewer QTL.

DeepSleepNet: A Model for Automatic Sleep Stage Scoring Based on Raw Single-Channel EEG.

PubMed

Supratak, Akara; Dong, Hao; Wu, Chao; Guo, Yike

2017-11-01

This paper proposes a deep learning model, named DeepSleepNet, for automatic sleep stage scoring based on raw single-channel EEG. Most of the existing methods rely on hand-engineered features, which require prior knowledge of sleep analysis. Only a few of them encode the temporal information, such as transition rules, which is important for identifying the next sleep stages, into the extracted features. In the proposed model, we utilize convolutional neural networks to extract time-invariant features, and bidirectional-long short-term memory to learn transition rules among sleep stages automatically from EEG epochs. We implement a two-step training algorithm to train our model efficiently. We evaluated our model using different single-channel EEGs (F4-EOG (left), Fpz-Cz, and Pz-Oz) from two public sleep data sets, that have different properties (e.g., sampling rate) and scoring standards (AASM and R&K). The results showed that our model achieved similar overall accuracy and macro F1-score (MASS: 86.2%-81.7, Sleep-EDF: 82.0%-76.9) compared with the state-of-the-art methods (MASS: 85.9%-80.5, Sleep-EDF: 78.9%-73.7) on both data sets. This demonstrated that, without changing the model architecture and the training algorithm, our model could automatically learn features for sleep stage scoring from different raw single-channel EEGs from different data sets without utilizing any hand-engineered features.

An integrated direct loop-mediated isothermal amplification microdevice incorporated with an immunochromatographic strip for bacteria detection in human whole blood and milk without a sample preparation step.

PubMed

Lee, Dohwan; Kim, Yong Tae; Lee, Jee Won; Kim, Do Hyun; Seo, Tae Seok

2016-05-15

We have developed an integrated direct loop-mediated isothermal amplification (Direct LAMP) microdevice incorporated with an immunochromatographic strip (ICS) to identify bacteria contaminated in real samples. The Direct LAMP is a novel isothermal DNA amplification technique which does not require thermal cycling steps as well as any sample preparation steps such as cell lysis and DNA extraction for amplifying specific target genes. In addition, the resultant amplicons were colorimetrically detected on the ICS, thereby enabling the entire genetic analysis process to be simplified. The two functional units (Direct LAMP and ICS) were integrated on a single device without use of the tedious and complicated microvalve and tubing systems. The utilization of a slidable plate allows us to manipulate the fluidic control in the microchannels manually and the sequential operation of the Direct LAMP and ICS detection could be performed by switching the slidable plate to each functional unit. Thus, the combination of the direct isothermal amplification without any sample preparation and thermal cycling steps, the ICS based amplicon detection by naked eyes, and the slidable plate to eliminate the microvalves in the integrated microdevice would be an ideal platform for point-of-care DNA diaganotics. On the integrated Direct LAMP-ICS microdevice, we could analyze Staphylococcus aureus (S. aureus) and Escherichia coli O157:H7 (E. coli O157:H7) contaminated in human whole blood or milk at a single-cell level within 1h. Copyright © 2015 Elsevier B.V. All rights reserved.

Analysis of organic compounds' degradation and electricity generation in anaerobic fluidized bed microbial fuel cell for coking wastewater treatment.

PubMed

Liu, Xinmin; Wu, Jianjun; Guo, Qingjie

2017-12-01

A single-chambered packing-type anaerobic fluidized microbial fuel cell (AFBMFC) with coking wastewater (CWW) as fuel was built to treat CWW, which not only has high treating efficiency, but also can convert organic matter in wastewater into electricity. AFBMFC was constructed by using anaerobic sludge that was domesticated as inoculation sludge, which was used to biochemically treat CWW. The organic compounds in CWW were extracted by liquid-liquid extraction step by step every day. The extraction phase was concentrated by a rotary evaporator and a nitrogen sweeping device and was analyzed by GC-MS. And the electricity-generation performances of AFBMFC were investigated. The results show that the composition of CWW was complicated, which mainly contains hydrocarbons, phenols, nitrogenous organic compounds, alcohols and aldehydes, esters and acids and so on. After a cycle of anaerobic biochemical treatment, the content of organic compounds in the effluent decreased significantly. After the treatment of AFBMFC, 99.9% phenols, 98.4% alcohol and aldehydes and 95.3% nitrogenous compounds were biodegraded. In the effluent, some new compounds (such as tricosane and dibutyl phthalate) were produced. The chemical oxygen demand (COD) of CWW decreased from 3372 to 559 mg/L in the closed-circuit microbial fuel cell, and the COD removal was 83.4 ± 1.0%. The maximum power density of AFBMFC was 2.13 ± 0.01 mW m -2 .

Multi-view video segmentation and tracking for video surveillance

NASA Astrophysics Data System (ADS)

Mohammadi, Gelareh; Dufaux, Frederic; Minh, Thien Ha; Ebrahimi, Touradj

2009-05-01

Tracking moving objects is a critical step for smart video surveillance systems. Despite the complexity increase, multiple camera systems exhibit the undoubted advantages of covering wide areas and handling the occurrence of occlusions by exploiting the different viewpoints. The technical problems in multiple camera systems are several: installation, calibration, objects matching, switching, data fusion, and occlusion handling. In this paper, we address the issue of tracking moving objects in an environment covered by multiple un-calibrated cameras with overlapping fields of view, typical of most surveillance setups. Our main objective is to create a framework that can be used to integrate objecttracking information from multiple video sources. Basically, the proposed technique consists of the following steps. We first perform a single-view tracking algorithm on each camera view, and then apply a consistent object labeling algorithm on all views. In the next step, we verify objects in each view separately for inconsistencies. Correspondent objects are extracted through a Homography transform from one view to the other and vice versa. Having found the correspondent objects of different views, we partition each object into homogeneous regions. In the last step, we apply the Homography transform to find the region map of first view in the second view and vice versa. For each region (in the main frame and mapped frame) a set of descriptors are extracted to find the best match between two views based on region descriptors similarity. This method is able to deal with multiple objects. Track management issues such as occlusion, appearance and disappearance of objects are resolved using information from all views. This method is capable of tracking rigid and deformable objects and this versatility lets it to be suitable for different application scenarios.

Optimization of total vaporization solid-phase microextraction (TV-SPME) for the determination of lipid profiles of Phormia regina, a forensically important blow fly species.

PubMed

Kranz, William; Carroll, Clinton; Dixon, Darren; Picard, Christine; Goodpaster, John

2017-11-01

A new method has been developed for the determination of fatty acids, sterols, and other lipids which naturally occur within pupae of the blow fly Phormia regina. The method relies upon liquid extraction in non-polar solvent, followed by derivatization using N,O-bis(trimethylsilyl)trifluoroacetamide (BSTFA) w/ 1% trimethylchlorsilane (TMCS) carried out inside the sample vial. The analysis is facilitated by total vaporization solid-phase microextraction (TV-SPME), with gas chromatography-mass spectrometry (GC-MS) serving as the instrumentation for analysis. The TV-SPME delivery technique is approximately a factor of five more sensitive than traditional liquid injection, which may alleviate the need for rotary evaporation, reconstitution, collection of high performance liquid chromatography fractions, and many of the other pre-concentration steps that are commonplace in the current literature. Furthermore, the ability to derivatize the liquid extract in a single easy step while increasing sensitivity represents an improvement over current derivatization methods. The most common lipids identified in fly pupae were various saturated and unsaturated fatty acids ranging from lauric acid (12:0) to arachinoic acid (20:4), as well as cholesterol. The concentrations of myristic acid (14:0), palmitelaidic acid (16:2), and palmitoleic acid (16:1) were the most reliable indicators of the age of the pupae. Graphical abstract Blow fly pupae were extracted prior to emerging as adults. The extracts were analyzed via total vaporization solid-phase microextraction (TV-SPME), revealing a complex mixture of lipids that could be associated with the age of the insect. This information may assist in determining a post-mortum interval (PMI) in a death investigation.

A new tunable dispersive liquid-liquid micro extraction method developed for the simultaneous preconcentration of lead and cadmium from lakes water: a multivariate study

NASA Astrophysics Data System (ADS)

Bilal, Muhammad; Kazi, Tasneem Gul; Afridi, Hassan Imran; Ali, Jamshed; Baig, Jameel Ahmed; Arain, Mohammad Balal; Khan, Mustafa

2017-08-01

A green tunable dispersive liquid-liquid micro extraction (TDLLME) technique was established for the simultaneous enrichment of lead (Pb) and cadmium (Cd) from different lakes water before analysis by flame atomic absorption spectrometry (FAAS). A solvent known as tunable polarity solvent (TPS), mixture of 1,8-diazabicyclo-[5.4.0]-undec-7-ene (DBU) and 1-decanol, has been employed as extractant in aqueous medium. In first step this mixture can be made polar by slowly bubbling the antisolvent trigger (CO2) through the solution, which makes a monophasic solution. During this step hydrophobic complexes of the metals with 8-hydroxy quinoline (8-HQ) were extracted by TPS. Then the mixture was switched back to hydrophobic one by heating and/or bubbling nitrogen, turning the mixture into two phases again. In second phase the metals were leached out from the complexes entrapped in TPS, by treating with a solution of nitric acid and exposing the mixture to CO2, which switched the mixture into single phase. Then N2 purging and/or heating again turned the mixture into two phases. The acidic aqueous phase containing the metals was introduced to FAAS for analysis, whereas TPS was recycled for next experiment. Different parameters, affecting the efficiency the technique, were optimized by multivariate approach. The method was applied to certified reference material of water and to a real sample spiked with standards of known concentration, to confirm its validity and accuracy. LOD obtained for Pb and Cd were 0.560 and 0.056 μg L- 1 respectively. The developed method was applied successfully to the real water samples of two lakes of Sindh, Pakistan.

Apical Extrusion of Intracanal Debris Using Two Engine Driven and Step-Back Instrumentation Techniques: An In-Vitro Study

PubMed Central

Kustarci, Alper; Akdemir, Neslihan; Siso, Seyda Herguner; Altunbas, Demet

2008-01-01

Objectives The purpose of this study was to compare in-vitro the amount of debris extruded apically from extracted teeth, using K3, Protaper rotary instruments and manual step-back technique. Methods Forty five human single-rooted mandibular premolar teeth were randomly divided into 3 groups. The teeth in 3 groups were instrumented until reaching the working length with K3, Protaper rotary instruments and K-type stainless steel instruments with manual step-back technique, respectively. Debris extruded from the apical foramen was collected into centrifuge tubes and the amount was determined. The data obtained were analyzed using Kruskal-Wallis one-way analysis of variance and Mann-Whitney U tests, with P=.05 as the level for statistical significance. Results Statistically significant difference was observed between K3, Protaper and step-back groups in terms of debris extrusion (P<.05). Step-back group had the highest mean debris weight, which was significantly different from the K3 and Protaper groups (P<.05). The lowest mean debris weight was related to K3 group, which was significantly different from the Protaper group (P<.05). Conclusions: Based on the results, all instrumentation techniques produced debris extrusion. The engine-driven Ni-Ti systems extruded significantly less apical debris than step-back technique. However, Protaper rotary instruments extruded significantly more debris than K3 rotary instruments. PMID:19212528

Apical extrusion of intracanal debris using two engine driven and step-back instrumentation techniques: an in-vitro study.

PubMed

Kustarci, Alper; Akdemir, Neslihan; Siso, Seyda Herguner; Altunbas, Demet

2008-10-01

The purpose of this study was to compare in-vitro the amount of debris extruded apically from extracted teeth, using K3, Protaper rotary instruments and manual step-back technique. Forty five human single-rooted mandibular premolar teeth were randomly divided into 3 groups. The teeth in 3 groups were instrumented until reaching the working length with K3, Protaper rotary instruments and K-type stainless steel instruments with manual step-back technique, respectively. Debris extruded from the apical foramen was collected into centrifuge tubes and the amount was determined. The data obtained were analyzed using Kruskal-Wallis one-way analysis of variance and Mann-Whitney U tests, with P=.05 as the level for statistical significance. Statistically significant difference was observed between K3, Protaper and step-back groups in terms of debris extrusion (P<.05). Step-back group had the highest mean debris weight, which was significantly different from the K3 and Protaper groups (P<.05). The lowest mean debris weight was related to K3 group, which was significantly different from the Protaper group (P<.05). Based on the results, all instrumentation techniques produced debris extrusion. The engine-driven Ni-Ti systems extruded significantly less apical debris than step-back technique. However, Protaper rotary instruments extruded significantly more debris than K3 rotary instruments.

Levels, distribution and bioavailability of transuranic elements released in the Palomares accident (Spain).

PubMed

Jiménez-Ramos, M C; Vioque, I; García-Tenorio, R; García León, M

2008-11-01

The current levels and distribution of the remaining transuranic contamination present in the terrestrial area affected by the nuclear Palomares accident have been evaluated through the determination of the Pu-isotopes and (241)Am concentrations in soils collected 35 years after the accident. In addition, after confirming that most of the contamination is present in particulate form, some bioavailability laboratory-based experiments, based on the use of single extractants, were performed as an essential step in order to study the behaviour of the Pu contamination in the soils from the affected areas.

Microwave-assisted extraction performed in low temperature and in vacuo for the extraction of labile compounds in food samples.

PubMed

Xiao, Xiaohua; Song, Wei; Wang, Jiayue; Li, Gongke

2012-01-27

In this study, low temperature vacuum microwave-assisted extraction, which simultaneous performed microwave-assisted extraction (MAE) in low temperature and in vacuo environment, was proposed. The influencing parameters including solid/liquid ratio, extraction temperature, extraction time, degree of vacuum and microwave power were discussed. The predominance of low temperature vacuum microwave-assisted extraction was investigated by comparing the extraction yields of vitamin C, β-carotene, aloin A and astaxanthin in different foods with that in MAE and solvent extraction, and 5.2-243% increments were obtained. On the other hand, the chemical kinetics of vitamin C and aloin A, which composed two different steps including the extraction step of analyte transferred from matrix into solvent and the decomposition step of analyte degraded in the extraction solvent, were proposed. All of the decomposition rates (K(2)) for the selected analyte in low temperature, in vacuo and in nitrogen atmosphere decreased significantly comparing with that in conventional MAE, which are in agreement with that obtained from experiments. Consequently, the present method was successfully applied to extract labile compound from different food samples. These results showed that low temperature and/or in vacuo environment in microwave-assisted extraction system was especially important to prevent the degradation of labile components and have good potential on the extraction of labile compound in foods, pharmaceutical and natural products. Copyright © 2011 Elsevier B.V. All rights reserved.

Extraction and purification of capsaicin from capsicum oleoresin using an aqueous two-phase system combined with chromatography.

PubMed

Fan, Yong; Lu, Yan-Min; Yu, Bin; Tan, Cong-Ping; Cui, Bo

2017-09-15

Capsaicin was extracted from capsicum oleoresin using an aqueous two-phase system (ATPS) composed of an ethylene oxide-propylene oxide (EOPO) copolymer, salt and ethanol. Capsaicin was concentrated in the top polymer-rich phase. To determine the optimal conditions, the partitioning of capsaicin in the ATPS was investigated, considering a single-factor experiment including the salt concentration, polymer concentration, buffer pH, ethanol concentration, sample loading and extraction duration. Response surface methodology was applied to investigate the effects of the polymer concentration, buffer pH and sample loading on capsaicin partitioning. A capsaicin yield of 95.5% was obtained using the optimal extraction system, which consisted of 16.3% UCON 50-HB-5100/10% K 2 HPO 4 /1% ethanol, a buffer pH of 4.35 and 0.24g of capsicum oleoresin. Capsaicin was purified from the capsaicinoid extract using a two-step macroporous adsorption resin (MAR) method. After purification using non-polar MAR ADS-17, the recovery and purity of capsaicin were 83.7% and 50.3%, respectively. After purification using weakly polar MAR AB-8, the recovery and purity of capsaicin were 88.0% and 85.1%, respectively. Copyright © 2017. Published by Elsevier B.V.

A rapid method for the extraction and analysis of carotenoids and other hydrophobic substances suitable for systems biology studies with photosynthetic bacteria.

PubMed

Bóna-Lovász, Judit; Bóna, Aron; Ederer, Michael; Sawodny, Oliver; Ghosh, Robin

2013-10-11

A simple, rapid, and inexpensive extraction method for carotenoids and other non-polar compounds present in phototrophic bacteria has been developed. The method, which has been extensively tested on the phototrophic purple non-sulphur bacterium Rhodospirillum rubrum, is suitable for extracting large numbers of samples, which is common in systems biology studies, and yields material suitable for subsequent analysis using HPLC and mass spectroscopy. The procedure is particularly suitable for carotenoids and other terpenoids, including quinones, bacteriochlorophyll a and bacteriopheophytin a, and is also useful for the analysis of polar phospholipids. The extraction procedure requires only a single step extraction with a hexane/methanol/water mixture, followed by HPLC using a Spherisorb C18 column, with a mobile phase consisting of acetone-water and a non-linear gradient of 50%-100% acetone. The method was employed for examining the carotenoid composition observed during microaerophilic growth of R. rubrum strains, and was able to determine 18 carotenoids, 4 isoprenoid-quinones, bacteriochlorophyll a and bacteriopheophytin a as well as four different phosphatidylglycerol species of different acyl chain compositions. The analytical procedure was used to examine the dynamics of carotenoid biosynthesis in the major and minor pathways operating simultaneously in a carotenoid biosynthesis mutant of R. rubrum.

Selective extraction and separation of oxymatrine from Sophora flavescens Ait. extract by silica-confined ionic liquid.

PubMed

Bi, Wentao; Tian, Minglei; Row, Kyung Ho

2012-01-01

This study highlighted the application of a two-stepped extraction method for extraction and separation of oxymatrine from Sophora flavescens Ait. extract by utilizing silica-confined ionic liquids as sorbent. The optimized silica-confined ionic liquid was firstly mixed with plant extract to adsorb oxymatrine. Simultaneously, some interference, such as matrine, was removed. The obtained suspension was then added to a cartridge for solid phase extraction. Through these two steps, target compound was adequately separated from interferences with 93.4% recovery. In comparison with traditional solid phase extraction, this method accelerates loading and reduces the use of organic solvents during washing. Moreover, the optimization of loading volume was simplified as optimization of solid/liquid ratio. Copyright © 2011 Elsevier B.V. All rights reserved.

Determination of aminophenols and phenol in hair colorants by ultrasound-assisted solid-phase dispersion extraction coupled with ion chromatography.

PubMed

Zhong, Zhixiong; Li, Gongke; Wu, Rong; Zhu, Binghui; Luo, Zhibin

2014-08-01

A simple and reliable ultrasound-assisted solid-phase dispersion extraction coupled with ion chromatography was developed for the determination of aminophenols and phenol. The highly viscous hair colorant was dispersed in solvents using anhydrous sodium sulfite having dual functions of dispersant and antioxidant. The use of anhydrous sodium sulfite did not change the sample volume because it could completely dissolve in solution after matrix dispersion. The extraction and cleanup were combined in one single step for simplifying operation. The extraction process could be rapidly accomplished within 9 min with high sample throughput under the synergistic effects of vibration, ultrasound, and heating. Satisfactory linearity was observed with correlation coefficients higher than 0.9992, and the limits of detection varied from 0.02 to 0.09 mg/L. The applicability of the proposed method was demonstrated by measuring the concentrations of aminophenols and phenol in 32 different commercial hair color products. The recoveries ranged from 86.4-101.2% with the relative standard deviations in the range of 0.52-4.3%. The method offers an attractive alternative for the analysis of trace phenols in complex matrices. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Back to basics: an evaluation of NaOH and alternative rapid DNA extraction protocols for DNA barcoding, genotyping, and disease diagnostics from fungal and oomycete samples.

PubMed

Osmundson, Todd W; Eyre, Catherine A; Hayden, Katherine M; Dhillon, Jaskirn; Garbelotto, Matteo M

2013-01-01

The ubiquity, high diversity and often-cryptic manifestations of fungi and oomycetes frequently necessitate molecular tools for detecting and identifying them in the environment. In applications including DNA barcoding, pathogen detection from plant samples, and genotyping for population genetics and epidemiology, rapid and dependable DNA extraction methods scalable from one to hundreds of samples are desirable. We evaluated several rapid extraction methods (NaOH, Rapid one-step extraction (ROSE), Chelex 100, proteinase K) for their ability to obtain DNA of quantity and quality suitable for the following applications: PCR amplification of the multicopy barcoding locus ITS1/5.8S/ITS2 from various fungal cultures and sporocarps; single-copy microsatellite amplification from cultures of the phytopathogenic oomycete Phytophthora ramorum; probe-based P. ramorum detection from leaves. Several methods were effective for most of the applications, with NaOH extraction favored in terms of success rate, cost, speed and simplicity. Frozen dilutions of ROSE and NaOH extracts maintained PCR viability for over 32 months. DNA from rapid extractions performed poorly compared to CTAB/phenol-chloroform extracts for TaqMan diagnostics from tanoak leaves, suggesting that incomplete removal of PCR inhibitors is an issue for sensitive diagnostic procedures, especially from plants with recalcitrant leaf chemistry. NaOH extracts exhibited lower yield and size than CTAB/phenol-chloroform extracts; however, NaOH extraction facilitated obtaining clean sequence data from sporocarps contaminated by other fungi, perhaps due to dilution resulting from low DNA yield. We conclude that conventional extractions are often unnecessary for routine DNA sequencing or genotyping of fungi and oomycetes, and recommend simpler strategies where source materials and intended applications warrant such use. © 2012 Blackwell Publishing Ltd.

Sensing cocaine in saliva with attenuated total reflection infrared (ATR-IR) spectroscopy combined with a one-step extraction method

NASA Astrophysics Data System (ADS)

Hans, Kerstin M.-C.; Gianella, Michele; Sigrist, Markus W.

2012-03-01

On-site drug tests have gained importance, e.g., for protecting the society from impaired drivers. Since today's drug tests are majorly only positive/negative, there is a great need for a reliable, portable and preferentially quantitative drug test. In the project IrSens we aim to bridge this gap with the development of an optical sensor platform based on infrared spectroscopy and focus on cocaine detection in saliva. We combine a one-step extraction method, a sample drying technique and infrared attenuated total reflection (ATR) spectroscopy. As a first step we have developed an extraction technique that allows us to extract cocaine from saliva to an almost infrared-transparent solvent and to record ATR spectra with a commercially available Fourier Transform-infrared spectrometer. To the best of our knowledge this is the first time that such a simple and easy-to-use one-step extraction method is used to transfer cocaine from saliva into an organic solvent and detect it quantitatively. With this new method we are able to reach a current limit of detection around 10 μg/ml. This new extraction method could also be applied to waste water monitoring and controlling caffeine content in beverages.

Bayesian modelling of uncertainties of Monte Carlo radiative-transfer simulations

NASA Astrophysics Data System (ADS)

Beaujean, Frederik; Eggers, Hans C.; Kerzendorf, Wolfgang E.

2018-04-01

One of the big challenges in astrophysics is the comparison of complex simulations to observations. As many codes do not directly generate observables (e.g. hydrodynamic simulations), the last step in the modelling process is often a radiative-transfer treatment. For this step, the community relies increasingly on Monte Carlo radiative transfer due to the ease of implementation and scalability with computing power. We show how to estimate the statistical uncertainty given the output of just a single radiative-transfer simulation in which the number of photon packets follows a Poisson distribution and the weight (e.g. energy or luminosity) of a single packet may follow an arbitrary distribution. Our Bayesian approach produces a posterior distribution that is valid for any number of packets in a bin, even zero packets, and is easy to implement in practice. Our analytic results for large number of packets show that we generalise existing methods that are valid only in limiting cases. The statistical problem considered here appears in identical form in a wide range of Monte Carlo simulations including particle physics and importance sampling. It is particularly powerful in extracting information when the available data are sparse or quantities are small.

Bayesian modelling of uncertainties of Monte Carlo radiative-transfer simulations

NASA Astrophysics Data System (ADS)

Beaujean, Frederik; Eggers, Hans C.; Kerzendorf, Wolfgang E.

2018-07-01

One of the big challenges in astrophysics is the comparison of complex simulations to observations. As many codes do not directly generate observables (e.g. hydrodynamic simulations), the last step in the modelling process is often a radiative-transfer treatment. For this step, the community relies increasingly on Monte Carlo radiative transfer due to the ease of implementation and scalability with computing power. We consider simulations in which the number of photon packets is Poisson distributed, while the weight assigned to a single photon packet follows any distribution of choice. We show how to estimate the statistical uncertainty of the sum of weights in each bin from the output of a single radiative-transfer simulation. Our Bayesian approach produces a posterior distribution that is valid for any number of packets in a bin, even zero packets, and is easy to implement in practice. Our analytic results for large number of packets show that we generalize existing methods that are valid only in limiting cases. The statistical problem considered here appears in identical form in a wide range of Monte Carlo simulations including particle physics and importance sampling. It is particularly powerful in extracting information when the available data are sparse or quantities are small.

Angle-dependent photodegradation over ZnO nanowire arrays on flexible paper substrates

PubMed Central

2014-01-01

In this study, we grew zinc oxide (ZnO) nanowire arrays on paper substrates using a two-step growth strategy. In the first step, we formed single-crystalline ZnO nanoparticles of uniform size distribution (ca. 4 nm) as seeds for the hydrothermal growth of the ZnO nanowire arrays. After spin-coating of these seeds onto paper, we grew ZnO nanowire arrays conformally on these substrates. The crystal structure of a ZnO nanowire revealed that the nanowires were single-crystalline and had grown along the c axis. Further visualization through annular bright field scanning transmission electron microscopy revealed that the hydrothermally grown ZnO nanowires possessed Zn polarity. From photocatalytic activity measurements of the ZnO nanowire (NW) arrays on paper substrate, we extracted rate constants of 0.415, 0.244, 0.195, and 0.08 s-1 for the degradation of methylene blue at incident angles of 0°, 30°, 60°, and 75°, respectively; that is, the photocatalytic activity of these ZnO nanowire arrays was related to the cosine of the incident angle of the UV light. Accordingly, these materials have promising applications in the design of sterilization systems and light-harvesting devices. PMID:25593556

Extraction of sediment-associated polycyclic aromatic hydrocarbons with granular activated carbon.

PubMed

Rakowska, M I; Kupryianchyk, D; Grotenhuis, T; Rijnaarts, H H M; Koelmans, A A

2013-02-01

Addition of activated carbon (AC) to sediments has been proposed as a method to reduce ecotoxicological risks of sediment-bound contaminants. The present study explores the effectiveness of granular AC (GAC) in extracting polycyclic aromatic hydrocarbon (PAH) from highly contaminated sediments. Four candidate GAC materials were screened in terms of PAH extraction efficiency using single-step 24-h GAC extractions, with traditional 24-h Tenax extraction as a reference. Subsequently, sorption of native PAHs to the best performing GAC 1240W (0.45-1.70 mm) was studied for sediment only and for GAC-sediment mixtures at different GAC-sediment weight ratios, using 76-µm polyoxymethylene (POM) passive samplers. Granular AC sorption parameters for PAHs were determined by subtracting the contribution of PAH sorption to sediment from PAH sorption to the GAC-sediment mixture. It appears that the binding of PAHs and the effectiveness of GAC to reduce sediment porewater concentrations were highly dependent on the GAC-sediment mixing ratio and hydrophobicity of the PAH. Despite the considerable fouling of GAC by organic matter and oil, 50 to 90% of the most available PAH was extracted by the GAC during a 28-d contact time, at a dose as low as 4%, which also is a feasible dose in field-scale applications aimed at cleaning the sediment by GAC addition and removal. Copyright © 2012 SETAC.

Comparison of Different Protein Extraction Methods for Gel-Based Proteomic Analysis of Ganoderma spp.

PubMed

Al-Obaidi, Jameel R; Saidi, Noor Baity; Usuldin, Siti Rokhiyah Ahmad; Hussin, Siti Nahdatul Isnaini Said; Yusoff, Noornabeela Md; Idris, Abu Seman

2016-04-01

Ganoderma species are a group of fungi that have the ability to degrade lignin polymers and cause severe diseases such as stem and root rot and can infect economically important plants and perennial crops such as oil palm, especially in tropical countries such as Malaysia. Unfortunately, very little is known about the complex interplay between oil palm and Ganoderma in the pathogenesis of the diseases. Proteomic technologies are simple yet powerful tools in comparing protein profile and have been widely used to study plant-fungus interaction. A critical step to perform a good proteome research is to establish a method that gives the best quality and a wide coverage of total proteins. Despite the availability of various protein extraction protocols from pathogenic fungi in the literature, no single extraction method was found suitable for all types of pathogenic fungi. To develop an optimized protein extraction protocol for 2-DE gel analysis of Ganoderma spp., three previously reported protein extraction protocols were compared: trichloroacetic acid, sucrose and phenol/ammonium acetate in methanol. The third method was found to give the most reproducible gels and highest protein concentration. Using the later method, a total of 10 protein spots (5 from each species) were successfully identified. Hence, the results from this study propose phenol/ammonium acetate in methanol as the most effective protein extraction method for 2-DE proteomic studies of Ganoderma spp.

Step-wise supercritical extraction of carbonaceous residua

DOEpatents

Warzinski, Robert P.

1987-01-01

A method of fractionating a mixture containing high boiling carbonaceous material and normally solid mineral matter includes processing with a plurality of different supercritical solvents. The mixture is treated with a first solvent of high critical temperature and solvent capacity to extract a large fraction as solute. The solute is released as liquid from solvent and successively treated with other supercritical solvents of different critical values to extract fractions of differing properties. Fractionation can be supplemented by solute reflux over a temperature gradient, pressure let down in steps and extractions at varying temperature and pressure values.

A simple protocol for Matrix Assisted Laser Desorption Ionization- time of flight-mass spectrometry (MALDI-TOF-MS) analysis of lipids and proteins in single microsamples of paintings.

PubMed

van der Werf, Inez D; Calvano, Cosima D; Palmisano, Francesco; Sabbatini, Luigia

2012-03-09

A simple protocol, based on Bligh-Dyer (BD) extraction followed by MALDI-TOF-MS analysis, for fast identification of paint binders in single microsamples is proposed. For the first time it is demonstrated that the BD method is effective for the simultaneous extraction of lipids and proteins from complex, and atypical matrices, such as pigmented paint layers. The protocol makes use of an alternative denaturing anionic detergent (RapiGest™) in order to improve efficiency of protein digestion and purification step. Detection of various lipid classes, such as triacylglycerols (TAGs) and phospholipids (PLs), and their oxidation by-products was accomplished, whereas proteins could be identified by peptide mass fingerprinting. The effect of pigments on ageing of lipids and proteins was also investigated. Finally, the proposed protocol was successfully applied to the study of a late-15th century Italian panel painting allowing the identification of various proteinaceous and lipid sections in organic binders, such as egg yolk, egg white, animal glue, casein, and drying oil. Copyright © 2011 Elsevier B.V. All rights reserved.

Extrusion of xylans extracted from corn cobs into biodegradable polymeric materials.

PubMed

Bahcegul, Erinc; Akinalan, Busra; Toraman, Hilal E; Erdemir, Duygu; Ozkan, Necati; Bakir, Ufuk

2013-12-01

Solvent casting technique, which comprises multiple energy demanding steps including the dissolution of a polymer in a solvent followed by the evaporation of the solvent from the polymer solution, is currently the main technique for the production of xylan based polymeric materials. The present study shows that sufficient water content renders arabinoglucuronoxylan (AGX) polymers extrudable, enabling the production of AGX based polymeric materials in a single step via extrusion, which is economically advantageous to solvent casting process for mass production. AGX polymers with water content of 27% were found to yield extrudates at an extrusion temperature of 90°C. The extruded strips showed very good mechanical properties with an ultimate tensile strength of 76 ± 6 MPa and elongation at break value of 35 ± 8%, which were superior to the mechanical properties of the strips obtained from polylactic acid. Copyright © 2013 Elsevier Ltd. All rights reserved.

Assembly and multiple gene expression of thermophilic enzymes in Escherichia coli for in vitro metabolic engineering.

PubMed

Ninh, Pham Huynh; Honda, Kohsuke; Sakai, Takaaki; Okano, Kenji; Ohtake, Hisao

2015-01-01

In vitro reconstitution of an artificial metabolic pathway is an emerging approach for the biocatalytic production of industrial chemicals. However, several enzymes have to be separately prepared (and purified) for the construction of an in vitro metabolic pathway, thereby limiting the practical applicability of this approach. In this study, genes encoding the nine thermophilic enzymes involved in a non-ATP-forming chimeric glycolytic pathway were assembled in an artificial operon and co-expressed in a single recombinant Escherichia coli strain. Gene expression levels of the thermophilic enzymes were controlled by their sequential order in the artificial operon. The specific activities of the recombinant enzymes in the cell-free extract of the multiple-gene-expression E. coli were 5.0-1,370 times higher than those in an enzyme cocktail prepared from a mixture of single-gene-expression strains, in each of which a single one of the nine thermophilic enzymes was overproduced. Heat treatment of a crude extract of the multiple-gene-expression cells led to the denaturation of indigenous proteins and one-step preparation of an in vitro synthetic pathway comprising only a limited number of thermotolerant enzymes. Coupling this in vitro pathway with other thermophilic enzymes including the H2 O-forming NADH oxidase or the malate/lactate dehydrogenase facilitated one-pot conversion of glucose to pyruvate or lactate, respectively. © 2014 Wiley Periodicals, Inc.

Effect of Calendula officinalis hydroalcoholic extract on passive avoidance learning and memory in streptozotocin-induced diabetic rats

PubMed Central

Moradkhani, Shirin; Salehi, Iraj; Abdolmaleki, Somayeh; Komaki, Alireza

2015-01-01

Background: Medicinal plants, owing to their different mechanisms such as antioxidants effects, may improve learning and memory impairments in diabetic rats. Calendula officinalis (CO), has a significant antioxidant activity. Aims: To examine the effect of hydroalcoholic extract of CO on passive avoidance learning (PAL) and memory in streptozotocin (STZ)-induced diabetic male rats. Settings and Design: A total of 32 adult male Wistar rats were randomly allocated to four groups: Control, diabetic, control + extract of CO and diabetic control + extract of CO groups with free access to regular rat diet. Subjects and Methods: Diabetes in diabetic rats was induced by single intraperitoneal injection of 60 mg/kg STZ. After confirmation of diabetes, oral administration of 300 mg/kg CO extract to extract-treated groups have been done. PAL was tested 8 weeks after onset of treatment, and blood glucose and body weight were measured in all groups at the beginning and end of the experiment. Statistical Analysis Used: The statistical analysis of data was performed by ANOVA followed by least significant difference post-hoc analysis. Results: Diabetes decreased learning and memory. Effect of CO extract in retention test (after 24 and 48 h) has been shown a significant decrease in step-through latency and increase in time spent in the dark compartment part. Also the extract partially improved hyperglycemia and reduced body weight. Conclusion: Taken together, CO extract can improve PAL and memory impairments in STZ-diabetic rats. This improvement may be due to its antioxidant, anticholinergic activities or its power to reduce hyperglycemia. PMID:26120230

Labile rhizosphere soil solution fraction for prediction of bioavailability of heavy metals and rare earth elements to plants.

PubMed

Shan, Xiao-Quan; Wang, Zhongwen; Wang, Weisheng; Zhang, Shuzhen; Wen, Bei

2003-02-01

A labile rhizosphere soil solution fraction has been recommended to predict the bioavailability of heavy metals and rare earth elements to plants. This method used moist rhizosphere soil in combination with a mixture of 0.01 mol L(-1) of low-molecular-weight organic acids (LMWOAs) as extractant. The extracted soil solutions were fractionated into two colloidal fractions of <0.45 microm (F(3)) and <0.2 microm (F(2)), and one truly dissolved fraction including free metal ions and inorganic and organic complexes (fractionr(0.2 microm, LMWOAs) approximately r(0.45 microm, LMWOAs). In the case of rare earth elements the good correlation was obtained for both the wheat roots and shoots. Generally, the correlation coefficients obtained by LMWAOs were better than that obtained by the first step of BCR method. Therefore, LMWAOs and F(lrss) were strongly recommended to predict the bioavailability of metals in soil pools to plants.

Biochar as a sorbent for chlorinated hydrocarbons - sorption and extraction experiments in single and bi-solute systems

NASA Astrophysics Data System (ADS)

Schreiter, I. J.; Wefer-Roehl, A.; Graber, E. R.; Schueth, C.

2016-12-01

Biochar (BC) is increasingly deemed a potential sorbent for contaminants in soil and water remediation, and brownfield restoration. In this study, sorption and extraction experiments were performed to assess the potential of three different BCs to sorb and retain the chlorinated hydrocarbons TCE and PCE. BCs studied were produced from wood chips, grain husk, and cattle manure at 450 °C. A commercially available activated carbon (AC) served as a reference. The sorption behaviour was studied in batch experiments in single solute and bi-solute systems. Resulting isotherms were fitted to the Freundlich model. To assess the desorption behaviour, a five step extraction scheme (water at 40°C, water at 80°C, methanol at 50°C, toluene at 50°C, and n-hexane at 50°) was developed utilizing Accelerated Solvent Extraction. Isotherms revealed distinct differences in sorption behaviour depending on BC feedstock. Sorption capacity ranked as follows: wood chip BC > grain husk BC > cattle manure BC for both contaminants. This sequence could be attributable to an increasing specific surface area and a decreasing ash content of the sorbents. It is noteworthy that all three BCs were more effective in adsorbing TCE, which is surprising, given the higher logKOWof PCE. The reverse trend was observed for the AC. In bi-solute experiments, PCE sorbed as good as or stronger than TCE, yet the total mass of sorbed compounds was higher. In contrast, AC showed a significant decrease of TCE sorption. Extraction experiments revealed that for all BCs a large fraction of the contaminants could not be readily desorbed. In all cases, water remobilized < 5 % of the total contaminant mass and up to 70 % could not be extracted by any of the solvents. The findings suggest that BC is a promising sorbent for mixed contaminant systems as it offers a diverse nature of sorption sites and is more effective in long-term stabilization than AC.

Automatic diagnosis of malaria based on complete circle-ellipse fitting search algorithm.

PubMed

Sheikhhosseini, M; Rabbani, H; Zekri, M; Talebi, A

2013-12-01

Diagnosis of malaria parasitemia from blood smears is a subjective and time-consuming task for pathologists. The automatic diagnostic process will reduce the diagnostic time. Also, it can be worked as a second opinion for pathologists and may be useful in malaria screening. This study presents an automatic method for malaria diagnosis from thin blood smears. According to this fact that malaria life cycle is started by forming a ring around the parasite nucleus, the proposed approach is mainly based on curve fitting to detect parasite ring in the blood smear. The method is composed of six main phases: stain object extraction step, which extracts candidate objects that may be infected by malaria parasites. This phase includes stained pixel extraction step based on intensity and colour, and stained object segmentation by defining stained circle matching. Second step is preprocessing phase which makes use of nonlinear diffusion filtering. The process continues with detection of parasite nucleus from resulted image of previous step according to image intensity. Fourth step introduces a complete search process in which the circle search step identifies the direction and initial points for direct least-square ellipse fitting algorithm. Furthermore in the ellipse searching process, although parasite shape is completed undesired regions with high error value are removed and ellipse parameters are modified. Features are extracted from the parasite candidate region instead of whole candidate object in the fifth step. By employing this special feature extraction way, which is provided by special searching process, the necessity of employing clump splitting methods is removed. Also, defining stained circle matching process in the first step speeds up the whole procedure. Finally, a series of decision rules are applied on the extracted features to decide on the positivity or negativity of malaria parasite presence. The algorithm is applied on 26 digital images which are provided from thin blood smear films. The images are contained 1274 objects which may be infected by parasite or healthy. Applying the automatic identification of malaria on provided database showed a sensitivity of 82.28% and specificity of 98.02%. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.

Electrolysis of a molten semiconductor

PubMed Central

Yin, Huayi; Chung, Brice; Sadoway, Donald R.

2016-01-01

Metals cannot be extracted by electrolysis of transition-metal sulfides because as liquids they are semiconductors, which exhibit high levels of electronic conduction and metal dissolution. Herein by introduction of a distinct secondary electrolyte, we reveal a high-throughput electro-desulfurization process that directly converts semiconducting molten stibnite (Sb2S3) into pure (99.9%) liquid antimony and sulfur vapour. At the bottom of the cell liquid antimony pools beneath cathodically polarized molten stibnite. At the top of the cell sulfur issues from a carbon anode immersed in an immiscible secondary molten salt electrolyte disposed above molten stibnite, thereby blocking electronic shorting across the cell. As opposed to conventional extraction practices, direct sulfide electrolysis completely avoids generation of problematic fugitive emissions (CO2, CO and SO2), significantly reduces energy consumption, increases productivity in a single-step process (lower capital and operating costs) and is broadly applicable to a host of electronically conductive transition-metal chalcogenides. PMID:27553525

Electrolysis of a molten semiconductor.

PubMed

Yin, Huayi; Chung, Brice; Sadoway, Donald R

2016-08-24

Metals cannot be extracted by electrolysis of transition-metal sulfides because as liquids they are semiconductors, which exhibit high levels of electronic conduction and metal dissolution. Herein by introduction of a distinct secondary electrolyte, we reveal a high-throughput electro-desulfurization process that directly converts semiconducting molten stibnite (Sb2S3) into pure (99.9%) liquid antimony and sulfur vapour. At the bottom of the cell liquid antimony pools beneath cathodically polarized molten stibnite. At the top of the cell sulfur issues from a carbon anode immersed in an immiscible secondary molten salt electrolyte disposed above molten stibnite, thereby blocking electronic shorting across the cell. As opposed to conventional extraction practices, direct sulfide electrolysis completely avoids generation of problematic fugitive emissions (CO2, CO and SO2), significantly reduces energy consumption, increases productivity in a single-step process (lower capital and operating costs) and is broadly applicable to a host of electronically conductive transition-metal chalcogenides.

Electrolysis of a molten semiconductor

NASA Astrophysics Data System (ADS)

Yin, Huayi; Chung, Brice; Sadoway, Donald R.

2016-08-01

Metals cannot be extracted by electrolysis of transition-metal sulfides because as liquids they are semiconductors, which exhibit high levels of electronic conduction and metal dissolution. Herein by introduction of a distinct secondary electrolyte, we reveal a high-throughput electro-desulfurization process that directly converts semiconducting molten stibnite (Sb2S3) into pure (99.9%) liquid antimony and sulfur vapour. At the bottom of the cell liquid antimony pools beneath cathodically polarized molten stibnite. At the top of the cell sulfur issues from a carbon anode immersed in an immiscible secondary molten salt electrolyte disposed above molten stibnite, thereby blocking electronic shorting across the cell. As opposed to conventional extraction practices, direct sulfide electrolysis completely avoids generation of problematic fugitive emissions (CO2, CO and SO2), significantly reduces energy consumption, increases productivity in a single-step process (lower capital and operating costs) and is broadly applicable to a host of electronically conductive transition-metal chalcogenides.

Direct capture of His₆-tagged proteins using megaporous cryogels developed for metal-ion affinity chromatography.

PubMed

Singh, Naveen Kumar; DSouza, Roy N; Bibi, Noor Shad; Fernández-Lahore, Marcelo

2015-01-01

Immobilized metal-ion affinity chromatography (IMAC) has been developed for the rapid isolation and purification of recombinant proteins. In this chapter, megaporous cryogels were synthesized having metal-ion affinity functionality, and their adsorptive properties were investigated. These cryogels have large pore sizes ranging from 10 to 100 μm with corresponding porosities between 80 and 90%. The synthesized IMAC-cryogel had a total ligand density of 770 μmol/g. Twelve milligram of a His6-tagged protein (NAD(P)H-dependent 2-cyclohexen-1-one-reductase) can be purified from a crude cell extract per gram of IMAC-cryogels. The protein binding capacity is increased with higher degrees of grafting, although a slight decrease in column efficiency may result. This chapter provides methodologies for a rapid single-step purification of recombinant His6-tagged proteins from crude cell extracts using IMAC-cryogels.

Fast single run of vanilla fingerprint markers on microfluidic-electrochemistry chip for confirmation of common frauds.

PubMed

Avila, Mónica; Zougagh, Mohammed; Escarpa, Alberto; Ríos, Angel

2009-10-01

A new strategy based on the fast separation of the fingerprint markers of Vanilla planifolia extracts and vanilla-related samples on microfluidic-electrochemistry chip is proposed. This methodology allowed the detection of all required markers for confirmation of common frauds in this field. The elution order was strategically connected with sequential sample screening and analyte confirmation steps, where first ethyl vanillin was detected to distinguish natural from adultered samples; second, vanillin as prominent marker in V. planifolia, but frequently added in its synthetic form; and third, the final detection of the fingerprint markers (p-hydroxybenzaldehyde, vanillic acid, and p-hydroxybenzoic acid) of V. planifolia with confirmation purposes. The reliability of the proposed methodology was demonstrated in the confirmation the natural or non-natural origin of vanilla in samples using V. planifolia extracts and other selected food samples containing this flavor.

Measurement of polycyclic aromatic hydrocarbon (PAHs) in interplanetary dust particles

NASA Technical Reports Server (NTRS)

Clemett, S. J.; Maechling, C. R.; Zare, R. N.; Swan, P. D.; Walker, R. M.

1993-01-01

We report here the first definitive measurements of specific organic molecules (polycyclic aromatic hydrocarbons (PAH's)) in interplanetary dust particles (IDP's). An improved version of the microbeam-two-step laser mass spectrometer was used for the analysis. Two IDP's gave similar mass spectra showing an abundance of PAH's. Control samples, including particles of probable terrestrial origin from the same stratospheric collector, gave either null results or quite different spectra. We conclude that the PAH's are probably indigenous to the IDP's and are not terrestrial contaminants. The instrument used to study the particles is a two-step laser mass spectrometer. Constituent neutral molecules of the sample are first desorbed with a pulsed infrared laser beam focussed to 40 micrometers. In the second step, PAH's in the desorbed plume are preferentially ionized by a pulsed UV laser beam. Resulting ions produced by resonant absorption are extracted into a reflectron time-of-flight mass spectrometer. This instrument has high spatial resolution, high ion transmission, unlimited mass range, and multichannel detection of all ion masses from a single laser shot.

Direct digestion of proteins in living cells into peptides for proteomic analysis.

PubMed

Chen, Qi; Yan, Guoquan; Gao, Mingxia; Zhang, Xiangmin

2015-01-01

To analyze the proteome of an extremely low number of cells or even a single cell, we established a new method of digesting whole cells into mass-spectrometry-identifiable peptides in a single step within 2 h. Our sampling method greatly simplified the processes of cell lysis, protein extraction, protein purification, and overnight digestion, without compromising efficiency. We used our method to digest hundred-scale cells. As far as we know, there is no report of proteome analysis starting directly with as few as 100 cells. We identified an average of 109 proteins from 100 cells, and with three replicates, the number of proteins rose to 204. Good reproducibility was achieved, showing stability and reliability of the method. Gene Ontology analysis revealed that proteins in different cellular compartments were well represented.

One-step displacement dispersive liquid-liquid microextraction coupled with graphite furnace atomic absorption spectrometry for the selective determination of methylmercury in environmental samples.

PubMed

Liang, Pei; Kang, Caiyan; Mo, Yajun

2016-01-01

A novel method for the selective determination of methylmercury (MeHg) was developed by one-step displacement dispersive liquid-liquid microextraction (D-DLLME) coupled with graphite furnace atomic absorption spectrometry. In the proposed method, Cu(II) reacted with diethyldithiocarbamate (DDTC) to form Cu-DDTC complex, which was used as the chelating agent instead of DDTC for the dispersive liquid-liquid microextraction (DLLME) of MeHg. Because the stability of MeHg-DDTC is higher than that of Cu-DDTC, MeHg can displace Cu from the Cu-DDTC complex and be preconcentrated in a single DLLME procedure. MeHg could be extracted into the extraction solvent phase at pH 6 while Hg(II) remained in the sample solution. Potential interference from co-existing metal ions with lower DDTC complex stability was largely eliminated without the need of any masking reagent. Under the optimal conditions, the limit of detection of this method was 13.6ngL(-1) (as Hg), and an enhancement factor of 81 was achieved with a sample volume of 5.0mL. The proposed method was successfully applied for the determination of trace MeHg in some environmental samples with satisfactory results. Copyright © 2015 Elsevier B.V. All rights reserved.

Comparison on genomic predictions using three GBLUP methods and two single-step blending methods in the Nordic Holstein population

PubMed Central

2012-01-01

Background A single-step blending approach allows genomic prediction using information of genotyped and non-genotyped animals simultaneously. However, the combined relationship matrix in a single-step method may need to be adjusted because marker-based and pedigree-based relationship matrices may not be on the same scale. The same may apply when a GBLUP model includes both genomic breeding values and residual polygenic effects. The objective of this study was to compare single-step blending methods and GBLUP methods with and without adjustment of the genomic relationship matrix for genomic prediction of 16 traits in the Nordic Holstein population. Methods The data consisted of de-regressed proofs (DRP) for 5 214 genotyped and 9 374 non-genotyped bulls. The bulls were divided into a training and a validation population by birth date, October 1, 2001. Five approaches for genomic prediction were used: 1) a simple GBLUP method, 2) a GBLUP method with a polygenic effect, 3) an adjusted GBLUP method with a polygenic effect, 4) a single-step blending method, and 5) an adjusted single-step blending method. In the adjusted GBLUP and single-step methods, the genomic relationship matrix was adjusted for the difference of scale between the genomic and the pedigree relationship matrices. A set of weights on the pedigree relationship matrix (ranging from 0.05 to 0.40) was used to build the combined relationship matrix in the single-step blending method and the GBLUP method with a polygenetic effect. Results Averaged over the 16 traits, reliabilities of genomic breeding values predicted using the GBLUP method with a polygenic effect (relative weight of 0.20) were 0.3% higher than reliabilities from the simple GBLUP method (without a polygenic effect). The adjusted single-step blending and original single-step blending methods (relative weight of 0.20) had average reliabilities that were 2.1% and 1.8% higher than the simple GBLUP method, respectively. In addition, the GBLUP method with a polygenic effect led to less bias of genomic predictions than the simple GBLUP method, and both single-step blending methods yielded less bias of predictions than all GBLUP methods. Conclusions The single-step blending method is an appealing approach for practical genomic prediction in dairy cattle. Genomic prediction from the single-step blending method can be improved by adjusting the scale of the genomic relationship matrix. PMID:22455934

Smoke regions extraction based on two steps segmentation and motion detection in early fire

NASA Astrophysics Data System (ADS)

Jian, Wenlin; Wu, Kaizhi; Yu, Zirong; Chen, Lijuan

2018-03-01

Aiming at the early problems of video-based smoke detection in fire video, this paper proposes a method to extract smoke suspected regions by combining two steps segmentation and motion characteristics. Early smoldering smoke can be seen as gray or gray-white regions. In the first stage, regions of interests (ROIs) with smoke are obtained by using two step segmentation methods. Then, suspected smoke regions are detected by combining the two step segmentation and motion detection. Finally, morphological processing is used for smoke regions extracting. The Otsu algorithm is used as segmentation method and the ViBe algorithm is used to detect the motion of smoke. The proposed method was tested on 6 test videos with smoke. The experimental results show the effectiveness of our proposed method over visual observation.

Improved method for the extraction and chromatographic analysis on a fused-core column of ellagitannins found in oak-aged wine.

PubMed

Navarro, María; Kontoudakis, Nikolaos; Canals, Joan Miquel; García-Romero, Esteban; Gómez-Alonso, Sergio; Zamora, Fernando; Hermosín-Gutiérrez, Isidro

2017-07-01

A new method for the analysis of ellagitannins observed in oak-aged wine is proposed, exhibiting interesting advantages with regard to previously reported analytical methods. The necessary extraction of ellagitannins from wine was simplified to a single step of solid phase extraction (SPE) using size exclusion chromatography with Sephadex LH-20 without the need for any previous SPE of phenolic compounds using reversed-phase materials. The quantitative recovery of wine ellagitannins requires a combined elution with methanol and ethyl acetate, especially for increasing the recovery of the less polar acutissimins. The chromatographic method was performed using a fused-core C18 column, thereby avoiding the coelution of main ellagitannins, such as vescalagin and roburin E. However, the very polar ellagitannins, namely, the roburins A, B and C, still partially coeluted, and their quantification was assisted by the MS detector. This methodology also enabled the analysis of free gallic and ellagic acids in the same chromatographic run. Copyright © 2017 Elsevier Ltd. All rights reserved.

Dimensionality Reduction Through Classifier Ensembles

NASA Technical Reports Server (NTRS)

Oza, Nikunj C.; Tumer, Kagan; Norwig, Peter (Technical Monitor)

1999-01-01

In data mining, one often needs to analyze datasets with a very large number of attributes. Performing machine learning directly on such data sets is often impractical because of extensive run times, excessive complexity of the fitted model (often leading to overfitting), and the well-known "curse of dimensionality." In practice, to avoid such problems, feature selection and/or extraction are often used to reduce data dimensionality prior to the learning step. However, existing feature selection/extraction algorithms either evaluate features by their effectiveness across the entire data set or simply disregard class information altogether (e.g., principal component analysis). Furthermore, feature extraction algorithms such as principal components analysis create new features that are often meaningless to human users. In this article, we present input decimation, a method that provides "feature subsets" that are selected for their ability to discriminate among the classes. These features are subsequently used in ensembles of classifiers, yielding results superior to single classifiers, ensembles that use the full set of features, and ensembles based on principal component analysis on both real and synthetic datasets.

Application of the BioMek 2000 Laboratory Automation Workstation and the DNA IQ System to the extraction of forensic casework samples.

PubMed

Greenspoon, Susan A; Ban, Jeffrey D; Sykes, Karen; Ballard, Elizabeth J; Edler, Shelley S; Baisden, Melissa; Covington, Brian L

2004-01-01

Robotic systems are commonly utilized for the extraction of database samples. However, the application of robotic extraction to forensic casework samples is a more daunting task. Such a system must be versatile enough to accommodate a wide range of samples that may contain greatly varying amounts of DNA, but it must also pose no more risk of contamination than the manual DNA extraction methods. This study demonstrates that the BioMek 2000 Laboratory Automation Workstation, used in combination with the DNA IQ System, is versatile enough to accommodate the wide range of samples typically encountered by a crime laboratory. The use of a silica coated paramagnetic resin, as with the DNA IQ System, facilitates the adaptation of an open well, hands off, robotic system to the extraction of casework samples since no filtration or centrifugation steps are needed. Moreover, the DNA remains tightly coupled to the silica coated paramagnetic resin for the entire process until the elution step. A short pre-extraction incubation step is necessary prior to loading samples onto the robot and it is at this step that most modifications are made to accommodate the different sample types and substrates commonly encountered with forensic evidentiary samples. Sexual assault (mixed stain) samples, cigarette butts, blood stains, buccal swabs, and various tissue samples were successfully extracted with the BioMek 2000 Laboratory Automation Workstation and the DNA IQ System, with no evidence of contamination throughout the extensive validation studies reported here.

Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site.

PubMed

Fuchs, Gabriele; Petrov, Alexey N; Marceau, Caleb D; Popov, Lauren M; Chen, Jin; O'Leary, Seán E; Wang, Richard; Carette, Jan E; Sarnow, Peter; Puglisi, Joseph D

2015-01-13

Translation initiation can occur by multiple pathways. To delineate these pathways by single-molecule methods, fluorescently labeled ribosomal subunits are required. Here, we labeled human 40S ribosomal subunits with a fluorescent SNAP-tag at ribosomal protein eS25 (RPS25). The resulting ribosomal subunits could be specifically labeled in living cells and in vitro. Using single-molecule Förster resonance energy transfer (FRET) between RPS25 and domain II of the hepatitis C virus (HCV) internal ribosome entry site (IRES), we measured the rates of 40S subunit arrival to the HCV IRES. Our data support a single-step model of HCV IRES recruitment to 40S subunits, irreversible on the initiation time scale. We furthermore demonstrated that after binding, the 40S:HCV IRES complex is conformationally dynamic, undergoing slow large-scale rearrangements. Addition of translation extracts suppresses these fluctuations, funneling the complex into a single conformation on the 80S assembly pathway. These findings show that 40S:HCV IRES complex formation is accompanied by dynamic conformational rearrangements that may be modulated by initiation factors.

Influence of VO2+ ions on structural and optical properties of potassium succinate-succinic acid single crystal for non-linear optical applications

NASA Astrophysics Data System (ADS)

Juliet sheela, K.; Subramanian, P.

2018-04-01

A transparent and good optical quality semi organic single crystal of vanadium doped potassium succinate-succinic acid (KSSA) was synthesized by slow evaporation technique at room temperature. The structural perfection was supported by the powder XRD of the KSSA-VO2+ single crystal. Optical behavior of the material was discovered from the absorption and transmission spectra of UV-vis-NIR characterization. Functional group and presence of metal ion in the specimen are depicted from FTIR traces. From the photoluminescence studies, emission of wavelength in the violet region (418 nm) at the excitation of 243 nm could be ascertained. EDAX, SEM measurements identify presence of elements and pictures the step-line growth and the imperfection presents in the grown crystal. EPR analysis extracts the information about the local site symmetry around the impurity ion, molecular orbital coefficients, admixture coefficients and ground state wave function of VO2+ doped KSSA single crystal. Second harmonic generation (SHG) efficiency of the grown crystal was investigated to explore the NLO characteristic of the material.

Joint Extraction of Entities and Relations Using Reinforcement Learning and Deep Learning.

PubMed

Feng, Yuntian; Zhang, Hongjun; Hao, Wenning; Chen, Gang

2017-01-01

We use both reinforcement learning and deep learning to simultaneously extract entities and relations from unstructured texts. For reinforcement learning, we model the task as a two-step decision process. Deep learning is used to automatically capture the most important information from unstructured texts, which represent the state in the decision process. By designing the reward function per step, our proposed method can pass the information of entity extraction to relation extraction and obtain feedback in order to extract entities and relations simultaneously. Firstly, we use bidirectional LSTM to model the context information, which realizes preliminary entity extraction. On the basis of the extraction results, attention based method can represent the sentences that include target entity pair to generate the initial state in the decision process. Then we use Tree-LSTM to represent relation mentions to generate the transition state in the decision process. Finally, we employ Q -Learning algorithm to get control policy π in the two-step decision process. Experiments on ACE2005 demonstrate that our method attains better performance than the state-of-the-art method and gets a 2.4% increase in recall-score.

Joint Extraction of Entities and Relations Using Reinforcement Learning and Deep Learning

PubMed Central

Zhang, Hongjun; Chen, Gang

2017-01-01

We use both reinforcement learning and deep learning to simultaneously extract entities and relations from unstructured texts. For reinforcement learning, we model the task as a two-step decision process. Deep learning is used to automatically capture the most important information from unstructured texts, which represent the state in the decision process. By designing the reward function per step, our proposed method can pass the information of entity extraction to relation extraction and obtain feedback in order to extract entities and relations simultaneously. Firstly, we use bidirectional LSTM to model the context information, which realizes preliminary entity extraction. On the basis of the extraction results, attention based method can represent the sentences that include target entity pair to generate the initial state in the decision process. Then we use Tree-LSTM to represent relation mentions to generate the transition state in the decision process. Finally, we employ Q-Learning algorithm to get control policy π in the two-step decision process. Experiments on ACE2005 demonstrate that our method attains better performance than the state-of-the-art method and gets a 2.4% increase in recall-score. PMID:28894463

Fully Disposable Manufacturing Concepts for Clinical and Commercial Manufacturing and Ballroom Concepts.

PubMed

Boedeker, Berthold; Goldstein, Adam; Mahajan, Ekta

2017-11-04

The availability and use of pre-sterilized disposables has greatly changed the methods used in biopharmaceuticals development and production, particularly from mammalian cell culture. Nowadays, almost all process steps from cell expansion, fermentation, cell removal, and purification to formulation and storage of drug substances can be carried out in disposables, although there are still limitations with single-use technologies, particularly in the areas of pretesting and quality control of disposables, bag and connections standardization and qualification, extractables and leachables (E/L) validation, and dependency on individual vendors. The current status of single-use technologies is summarized for all process unit operations using a standard mAb process as an example. In addition, current pros and cons of using disposables are addressed in a comparative way, including quality control and E/L validation.The continuing progress in developing single-use technologies has an important impact on manufacturing facilities, resulting in much faster, less expensive and simpler plant design, start-up, and operation, because cell culture process steps are no longer performed in hard-piped unit operations. This leads to simpler operations in a lab-like environment. Overall it enriches the current landscape of available facilities from standard hard-piped to hard-piped/disposables hybrid to completely single-use-based production plants using the current segregation and containment concept. At the top, disposables in combination with completely and functionally closed systems facilitate a new, revolutionary design of ballroom facilities without or with much less segregation, which enables us to perform good manufacturing practice manufacturing of different products simultaneously in unclassified but controlled areas.Finally, single-use processing in lab-like shell facilities is a big enabler of transferring and establishing production in emergent countries, and this is described in more detail in 7. Graphical Abstract.

Development and validation of a solid-phase extraction method using anion exchange sorbent for the analysis of cannabinoids in plasma and serum by gas chromatography-mass spectrometry.

PubMed

Gasse, Angela; Pfeiffer, Heidi; Köhler, Helga; Schürenkamp, Jennifer

2016-07-01

The aim of this work was to develop and validate a solid-phase extraction (SPE) method for the analysis of cannabinoids with emphasis on a very extensive and effective matrix reduction in order to ensure constant good results in selectivity and sensitivity regardless of the applied measuring technology. This was obtained by the use of an anion exchange sorbent (AXS) and the purposive ionic interaction between matrix components and this sorbent material. In a first step, the neutral cannabinoids ∆9-tetrahydrocannabinol (THC) and 11-hydroxy-∆9-tetrahydrocannabinol (11-OH-THC) were eluted, leaving 11-nor-9-carboxy-∆9-tetrahydrocannabinol (THC-COOH) and the main interfering matrix components bound to the AXS. In a second step, exploiting differences in pH and polarity, it was possible to separate matrix components and THC-COOH, thereby yielding a clean elution of THC-COOH into the same collecting tube as THC and 11-OH-THC. Even when using a simple measuring technology like gas chromatography with single quadrupole mass spectrometry, this two-step elution allows for an obvious decrease in number and intensity of matrix interference in the chromatogram. Hence, in both plasma and serum, the AXS extracts resulted in very good selectivity. Limits of detection and limits of quantification were below 0.25 and 0.35 ng/mL for the neutral cannabinoids in both matrices, 2.0 and 3.0 ng/mL in plasma and 1.6 and 3.3 ng/mL in serum for THC-COOH. The recoveries were ≥79.8 % for all analytes. Interday and intraday imprecisions ranged from 0.8 to 6.1 % relative standard deviation, and accuracy bias ranged from -12.6 to 3.6 %.

Monocular precrash vehicle detection: features and classifiers.

PubMed

Sun, Zehang; Bebis, George; Miller, Ronald

2006-07-01

Robust and reliable vehicle detection from images acquired by a moving vehicle (i.e., on-road vehicle detection) is an important problem with applications to driver assistance systems and autonomous, self-guided vehicles. The focus of this work is on the issues of feature extraction and classification for rear-view vehicle detection. Specifically, by treating the problem of vehicle detection as a two-class classification problem, we have investigated several different feature extraction methods such as principal component analysis, wavelets, and Gabor filters. To evaluate the extracted features, we have experimented with two popular classifiers, neural networks and support vector machines (SVMs). Based on our evaluation results, we have developed an on-board real-time monocular vehicle detection system that is capable of acquiring grey-scale images, using Ford's proprietary low-light camera, achieving an average detection rate of 10 Hz. Our vehicle detection algorithm consists of two main steps: a multiscale driven hypothesis generation step and an appearance-based hypothesis verification step. During the hypothesis generation step, image locations where vehicles might be present are extracted. This step uses multiscale techniques not only to speed up detection, but also to improve system robustness. The appearance-based hypothesis verification step verifies the hypotheses using Gabor features and SVMs. The system has been tested in Ford's concept vehicle under different traffic conditions (e.g., structured highway, complex urban streets, and varying weather conditions), illustrating good performance.

A simplified bioprocess for human alpha-fetoprotein production from inclusion bodies.

PubMed

Leong, Susanna S J; Middelberg, Anton P J

2007-05-01

A simple and effective Escherichia coli (E. coli) bioprocess is demonstrated for the preparation of recombinant human alpha-fetoprotein (rhAFP), a pharmaceutically promising protein that has important immunomodulatory functions. The new rhAFP process employs only unit operations that are easy to scale and validate, and reduces the complexity embedded in existing inclusion body processing methods. A key requirement in the establishment of this process was the attainment of high purity rhAFP prior to protein refolding because (i) rhAFP binds easily to hydrophobic contaminants once refolded, and (ii) rhAFP aggregates during renaturation, in a contaminant- dependent way. In this work, direct protein extraction from cell suspension was coupled with a DNA precipitation-centrifugation step prior to purification using two simple chromatographic steps. Refolding was conducted using a single-step, redox-optimized dilution refolding protocol, with refolding success determined by reversed phase HPLC analysis, ELISA, and circular dichroism spectroscopy. Quantitation of DNA and protein contaminant loads after each unit operation showed that contaminant levels were reduced to levels comparable to traditional flowsheets. Protein microchemical modification due to carbamylation in this urea-based process was identified and minimized, yielding a final refolded and purified product that was significantly purified from carbamylated variants. Importantly, this work conclusively demonstrates, for the first time, that a chemical extraction process can substitute the more complex traditional inclusion body processing flowsheet, without compromising product purity and yield. This highly intensified and simplified process is expected to be of general utility for the preparation of other therapeutic candidates expressed as inclusion bodies. (c) 2006 Wiley Periodicals, Inc.

A simplified protocol for molecular identification of Eimeria species in field samples.

PubMed

Haug, Anita; Thebo, Per; Mattsson, Jens G

2007-05-15

This study aimed to find a fast, sensitive and efficient protocol for molecular identification of chicken Eimeria spp. in field samples. Various methods for each of the three steps of the protocol were evaluated: oocyst wall rupturing methods, DNA extraction methods, and identification of species-specific DNA sequences by PCR. We then compared and evaluated five complete protocols. Three series of oocyst suspensions of known number of oocysts from Eimeria mitis, Eimeria praecox, Eimeria maxima and Eimeria tenella were prepared and ground using glass beads or mini-pestle. DNA was extracted from ruptured oocysts using commercial systems (GeneReleaser, Qiagen Stoolkit and Prepman) or phenol-chloroform DNA extraction, followed by identification of species-specific ITS-1 sequences by optimised single species PCR assays. The Stoolkit and Prepman protocols showed insufficient repeatability, and the former was also expensive and relatively time-consuming. In contrast, both the GeneReleaser protocol and phenol-chloroform protocols were robust and sensitive, detecting less than 0.4 oocysts of each species per PCR. Finally, we evaluated our new protocol on 68 coccidia positive field samples. Our data suggests that rupturing the oocysts by mini-pestle grinding, preparing the DNA with GeneReleaser, followed by optimised single species PCR assays, makes a robust and sensitive procedure for identifying chicken Eimeria species in field samples. Importantly, it also provides minimal hands-on-time in the pre-PCR process, lower contamination risk and no handling of toxic chemicals.

Online in-tube microextractor coupled with UV-Vis spectrophotometer for bisphenol A detection.

PubMed

Poorahong, Sujittra; Thammakhet, Chongdee; Thavarungkul, Panote; Kanatharana, Proespichaya

2013-01-01

A simple and high extraction efficiency online in-tube microextractor (ITME) was developed for bisphenol A (BPA) detection in water samples. The ITME was fabricated by a stepwise electrodeposition of polyaniline, polyethylene glycol and polydimethylsiloxane composite (CPANI) inside a silico-steel tube. The obtained ITME coupled with UV-Vis detection at 278 nm was investigated. By this method, the extraction and pre-concentration of BPA in water were carried out in a single step. Under optimum conditions, the system provided a linear dynamic range of 0.1 to 100 μM with a limit of detection of 20 nM (S/N ≥3). A single in-tube microextractor had a good stability of more than 60 consecutive injections for 10.0 μM BPA with a relative standard deviation of less than 4%. Moreover, a good tube-to-tube reproducibility and precision were obtained. The system was applied to detect BPA in water samples from six brands of baby bottles and the results showed good agreement with those obtained from the conventional GC-MS method. Acceptable percentage recoveries from the spiked water samples were obtained, ranging from 83-102% for this new method compared with 73-107% for the GC-MS standard method. This new in-tube CPANI microextractor provided an excellent extraction efficiency and a good reproducibility. In addition, it can also be easily applied for the analysis of other polar organic compounds contaminated in water sample.

Development of an efficient fractionation method for the preparative separation of sesquiterpenoids from Tussilago farfara by counter-current chromatography.

PubMed

Song, Kwangho; Lee, Kyoung Jin; Kim, Yeong Shik

2017-03-17

A novel application of counter-current chromatography (CCC) to enrich plant extracts using direct and continuous injection (CCC-DCI) was developed to fractionate sesquiterpenoids from the buds of Tussilago farfara L. In this study, an n-hexane-acetonitrile-water (HAcW) solvent system was separately pumped into the CCC column, and an extraction solution (45% acetonitrile) was directly and continuously injected into the CCC column. Since the extraction solution was used as a mobile phase in this method, solvent consumption could be greatly reduced. To enrich the extraction solution (315.9g/5.4L), only 4.2L water, 4.6L acetonitrile, and 1.2L n-hexane were used, including the extraction step. Finally, 6.8g of a sesquiterpenoid-enriched (STE) fraction was obtained from the crude extract (315.9g) of Tussilago farfara (1kg) in a single CCC run with a separation time of 8.5h. The sample injection capacity of CCC-DCI was greater than 300g; this amount of sample could not be handled in conventional CCC or other fractionation methods with the same column volume. Moreover, three major sesquiterpenoids (1: tussilagone, 2: 14-acetoxy-7β-(3'-ethyl cis-crotonoyloxy)-1α-(2'-methylburyryloxy)-notonipetranone, and 3: 7β-(3'-ethyl cis-crotonoyloxy)-1α-(2'-methylburyryloxy)-3, 14-dehydro-Z-notonipetranone) were purified from the STE fraction by CCC, and their chemical structures were elucidated by 1 H NMR and 13 C NMR. A quantification study was conducted, and the contents of compounds 1-3 in the CCC-DCI fraction were higher than those of conventional multi-step fractionations performed in series: solvent partitioning and open column chromatography. Furthermore, the average CCC-DCI recoveries were 96.1% (1), 96.9% (2), and 94.6% (3), whereas the open column chromatography recoveries were 77.7% (1), 66.5% (2), and 58.4% (3). The developed method demonstrates that CCC is a useful technique for enriching target components from natural products. Copyright © 2017 Elsevier B.V. All rights reserved.

Phytochemistry of cimicifugic acids and associated bases in Cimicifuga racemosa root extracts.

PubMed

Gödecke, Tanja; Nikolic, Dejan; Lankin, David C; Chen, Shao-Nong; Powell, Sharla L; Dietz, Birgit; Bolton, Judy L; van Breemen, Richard B; Farnsworth, Norman R; Pauli, Guido F

2009-01-01

Earlier studies reported serotonergic activity for cimicifugic acids (CA) isolated from Cimicifuga racemosa. The discovery of strongly basic alkaloids, cimipronidines, from the active extract partition and evaluation of previously employed work-up procedures has led to the hypothesis of strong acid/base association in the extract. Re-isolation of the CAs was desired to permit further detailed studies. Based on the acid/base association hypothesis, a new separation scheme of the active partition was required, which separates acids from associated bases. A new 5-HT(7) bioassay guided work-up procedure was developed that concentrates activity into one partition. The latter was subjected to a new two-step centrifugal partitioning chromatography (CPC) method, which applies pH zone refinement gradient (pHZR CPC) to dissociate the acid/base complexes. The resulting CA fraction was subjected to a second CPC step. Fractions and compounds were monitored by (1)H NMR using a structure-based spin-pattern analysis facilitating dereplication of the known acids. Bioassay results were obtained for the pHZR CPC fractions and for purified CAs. A new CA was characterised. While none of the pure CAs was active, the serotonergic activity was concentrated in a single pHZR CPC fraction, which was subsequently shown to contain low levels of the potent 5-HT(7) ligand, N(omega)-methylserotonin. This study shows that CAs are not responsible for serotonergic activity in black cohosh. New phytochemical methodology (pHZR CPC) and a sensitive dereplication method (LC-MS) led to the identification of N(omega)-methylserotonin as serotonergic active principle. Copyright (c) 2009 John Wiley & Sons, Ltd.

Phytochemistry of Cimicifugic Acids and Associated Bases in Cimicifuga racemosa Root Extracts

PubMed Central

GÖdecke, Tanja; Nikolic, Dejan; Lankin, David C.; Chen, Shao-Nong; Powell, Sharla L.; Dietz, Birgit; Bolton, Judy L.; Van Breemen, Richard B.; Farnsworth, Norman R.; Pauli, Guido F.

2009-01-01

Introduction Earlier studies reported serotonergic activity for cimicifugic acids (CA) isolated from Cimicifuga racemosa. The discovery of strongly basic alkaloids, cimipronidines, from the active extract partition and evaluation of previously employed work-up procedures has led to the hypothesis of strong acid/base association in the extract. Objective Re-isolation of the CAs was desired to permit further detailed studies. Based on the acid/base association hypothesis, a new separation scheme of the active partition was required, which separates acids from associated bases. Methodology A new 5-HT7 bioassay guided work-up procedure was developed that concentrates activity into one partition. The latter was subjected to a new 2-step centrifugal partitioning chromatography (CPC) method, which applies pH zone refinement gradient (pHZR CPC) to dissociate the acid/base complexes. The resulting CA fraction was subjected to a second CPC step. Fractions and compounds were monitored by 1H NMR using a structure based spin-pattern analysis facilitating dereplication of the known acids. Bioassay results were obtained for the pHZR CPC fractions and for purified CAs. Results A new CA was characterized. While none of the pure CAs was active, the serotonergic activity was concentrated in a single pHZR CPC fraction, which was subsequently shown to contain low levels of the potent 5-HT7 ligand, Nω–methylserotonin. Conclusion This study shows that CAs are not responsible for serotonergic activity in black cohosh. New phytochemical methodology (pHZR CPC) and a sensitive dereplication method (LC-MS) led to the identification of Nω–methylserotonin as serotonergic active principle. PMID:19140115

[Investigation of stages of chemical leaching and biooxidation during the extraction of gold from sulfide concentrates].

PubMed

Murav'ev, M I; Fomchenko, N V; Kondrat'eva, T V

2015-01-01

We examined the chemical leaching and biooxidation stages in a two-stage biooxidation process of an auriferous sulfide concentrate containing pyrrhotite, arsenopyrite and pyrite. Chemical leaching of the concentrate (slurry density at 200 g/L) by ferric sulfate biosolvent (initial concentration at 35.6 g/L), which was obtained by microbial oxidation of ferrous sulfate for 2 hours at 70°C at pH 1.4, was allowed to oxidize 20.4% ofarsenopyrite and 52.1% of sulfur. The most effective biooxidation of chemically leached concentrate was observed at 45°C in the presence of yeast extract. Oxidation of the sulfide concentrate in a two-step process proceeded more efficiently than in one-step. In a two-step mode, gold extraction from the precipitate was 10% higher and the content of elemental sulfur was two times lower than in a one-step process.

Bioaerosol DNA Extraction Technique from Air Filters Collected from Marine and Freshwater Locations

NASA Astrophysics Data System (ADS)

Beckwith, M.; Crandall, S. G.; Barnes, A.; Paytan, A.

2015-12-01

Bioaerosols are composed of microorganisms suspended in air. Among these organisms include bacteria, fungi, virus, and protists. Microbes introduced into the atmosphere can drift, primarily by wind, into natural environments different from their point of origin. Although bioaerosols can impact atmospheric dynamics as well as the ecology and biogeochemistry of terrestrial systems, very little is known about the composition of bioaerosols collected from marine and freshwater environments. The first step to determine composition of airborne microbes is to successfully extract environmental DNA from air filters. We asked 1) can DNA be extracted from quartz (SiO2) air filters? and 2) how can we optimize the DNA yield for downstream metagenomic sequencing? Aerosol filters were collected and archived on a weekly basis from aquatic sites (USA, Bermuda, Israel) over the course of 10 years. We successfully extracted DNA from a subsample of ~ 20 filters. We modified a DNA extraction protocol (Qiagen) by adding a beadbeating step to mechanically shear cell walls in order to optimize our DNA product. We quantified our DNA yield using a spectrophotometer (Nanodrop 1000). Results indicate that DNA can indeed be extracted from quartz filters. The additional beadbeating step helped increase our yield - up to twice as much DNA product was obtained compared to when this step was omitted. Moreover, bioaerosol DNA content does vary across time. For instance, the DNA extracted from filters from Lake Tahoe, USA collected near the end of June decreased from 9.9 ng/μL in 2007 to 3.8 ng/μL in 2008. Further next-generation sequencing analysis of our extracted DNA will be performed to determine the composition of these microbes. We will also model the meteorological and chemical factors that are good predictors for microbial composition for our samples over time and space.

Quantitative Analysis of Bioactive Compounds from Aromatic Plants by Means of Dynamic Headspace Extraction and Multiple Headspace Extraction-Gas Chromatography-Mass Spectrometry.

PubMed

Omar, Jone; Olivares, Maitane; Alonso, Ibone; Vallejo, Asier; Aizpurua-Olaizola, Oier; Etxebarria, Nestor

2016-04-01

Seven monoterpenes in 4 aromatic plants (sage, cardamom, lavender, and rosemary) were quantified in liquid extracts and directly in solid samples by means of dynamic headspace-gas chromatography-mass spectrometry (DHS-GC-MS) and multiple headspace extraction-gas chromatography-mass spectrometry (MHSE), respectively. The monoterpenes were 1st extracted by means of supercritical fluid extraction (SFE) and analyzed by an optimized DHS-GC-MS. The optimization of the dynamic extraction step and the desorption/cryo-focusing step were tackled independently by experimental design assays. The best working conditions were set at 30 °C for the incubation temperature, 5 min of incubation time, and 40 mL of purge volume for the dynamic extraction step of these bioactive molecules. The conditions of the desorption/cryo-trapping step from the Tenax TA trap were set at follows: the temperature was increased from 30 to 300 °C at 150 °C/min, although the cryo-trapping was maintained at -70 °C. In order to estimate the efficiency of the SFE process, the analysis of monoterpenes in the 4 aromatic plants was directly carried out by means of MHSE because it did not require any sample preparation. Good linearity (r2) > 0.99) and reproducibility (relative standard deviation % <12) was obtained for solid and liquid quantification approaches, in the ranges of 0.5 to 200 ng and 10 to 500 ng/mL, respectively. The developed methods were applied to analyze the concentration of 7 monoterpenes in aromatic plants obtaining concentrations in the range of 2 to 6000 ng/g and 0.25 to 110 μg/mg, respectively. © 2016 Institute of Food Technologists®

Validation of an updated fractionation and indirect speciation procedure for inorganic arsenic in oxic and suboxic soils and sediments.

PubMed

Lock, Alan; Wallschläger, Dirk; McMurdo, Colin; Tyler, Laura; Belzile, Nelson; Spiers, Graeme

2016-12-01

A sequential extraction procedure (SEP) for the speciation analysis of As(III) and As(V) in oxic and suboxic soils and sediments was validated using a natural lake sediment and three certified reference materials, as well as spike recoveries of As(III) and As(V). Many of the extraction steps have been previously validated making the procedure useful for comparisons to similar previous SEP studies. The novel aspect of this research is the validation for the SEP to maintain As(III) and As(V) species. The proposed five step extraction procedure includes the extraction agents (NH 4 ) 2 SO 4 , NH 4 H 2 PO 4 , H 3 PO 4  + NH 2 OH·HCl, oxalate + ascorbic acid (heated), and HNO 3  + HCl + HF, targeting operationally defined easily exchangeable, strongly sorbed, amorphous Fe oxide bound, crystalline Fe oxide bound, and residual As fractions, respectively. The third extraction step, H 3 PO 4  + NH 2 OH·HCl, has not been previously validated for fraction selectivity. We present evidence for this extraction step to target As complexed with amorphous Fe oxides when used in the SEP proposed here. All solutions were analyzed on ICP-MS. The greatest concentrations of As were extracted from the amorphous Fe oxide fraction and the dominant species was As(V). Lake sediment materials were found to have higher As(III) concentrations than the soil materials. Because different soils/sediments have different chemical characteristics, maintenance of As species during extractions must be validated for specific soil/sediment types using spiking experiments. Copyright © 2016 Elsevier Ltd. All rights reserved.

Lipid extraction from microalgae using a single ionic liquid

DOEpatents

Salvo, Roberto Di; Reich, Alton; Dykes, Jr., H. Waite H.; Teixeira, Rodrigo

2013-05-28

A one-step process for the lysis of microalgae cell walls and separation of the cellular lipids for use in biofuel production by utilizing a hydrophilic ionic liquid, 1-butyl-3-methylimidazolium. The hydrophilic ionic liquid both lyses the microalgae cell walls and forms two immiscible layers, one of which consists of the lipid contents of the lysed cells. After mixture of the hydrophilic ionic liquid with a suspension of microalgae cells, gravity causes a hydrophobic lipid phase to move to a top phase where it is removed from the mixture and purified. The hydrophilic ionic liquid is recycled to lyse new microalgae suspensions.

Preparative isolation and purification of capsaicin and dihydrocapsaicin from Capsici Fructus using supercritical fluid extraction combined with high speed countercurrent chromatography.

PubMed

Yan, Rongwei; Zhao, Leilei; Tao, Junfei; Zou, Yong; Xu, Xinjun

2018-05-01

Supercritical fluid extraction with CO 2 (SFE-CO 2 ) was utilized for extraction of capsaicin (CA) and dihydrocapsaicin (DHCA) from Capsici Fructus, and then a two-step enrichment method for separating capsaicinoids from SFE-CO 2 extracts was developed. The process involved extraction with aqueous methanol and crystallization by alkali extraction and acid precipitation. Finally, a consecutive high-speed countercurrent chromatography (HSCCC) separation method was successfully applied in the purification of CA and DHCA from capsaicinoid crystal. The extraction pressure, extraction temperature and volume of co-solvent were optimized at 33 MPa, 41 °C and 75 mL, respectively, using response surface methodology; the extraction rates of CA and DHCA were about 93.18% and 93.49%, respectively. 407.43 mg capsaicinoid crystal was isolated from the SFE-CO 2 extracts obtained from 100 g capsicum powder by the two-step enrichment method. About 506 mg and 184 mg CA and DHCA with purities up to 98.31% and 96.68%, respectively, were obtained from 1 g capsaicinoid crystal in one HSCCC of three consecutive sample loadings without exchanging any solvent system. This method comprising SFE-CO 2 , a two-step enrichment and HSCCC was efficient, powerful and practical for the large-scale preparation of CA and DHCA from Capsici Fructus with high purity and high yield. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Daymet: Daily Surface Weather Data on a 1-km Grid for North America, Version 2.

NASA Astrophysics Data System (ADS)

Devarakonda, R.

2014-12-01

Daymet: Daily Surface Weather Data and Climatological Summaries provides gridded estimates of daily weather parameters for North America, including daily continuous surfaces of minimum and maximum temperature, precipitation occurrence and amount, humidity, shortwave radiation, snow water equivalent, and day length. The current data product (Version 2) covers the period January 1, 1980 to December 31, 2013 [1]. Data are available on a daily time step at a 1-km x 1-km spatial resolution in Lambert Conformal Conic projection with a spatial extent that covers the North America as meteorological station density allows. Daymet data can be downloaded from 1) the ORNL Distributed Active Archive Center (DAAC) search and order tools (http://daac.ornl.gov/cgi-bin/cart/add2cart.pl?add=1219) or directly from the DAAC FTP site (http://daac.ornl.gov/cgi-bin/dsviewer.pl?ds_id=1219) and 2) the Single Pixel Tool (http://daymet.ornl.gov/singlepixel.html) and THREDDS (Thematic Real-time Environmental Data Services) Data Server (TDS) (http://daymet.ornl.gov/thredds_mosaics.html). The Single Pixel Data Extraction Tool [2] allows users to enter a single geographic point by latitude and longitude in decimal degrees. A routine is executed that translates the (lon, lat) coordinates into projected Daymet (x,y) coordinates. These coordinates are used to access the Daymet database of daily-interpolated surface weather variables. The Single Pixel Data Extraction Tool also provides the option to download multiple coordinates programmatically. The ORNL DAAC's TDS provides customized visualization and access to Daymet time series of North American mosaics. Users can subset and download Daymet data via a variety of community standards, including OPeNDAP, NetCDF Subset service, and Open Geospatial Consortium (OGC) Web Map/Coverage Service. References: [1] Thornton, P. E., Thornton, M. M., Mayer, B. W., Wilhelmi, N., Wei, Y., Devarakonda, R., & Cook, R. (2012). "Daymet: Daily surface weather on a 1 km grid for North America, 1980-2008". Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center for Biogeochemical Dynamics (DAAC), 1. [2] Devarakonda R., et al. 2012. Daymet: Single Pixel Data Extraction Tool. Available [http://daymet.ornl.go/singlepixel.html].

The effect of different solvents and number of extraction steps on the polyphenol content and antioxidant capacity of basil leaves (Ocimum basilicum L.) extracts.

PubMed

Złotek, Urszula; Mikulska, Sylwia; Nagajek, Małgorzata; Świeca, Michał

2016-09-01

The objectives of this study were to determine best conditions for the extraction of phenolic compounds from fresh, frozen and lyophilized basil leaves. The acetone mixtures with the highest addition of acetic acid extracted most of the phenolic compounds when fresh and freeze-dried material have been used. The three times procedure was more effective than once shaking procedure in most of the extracts obtained from fresh basil leaves - unlike the extracts derived from frozen material. Surprisingly, there were not any significant differences in the content of phenolics between the two used procedures in the case of lyophilized basil leaves used for extraction. Additionally, the positive correlation between the phenolic compounds content and antioxidant activity of the studied extracts has been noted. It is concluded that the acetone mixtures were more effective than the methanol ones for polyphenol extraction. The number of extraction steps in most of the cases was also a statistically significant factor affecting the yield of phenolic extraction as well as antioxidant potential of basil leaf extracts.

Arsenic in coal of the Thar coalfield, Pakistan, and its behavior during combustion.

PubMed

Ali, Jamshed; Kazi, Tasneem G; Baig, Jameel A; Afridi, Hassan I; Arain, Mariam S; Brahman, Kapil D; Naeemullah; Panhwar, Abdul H

2015-06-01

The aim of the current study is to evaluate the occurrence of arsenic in coal collected from Thar coalfield, Pakistan, and its behavior during the combustion. Fractionation of arsenic (As) in coal samples was carried out by Community Bureau of Reference sequential extraction scheme (BCR-SES) and single-step-based BCR method (BCR-SS). These methods are validated using the certified reference material of sediment BCR 701 and standard addition method. The stepwise fractions of As in laboratory-made ash (LMA) have been also investigated. The extractable As content associated with different phases in coal and LMA samples were analyzed by electrothermal atomic absorption spectrophotometer. The extraction efficiency of As by BCR-SS was slightly higher than BCR-SES, while the difference was not significant (p < 0.05). The BCR-SS method is a time-saving method because it can reduce the extraction time from 51 to 22 h. The As contents in LMA revealed that during combustion of the coal, >85 % of As may be released into atmosphere. The relative mobility of As in the coal samples was found in increasing order as follows: oxidizable fraction < reducible fraction < acid soluble fraction. The total and extractable As obtained by BCR-SES and BCR-SS were higher in coal samples of block III as compared to block V (p > 0.05).

Tocopherol fate in plasma and liver of streptozotocin-treated rats that orally received antioxidants and Spirulina extracts.

PubMed

García-Martínez, D; Rupérez, F J; Ugarte, P; Barbas, C

2007-07-01

Streptozotocin-induced diabetic rats constitute a model of oxidative stress, and vitamin E continues to be a topic of speculation in this area. On the other hand, marine extracts, particularly microalgae extracts obtained with environmentally clean technologies and which demonstrate antioxidant activity in vitro, are a potential source of in vivo antioxidant defense. We have studied the alpha-tocopherol content in the plasma and liver of diabetic rats after 7 and 14 days under the condition, and before and after the treatment with vitamin E and C, as well as with different Spirulina extracts, as compared with the corresponding controls. The improvement of analytical methodology related to the determination of alpha-tocopherol in the plasma and liver of rats was also considered. To do this, a method previously developed for plasma, employing a single extraction step, was adapted and validated for liver after minor modifications. Moreover, stability of alpha-tocopherol in plasma of diabetic and control animals was compared in different storage conditions. Results showed that diabetic plasma strongly influences stability of alpha-tocopherol, even at -20 degrees C, but samples are stable for at least one year at -80 degrees C. Finally, regarding supplementation, results indicate that supplementation with alpha-tocopherol increases stored alpha-tocopherol in liver, but not in plasma, but this availability is strongly dependent on the stage of diabetes of the animal. Extracts of Spirulina platensis, despite showing antioxidant activity in vitro, increased alpha-tocopherol concentration in neither plasma nor liver.

Novel method for the rapid and specific extraction of multiple β2 -agonist residues in food by tailor-made Monolith-MIPs extraction disks and detection by gas chromatography with mass spectrometry.

PubMed

Liu, Haibo; Gan, Ning; Chen, Yinji; Ding, Qingqing; Huang, Jie; Lin, Saichai; Cao, Yuting; Li, Tianhua

2016-09-01

A quick and specific pretreatment method based on a series of extraction clean-up disks, consisting of molecularly imprinted polymer monoliths and C18 adsorbent, was developed for the specific enrichment of salbutamol and clenbuterol residues in food. The molecularly imprinted monolithic polymer disk was synthesized using salbutamol as a template through a one-step synthesis process. It can simultaneously and specifically recognize salbutamol and clenbuterol. The monolithic polymer disk and series of C18 disks were assembled with a syringe to form a set of tailor-made devices for the extraction of target molecules. In a single run, salbutamol and clenbuterol can be specifically extracted, cleaned, and eluted by methanol/acetic acid/H2 O. The target molecules, after a silylation derivatization reaction were detected by gas chromatography-mass spectrometry. The parameters including solvent desorption, sample pH, and the cycles of reloading were investigated and discussed. Under the optimized extraction and clean-up conditions, the limits of detection and quantitation were determined as 0.018-0.022 and 0.042-0.049 ng/g for salbutamol and clenbuterol, respectively. The assay described was convenient, rapid, and specific; thereby potentially efficient in the high-throughput analysis of β2 -agonists residues in real food samples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Standard Operating Procedure for the Grinding and Extraction of Lead in Paint using Nitric Acid and a Rotor/Stator System Powered by a High Speed Motor

EPA Science Inventory

This Standard Operating Procedure (SOP) describes a new, rapid, and relatively inexpensive one step procedure which grinds the paint samples removed from the substrate and simultaneously quantitatively extracts the Pb from the paint in only one step in preparation for quantitativ...

Transparent DNA/RNA Co-extraction Workflow Protocol Suitable for Inhibitor-Rich Environmental Samples That Focuses on Complete DNA Removal for Transcriptomic Analyses

PubMed Central

Lim, Natalie Y. N.; Roco, Constance A.; Frostegård, Åsa

2016-01-01

Adequate comparisons of DNA and cDNA libraries from complex environments require methods for co-extraction of DNA and RNA due to the inherent heterogeneity of such samples, or risk bias caused by variations in lysis and extraction efficiencies. Still, there are few methods and kits allowing simultaneous extraction of DNA and RNA from the same sample, and the existing ones generally require optimization. The proprietary nature of kit components, however, makes modifications of individual steps in the manufacturer’s recommended procedure difficult. Surprisingly, enzymatic treatments are often performed before purification procedures are complete, which we have identified here as a major problem when seeking efficient genomic DNA removal from RNA extracts. Here, we tested several DNA/RNA co-extraction commercial kits on inhibitor-rich soils, and compared them to a commonly used phenol-chloroform co-extraction method. Since none of the kits/methods co-extracted high-quality nucleic acid material, we optimized the extraction workflow by introducing small but important improvements. In particular, we illustrate the need for extensive purification prior to all enzymatic procedures, with special focus on the DNase digestion step in RNA extraction. These adjustments led to the removal of enzymatic inhibition in RNA extracts and made it possible to reduce genomic DNA to below detectable levels as determined by quantitative PCR. Notably, we confirmed that DNase digestion may not be uniform in replicate extraction reactions, thus the analysis of “representative samples” is insufficient. The modular nature of our workflow protocol allows optimization of individual steps. It also increases focus on additional purification procedures prior to enzymatic processes, in particular DNases, yielding genomic DNA-free RNA extracts suitable for metatranscriptomic analysis. PMID:27803690

Performances of different protocols for exocellular polysaccharides extraction from milk acid gels: Application to yogurt.

PubMed

Nguyen, An Thi-Binh; Nigen, Michaël; Jimenez, Luciana; Ait-Abderrahim, Hassina; Marchesseau, Sylvie; Picart-Palmade, Laetitia

2018-01-15

Dextran or xanthan were used as model exocellular polysaccharides (EPS) to compare the extraction efficiency of EPS from skim milk acid gels using three different protocols. Extraction yields, residual protein concentrations and the macromolecular properties of extracted EPS were determined. For both model EPS, the highest extraction yield (∼80%) was obtained when samples were heated in acidic conditions at the first step of extraction (Protocol 1). Protocols that contained steps of acid/ethanol precipitation without heating (Protocols 2 and 3) show lower extraction yields (∼55%) but allow a better preservation of the EPS macromolecular properties. Changing the pH of acid gels up to 7 before extraction (Protocol 3) improved the extraction yield of anionic EPS without effect on the macromolecular properties of EPS. Protocol 1 was then applied for the quantification of EPS produced during the yogurt fermentation, while Protocol 3 was dedicated to their macromolecular characterization. Copyright © 2017 Elsevier Ltd. All rights reserved.

Extractables analysis of single-use flexible plastic biocontainers.

PubMed

Marghitoiu, Liliana; Liu, Jian; Lee, Hans; Perez, Lourdes; Fujimori, Kiyoshi; Ronk, Michael; Hammond, Matthew R; Nunn, Heather; Lower, Asher; Rogers, Gary; Nashed-Samuel, Yasser

2015-01-01

Studies of the extractable profiles of bioprocessing components have become an integral part of drug development efforts to minimize possible compromise in process performance, decrease in drug product quality, and potential safety risk to patients due to the possibility of small molecules leaching out from the components. In this study, an effective extraction solvent system was developed to evaluate the organic extractable profiles of single-use bioprocess equipment, which has been gaining increasing popularity in the biopharmaceutical industry because of the many advantages over the traditional stainless steel-based bioreactors and other fluid mixing and storage vessels. The chosen extraction conditions were intended to represent aggressive conditions relative to the application of single-use bags in biopharmaceutical manufacture, in which aqueous based systems are largely utilized. Those extraction conditions, along with a non-targeted analytical strategy, allowed for the generation and identification of an array of extractable compounds; a total of 53 organic compounds were identified from four types of commercially available single-use bags, the majority of which are degradation products of polymer additives. The success of this overall extractables analysis strategy was reflected partially by the effectiveness in the extraction and identification of a compound that was later found to be highly detrimental to mammalian cell growth. The usage of single-use bioreactors has been increasing in biopharmaceutical industry because of the appealing advantages that it promises regarding to the cleaning, sterilization, operational flexibility, and so on, during manufacturing of biologics. However, compared to its conventional counterparts based mainly on stainless steel, single-use bioreactors are more susceptible to potential problems associated with compound leaching into the bioprocessing fluid. As a result, extractable profiling of the single-use system has become essential in the qualification of such systems for its use in drug manufacturing. The aim of this study is to evaluate the effectiveness of an extraction solvent system developed to study the extraction profile of single-use bioreactors in which aqueous-based systems are largely used. The results showed that with a non-targeted analytical approach, the extraction solvent allowed the generation and identification of an array of extractable compounds from four commercially available single-use bioreactors. Most of extractables are degradation products of polymer additives, among which was a compound that was later found to be highly detrimental to mammalian cell growth. © PDA, Inc. 2015.

Simultaneous analysis of 70 pesticides using HPlc/MS/MS: a comparison of the multiresidue method of Klein and Alder and the QuEChERS method.

PubMed

Riedel, Melanie; Speer, Karl; Stuke, Sven; Schmeer, Karl

2010-01-01

Since 2003, two new multipesticide residue methods for screening crops for a large number of pesticides, developed by Klein and Alder and Anastassiades et al. (Quick, Easy, Cheap, Effective, Rugged, and Safe; QuEChERS), have been published. Our intention was to compare these two important methods on the basis of their extraction efficiency, reproducibility, ruggedness, ease of use, and speed. In total, 70 pesticides belonging to numerous different substance classes were analyzed at two concentration levels by applying both methods, using five different representative matrixes. In the case of the QuEChERS method, the results of the three sample preparation steps (crude extract, extract after SPE, and extract after SPE and acidification) were compared with each other and with the results obtained with the Klein and Alder method. The extraction efficiencies of the QuEChERS method were far higher, and the sample preparation was much quicker when the last two steps were omitted. In most cases, the extraction efficiencies after the first step were approximately 100%. With extraction efficiencies of mostly less than 70%, the Klein and Alder method did not compare favorably. Some analytes caused problems during evaluation, mostly due to matrix influences.

Proton irradiation of [18O]O2: production of [18F]F2 and [18F]F2 + [18F] OF2.

PubMed

Bishop, A; Satyamurthy, N; Bida, G; Hendry, G; Phelps, M; Barrio, J R

1996-04-01

The production of 18F electrophilic reagents via the 18O(p,n)18F reaction has been investigated in small-volume target bodies made of aluminum, copper, gold-plated copper and nickel, having straight or conical bore shapes. Three irradiation protocols-single-step, two-step and modified two-step-were used for the recovery of the 18F activity. The single-step irradiation protocol was tested in all the target bodies. Based on the single-step performance, aluminum targets were utilized extensively in the investigation of the two-step and modified two-step irradiation protocols. With an 11-MeV cyclotron and using the two-step irradiation protocol, > 1Ci [18F]F2 was recovered reproducibly from an aluminum target body. Probable radical mechanisms for the formation of OF2 and FONO2 (fluorine nitrate) in the single-step and modified two-step targets are proposed based on the amount of ozone generated and the nitrogen impurity present in the target gases, respectively.

Driving qubit phase gates with sech shaped pulses

NASA Astrophysics Data System (ADS)

Long, Junling; Ku, Hsiang-Sheng; Wu, Xian; Lake, Russell; Barnes, Edwin; Economou, Sophia; Pappas, David

As shown in 1932 by Rozen and Zener, the Rabi model has a unique solution whereby, for a given pulse length or amplitude, a sech(t/sigma) shaped pulse can be used to drive complete oscillations around the Bloch sphere that are independent of detuning with only a resultant detuning-dependent phase accumulation. Using this property, single qubit phase gates and two-qubit CZ gates have been proposed. In this work we explore the effect of different drive pulse shapes, i.e. square, Gaussian, and sech, as a function of detuning for Rabi oscillations of a superconducting transmon qubit. An arbitrary, single-qubit phase gate is demonstrated with the sech(t/sigma) pulse, and full tomography is performed to extract the fidelity. This is the first step towards high fidelity, low leakage two qubit CZ gates, and illustrates the efficacy of using analytic solutions of the qubit drive prior to optimal pulse shaping.

Multiresidue analysis of sulfonamides, quinolones, and tetracyclines in animal tissues by ultra-high performance liquid chromatography-tandem mass spectrometry.

PubMed

Zhang, Zhiwen; Li, Xiaowei; Ding, Shuangyang; Jiang, Haiyang; Shen, Jianzhong; Xia, Xi

2016-08-01

A multiresidue method for the efficient identification and quantification of 38 compounds from 3 different classes of antibiotics (tetracyclines, sulfonamides, and quinolones) in animal tissues has been developed. The method optimization involved the selection of extraction solutions, comparison of different solid-phase extraction cartridges and different mobile phases. As a result, the samples were extracted with Mcllvaine and phosphate buffers, followed by clean-up step based on solid-phase extraction with Oasis HLB cartridge. All compounds were determined by ultra-high performance liquid chromatography-tandem mass spectrometry, in one single injection with a chromatographic run time of only 9min. The method efficiency was evaluated in 5 tissues including muscle, liver, and kidney, and the mean recoveries ranged from 54% to 102%, with inter-day relative standard deviation lower than 14%. The limits of quantification were between 0.5 and 10μg/kg, which were satisfactory to support future surveillance monitoring. The developed method was applied to the analysis of swine liver and chicken samples from local markets, and sulfamethazine was the most commonly detected compound in the animal samples, with the highest residue level of 998μg/kg. Copyright © 2016 Elsevier Ltd. All rights reserved.

Nucleic acid purification from plants, animals and microbes in under 30 seconds

PubMed Central

Zou, Yiping; Wang, Yuling; Wee, Eugene; Turni, Conny; Blackall, Patrick J.; Trau, Matt; Botella, Jose Ramon

2017-01-01

Nucleic acid amplification is a powerful molecular biology tool, although its use outside the modern laboratory environment is limited due to the relatively cumbersome methods required to extract nucleic acids from biological samples. To address this issue, we investigated a variety of materials for their suitability for nucleic acid capture and purification. We report here that untreated cellulose-based paper can rapidly capture nucleic acids within seconds and retain them during a single washing step, while contaminants present in complex biological samples are quickly removed. Building on this knowledge, we have successfully created an equipment-free nucleic acid extraction dipstick methodology that can obtain amplification-ready DNA and RNA from plants, animals, and microbes from difficult biological samples such as blood and leaves from adult trees in less than 30 seconds. The simplicity and speed of this method as well as the low cost and availability of suitable materials (e.g., common paper towelling), means that nucleic acid extraction is now more accessible and affordable for researchers and the broader community. Furthermore, when combined with recent advancements in isothermal amplification and naked eye DNA visualization techniques, the dipstick extraction technology makes performing molecular diagnostic assays achievable in limited resource settings including university and high school classrooms, field-based environments, and developing countries. PMID:29161268

Liposomes Size Engineering by Combination of Ethanol Injection and Supercritical Processing.

PubMed

Santo, Islane Espirito; Campardelli, Roberta; Albuquerque, Elaine Cabral; Vieira De Melo, Silvio A B; Reverchon, Ernesto; Della Porta, Giovanna

2015-11-01

Supercritical fluid extraction using a high-pressure packed tower is proposed not only to remove the ethanol residue from liposome suspensions but also to affect their size and distribution leading the production of nanosomes. Different operating pressures, temperatures, and gas to liquid ratios were explored and ethanol was successfully extracted up to a value of 400 ppm; liposome size and distribution were also reduced by the supercritical processing preserving their integrity, as confirmed by Z-potential data and Trasmission Electron Microscopy observations. Operating at 120 bar and 38°C, nanosomes with a mean diameter of about 180 ± 40 nm and good storage stability were obtained. The supercritical processing did not interfere on drug encapsulation, and no loss of entrapped drug was observed when the water-soluble fluorescein was loaded as a model compound. Fluorescein encapsulation efficiency was 30% if pure water was used during the supercritical extraction as processing fluid; whereas an encapsulation efficiency of 90% was obtained if the liposome suspension was processed in water/fluorescein solution. The described technology is easy to scale up to an industrial production and merge in one step the solvent extraction, liposome size engineering, and an excellent drug encapsulation in a single operation unit. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Determination of anthelmintic drug residues in milk using ultra high performance liquid chromatography-tandem mass spectrometry with rapid polarity switching.

PubMed

Whelan, Michelle; Kinsella, Brian; Furey, Ambrose; Moloney, Mary; Cantwell, Helen; Lehotay, Steven J; Danaher, Martin

2010-07-02

A new UHPLC-MS/MS (ultra high performance liquid chromatography coupled to tandem mass spectrometry) method was developed and validated to detect 38 anthelmintic drug residues, consisting of benzimidazoles, avermectins and flukicides. A modified QuEChERS-type extraction method was developed with an added concentration step to detect most of the analytes at <1 microg kg(-1) levels in milk. Anthelmintic residues were extracted into acetonitrile using magnesium sulphate and sodium chloride to induce liquid-liquid partitioning followed by dispersive solid phase extraction for cleanup. The extract was concentrated into dimethyl sulphoxide, which was used as a keeper to ensure analytes remain in solution. Using rapid polarity switching in electrospray ionisation, a single injection was capable of detecting both positively and negatively charged ions in a 13 min run time. The method was validated at two levels: the unapproved use level and at the maximum residue level (MRL) according to Commission Decision (CD) 2002/657/EC criteria. The decision limit (CCalpha) of the method was in the range of 0.14-1.9 and 11-123 microg kg(-1) for drugs validated at unapproved and MRL levels, respectively. The performance of the method was successfully verified for benzimidazoles and levamisole by participating in a proficiency study.

Extraction of hyaluronic acid (HA) from rooster comb and characterization using flow field-flow fractionation (FlFFF) coupled with multiangle light scattering (MALS).

PubMed

Kang, Dong Young; Kim, Won-Suk; Heo, In Sook; Park, Young Hun; Lee, Seungho

2010-11-01

Hyaluronic acid (HA) was extracted in a relatively large scale from rooster comb using a method similar to that reported previously. The extraction method was modified to simplify and to reduce time and cost in order to accommodate a large-scale extraction. Five hundred grams of frozen rooster combs yielded about 500 mg of dried HA. Extracted HA was characterized using asymmetrical flow field-flow fractionation (AsFlFFF) coupled online to a multiangle light scattering detector and a refractive index detector to determine the molecular size, molecular weight (MW) distribution, and molecular conformation of HA. For characterization of HA, AsFlFFF was operated by a simplified two-step procedure, instead of the conventional three-step procedure, where the first two steps (sample loading and focusing) were combined into one to avoid the adsorption of viscous HA onto the channel membrane. The simplified two-step AsFlFFF yielded reasonably good separations of HA molecules based on their MWs. The weight average MW (M(w) ) and the average root-mean-square (RMS) radius of HA extracted from rooster comb were 1.20×10(6) and 94.7 nm, respectively. When the sample solution was filtered through a 0.45 μm disposable syringe filter, they were reduced down to 3.8×10(5) and 50.1 nm, respectively. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lower limb muscle moments and power during recovery from forward loss of balance in male and female single and multiple steppers.

PubMed

Carty, Christopher P; Cronin, Neil J; Lichtwark, Glen A; Mills, Peter M; Barrett, Rod S

2012-12-01

Studying recovery responses to loss of balance may help to explain why older adults are susceptible to falls. The purpose of the present study was to assess whether male and female older adults, that use a single or multiple step recovery strategy, differ in the proportion of lower limb strength used and power produced during the stepping phase of balance recovery. Eighty-four community-dwelling older adults (47 men, 37 women) participated in the study. Isometric strength of the ankle, knee and hip joint flexors and extensors was assessed using a dynamometer. Loss of balance was induced by releasing participants from a static forward lean (4 trials at each of 3 forward lean angles). Participants were instructed to recover with a single step and were subsequently classified as using a single or multiple step recovery strategy for each trial. (1) Females were weaker than males and the proportion of females that were able to recover with a single step were lower than for males at each lean magnitude. (2) Multiple compared to single steppers used a significantly higher proportion of their hip extension strength and produced less knee and ankle joint peak power during stepping, at the intermediate lean angle. Strength deficits in female compared to male participants may explain why a lower proportion of female participants were able to recover with a single step. The inability to generate sufficient power in the stepping limb appears to be a limiting factor in single step recovery from forward loss of balance. Crown Copyright © 2012. Published by Elsevier Ltd. All rights reserved.

Single-trial laser-evoked potentials feature extraction for prediction of pain perception.

PubMed

Huang, Gan; Xiao, Ping; Hu, Li; Hung, Yeung Sam; Zhang, Zhiguo

2013-01-01

Pain is a highly subjective experience, and the availability of an objective assessment of pain perception would be of great importance for both basic and clinical applications. The objective of the present study is to develop a novel approach to extract pain-related features from single-trial laser-evoked potentials (LEPs) for classification of pain perception. The single-trial LEP feature extraction approach combines a spatial filtering using common spatial pattern (CSP) and a multiple linear regression (MLR). The CSP method is effective in separating laser-evoked EEG response from ongoing EEG activity, while MLR is capable of automatically estimating the amplitudes and latencies of N2 and P2 from single-trial LEP waveforms. The extracted single-trial LEP features are used in a Naïve Bayes classifier to classify different levels of pain perceived by the subjects. The experimental results show that the proposed single-trial LEP feature extraction approach can effectively extract pain-related LEP features for achieving high classification accuracy.

Investigation of reductive dechlorination supported by natural organic carbon

USGS Publications Warehouse

Rectanus, H.V.; Widdowson, M.A.; Chapelle, F.H.; Kelly, C.A.; Novak, J.T.

2007-01-01

Because remediation timeframes using monitored natural attenuation may span decades or even centuries at chlorinated solvent sites, new approaches are needed to assess the long-term sustainability of reductive dechlorination in ground water systems. In this study, extraction procedures were used to investigate the mass of indigenous organic carbon in aquifer sediment, and experiments were conducted to determine if the extracted carbon could support reductive dechlorination of chloroethenes. Aquifer sediment cores were collected from a site without an anthropogenic source of organic carbon where organic carbon varied from 0.02% to 0.12%. Single extraction results showed that 1% to 28% of sediment-associated organic carbon and 2% to 36% of the soft carbon were removed depending on nature and concentration of the extracting solution (Nanopure water; 0.1%, 0.5%, and 1.0% sodium pyrophosphate; and 0.5 N sodium hydroxide). Soft carbon is defined as organic carbon oxidized with potassium persulfate and is assumed to serve as a source of biodegradable carbon within the aquifer. Biodegradability studies demonstrated that 20% to 40% of extracted organic carbon was biodegraded aerobically and anaerobically by soil microorganisms in relatively brief tests (45 d). A five-step extraction procedure consisting of 0.1% pyrophosphate and base solutions was investigated to quantify bioavailable organic carbon. Using the extracted carbon as the sole electron donor source, tetrachloroethene was transformed to cis-1,2- dichloroethene and vinyl chloride in anaerobic enrichment culture experiments. Hydrogen gas was produced at levels necessary to sustain reductive dechlorination (>1 nM). ?? 2007 National Ground Water Association.

Rapid determination of the volatile components in tobacco by ultrasound-microwave synergistic extraction coupled to headspace solid-phase microextraction with gas chromatography-mass spectrometry.

PubMed

Yang, Yanqin; Chu, Guohai; Zhou, Guojun; Jiang, Jian; Yuan, Kailong; Pan, Yuanjiang; Song, Zhiyu; Li, Zuguang; Xia, Qian; Lu, Xinbo; Xiao, Weiqiang

2016-03-01

An ultrasound-microwave synergistic extraction coupled to headspace solid-phase microextraction was first employed to determine the volatile components in tobacco samples. The method combined the advantages of ultrasound, microwave, and headspace solid-phase microextraction. The extraction, separation, and enrichment were performed in a single step, which could greatly simplify the operation and reduce the whole pretreatment time. In the developed method, several experimental parameters, such as fiber type, ultrasound power, and irradiation time, were optimized to improve sampling efficiency. Under the optimal conditions, there were 37, 36, 34, and 36 components identified in tobacco from Guizhou, Hunan, Yunnan, and Zimbabwe, respectively, including esters, heterocycles, alkanes, ketones, terpenoids, acids, phenols, and alcohols. The compound types were roughly the same while the contents were varied from different origins due to the disparity of their growing conditions, such as soil, water, and climate. In addition, the ultrasound-microwave synergistic extraction coupled to headspace solid-phase microextraction method was compared with the microwave-assisted extraction coupled to headspace solid-phase microextraction and headspace solid-phase microextraction methods. More types of volatile components were obtained by using the ultrasound-microwave synergistic extraction coupled to headspace solid-phase microextraction method, moreover, the contents were high. The results indicated that the ultrasound-microwave synergistic extraction coupled to headspace solid-phase microextraction technique was a simple, time-saving and highly efficient approach, which was especially suitable for analysis of the volatile components in tobacco. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Critical evaluation of the ability of sequential extraction procedures to quantify discrete forms of selenium in sediments and soils.

PubMed

Wright, Michael T; Parker, David R; Amrhein, Christopher

2003-10-15

Sequential extraction procedures (SEPs) have been widely used to characterize the mobility, bioavailibility, and potential toxicity of trace elements in soils and sediments. Although oft-criticized, these methods may perform best with redox-labile elements (As, Hg, Se) for which more discrete biogeochemical phases may arise from variations in oxidation number. We critically evaluated two published SEPs for Se for their specificity and precision by applying them to four discrete components in an inert silica matrix: soluble Se(VI) (selenate), Se(IV) (selenite) adsorbed onto goethite, elemental Se, and a metal selenide (FeSe; achavalite). These were extracted both individually and in a mixed model sediment. The more selective of the two procedures was modified to further improve its selectivity (SEP 2M). Both SEP 1 and SEP 2M quantitatively recovered soluble selenate but yielded incomplete recoveries of adsorbed selenite (64% and 81%, respectively). SEP 1 utilizes 0.1 M K2S2O8 to target "organically associated" Se, but this extractant also solubilized most of the elemental (64%) and iron selenide (91%) components of the model sediment. In SEP 2M, the Na2SO3 used in step III is effective in extracting elemental Se but also extracted 17% of the Se from the iron selenide, such that the elemental fraction would be overestimated should both forms coexist. Application of SEP 2M to eight wetland sediments further suggested that the Na2SO3 in step III extracts some organically associated Se, so a NaOH extraction was inserted beforehand to yield a further modification, SEP 2OH. Results using this five-step procedure suggested that the four-step SEP 2M could overestimate elemental Se by as much as 43% due to solubilization of organic Se. Although still imperfect in its selectivity, SEP 20H may be the most suitable procedure for routine, accurate fractionation of Se in soils and sediments. However, the strong oxidant (NaOCl) used in the final step cannot distinguish between refractory organic forms of Se and pyritic Se that might form under sulfur-reducing conditions.

Single-step electrodeposition of CIS thin films with the complexing agent triethanolamine

NASA Astrophysics Data System (ADS)

Chiu, Yu-Shuen; Hsieh, Mu-Tao; Chang, Chih-Min; Chen, Chun-Shuo; Whang, Thou-Jen

2014-04-01

Some difficulties have long been encountered by single-step electrodeposition such as the optimization of electrolyte composition, deposition potentials, deposition time, and pH values. The approach of introducing ternary components into single-step electrodeposition is rather challenging especially due to the different values of the equilibrium potential for each constituent. Complexing agents play an important role in single-step electrodeposition of CuInSe2 (CIS), since the equilibrium potential of every constituent can be brought closer to each other when complexing agents are employed. In this work, single-step electrodeposition of CIS was enhanced by adding triethanolamine (TEA) into deposition bath, the CIS thin films were improved consequently in the form of polycrystalline cauliflower structures through the examination of SEM images and XRD patterns. The optimum composition of the solution for single-step electrodeposition of CIS is found to be 5 mM CuCl2, 22 mM InCl3, and 22 mM SeO2 at pH 1.5 with 0.1 M TEA. The structures, compositions, and morphologies of as-deposited and of annealed films were investigated.

An approach to predict Sudden Cardiac Death (SCD) using time domain and bispectrum features from HRV signal.

PubMed

Houshyarifar, Vahid; Chehel Amirani, Mehdi

2016-08-12

In this paper we present a method to predict Sudden Cardiac Arrest (SCA) with higher order spectral (HOS) and linear (Time) features extracted from heart rate variability (HRV) signal. Predicting the occurrence of SCA is important in order to avoid the probability of Sudden Cardiac Death (SCD). This work is a challenge to predict five minutes before SCA onset. The method consists of four steps: pre-processing, feature extraction, feature reduction, and classification. In the first step, the QRS complexes are detected from the electrocardiogram (ECG) signal and then the HRV signal is extracted. In second step, bispectrum features of HRV signal and time-domain features are obtained. Six features are extracted from bispectrum and two features from time-domain. In the next step, these features are reduced to one feature by the linear discriminant analysis (LDA) technique. Finally, KNN and support vector machine-based classifiers are used to classify the HRV signals. We used two database named, MIT/BIH Sudden Cardiac Death (SCD) Database and Physiobank Normal Sinus Rhythm (NSR). In this work we achieved prediction of SCD occurrence for six minutes before the SCA with the accuracy over 91%.

Current lipid extraction methods are significantly enhanced adding a water treatment step in Chlorella protothecoides.

PubMed

Ren, Xiaojie; Zhao, Xinhe; Turcotte, François; Deschênes, Jean-Sébastien; Tremblay, Réjean; Jolicoeur, Mario

2017-02-11

Microalgae have the potential to rapidly accumulate lipids of high interest for the food, cosmetics, pharmaceutical and energy (e.g. biodiesel) industries. However, current lipid extraction methods show efficiency limitation and until now, extraction protocols have not been fully optimized for specific lipid compounds. The present study thus presents a novel lipid extraction method, consisting in the addition of a water treatment of biomass between the two-stage solvent extraction steps of current extraction methods. The resulting modified method not only enhances lipid extraction efficiency, but also yields a higher triacylglycerols (TAG) ratio, which is highly desirable for biodiesel production. Modification of four existing methods using acetone, chloroform/methanol (Chl/Met), chloroform/methanol/H 2 O (Chl/Met/H 2 O) and dichloromethane/methanol (Dic/Met) showed respective lipid extraction yield enhancement of 72.3, 35.8, 60.3 and 60.9%. The modified acetone method resulted in the highest extraction yield, with 68.9 ± 0.2% DW total lipids. Extraction of TAG was particularly improved with the water treatment, especially for the Chl/Met/H 2 O and Dic/Met methods. The acetone method with the water treatment led to the highest extraction level of TAG with 73.7 ± 7.3 µg/mg DW, which is 130.8 ± 10.6% higher than the maximum value obtained for the four classical methods (31.9 ± 4.6 µg/mg DW). Interestingly, the water treatment preferentially improved the extraction of intracellular fractions, i.e. TAG, sterols, and free fatty acids, compared to the lipid fractions of the cell membranes, which are constituted of phospholipids (PL), acetone mobile polar lipids and hydrocarbons. Finally, from the 32 fatty acids analyzed for both neutral lipids (NL) and polar lipids (PL) fractions, it is clear that the water treatment greatly improves NL-to-PL ratio for the four standard methods assessed. Water treatment of biomass after the first solvent extraction step helps the subsequent release of intracellular lipids in the second extraction step, thus improving the global lipids extraction yield. In addition, the water treatment positively modifies the intracellular lipid class ratios of the final extract, in which TAG ratio is significantly increased without changes in the fatty acids composition. The novel method thus provides an efficient way to improve lipid extraction yield of existing methods, as well as selectively favoring TAG, a lipid of the upmost interest for biodiesel production.

Recovery of viruses from water by a modified flocculation procedure for second-step concentration.

PubMed Central

Dahling, D R; Wright, B A

1986-01-01

A reduction in virus recovery efficiencies stemming from a change in the commercial processing of powdered beef extract was reversed by the addition of Celite analytical filter aid. Supplementing beef extract with this silicate is recommended as a modification to the organic flocculation procedure for second-step concentration in monitoring for waterborne viruses. Considerable differences in virus recovery were found among lots of beef extract and Celite preparations; this indicates that the performance of each lot of these substances should be checked before use. PMID:3015024

Extraction and isolation of catechins from tea.

PubMed

Vuong, Quan V; Golding, John B; Nguyen, Minh; Roach, Paul D

2010-11-01

Tea is a major source of catechins, which have become well known for their antioxidant potential. Numerous human, animal, and in vitro studies have linked tea catechins with prevention of certain types of cancers, reduction of the risks for obesity, diabetes, and cardiovascular disease, and improvement of the immune system. Tea catechins are widely used in various neutraceuticals, pharmaceuticals, and cosmetics for either enhancing product shelf-life or for enhancing human health. Thus, the demand for catechins has increased considerably. Catechins have been extracted and isolated from tea leaves by numerous methods through several steps including: treatment of the tea leaves, extraction of catechins from teas into solvents, isolation of catechins from other extracted components, and drying the preparations to obtain catechin extracts in a powder form. This paper outlines the physical and chemical properties of the tea catechins and reviews the extraction steps of the various extraction methods, as a basis to improve and further develop the extraction and isolation of the tea catechins.

Revisiting chlorophyll extraction methods in biological soil crusts - methodology for determination of chlorophyll a and chlorophyll a + b as compared to previous methods

NASA Astrophysics Data System (ADS)

Caesar, Jennifer; Tamm, Alexandra; Ruckteschler, Nina; Lena Leifke, Anna; Weber, Bettina

2018-03-01

Chlorophyll concentrations of biological soil crust (biocrust) samples are commonly determined to quantify the relevance of photosynthetically active organisms within these surface soil communities. Whereas chlorophyll extraction methods for freshwater algae and leaf tissues of vascular plants are well established, there is still some uncertainty regarding the optimal extraction method for biocrusts, where organism composition is highly variable and samples comprise major amounts of soil. In this study we analyzed the efficiency of two different chlorophyll extraction solvents, the effect of grinding the soil samples prior to the extraction procedure, and the impact of shaking as an intermediate step during extraction. The analyses were conducted on four different types of biocrusts. Our results show that for all biocrust types chlorophyll contents obtained with ethanol were significantly lower than those obtained using dimethyl sulfoxide (DMSO) as a solvent. Grinding of biocrust samples prior to analysis caused a highly significant decrease in chlorophyll content for green algal lichen- and cyanolichen-dominated biocrusts, and a tendency towards lower values for moss- and algae-dominated biocrusts. Shaking of the samples after each extraction step had a significant positive effect on the chlorophyll content of green algal lichen- and cyanolichen-dominated biocrusts. Based on our results we confirm a DMSO-based chlorophyll extraction method without grinding pretreatment and suggest the addition of an intermediate shaking step for complete chlorophyll extraction (see Supplement S6 for detailed manual). Determination of a universal chlorophyll extraction method for biocrusts is essential for the inter-comparability of publications conducted across all continents.

Pelvic Inflammatory Disease

MedlinePlus

... No single step can protect you from every single type of STI. Can women who have sex with women get PID? Yes. ... No single step can protect you from every single type of STI. Can women who have sex with women get PID? Yes. ...

Lipid extraction from isolated single nerve cells

NASA Technical Reports Server (NTRS)

Krasnov, I. V.

1977-01-01

A method of extracting lipids from single neurons isolated from lyophilized tissue is described. The method permits the simultaneous extraction of lipids from 30-40 nerve cells and for each cell provides equal conditions of solvent removal at the conclusion of extraction.

Two-step liquid phase microextraction combined with capillary electrophoresis: a new approach to simultaneous determination of basic and zwitterionic compounds.

PubMed

Nojavan, Saeed; Moharami, Arezoo; Fakhari, Ali Reza

2012-08-01

In this work, two-step hollow fiber-based liquid-phase microextraction procedure was evaluated for extraction of the zwitterionic cetirizine (CTZ) and basic hydroxyzine (HZ) in human plasma. In the first step of extraction, the pH of sample was adjusted at 5.0 in order to promote liquid-phase microextraction of the zwitterionic CTZ. In the second step, the pH of sample was increased up to 11.0 for extraction of basic HZ. In this procedure, the extraction times for the first and the second steps were 30 and 20 min, respectively. Owing to the high ratio between the volumes of donor phase and acceptor phase, CTZ and HZ were enriched by factors of 280 and 355, respectively. The linearity of the analytical method was investigated for both compounds in the range of 10-500 ng mL(-1) (R(2) > 0.999). Limit of quantification (S/N = 10) for CTZ and HZ was 10 ng mL(-1) , while the limit of detection was 3 ng mL(-1) for both compounds at a signal to noise ratio of 3:1. Intraday and interday relative standard deviations (RSDs, n = 6) were in the range of 6.5-16.2%. This procedure enabled CTZ and HZ to be analyzed simultaneously by capillary electrophoresis. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Organic solvent-free air-assisted liquid-liquid microextraction for optimized extraction of illegal azo-based dyes and their main metabolite from spices, cosmetics and human bio-fluid samples in one step.

PubMed

Barfi, Behruz; Asghari, Alireza; Rajabi, Maryam; Sabzalian, Sedigheh

2015-08-15

Air-assisted liquid-liquid microextraction (AALLME) has unique capabilities to develop as an organic solvent-free and one-step microextraction method, applying ionic-liquids as extraction solvent and avoiding centrifugation step. Herein, a novel and simple eco-friendly method, termed one-step air-assisted liquid-liquid microextraction (OS-AALLME), was developed to extract some illegal azo-based dyes (including Sudan I to IV, and Orange G) from food and cosmetic products. A series of experiments were investigated to achieve the most favorable conditions (including extraction solvent: 77μL of 1-Hexyl-3-methylimidazolium hexafluorophosphate; sample pH 6.3, without salt addition; and extraction cycles: 25 during 100s of sonication) using a central composite design strategy. Under these conditions, limits of detection, linear dynamic ranges, enrichment factors and consumptive indices were in the range of 3.9-84.8ngmL(-1), 0.013-3.1μgmL(-1), 33-39, and 0.13-0.15, respectively. The results showed that -as well as its simplicity, fastness, and use of no hazardous disperser and extraction solvents- OS-AALLME is an enough sensitive and efficient method for the extraction of these dyes from complex matrices. After optimization and validation, OS-AALLME was applied to estimate the concentration of 1-amino-2-naphthol in human bio-fluids as a main reductive metabolite of selected dyes. Levels of 1-amino-2-naphthol in plasma and urinary excretion suggested that this compound may be used as a new potential biomarker of these dyes in human body. Copyright © 2015 Elsevier B.V. All rights reserved.

Voltage-step pulsed electromembrane as a novel view of electrical field-induced liquid-phase microextraction.

PubMed

Rezazadeh, Maryam; Yamini, Yadollah; Seidi, Shahram; Arjomandi-Behzad, Leila

2014-01-10

In the present work, the effect of application of voltage steps on extraction efficiency of pulsed electromembrane extraction (PEME) was investigated for the first time. The effects of voltage variations including initial and final voltages, number of steps between the initial and final voltages as well as their time durations were studied on the extraction efficiencies of three different classes of analytes. These classes include amitriptyline (AMI) and nortriptyline (NOR) as more hydrophobic analytes, diclofenac (DIC) and mefenamic acid (MEF) as acidic drugs and salbutamol (SB) and terbutaline (TB) as hydrophilic compounds. It was anticipated that the application of high voltages is not necessary at the beginning of the extraction, since large amounts of target analytes exist around the supported liquid membrane (SLM)/sample solution interface. So, they could be easily transferred into the acceptor phase utilizing lower voltages. Results showed that the benefits of voltage-step PEME (VS-PEME) are more obvious in systems with low electrical resistance (regarding the SLM composition). Efficiencies of VS-PEME for extraction of AMI and NOR (96% and 89% for AMI and NOR, respectively) were comparable with those achieved from applying a constant voltage (95% for AMI and 83% for NOR). However, recoveries from the VS-PEME of DIC and MEF (53% and 44% for DIC and MEF, respectively) were significantly higher than those from the application of a constant voltage (33% for DIC and 31% for MEF). Also, recoveries obtained from the VS-PEME for SB and TB were approximately 3 orders of magnitude greater than those from a constant voltage. Moreover, it was demonstrated that in all cases analytes could effectively be extracted at the beginning of extraction by applying low voltages. Copyright © 2013 Elsevier B.V. All rights reserved.

Bioavailability and mobility of organic contaminants in soil: new three-step ecotoxicological evaluation.

PubMed

Prokop, Zbyněk; Nečasová, Anežka; Klánová, Jana; Čupr, Pavel

2016-03-01

A novel approach was developed for rapid assessment of bioavailability and potential mobility of contaminants in soil. The response of the same test organism to the organic extract, water extract and solid phase of soil was recorded and compared. This approach was designed to give an initial estimate of the total organic toxicity (response to organic extractable fraction), as well as the mobile (response to water extract) and bioavailable fraction (response to solid phase) of soil samples. Eighteen soil samples with different levels of pollution and content of organic carbon were selected to validate the novel three-step ecotoxicological evaluation approach. All samples were chemically analysed for priority contaminants, including aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), hexachlorocyclohexane (HCH) and dichlordiphenyltrichloroethane (DDT). The ecotoxicological evaluation involved determination of toxicity of the organic, mobile and bioavailable fractions of soil to the test organism, bacterium Bacillus cereus. We found a good correlation between the chemical analysis and the toxicity of organic extract. The low toxicity of water extracts indicated low water solubility, and thus, low potential mobility of toxic contaminants present in the soil samples. The toxicity of the bioavailable fraction was significantly greater than the toxicity of water-soluble (mobile) fraction of the contaminants as deduced from comparing untreated samples and water extracts. The bioavailability of the contaminants decreased with increasing concentrations of organic carbon in evaluated soil samples. In conclusion, the three-step ecotoxicological evaluation utilised in this study can give a quick insight into soil contamination in context with bioavailability and mobility of the contaminants present. This information can be useful for hazard identification and risk assessment of soil-associated contaminants. Graphical Abstract New three-step ecotoxicological evaluation by using the same organism.

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.

Facile and rapid DNA extraction and purification from food matrices using IFAST (immiscible filtration assisted by surface tension).

PubMed

Strotman, Lindsay N; Lin, Guangyun; Berry, Scott M; Johnson, Eric A; Beebe, David J

2012-09-07

Extraction and purification of DNA is a prerequisite to detection and analytical techniques. While DNA sample preparation methods have improved over the last few decades, current methods are still time consuming and labor intensive. Here we demonstrate a technology termed IFAST (Immiscible Filtration Assisted by Surface Tension), that relies on immiscible phase filtration to reduce the time and effort required to purify DNA. IFAST replaces the multiple wash and centrifugation steps required by traditional DNA sample preparation methods with a single step. To operate, DNA from lysed cells is bound to paramagnetic particles (PMPs) and drawn through an immiscible fluid phase barrier (i.e. oil) by an external handheld magnet. Purified DNA is then eluted from the PMPs. Here, detection of Clostridium botulinum type A (BoNT/A) in food matrices (milk, orange juice), a bioterrorism concern, was used as a model system to establish IFAST's utility in detection assays. Data validated that the DNA purified by IFAST was functional as a qPCR template to amplify the bont/A gene. The sensitivity limit of IFAST was comparable to the commercially available Invitrogen ChargeSwitch® method. Notably, pathogen detection via IFAST required only 8.5 μL of sample and was accomplished in five-fold less time. The simplicity, rapidity and portability of IFAST offer significant advantages when compared to existing DNA sample preparation methods.

Bypassing bacterial infection in phage display by sequencing DNA released from phage particles.

PubMed

Villequey, Camille; Kong, Xu-Dong; Heinis, Christian

2017-11-01

Phage display relies on a bacterial infection step in which the phage particles are replicated to perform multiple affinity selection rounds and to enable the identification of isolated clones by DNA sequencing. While this process is efficient for wild-type phage, the bacterial infection rate of phage with mutant or chemically modified coat proteins can be low. For example, a phage mutant with a disulfide-free p3 coat protein, used for the selection of bicyclic peptides, has a more than 100-fold reduced infection rate compared to the wild-type. A potential strategy for bypassing the bacterial infection step is to directly sequence DNA extracted from phage particles after a single round of phage panning using high-throughput sequencing. In this work, we have quantified the fraction of phage clones that can be identified by directly sequencing DNA from phage particles. The results show that the DNA of essentially all of the phage particles can be 'decoded', and that the sequence coverage for mutants equals that of amplified DNA extracted from cells infected with wild-type phage. This procedure is particularly attractive for selections with phage that have a compromised infection capacity, and it may allow phage display to be performed with particles that are not infective at all. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Extracapsular cataract extraction training: junior ophthalmology residents' self-reported satisfaction level with their proficiency and initial learning barrier.

PubMed

Ting, Daniel Shu Wei; Tan, Sarah; Lee, Shu Yen; Rosman, Mohamad; Aw, Ai Tee; Yeo, Ian Yew San

2015-07-01

To investigate residents' self-reported satisfaction level with their proficiency in extracapsular cataract extraction (ECCE) surgery and the initial barriers to learning the procedure. This is a single-centre prospective descriptive case series involving eight first-year ophthalmology residents in Singapore National Eye Center. We recorded the demographics, frequency of review by the residents of their own surgical videos and their satisfaction level with their proficiency at each of the ECCE steps using a 5-point Likert scale. All ECCE surgical videos between October 2013 and May 2014 were collected and analysed for the overall time taken for the surgery and the time taken to perform the individual steps of the procedure. The mean age of the residents was 27.6 ± 1.5 years and 62.5% (5/8) were women. More than half (62.5%, 5/8) reviewed their own surgical videos while 37.5% (3/8) discussed the surgical videos with their peers or supervisors. Of the ECCE steps, the residents were most dissatisfied with their proficiency in performing irrigation and aspiration (87.5%, 7/8), followed by suturing (62.5%, 5/8), intraocular lens insertion (62.5%, 5/8) and tin can capsulotomy (62.5%, 5/8). The average time taken for each ECCE case was 55.0 ± 12.2 min and, of all the steps, most time was spent on suturing (20.5 ± 6.8 min), followed by irrigation and aspiration (5.5 ± 3.6 min) and tin can capsulotomy (3.3 ± 1.8 min). The first-year ophthalmology residents were most dissatisfied with their proficiency in irrigation/aspiration, suturing and tin can capsulotomy. More training needs to be directed to these areas during teaching sessions in the operating room, wet laboratory or cataract simulation training sessions. 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.

THE LIBERATION OF ARSENOSUGARS FROM MATRIX COMPONENTS IN DIFFICULT TO EXTRACT SEAFOOD SAMPLES UTILIZING TMAOH/ACETIC ACID SEQUENTIALLY IN A TWO-STAGE EXTRACTION PROCESS

EPA Science Inventory

Sample extraction is one of the most important steps in arsenic speciation analysis of solid dietary samples. One of the problem areas in this analysis is the partial extraction of arsenicals from seafood samples. The partial extraction allows the toxicity of the extracted arse...

A successful backward step correlates with hip flexion moment of supporting limb in elderly people.

PubMed

Takeuchi, Yahiko

2018-01-01

The objective of this study was to determine the positional relationship between the center of mass (COM) and the center of pressure (COP) at the time of step landing, and to examine their relationship with the joint moments exerted by the supporting limb, with regard to factors of the successful backward step response. The study population comprised 8 community-dwelling elderly people that were observed to take successive multi steps after the landing of a backward stepping. Using a motion capture system and force plate, we measured the COM, COP and COM-COP deviation distance on landing during backward stepping. In addition, we measured the moment of the supporting limb joint during backward stepping. The multi-step data were compared with data from instances when only one step was taken (single-step). Variables that differed significantly between the single- and multi-step data were used as objective variables and the joint moments of the supporting limb were used as explanatory variables in single regression analyses. The COM-COP deviation in the anteroposterior was significantly larger in the single-step. A regression analysis with COM-COP deviation as the objective variable obtained a significant regression equation in the hip flexion moment (R2 = 0.74). The hip flexion moment of supporting limb was shown to be a significant explanatory variable in both the PS and SS phases for the relationship with COM-COP distance. This study found that to create an appropriate backward step response after an external disturbance (i.e. the ability to stop after 1 step), posterior braking of the COM by a hip flexion moment are important during the single-limbed standing phase.

A simplified strategy for studying the etiology of viral diseases: Apple stem grooving virus as a case study.

PubMed

Dhir, Sunny; Walia, Yashika; Zaidi, A A; Hallan, Vipin

2015-03-01

A simple method to amplify infective, complete genomes of single stranded RNA viruses by long distance PCR (LD PCR) from woody plant tissues is described in detail. The present protocol eliminates partial purification of viral particles and the amplification is achieved in three steps: (i) easy preparation of template RNA by incorporating a pre processing step before loading onto the column (ii) reverse transcription by AMV or Superscript reverse transcriptase and (iii) amplification of cDNA by LD PCR using LA or Protoscript Taq DNA polymerase. Incorporation of a preprocessing step helped to isolate consistent quality RNA from recalcitrant woody tissues such as apple, which was critical for efficient amplification of the complete genomes of Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV) and Apple chlorotic leaf spot virus (ACLSV). Complete genome of ASGV was cloned under T7 RNA polymerase promoter and was confirmed to be infectious through transcript inoculation producing symptoms similar to the wild type virus. This is the first report for the largest RNA virus genome amplified by PCR from total nucleic acid extracts of woody plant tissues. Copyright © 2014 Elsevier B.V. All rights reserved.

Benign Synthesis of Black Microspheres of Anatase TiO2 with Paramagnetic Oxygen Vacancies through NH3 Treatment.

PubMed

Maqbool, Qysar; Srivastava, Aasheesh

2017-10-09

Coloured TiO 2 is coveted for its ability to extract energy from the visible region of electromagnetic spectrum. Here a facile synthesis of black anatase titania microspheres (B-TiO 2 ) through a two-step process is reported. In the first step, amorphous white TiO 2 microspheres (W-TiO 2 ) are obtained by hydrolysing titanium tetraisopropoxide by ammonia vapours in ethanol. In the second step, the W-TiO 2 is thermally annealed at 500 °C to obtain B-TiO 2 . The diffuse reflectance analysis showed that B-TiO 2 absorbs across visible spectrum with absorption extending well into NIR region. Raman scattering together with EPR analysis showed compelling evidence of the existence of oxygen deficiency within the crystal in B-TiO 2 that induces black colouration in the sample. The defects present in the black anatase sample were confirmed to be single-electron-trapped (or paramagnetic) oxygen vacancies (V o ⋅) by XPS and EPR studies. The magnetic susceptibility studies showed existence of antiferromagnetic interactions between these unpaired electron spins. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Scan Line Based Road Marking Extraction from Mobile LiDAR Point Clouds.

PubMed

Yan, Li; Liu, Hua; Tan, Junxiang; Li, Zan; Xie, Hong; Chen, Changjun

2016-06-17

Mobile Mapping Technology (MMT) is one of the most important 3D spatial data acquisition technologies. The state-of-the-art mobile mapping systems, equipped with laser scanners and named Mobile LiDAR Scanning (MLS) systems, have been widely used in a variety of areas, especially in road mapping and road inventory. With the commercialization of Advanced Driving Assistance Systems (ADASs) and self-driving technology, there will be a great demand for lane-level detailed 3D maps, and MLS is the most promising technology to generate such lane-level detailed 3D maps. Road markings and road edges are necessary information in creating such lane-level detailed 3D maps. This paper proposes a scan line based method to extract road markings from mobile LiDAR point clouds in three steps: (1) preprocessing; (2) road points extraction; (3) road markings extraction and refinement. In preprocessing step, the isolated LiDAR points in the air are removed from the LiDAR point clouds and the point clouds are organized into scan lines. In the road points extraction step, seed road points are first extracted by Height Difference (HD) between trajectory data and road surface, then full road points are extracted from the point clouds by moving least squares line fitting. In the road markings extraction and refinement step, the intensity values of road points in a scan line are first smoothed by a dynamic window median filter to suppress intensity noises, then road markings are extracted by Edge Detection and Edge Constraint (EDEC) method, and the Fake Road Marking Points (FRMPs) are eliminated from the detected road markings by segment and dimensionality feature-based refinement. The performance of the proposed method is evaluated by three data samples and the experiment results indicate that road points are well extracted from MLS data and road markings are well extracted from road points by the applied method. A quantitative study shows that the proposed method achieves an average completeness, correctness, and F-measure of 0.96, 0.93, and 0.94, respectively. The time complexity analysis shows that the scan line based road markings extraction method proposed in this paper provides a promising alternative for offline road markings extraction from MLS data.

Scan Line Based Road Marking Extraction from Mobile LiDAR Point Clouds†

PubMed Central

Yan, Li; Liu, Hua; Tan, Junxiang; Li, Zan; Xie, Hong; Chen, Changjun

2016-01-01

Mobile Mapping Technology (MMT) is one of the most important 3D spatial data acquisition technologies. The state-of-the-art mobile mapping systems, equipped with laser scanners and named Mobile LiDAR Scanning (MLS) systems, have been widely used in a variety of areas, especially in road mapping and road inventory. With the commercialization of Advanced Driving Assistance Systems (ADASs) and self-driving technology, there will be a great demand for lane-level detailed 3D maps, and MLS is the most promising technology to generate such lane-level detailed 3D maps. Road markings and road edges are necessary information in creating such lane-level detailed 3D maps. This paper proposes a scan line based method to extract road markings from mobile LiDAR point clouds in three steps: (1) preprocessing; (2) road points extraction; (3) road markings extraction and refinement. In preprocessing step, the isolated LiDAR points in the air are removed from the LiDAR point clouds and the point clouds are organized into scan lines. In the road points extraction step, seed road points are first extracted by Height Difference (HD) between trajectory data and road surface, then full road points are extracted from the point clouds by moving least squares line fitting. In the road markings extraction and refinement step, the intensity values of road points in a scan line are first smoothed by a dynamic window median filter to suppress intensity noises, then road markings are extracted by Edge Detection and Edge Constraint (EDEC) method, and the Fake Road Marking Points (FRMPs) are eliminated from the detected road markings by segment and dimensionality feature-based refinement. The performance of the proposed method is evaluated by three data samples and the experiment results indicate that road points are well extracted from MLS data and road markings are well extracted from road points by the applied method. A quantitative study shows that the proposed method achieves an average completeness, correctness, and F-measure of 0.96, 0.93, and 0.94, respectively. The time complexity analysis shows that the scan line based road markings extraction method proposed in this paper provides a promising alternative for offline road markings extraction from MLS data. PMID:27322279

Automated extraction of pleural effusion in three-dimensional thoracic CT images

NASA Astrophysics Data System (ADS)

Kido, Shoji; Tsunomori, Akinori

2009-02-01

It is important for diagnosis of pulmonary diseases to measure volume of accumulating pleural effusion in threedimensional thoracic CT images quantitatively. However, automated extraction of pulmonary effusion correctly is difficult. Conventional extraction algorithm using a gray-level based threshold can not extract pleural effusion from thoracic wall or mediastinum correctly, because density of pleural effusion in CT images is similar to those of thoracic wall or mediastinum. So, we have developed an automated extraction method of pulmonary effusion by use of extracting lung area with pleural effusion. Our method used a template of lung obtained from a normal lung for segmentation of lungs with pleural effusions. Registration process consisted of two steps. First step was a global matching processing between normal and abnormal lungs of organs such as bronchi, bones (ribs, sternum and vertebrae) and upper surfaces of livers which were extracted using a region-growing algorithm. Second step was a local matching processing between normal and abnormal lungs which were deformed by the parameter obtained from the global matching processing. Finally, we segmented a lung with pleural effusion by use of the template which was deformed by two parameters obtained from the global matching processing and the local matching processing. We compared our method with a conventional extraction method using a gray-level based threshold and two published methods. The extraction rates of pleural effusions obtained from our method were much higher than those obtained from other methods. Automated extraction method of pulmonary effusion by use of extracting lung area with pleural effusion is promising for diagnosis of pulmonary diseases by providing quantitative volume of accumulating pleural effusion.

Diagnosis of combined faults in Rotary Machinery by Non-Naive Bayesian approach

NASA Astrophysics Data System (ADS)

Asr, Mahsa Yazdanian; Ettefagh, Mir Mohammad; Hassannejad, Reza; Razavi, Seyed Naser

2017-02-01

When combined faults happen in different parts of the rotating machines, their features are profoundly dependent. Experts are completely familiar with individuals faults characteristics and enough data are available from single faults but the problem arises, when the faults combined and the separation of characteristics becomes complex. Therefore, the experts cannot declare exact information about the symptoms of combined fault and its quality. In this paper to overcome this drawback, a novel method is proposed. The core idea of the method is about declaring combined fault without using combined fault features as training data set and just individual fault features are applied in training step. For this purpose, after data acquisition and resampling the obtained vibration signals, Empirical Mode Decomposition (EMD) is utilized to decompose multi component signals to Intrinsic Mode Functions (IMFs). With the use of correlation coefficient, proper IMFs for feature extraction are selected. In feature extraction step, Shannon energy entropy of IMFs was extracted as well as statistical features. It is obvious that most of extracted features are strongly dependent. To consider this matter, Non-Naive Bayesian Classifier (NNBC) is appointed, which release the fundamental assumption of Naive Bayesian, i.e., the independence among features. To demonstrate the superiority of NNBC, other counterpart methods, include Normal Naive Bayesian classifier, Kernel Naive Bayesian classifier and Back Propagation Neural Networks were applied and the classification results are compared. An experimental vibration signals, collected from automobile gearbox, were used to verify the effectiveness of the proposed method. During the classification process, only the features, related individually to healthy state, bearing failure and gear failures, were assigned for training the classifier. But, combined fault features (combined gear and bearing failures) were examined as test data. The achieved probabilities for the test data show that the combined fault can be identified with high success rate.

Conversion and recovery of saponifiable lipids from microalgae using a nonpolar solvent via lipase-assisted extraction.

PubMed

Law, Sam Q K; Halim, Ronald; Scales, Peter J; Martin, Gregory J O

2018-07-01

A single-step method for transesterifying and recovering lipids in concentrated slurries (ca 20% w/w solids) of ruptured microalgae is presented. A soluble Rhizomucor miehei lipase (RML) was used to directly transesterify the lipids in the marine microalgae Nannochloropsis salina. This allowed both triglycerides (TAG) and polar saponifiable lipids to be recovered as fatty acid methyl esters (FAME) using a nonpolar solvent (hexane). Up to 90 wt% of the total saponifiable lipids (SL) were converted to FAME within 24 h, approximately 75% of which was recovered in the hexane by centrifugation. Two pathways for the conversion and recovery of polar lipids were identified. The water in the slurry buffered against potential lipase inhibition by methanol, but necessitated a high methanol dose for maximal FAME conversion. Nonetheless the method enables the recovery of polar lipids as FAME while avoiding the need for both drying of the biomass and a downstream transesterification step. Copyright © 2018 Elsevier Ltd. All rights reserved.

Proteome Speciation by Mass Spectrometry: Characterization of Composite Protein Mixtures in Milk Replacers.

PubMed

Gaspari, Marco; Chiesa, Luca; Nicastri, Annalisa; Gabriele, Caterina; Harper, Valeria; Britti, Domenico; Cuda, Giovanni; Procopio, Antonio

2016-12-06

The ability of tandem mass spectrometry to determine the primary structure of proteolytic peptides can be exploited to trace back the organisms from which the corresponding proteins were extracted. This information can be important when food products, such as protein powders, can be supplemented with lower-quality starting materials. In order to dissect the origin of proteinaceous material composing a given unknown mixture, a two-step database search strategy for bottom-up nanoscale liquid chromatography-tandem mass spectrometry (nanoLC-MS/MS) data was implemented. A single nanoLC-MS/MS analysis was sufficient not only to determine the qualitative composition of the mixtures under examination, but also to assess the relative percent composition of the various proteomes, if dedicated calibration curves were previously generated. The approach of two-step database search for qualitative analysis and proteome total ion current (pTIC) calculation for quantitative analysis was applied to several binary and ternary mixtures which mimic the composition of milk replacers typically used in calf feeding.

Accelerated x-ray scatter projection imaging using multiple continuously moving pencil beams

NASA Astrophysics Data System (ADS)

Dydula, Christopher; Belev, George; Johns, Paul C.

2017-03-01

Coherent x-ray scatter varies with angle and photon energy in a manner dependent on the chemical composition of the scattering material, even for amorphous materials. Therefore, images generated from scattered photons can have much higher contrast than conventional projection radiographs. We are developing a scatter projection imaging prototype at the BioMedical Imaging and Therapy (BMIT) facility of the Canadian Light Source (CLS) synchrotron in Saskatoon, Canada. The best images are obtained using step-and-shoot scanning with a single pencil beam and area detector to capture sequentially the scatter pattern for each primary beam location on the sample. Primary x-ray transmission is recorded simultaneously using photodiodes. The technological challenge is to acquire the scatter data in a reasonable time. Using multiple pencil beams producing partially-overlapping scatter patterns reduces acquisition time but increases complexity due to the need for a disentangling algorithm to extract the data. Continuous sample motion, rather than step-and-shoot, also reduces acquisition time at the expense of introducing motion blur. With a five-beam (33.2 keV, 3.5 mm2 beam area) continuous sample motion configuration, a rectangular array of 12 x 100 pixels with 1 mm sampling width has been acquired in 0.4 minutes (3000 pixels per minute). The acquisition speed is 38 times the speed for single beam step-and-shoot. A system model has been developed to calculate detected scatter patterns given the material composition of the object to be imaged. Our prototype development, image acquisition of a plastic phantom and modelling are described.

Performance evaluation testing of wells in the gradient control system at a federally operated Confined Disposal Facility using single well aquifer tests, East Chicago, Indiana

USGS Publications Warehouse

Lampe, David C.; Unthank, Michael D.

2016-12-08

The U.S. Geological Survey (USGS) performed tests to evaluate the hydrologic connection between the open interval of the well and the surrounding Calumet aquifer in response to fouling of extraction well pumps onsite. Two rounds of air slug testing were performed on seven monitoring wells and step drawdown and subsequent recovery tests on three extraction wells on a U.S. Army Corps of Engineers Confined Disposal Facility (CDF) in East Chicago, Indiana. The wells were tested in 2014 and again in 2015. The extraction and monitoring wells are part of the gradient control system that establishes an inward gradient around the perimeter of the facility. The testing established a set of protocols that site personnel can use to evaluate onsite well integrity and develop a maintenance procedure to evaluate future well performance.The results of the slug test analysis data indicate that the hydraulic connection of the well screen to the surrounding aquifer material in monitoring wells on the CDF and the reliability of hydraulic conductivity estimates of the surrounding geologic media could be increased by implementing well development maintenance. Repeated air slug tests showed increasing hydraulic conductivity until, in the case of the monitoring wells located outside of the groundwater cutoff wall (MW–4B, MW–11B, MW–14B), the difference in hydraulic conductivity from test to test decreased, indicating the results were approaching the optimal hydraulic connection between the aquifer and the well screen. Hydraulic conductivity values derived from successive tests in monitoring well D40, approximately 0.25 mile south of the CDF, were substantially higher than those derived from wells on the CDF property. Also, values did not vary from test to test like those measured in monitoring wells located on the CDF property, which indicated that a process may be affecting the connectivity of the wells on the CDF property to the Calumet aquifer. Derived hydraulic conductivity values from the initial air slug test during the 2015 testing period for MW–11A and MW–14A are an order of magnitude less than those derived from the final test during the 2014 testing period indicating the development of a low conductivity skin between the final test of the 2014 testing period and the beginning of the 2015 testing period that created a decrease in the connection of the monitoring well screen to the surrounding aquifer material.Repeated step drawdown and recovery testing of the extraction wells tested during this study provided results that indicate a slight increase in the development of a skin and a decrease in the connectivity of the extraction wells with the Calumet aquifer. Hydraulic conductivity values obtained from the test results were relatively similar in EW–4B and EW–14A but were substantially lower for EW–11C. This difference may be due to the presence of finer grained silt deposits in the area surrounding well nest 11. Skin factors calculated during the step drawdown and recovery analysis were lowest in EW–11C and relatively similar in EW–4B and EW–14A. Calculated skin factors increased slightly in the analysis of data collected in 2015 from that collected in 2014.Comparisons of the specific-capacity values calculated from well development data collected following extraction well installation to those calculated during the single well aquifer tests at EW–4B, EW–14A and EW–11C indicate that the productivity of extraction wells on the CDF property has diminished since 2008. Values calculated for monitoring wells MW–4A, MW–11A, and MW–14A were used to evaluate the decrease in air slug derived hydraulic conductivity for monitoring wells within the groundwater cutoff wall between testing in 2014 and 2015.Results from testing by this study indicate that implementation of an air slug testing regimen of the monitoring wells that control the gradient control system at the CDF throughout the course of a year may help sustain the connectivity between the monitoring wells and the surrounding aquifer and provide data to evaluate the need for different types of well development approaches to address chemical or biological fouling issues. Repeated step drawdown and recovery testing of the extraction wells tested during this study provided results that indicate a slight increase in the development of a skin and a decrease in the connectivity of the extraction wells with the Calumet aquifer. Implementation of a specific capacity testing regimen can provide data to record and track well condition through time for individual extraction wells. Results from aquifer testing by this study indicate that specific capacity test results, when paired with recovery testing, provide useful data to measure the development of any low conductivity wellbore skin through the skin factors derived for the individual extraction wells. An initial annual schedule of specific capacity and recovery tests would provide sufficient data to identify substantial short-term changes in the operating condition of the extraction wells.

Analysis of Intracellular Metabolites from Microorganisms: Quenching and Extraction Protocols

PubMed Central

Villas-Boas, Silas G.; Aggio, Raphael

2017-01-01

Sample preparation is one of the most important steps in metabolome analysis. The challenges of determining microbial metabolome have been well discussed within the research community and many improvements have already been achieved in last decade. The analysis of intracellular metabolites is particularly challenging. Environmental perturbations may considerably affect microbial metabolism, which results in intracellular metabolites being rapidly degraded or metabolized by enzymatic reactions. Therefore, quenching or the complete stop of cell metabolism is a pre-requisite for accurate intracellular metabolite analysis. After quenching, metabolites need to be extracted from the intracellular compartment. The choice of the most suitable metabolite extraction method/s is another crucial step. The literature indicates that specific classes of metabolites are better extracted by different extraction protocols. In this review, we discuss the technical aspects and advancements of quenching and extraction of intracellular metabolite analysis from microbial cells. PMID:29065530

Green procedure with a green solvent for fats and oils' determination. Microwave-integrated Soxhlet using limonene followed by microwave Clevenger distillation.

PubMed

Virot, Matthieu; Tomao, Valérie; Ginies, Christian; Visinoni, Franco; Chemat, Farid

2008-07-04

Here is described a green and original alternative procedure for fats and oils' determination in oleaginous seeds. Extractions were carried out using a by-product of the citrus industry as extraction solvent, namely d-limonene, instead of hazardous petroleum solvents such as n-hexane. The described method is achieved in two steps using microwave energy: at first, extractions are attained using microwave-integrated Soxhlet, followed by the elimination of the solvent from the medium using a microwave Clevenger distillation in the second step. Oils extracted from olive seeds were compared with both conventional Soxhlet and microwave-integrated Soxhlet extraction procedures performed with n-hexane in terms of qualitative and quantitative determination. No significant difference was obtained between each extract allowing us to conclude that the proposed method is effective and valuable.

High-throughput, automated extraction of DNA and RNA from clinical samples using TruTip technology on common liquid handling robots.

PubMed

Holmberg, Rebecca C; Gindlesperger, Alissa; Stokes, Tinsley; Brady, Dane; Thakore, Nitu; Belgrader, Philip; Cooney, Christopher G; Chandler, Darrell P

2013-06-11

TruTip is a simple nucleic acid extraction technology whereby a porous, monolithic binding matrix is inserted into a pipette tip. The geometry of the monolith can be adapted for specific pipette tips ranging in volume from 1.0 to 5.0 ml. The large porosity of the monolith enables viscous or complex samples to readily pass through it with minimal fluidic backpressure. Bi-directional flow maximizes residence time between the monolith and sample, and enables large sample volumes to be processed within a single TruTip. The fundamental steps, irrespective of sample volume or TruTip geometry, include cell lysis, nucleic acid binding to the inner pores of the TruTip monolith, washing away unbound sample components and lysis buffers, and eluting purified and concentrated nucleic acids into an appropriate buffer. The attributes and adaptability of TruTip are demonstrated in three automated clinical sample processing protocols using an Eppendorf epMotion 5070, Hamilton STAR and STARplus liquid handling robots, including RNA isolation from nasopharyngeal aspirate, genomic DNA isolation from whole blood, and fetal DNA extraction and enrichment from large volumes of maternal plasma (respectively).

Unexpectedly large difference of the electron density at the nucleus in the 4p ^2{P}_{{1}/{2},{3}/{2}} fine-structure doublet of Ca^+

NASA Astrophysics Data System (ADS)

Shi, C.; Gebert, F.; Gorges, C.; Kaufmann, S.; Nörtershäuser, W.; Sahoo, B. K.; Surzhykov, A.; Yerokhin, V. A.; Berengut, J. C.; Wolf, F.; Heip, J. C.; Schmidt, P. O.

2017-01-01

We measured the isotope shift in the ^2{S}_{{1}/{2}} → ^2{P}_{{3}/{2}} (D2) transition in singly ionized calcium ions using photon recoil spectroscopy. The high accuracy of the technique enables us to compare the difference between the isotope shifts of this transition to the previously measured isotopic shifts of the ^2{S}_{{1}/{2}} → ^2{P}_{{1}/{2}} (D1) line. This so-called splitting isotope shift is extracted and exhibits a clear signature of field shift contributions. From the data, we were able to extract the small difference of the field shift coefficient and mass shifts between the two transitions with high accuracy. This J-dependence is of relativistic origin and can be used to benchmark atomic structure calculations. As a first step, we use several ab initio atomic structure calculation methods to provide more accurate values for the field shift constants and their ratio. Remarkably, the high-accuracy value for the ratio of the field shift constants extracted from the experimental data is larger than all available theoretical predictions.

Comparison of bioavailable vanadium in alfalfa rhizosphere soil extracted by an improved BCR procedure and EDTA, HCl, and NaNO₃ single extractions in a pot experiment with V-Cd treatments.

PubMed

Yang, Jie; Teng, Yanguo; Zuo, Rui; Song, Liuting

2015-06-01

The BCR sequential extraction procedure was compared with EDTA, HCl, and NaNO3 single extractions for evaluating vanadium bioavailability in alfalfa rhizosphere soil. The amounts of vanadium extracted by these methods were in the following order: BCR (bioavailable V) > EDTA ≈ HCl > NaNO3. Both correlation analysis and stepwise regression were adopted to illustrate the extractable vanadium between different reagents. The correlation coefficients between extracted vanadium and the vanadium contents in alfalfa roots were R NaNO3 = 0.948, R HCl = 0.902, R EDTA = 0.816, and R bioavailable V = 0.819. The stepwise multiple regression equation of the NaNO3 extraction was the most significant at a 95 % confidence interval. The influence of pH, total organic carbon, and cadmium content of soil to vanadium bioavailability were not definite. In summary, both the BCR sequential extraction and the single extraction methods were valid approaches for predicting vanadium bioavailability in alfalfa rhizosphere soil, especially the single extractions.

Solid-phase microextraction of methadone in urine samples by electrochemically co-deposited sol-gel/Cu nanocomposite fiber.

PubMed

Mohammadiazar, Sirwan; Hasanli, Fateme; Maham, Mehdi; Payami Samarin, Somayeh

2017-08-01

Electrochemically co-deposited sol-gel/Cu nanocomposites have been introduced as a novel, simple and single-step technique for preparation of solid-phase microextraction (SPME) coating to extract methadone (MDN) (a synthetic opioid) in urine samples. The porous surface structure of the sol-gel/Cu nanocomposite coating was revealed by scanning electron microscopy. Direct immersion SPME followed by HPLC-UV determination was employed. The factors influencing the SPME procedure, such as the salt content, desorption solvent type, pH and equilibration time, were optimized. The best conditions were obtained with no salt content, acetonitrile as desorption solvent type, pH 9 and 10 min equilibration time. The calibration graphs for urine samples showed good linearity. The detection limit was about 0.2 ng mL -1 . Also, the novel method for preparation of nanocomposite fiber was compared with previously reported techniques for MDN determination. The results show that the novel nanocomposite fiber has relatively high extraction efficiency. Copyright © 2016 John Wiley & Sons, Ltd.

Noncatalytic transformation of the crude lipid of ChlorellaI vulgaris into fatty acid methyl ester (FAME) with charcoal via a thermo-chemical process.

PubMed

Kwon, Eilhann E; Jeon, Young Jae; Yi, Haakrho

2013-02-01

The noncatalytic transformation of the crude lipid of Chlorella vulgaris (C. vulgaris) into fatty acid methyl ester (FAME) via a thermo-chemical process was mainly investigated in this work. The crude lipid of C. vulgaris was recovered by means of solvent extraction from C. vulgaris cultivated in a raceway pond. The conventional catalyzed transesterification of crude lipid of C. vulgaris is notably inhibited by the impurities contained in the crude lipid of C. vulgaris. These impurities are inevitably derived from the solvent extraction process for C. vulgaris. However, this work presents the noncatalytic transesterification of microalgal lipid into FAME, which could be an alternative option. For example, the noncatalytic transformation of microalgal lipid into FAME provides evidence that the esterification of free fatty acids (FFAs) and the transesterification of triglycerides can be combined into a single step less susceptible to the impurities and with a high conversion efficiency (∼97%). Copyright © 2012 Elsevier Ltd. All rights reserved.

Electrolysis of a molten semiconductor

DOE PAGES

Yin, Huayi; Chung, Brice; Sadoway, Donald R.

2016-08-24

Metals cannot be extracted by electrolysis of transition-metal sulfides because as liquids they are semiconductors, which exhibit high levels of electronic conduction and metal dissolution. Herein by introduction of a distinct secondary electrolyte, we reveal a high-throughput electro-desulfurization process that directly converts semiconducting molten stibnite (Sb 2S 3) into pure (99.9%) liquid antimony and sulfur vapour. At the bottom of the cell liquid antimony pools beneath cathodically polarized molten stibnite. At the top of the cell sulfur issues from a carbon anode immersed in an immiscible secondary molten salt electrolyte disposed above molten stibnite, thereby blocking electronic shorting across themore » cell. In conclusion, as opposed to conventional extraction practices, direct sulfide electrolysis completely avoids generation of problematic fugitive emissions (CO 2, CO and SO 2), significantly reduces energy consumption, increases productivity in a single-step process (lower capital and operating costs) and is broadly applicable to a host of electronically conductive transition-metal chalcogenides.« less

The monocarboxylate carrier from bovine heart mitochondria: partial purification and its substrate-transporting properties in a reconstituted system.

PubMed

Nałecz, K A; Bolli, R; Wojtczak, L; Azzi, A

1986-08-13

The monocarboxylate (pyruvate) carrier from bovine heart mitochondria was extracted from submitochondrial particles with Triton X-114 in the presence of cardiolipin. By a single hydroxylapatite chromatography step a 125-fold purification of the carrier protein could be achieved. High pyruvate/pyruvate-exchange activity was recovered, when the protein was reconstituted into phospholipid vesicles. No transport activity was observed, when the isolation occurred in the absence of phospholipids. The 2-cyano-4-hydroxycinnamate sensitive pyruvate exchange reaction was strongly temperature sensitive and dependent on the amount of protein reconstituted. Other 2-ketoacids caused competitive inhibition of the pyruvate uptake. Inhibitors of other mitochondrial carries, however, had very low or no effect on the monocarboxylate exchange. The influence of different -SH group reagents on the measured pyruvate/pyruvate-exchange in the reconstituted system was similar to the one observed with intact mitochondria. It is concluded that the described procedures for extraction, purification and reconstitution of the mitochondrial monocarboxylate carrier conserved the functional properties of the protein.

Lippia javanica: a cheap natural source for the synthesis of antibacterial silver nanocolloid

NASA Astrophysics Data System (ADS)

Kumar, Santosh; Singh, Mukesh; Halder, Dipankar; Mitra, Atanu

2016-10-01

Aqueous silver nanocolloid was synthesized in a single step by a biogenic approach using aqueous leaf extract of Lippia javanica plant which acts as both reducing as well as capping agent. The as-synthesized silver nanoparticles were characterized by UV-visible absorption spectroscopy, high-resolution transmission electron microscopy and Fourier transform infrared spectroscopy (FTIR). The UV-Vis absorption spectra of colloidal silver nanoparticles showed characteristic surface plasmon resonance peak centered at a wavelength of 415 nm. The kinetic study showed that the reduction process was complete within 2 h of time. The TEM analysis showed that most of the particles were spherical in shape and their average diameter was about 17.5 nm. FTIR study confirmed the presence of some organic functional groups in leaf extract and their participation during the reduction as well as stabilization process. In addition, the as-synthesized silver nanoparticles showed antimicrobial activity against clinically isolated pathogenic strain of E. coli and B. subtilis.

Extracting metalworking fluid aerosol samples in cassettes by provisional ASTM and NIOSH methods.

PubMed

Harper, Martin

2002-01-01

Recent provisional methods for the determination of metalworking fluid aerosol in workplace air involve a solvent extraction procedure to separate the nonvolatile fraction of the fluid from insoluble material such as metal turnings and dirt. The procedure calls for preweighing a filter (W1) and assembling it into a cassette and taking a sample. In the laboratory the filter is removed from the cassette, desiccated to remove any collected water or other volatile substances, and weighed again (W2). The filter is then extracted in an organic solvent blend, allowed to dry, and weighed a final time (W3). The total weight collected by the filter is given by (W2-W1), and the weight of (nonvolatile) metalworking fluid collected is given by (W2-W3). The extraction step can take place within a cassette housing if it is relatively inert to the solvent blend used. The extraction of four metalworking fluids (straight oil, soluble oil, synthetic and semisynthetic) within disposable polypropylene cassettes was investigated using the same protocol used to evaluate the original method. For all fluids the extraction efficiency was greater than 95% with a precision better than 5%. The mean blank contribution to the extraction step was 16 micrograms. Blanks were also evaluated after storage, and after transport and storage. A small additional blank contribution could be removed by desiccation. The limits of detection and quantitation of the extraction step were calculated to be 28 and 94 micrograms, respectively.

Synthetical Analysis for Morphology, biological Species, and stable Isotopes (SAMSI) of single-cell planktonic foraminifer

NASA Astrophysics Data System (ADS)

Ujiie, Y.; Kimoto, K.; Ishimura, T.

2017-12-01

Planktonic foraminifers are widely used in the studies of paleontology and paleoceanography, because the morphology of their calcareous shells is enough highly variable to identify the morphospecies and the chemical composition of the shells reflect ambient seawater condition. Although the morphospecies were believed to represent environments associating with latitudinal temperature range of the world ocean, molecular phylogeographic studies have unveiled the presence of multiple biological species in a single morphospecies and their species-specific distributions. This implicates the actual complexity of planktonic foraminiferal ecology. Conversely, these biological species have a high potential for providing novel ecological and environmental information to us. In order to reassess the morphological and geochemical characters of biological species, the DNA extraction method with the guanidium isothiocyanate buffer was developed to preserve the calcareous shells. The present study carefully tested the physical and chemical damages of the DNA extraction process to the shells, by our novel approaches with geochemical analysis of the shells after non-destructive analysis for morphometrics on a same specimen. First, we checked the changes of the shell densities between pre- and post-DNA extraction by using the micro-focus X-ray CT (MXCT) scanning. Based on the simultaneous measurement of a sample and the standard material, we confirmed no significant changes to the shell densities through the DNA extraction process. As a next step, we compared stable oxygen and carbon isotopes among individuals of three sample sets: (1) no chemical and incubation as control, (2) incubation in the DNA extraction buffer at 65-70°C for 40 minutes as standard way, and (3) incubation in the DNA extraction buffer at 65-70°C for 120 minutes, by using the microscale isotopic analytical system (MICAL3c). Consequently, there were no significant differences among the three sample sets. These examinations clearly certified that we define morphological and geochemical features from same specimens after genetic identification. Thus, our novel approach (SAMSI) provides future studies to establish the accurate ecological and environmental proxies both in the modern and past oceans.

Biochar as a sorbent for chlorinated hydrocarbons - sorption and extraction experiments in single and bi-solute systems

NASA Astrophysics Data System (ADS)

Schreiter, Inga J.; Wefer-Roehl, Annette; Graber, Ellen R.; Schüth, Christoph

2017-04-01

Biochar (BC) is increasingly deemed a potential sorbent for contaminants in soil and water remediation, and brownfield restoration. In this study, sorption and extraction experiments were performed to assess the potential of three different BCs to sorb and retain the chlorinated hydrocarbons trichloroethylene (TCE) and tetrachloroethylene (PCE). BCs studied were produced from wood chips, grain husk, and cattle manure at 450 °C. A commercially available activated carbon (AC) served as a reference. The sorption behaviour was studied in batch experiments in single solute and bi-solute systems. Resulting isotherms were fitted to the Freundlich model. To assess the desorption behaviour, a five-step extraction scheme (water at 40°C, water at 80°C, methanol at 50°C, toluene at 50°C, and n-hexane at 50°) was developed, utilizing Accelerated Solvent Extraction. Isotherms revealed distinct differences in sorption behaviour depending on BC feedstock. Sorption capacity ranked as follows: wood chip BC > grain husk BC > cattle manure BC for both contaminants. This sequence could be attributable to an increasing specific surface area, an increasing amount of carbon, and a decreasing ash content of the sorbents. It is noteworthy that all three BCs were more effective in adsorbing TCE, which is surprising, given the higher logKow of PCE. The reverse was observed for the AC. Here, sorption is purely driven by the hydrophobicity of the compound rather than sorbent properties. In bi-solute experiments, PCE sorbed as good as or stronger than TCE, yet the total mass of sorbed compounds increased slightly. In contrast, AC showed a significant decrease of TCE sorption and no significant changes in the total mass sorbed. Extraction experiments revealed that for all BCs a large fraction of the contaminants could not be readily desorbed. In all cases, water remobilized < 5 % of the total contaminant mass and up to 70 % could not be extracted by any of the solvents. The findings suggest that BC is a promising sorbent for mixed contaminant systems as it offers a diverse nature of sorption sites and is more effective in long-term immobilization than AC.

Preconcentration of DNA using magnetic ionic liquids that are compatible with real-time PCR for rapid nucleic acid quantification.

PubMed

Emaus, Miranda N; Clark, Kevin D; Hinners, Paige; Anderson, Jared L

2018-04-28

Nucleic acid extraction and purification represents a major bottleneck in DNA analysis. Traditional methods for DNA purification often require reagents that may inhibit quantitative polymerase chain reaction (qPCR) if not sufficiently removed from the sample. Approaches that employ magnetic beads may exhibit lower extraction efficiencies due to sedimentation and aggregation. In this study, four hydrophobic magnetic ionic liquids (MILs) were investigated as DNA extraction solvents with the goal of improving DNA enrichment factors and compatibility with downstream bioanalytical techniques. By designing custom qPCR buffers, we directly incorporated DNA-enriched MILs including trihexyl(tetradecyl)phosphonium tris(hexafluoroacetylaceto)nickelate(II) ([P 6,6,6,14 + ][Ni(hfacac) 3 - ]), [P 6,6,6,14 + ] tris(hexafluoroacetylaceto)colbaltate(II) ([Co(hfacac) 3 - ]), [P 6,6,6,14 + ] tris(hexafluoroacetylaceto)manganate(II) ([Mn(hfacac) 3 - ]), or [P 6,6,6,14 + ] tetrakis(hexafluoroacetylaceto)dysprosate(III) ([Dy(hfacac) 4 - ]) into reaction systems, thereby circumventing the need for time-consuming DNA recovery steps. Incorporating MILs into the reaction buffer did not significantly impact the amplification efficiency of the reaction (91.1%). High enrichment factors were achieved using the [P 6,6,6,14 + ][Ni(hfacac) 3 - ] MIL for the extraction of single-stranded and double-stranded DNA with extraction times as short as 2 min. When compared to a commercial magnetic bead-based platform, the [P 6,6,6,14 + ][Ni(hfacac) 3 - ] MIL was capable of producing higher enrichment factors for single-stranded DNA and similar enrichment factors for double-stranded DNA. The MIL-based method was applied for the extraction and direct qPCR amplification of mutation prone-KRAS oncogene fragment in plasma samples. Graphical abstract Magnetic ionic liquid solvents are shown to preconcentrate sufficient KRAS DNA template from an aqueous solution in as short as 2 min without using chaotropic salts or toxic organic solvents. By using custom-designed qPCR buffers, DNA can be directly amplified and quantified from four MILs examined in this study.

Unexpected Reaction Pathway for butyrylcholinesterase-catalyzed inactivation of “hunger hormone” ghrelin

NASA Astrophysics Data System (ADS)

Yao, Jianzhuang; Yuan, Yaxia; Zheng, Fang; Zhan, Chang-Guo

2016-02-01

Extensive computational modeling and simulations have been carried out, in the present study, to uncover the fundamental reaction pathway for butyrylcholinesterase (BChE)-catalyzed hydrolysis of ghrelin, demonstrating that the acylation process of BChE-catalyzed hydrolysis of ghrelin follows an unprecedented single-step reaction pathway and the single-step acylation process is rate-determining. The free energy barrier (18.8 kcal/mol) calculated for the rate-determining step is reasonably close to the experimentally-derived free energy barrier (~19.4 kcal/mol), suggesting that the obtained mechanistic insights are reasonable. The single-step reaction pathway for the acylation is remarkably different from the well-known two-step acylation reaction pathway for numerous ester hydrolysis reactions catalyzed by a serine esterase. This is the first time demonstrating that a single-step reaction pathway is possible for an ester hydrolysis reaction catalyzed by a serine esterase and, therefore, one no longer can simply assume that the acylation process must follow the well-known two-step reaction pathway.

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.

Sequential electrokinetic treatment and oxalic acid extraction for the removal of Cu, Cr and As from wood.

PubMed

Isosaari, Pirjo; Marjavaara, Pieti; Lehmus, Eila

2010-10-15

Removal of Cu, Cr and As from utility poles treated with chromated copper arsenate (CCA) was investigated using different one- to three-step combinations of oxalic acid extraction and electrokinetic treatment. The experiments were carried out at room temperature, using 0.8% oxalic acid and 30 V (200 V/m) of direct current (DC) or alternating current in combination (DC/AC). Six-hour extraction removed only 15%, 11% and 28% and 7-day electrokinetic treatment 57%, 0% and 17% of Cu, Cr and As from wood chips, respectively. The best combination for all the metals was a three-step process consisting of pre-extraction, electrokinetics and post-extraction steps, yielding removals of 67% for Cu, 64% for Cr and 81% for As. Oxalic acid extraction prior to electrokinetic treatment was deleterious to further removal of Cu, but it was necessary for Cr and As removal. Chemical equilibrium modelling was used to explain the differences in the behaviour of Cu, Cr and As. Due to the dissimilar nature of these metals, it appeared that even more process sequences and/or stricter control of the process conditions would be needed to obtain the >99% removals required for safe recycling of the purified wood material. 2010 Elsevier B.V. All rights reserved.

Hybrid Signal Processing Technique to Improve the Defect Estimation in Ultrasonic Non-Destructive Testing of Composite Structures

PubMed Central

Raisutis, Renaldas; Samaitis, Vykintas

2017-01-01

This work proposes a novel hybrid signal processing technique to extract information on disbond-type defects from a single B-scan in the process of non-destructive testing (NDT) of glass fiber reinforced plastic (GFRP) material using ultrasonic guided waves (GW). The selected GFRP sample has been a segment of wind turbine blade, which possessed an aerodynamic shape. Two disbond type defects having diameters of 15 mm and 25 mm were artificially constructed on its trailing edge. The experiment has been performed using the low-frequency ultrasonic system developed at the Ultrasound Institute of Kaunas University of Technology and only one side of the sample was accessed. A special configuration of the transmitting and receiving transducers fixed on a movable panel with a separation distance of 50 mm was proposed for recording the ultrasonic guided wave signals at each one-millimeter step along the scanning distance up to 500 mm. Finally, the hybrid signal processing technique comprising the valuable features of the three most promising signal processing techniques: cross-correlation, wavelet transform, and Hilbert–Huang transform has been applied to the received signals for the extraction of defects information from a single B-scan image. The wavelet transform and cross-correlation techniques have been combined in order to extract the approximated size and location of the defects and measurements of time delays. Thereafter, Hilbert–Huang transform has been applied to the wavelet transformed signal to compare the variation of instantaneous frequencies and instantaneous amplitudes of the defect-free and defective signals. PMID:29232845

Contribution of lower limb eccentric work and different step responses to balance recovery among older adults.

PubMed

Nagano, Hanatsu; Levinger, Pazit; Downie, Calum; Hayes, Alan; Begg, Rezaul

2015-09-01

Falls during walking reflect susceptibility to balance loss and the individual's capacity to recover stability. Balance can be recovered using either one step or multiple steps but both responses are impaired with ageing. To investigate older adults' (n=15, 72.5±4.8 yrs) recovery step control a tether-release procedure was devised to induce unanticipated forward balance loss. Three-dimensional position-time data combined with foot-ground reaction forces were used to measure balance recovery. Dependent variables were; margin of stability (MoS) and available response time (ART) for spatial and temporal balance measures in the transverse and sagittal planes; lower limb joint angles and joint negative/positive work; and spatio-temporal gait parameters. Relative to multi-step responses, single-step recovery was more effective in maintaining balance, indicated by greater MoS and longer ART. MoS in the sagittal plane measure and ART in the transverse plane distinguished single step responses from multiple steps. When MoS and ART were negative (<0), balance was not secured and additional steps would be required to establish the new base of support for balance recovery. Single-step responses demonstrated greater step length and velocity and when the recovery foot landed, greater centre of mass downward velocity. Single-step strategies also showed greater ankle dorsiflexion, increased knee maximum flexion and more negative work at the ankle and knee. Collectively these findings suggest that single-step responses are more effective in forward balance recovery by directing falling momentum downward to be absorbed as lower limb eccentric work. Copyright © 2015 Elsevier B.V. All rights reserved.

Semi-automatic building extraction in informal settlements from high-resolution satellite imagery

NASA Astrophysics Data System (ADS)

Mayunga, Selassie David

The extraction of man-made features from digital remotely sensed images is considered as an important step underpinning management of human settlements in any country. Man-made features and buildings in particular are required for varieties of applications such as urban planning, creation of geographical information systems (GIS) databases and Urban City models. The traditional man-made feature extraction methods are very expensive in terms of equipment, labour intensive, need well-trained personnel and cannot cope with changing environments, particularly in dense urban settlement areas. This research presents an approach for extracting buildings in dense informal settlement areas using high-resolution satellite imagery. The proposed system uses a novel strategy of extracting building by measuring a single point at the approximate centre of the building. The fine measurement of the building outlines is then effected using a modified snake model. The original snake model on which this framework is based, incorporates an external constraint energy term which is tailored to preserving the convergence properties of the snake model; its use to unstructured objects will negatively affect their actual shapes. The external constrained energy term was removed from the original snake model formulation, thereby, giving ability to cope with high variability of building shapes in informal settlement areas. The proposed building extraction system was tested on two areas, which have different situations. The first area was Tungi in Dar Es Salaam, Tanzania where three sites were tested. This area is characterized by informal settlements, which are illegally formulated within the city boundaries. The second area was Oromocto in New Brunswick, Canada where two sites were tested. Oromocto area is mostly flat and the buildings are constructed using similar materials. Qualitative and quantitative measures were employed to evaluate the accuracy of the results as well as the performance of the system. The qualitative and quantitative measures were based on visual inspection and by comparing the measured coordinates to the reference data respectively. In the course of this process, a mean area coverage of 98% was achieved for Dar Es Salaam test sites, which globally indicated that the extracted building polygons were close to the ground truth data. Furthermore, the proposed system saved time to extract a single building by 32%. Although the extracted building polygons are within the perimeter of ground truth data, visually some of the extracted building polygons were somewhat distorted. This implies that interactive post-editing process is necessary for cartographic representation.

Simple and sensitive method for quantification of fluorescent enzymatic mature and senescent crosslinks of collagen in bone hydrolysate using single-column high performance liquid chromatography.

PubMed

Viguet-Carrin, S; Gineyts, E; Bertholon, C; Delmas, P D

2009-01-01

A rapid high performance liquid chromatographic method was developed including an internal standard for the measurement of mature and senescent crosslinks concentration in non-demineralized bone hydrolysates. To avoid the demineralization which is a tedious step, we developed a method based on the use of a solid-phase extraction procedure to clean-up the samples. It resulted in sensitive and accurate measurements: the detection limits as low as 0.2 pmol for the pyridimium crosslinks and 0.02 pmol for the pentosidine. The inter- and intra-assay coefficients of variation were as low as 5% and 2%, respectively, for all crosslinks.

IRIS: A database application system for diseases identification using FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Arshad, Ahmad Zulhilmi; Munajat, Yusof; Ibrahim, Raja Kamarulzaman Raja; Mahmood, Nasrul Humaimi

2015-05-01

Infrared information on diseases identification system (IRIS) is an application for diseases identification and analysis by using Fourier transform infrared (FTIR) spectroscopy. This is the preliminary step to gather information from the secondary data which was extracted from recognized various research and scientific paper, which are combined into a single database as in IRIS for our purpose of study. The importance of this database is to examine the fingerprint differences between normal and diseases cell or tissue. With the implementation of this application is it hopes that the diseases identification using FTIR spectroscopy would be more reliable and may assist either physicians, pathologists, or researchers to diagnose the certain type of disease efficiently.

Two-step voltage dual electromembrane extraction: A new approach to simultaneous extraction of acidic and basic drugs.

PubMed

Asadi, Sakine; Nojavan, Saeed

2016-06-07

In the present work, acidic and basic drugs were simultaneously extracted by a novel method of high efficiency herein referred to as two-step voltage dual electromembrane extraction (TSV-DEME). Optimizing effective parameters such as composition of organic liquid membrane, pH values of donor and acceptor solutions, voltage and duration of each step, the method had its figures of merit investigated in pure water, human plasma, wastewater, and breast milk samples. Simultaneous extraction of acidic and basic drugs was done by applying potentials of 150 V and 400 V for 6 min and 19 min as the first and second steps, respectively. The model compounds were extracted from 4 mL of sample solution (pH = 6) into 20 μL of each acceptor solution (32 mM NaOH for acidic drugs and 32 mM HCL for basic drugs). 1-Octanol was immobilized within the pores of a porous hollow fiber of polypropylene, as the supported liquid membrane (SLM) for acidic drugs, and 2-ethyle hexanol, as the SLM for basic drugs. The proposed TSV-DEME technique provided good linearity with the resulting correlation coefficients ranging from 0.993 to 0.998 over a concentration range of 1-1000 ng mL(-1). The limit of detections of the drugs were found to range within 0.3-1.5 ng mL(-1), while the corresponding repeatability ranged from 7.7 to 15.5% (n = 4). The proposed method was further compared to simple dual electromembrane extraction (DEME), indicating significantly higher recoveries for TSV-DEME procedure (38.1-68%), as compared to those of simple DEME procedure (17.7-46%). Finally, the optimized TSV-DEME was applied to extract and quantify model compounds in breast milk, wastewater, and plasma samples. Copyright © 2016 Elsevier B.V. All rights reserved.

DNA confinement in nanochannels: physics and biological applications

NASA Astrophysics Data System (ADS)

Reisner, Walter; Pedersen, Jonas N.; Austin, Robert H.

2012-10-01

DNA is the central storage molecule of genetic information in the cell, and reading that information is a central problem in biology. While sequencing technology has made enormous advances over the past decade, there is growing interest in platforms that can readout genetic information directly from long single DNA molecules, with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need for ensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloning and molecular amplification steps (thus enabling direct assessment of the genome in its native state). In this review, we will discuss how the information contained in genomic-length single DNA molecules can be accessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules will stretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel for analysis. We will first review the fundamental physics of DNA nanochannel confinement—including the effect of varying ionic strength—and then discuss recent applications of these systems to genomic mapping. Apart from the intense biological interest in extracting linear sequence information from elongated DNA molecules, from a physics view these systems are fascinating as they enable probing of single-molecule conformation in environments with dimensions that intersect key physical length-scales in the 1 nm to 100 µm range.

Study of flavour compounds from orange juices by HS-SPME and GC-MS

NASA Astrophysics Data System (ADS)

Schmutzer, G.; Avram, V.; Covaciu, F.; Feher, I.; Magdas, A.; David, L.; Moldovan, Z.

2013-11-01

The flavour of the orange juices, which gives the taste and odour of the product, is an important criterion about the products quality for consumers. A fresh single strength and two commercial orange juices (obtained from concentrate) flavour profile were studied using a selective and sensitive gas chromatography - mass spectrometry (GC-MS) analytical system, after a solvent free, single step preconcentration and extraction technique, the headspace solid phase microextraction (HP-SPME). In the studied orange juices 55 flavour compounds were detected and classified as belonging to the esters, alcohols, ketones, monoterpenes and sesquiterpenes chemical families. The fresh single strength orange juice was characterized by high amount of esters, monoterpenes and sesquiterpenes. Limonene and valencene were the most abundant flavours in this fresh natural orange juice. Alcohols and ketones were found in higher concentration in the commercial orange juices made from concentrate, than in the single strength products. Nevertheless, in commercial juices the most abundant flavour was limonene and α-terpineol. The results highlight clear differences between fresh singles strength orange juice and juice from concentrate. The orange juices reconstructed from concentrate, made in Romania, present low quantity of flavour compounds, suggesting the absence or a low rearomatization process, but extraneous components were not detected.

DNA confinement in nanochannels: physics and biological applications.

PubMed

Reisner, Walter; Pedersen, Jonas N; Austin, Robert H

2012-10-01

DNA is the central storage molecule of genetic information in the cell, and reading that information is a central problem in biology. While sequencing technology has made enormous advances over the past decade, there is growing interest in platforms that can readout genetic information directly from long single DNA molecules, with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need for ensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloning and molecular amplification steps (thus enabling direct assessment of the genome in its native state). In this review, we will discuss how the information contained in genomic-length single DNA molecules can be accessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules will stretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel for analysis. We will first review the fundamental physics of DNA nanochannel confinement--including the effect of varying ionic strength--and then discuss recent applications of these systems to genomic mapping. Apart from the intense biological interest in extracting linear sequence information from elongated DNA molecules, from a physics view these systems are fascinating as they enable probing of single-molecule conformation in environments with dimensions that intersect key physical length-scales in the 1 nm to 100 µm range.

A Single-Step Enrichment Medium for Nonchromogenic Isolation of Healthy and Cold-Injured Salmonella spp. from Fresh Vegetables.

PubMed

Kim, Hong-Seok; Choi, Dasom; Kang, Il-Byeong; Kim, Dong-Hyeon; Yim, Jin-Hyeok; Kim, Young-Ji; Chon, Jung-Whan; Oh, Deog-Hwan; Seo, Kun-Ho

2017-02-01

Culture-based detection of nontyphoidal Salmonella spp. in foods requires at least four working days; therefore, new detection methods that shorten the test time are needed. In this study, we developed a novel single-step Salmonella enrichment broth, SSE-1, and compared its detection capability with that of commercial single-step ONE broth-Salmonella (OBS) medium and a conventional two-step enrichment method using buffered peptone water and Rappaport-Vassiliadis soy broth (BPW-RVS). Minimally processed lettuce samples were artificially inoculated with low levels of healthy and cold-injured Salmonella Enteritidis (10 0 or 10 1 colony-forming unit/25 g), incubated in OBS, BPW-RVS, and SSE-1 broths, and streaked on xylose lysine deoxycholate (XLD) agar. Salmonella recoverability was significantly higher in BPW-RVS (79.2%) and SSE-1 (83.3%) compared to OBS (39.3%) (p < 0.05). Our data suggest that the SSE-1 single-step enrichment broth could completely replace two-step enrichment with reduced enrichment time from 48 to 24 h, performing better than commercial single-step enrichment medium in the conventional nonchromogenic Salmonella detection, thus saving time, labor, and cost.

Integrated experimental and technoeconomic evaluation of two-stage Cu-catalyzed alkaline-oxidative pretreatment of hybrid poplar.

PubMed

Bhalla, Aditya; Fasahati, Peyman; Particka, Chrislyn A; Assad, Aline E; Stoklosa, Ryan J; Bansal, Namita; Semaan, Rachel; Saffron, Christopher M; Hodge, David B; Hegg, Eric L

2018-01-01

When applied to recalcitrant lignocellulosic feedstocks, multi-stage pretreatments can provide more processing flexibility to optimize or balance process outcomes such as increasing delignification, preserving hemicellulose, and maximizing enzymatic hydrolysis yields. We previously reported that adding an alkaline pre-extraction step to a copper-catalyzed alkaline hydrogen peroxide (Cu-AHP) pretreatment process resulted in improved sugar yields, but the process still utilized relatively high chemical inputs (catalyst and H 2 O 2 ) and enzyme loadings. We hypothesized that by increasing the temperature of the alkaline pre-extraction step in water or ethanol, we could reduce the inputs required during Cu-AHP pretreatment and enzymatic hydrolysis without significant loss in sugar yield. We also performed technoeconomic analysis to determine if ethanol or water was the more cost-effective solvent during alkaline pre-extraction and if the expense associated with increasing the temperature was economically justified. After Cu-AHP pretreatment of 120 °C NaOH-H 2 O pre-extracted and 120 °C NaOH-EtOH pre-extracted biomass, approximately 1.4-fold more total lignin was solubilized (78% and 74%, respectively) compared to the 30 °C NaOH-H 2 O pre-extraction (55%) carried out in a previous study. Consequently, increasing the temperature of the alkaline pre-extraction step to 120 °C in both ethanol and water allowed us to decrease bipyridine and H 2 O 2 during Cu-AHP and enzymes during hydrolysis with only a small reduction in sugar yields compared to 30 °C alkaline pre-extraction. Technoeconomic analysis indicated that 120 °C NaOH-H 2 O pre-extraction has the lowest installed ($246 million) and raw material ($175 million) costs compared to the other process configurations. We found that by increasing the temperature of the alkaline pre-extraction step, we could successfully lower the inputs for pretreatment and enzymatic hydrolysis. Based on sugar yields as well as capital, feedstock, and operating costs, 120 °C NaOH-H 2 O pre-extraction was superior to both 120 °C NaOH-EtOH and 30 °C NaOH-H 2 O pre-extraction.

Evaluation of sequential extraction procedures for soluble and insoluble hexavalent chromium compounds in workplace air samples.

PubMed

Ashley, Kevin; Applegate, Gregory T; Marcy, A Dale; Drake, Pamela L; Pierce, Paul A; Carabin, Nathalie; Demange, Martine

2009-02-01

Because toxicities may differ for Cr(VI) compounds of varying solubility, some countries and organizations have promulgated different occupational exposure limits (OELs) for soluble and insoluble hexavalent chromium (Cr(VI)) compounds, and analytical methods are needed to determine these species in workplace air samples. To address this need, international standard methods ASTM D6832 and ISO 16740 have been published that describe sequential extraction techniques for soluble and insoluble Cr(VI) in samples collected from occupational settings. However, no published performance data were previously available for these Cr(VI) sequential extraction procedures. In this work, the sequential extraction methods outlined in the relevant international standards were investigated. The procedures tested involved the use of either deionized water or an ammonium sulfate/ammonium hydroxide buffer solution to target soluble Cr(VI) species. This was followed by extraction in a sodium carbonate/sodium hydroxide buffer solution to dissolve insoluble Cr(VI) compounds. Three-step sequential extraction with (1) water, (2) sulfate buffer and (3) carbonate buffer was also investigated. Sequential extractions were carried out on spiked samples of soluble, sparingly soluble and insoluble Cr(VI) compounds, and analyses were then generally carried out by using the diphenylcarbazide method. Similar experiments were performed on paint pigment samples and on airborne particulate filter samples collected from stainless steel welding. Potential interferences from soluble and insoluble Cr(III) compounds, as well as from Fe(II), were investigated. Interferences from Cr(III) species were generally absent, while the presence of Fe(II) resulted in low Cr(VI) recoveries. Two-step sequential extraction of spiked samples with (first) either water or sulfate buffer, and then carbonate buffer, yielded quantitative recoveries of soluble Cr(VI) and insoluble Cr(VI), respectively. Three-step sequential extraction gave excessively high recoveries of soluble Cr(VI), low recoveries of sparingly soluble Cr(VI), and quantitative recoveries of insoluble Cr(VI). Experiments on paint pigment samples using two-step extraction with water and carbonate buffer yielded varying percentages of relative fractions of soluble and insoluble Cr(VI). Sequential extractions of stainless steel welding fume air filter samples demonstrated the predominance of soluble Cr(VI) compounds in such samples. The performance data obtained in this work support the Cr(VI) sequential extraction procedures described in the international standards.

Integrated experimental and technoeconomic evaluation of two-stage Cu-catalyzed alkaline–oxidative pretreatment of hybrid poplar

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

Bhalla, Aditya; Fasahati, Peyman; Particka, Chrislyn A.

When applied to recalcitrant lignocellulosic feedstocks, multi-stage pretreatments can provide more processing flexibility to optimize or balance process outcomes such as increasing delignification, preserving hemicellulose, and maximizing enzymatic hydrolysis yields. We previously reported that adding an alkaline pre-extraction step to a copper-catalyzed alkaline hydrogen peroxide (Cu-AHP) pretreatment process resulted in improved sugar yields, but the process still utilized relatively high chemical inputs (catalyst and H 2O 2) and enzyme loadings. We hypothesized that by increasing the temperature of the alkaline pre-extraction step in water or ethanol, we could reduce the inputs required during Cu-AHP pretreatment and enzymatic hydrolysis without significantmore » loss in sugar yield. We also performed technoeconomic analysis to determine if ethanol or water was the more cost-effective solvent during alkaline pre-extraction and if the expense associated with increasing the temperature was economically justified. After Cu-AHP pretreatment of 120 °C NaOH-H 2O pre-extracted and 120 °C NaOH-EtOH pre-extracted biomass, approximately 1.4-fold more total lignin was solubilized (78% and 74%, respectively) compared to the 30 °C NaOH-H 2O pre-extraction (55%) carried out in a previous study. Consequently, increasing the temperature of the alkaline pre-extraction step to 120 °C in both ethanol and water allowed us to decrease bipyridine and H 2O 2 during Cu-AHP and enzymes during hydrolysis with only a small reduction in sugar yields compared to 30 °C alkaline pre-extraction. Technoeconomic analysis indicated that 120 °C NaOH-H 2O pre-extraction has the lowest installed ($246 million) and raw material (175 million) costs compared to the other process configurations. We found that by increasing the temperature of the alkaline pre-extraction step, we could successfully lower the inputs for pretreatment and enzymatic hydrolysis. Based on sugar yields as well as capital, feedstock, and operating costs, 120 °C NaOH-H 2O pre-extraction was superior to both 120 °C NaOH-EtOH and 30 °C NaOH-H 2O pre-extraction.« less

Integrated experimental and technoeconomic evaluation of two-stage Cu-catalyzed alkaline–oxidative pretreatment of hybrid poplar

DOE PAGES

Bhalla, Aditya; Fasahati, Peyman; Particka, Chrislyn A.; ...

2018-05-17

When applied to recalcitrant lignocellulosic feedstocks, multi-stage pretreatments can provide more processing flexibility to optimize or balance process outcomes such as increasing delignification, preserving hemicellulose, and maximizing enzymatic hydrolysis yields. We previously reported that adding an alkaline pre-extraction step to a copper-catalyzed alkaline hydrogen peroxide (Cu-AHP) pretreatment process resulted in improved sugar yields, but the process still utilized relatively high chemical inputs (catalyst and H 2O 2) and enzyme loadings. We hypothesized that by increasing the temperature of the alkaline pre-extraction step in water or ethanol, we could reduce the inputs required during Cu-AHP pretreatment and enzymatic hydrolysis without significantmore » loss in sugar yield. We also performed technoeconomic analysis to determine if ethanol or water was the more cost-effective solvent during alkaline pre-extraction and if the expense associated with increasing the temperature was economically justified. After Cu-AHP pretreatment of 120 °C NaOH-H 2O pre-extracted and 120 °C NaOH-EtOH pre-extracted biomass, approximately 1.4-fold more total lignin was solubilized (78% and 74%, respectively) compared to the 30 °C NaOH-H 2O pre-extraction (55%) carried out in a previous study. Consequently, increasing the temperature of the alkaline pre-extraction step to 120 °C in both ethanol and water allowed us to decrease bipyridine and H 2O 2 during Cu-AHP and enzymes during hydrolysis with only a small reduction in sugar yields compared to 30 °C alkaline pre-extraction. Technoeconomic analysis indicated that 120 °C NaOH-H 2O pre-extraction has the lowest installed ($246 million) and raw material (175 million) costs compared to the other process configurations. We found that by increasing the temperature of the alkaline pre-extraction step, we could successfully lower the inputs for pretreatment and enzymatic hydrolysis. Based on sugar yields as well as capital, feedstock, and operating costs, 120 °C NaOH-H 2O pre-extraction was superior to both 120 °C NaOH-EtOH and 30 °C NaOH-H 2O pre-extraction.« less

Design and application of PDF model for extracting

NASA Astrophysics Data System (ADS)

Xiong, Lei

2013-07-01

In order to change the steps of contributions in editorial department system from two steps to one, this paper advocates that the technology of extracting the information of PDF files should be transplanted from PDF reader into IEEE Xplore contribution system and that it should be combined with uploading in batch skillfully to enable editors to upload PDF files about 1GB in batch for once. Computers will extract the information of the title, author, address, mailbox, abstract and key words of thesis voluntarily for later retrieval so as to save plenty of labor, material and finance for editorial department.

Natural deep eutectic solvent mediated pretreatment of rice straw: bioanalytical characterization of lignin extract and enzymatic hydrolysis of pretreated biomass residue.

PubMed

Kumar, Adepu K; Parikh, Bhumika S; Pravakar, Mohanty

2016-05-01

The present investigation demonstrated pretreatment of lignocellulosic biomass rice straw using natural deep eutectic solvents (NADESs), and separation of high-quality lignin and holocellulose in a single step. Qualitative analysis of the NADES extract showed that the extracted lignin was of high purity (>90 %), and quantitative analysis showed that nearly 60 ± 5 % (w/w) of total lignin was separated from the lignocellulosic biomass. Addition of 5.0 % (v/v) water during pretreatment significantly enhanced the total lignin extraction, and nearly 22 ± 3 % more lignin was released from the residual biomass into the NADES extract. X-ray diffraction studies of the untreated and pretreated rice straw biomass showed that the crystallinity index ratio was marginally decreased from 46.4 to 44.3 %, indicating subtle structural alterations in the crystalline and amorphous regions of the cellulosic fractions. Thermogravimetric analysis of the pretreated biomass residue revealed a slightly higher T dcp (295 °C) compared to the T dcp (285 °C) of untreated biomass. Among the tested NADES reagents, lactic acid/choline chloride at molar ratio of 5:1 extracted maximum lignin of 68 ± 4 mg g(-1) from the rice straw biomass, and subsequent enzymatic hydrolysis of the residual holocellulose enriched biomass showed maximum reducing sugars of 333 ± 11 mg g(-1) with a saccharification efficiency of 36.0 ± 3.2 % in 24 h at 10 % solids loading.

Magnetic Beads-Based Sensor with Tailored Sensitivity for Rapid and Single-Step Amperometric Determination of miRNAs.

PubMed

Vargas, Eva; Torrente-Rodríguez, Rebeca M; Ruiz-Valdepeñas Montiel, Víctor; Povedano, Eloy; Pedrero, María; Montoya, Juan J; Campuzano, Susana; Pingarrón, José M

2017-11-09

This work describes a sensitive amperometric magneto-biosensor for single-step and rapid determination of microRNAs (miRNAs). The developed strategy involves the use of direct hybridization of the target miRNA (miRNA-21) with a specific biotinylated DNA probe immobilized on streptavidin-modified magnetic beads (MBs), and labeling of the resulting heteroduplexes with a specific DNA-RNA antibody and the bacterial protein A (ProtA) conjugated with an horseradish peroxidase (HRP) homopolymer (Poly-HRP40) as an enzymatic label for signal amplification. Amperometric detection is performed upon magnetic capture of the modified MBs onto the working electrode surface of disposable screen-printed carbon electrodes (SPCEs) using the H₂O₂/hydroquinone (HQ) system. The magnitude of the cathodic signal obtained at -0.20 V (vs. the Ag pseudo-reference electrode) demonstrated linear dependence with the concentration of the synthetic target miRNA over the 1.0 to 100 pM range. The method provided a detection limit (LOD) of 10 attomoles (in a 25 μL sample) without any target miRNA amplification in just 30 min (once the DNA capture probe-MBs were prepared). This approach shows improved sensitivity compared with that of biosensors constructed with the same anti-DNA-RNA Ab as capture instead of a detector antibody and further labeling with a Strep-HRP conjugate instead of the Poly-HRP40 homopolymer. The developed strategy involves a single step working protocol, as well as the possibility to tailor the sensitivity by enlarging the length of the DNA/miRNA heteroduplexes using additional probes and/or performing the labelling with ProtA conjugated with homopolymers prepared with different numbers of HRP molecules. The practical usefulness was demonstrated by determination of the endogenous levels of the mature target miRNA in 250 ng raw total RNA (RNA t ) extracted from human mammary epithelial normal (MCF-10A) and cancer (MCF-7) cells and tumor tissues.

The stepping behavior analysis of pedestrians from different age groups via a single-file experiment

NASA Astrophysics Data System (ADS)

Cao, Shuchao; Zhang, Jun; Song, Weiguo; Shi, Chang'an; Zhang, Ruifang

2018-03-01

The stepping behavior of pedestrians with different age compositions in single-file experiment is investigated in this paper. The relation between step length, step width and stepping time are analyzed by using the step measurement method based on the calculation of curvature of the trajectory. The relations of velocity-step width, velocity-step length and velocity-stepping time for different age groups are discussed and compared with previous studies. Finally effects of pedestrian gender and height on stepping laws and fundamental diagrams are analyzed. The study is helpful for understanding pedestrian dynamics of movement. Meanwhile, it offers experimental data to develop a microscopic model of pedestrian movement by considering stepping behavior.

Solid-phase extraction using bis(indolyl)methane-modified silica reinforced with multiwalled carbon nanotubes for the simultaneous determination of flavonoids and aromatic organic acid preservatives.

PubMed

Wang, Na; Liao, Yuan; Wang, Jiamin; Tang, Sheng; Shao, Shijun

2015-12-01

A novel bis(indolyl)methane-modified silica reinforced with multiwalled carbon nanotubes sorbent for solid-phase extraction was designed and synthesized by chemical immobilization of nitro-substituted 3,3'-bis(indolyl)methane on silica modified with multiwalled carbon nanotubes. Coupled with high-performance liquid chromatography analysis, the extraction properties of the sorbent were evaluated for flavonoids and aromatic organic acid compounds. Under optimum conditions, the sorbent can simultaneously extract five flavonoids and two aromatic organic acid preservatives in aqueous solutions in a single-step solid-phase extraction procedure. Wide linear ranges were obtained with correlation coefficients (R(2) ) ranging from 0.9843 to 0.9976, and the limits of detection were in the range of 0.5-5 μg/L for the compounds tested. Compared with the silica modified with multiwalled carbon nanotubes sorbent and the nitro-substituted 3,3'-bis(indolyl)methane-modified silica sorbent, the developed sorbent exhibited higher extraction efficiency toward the selected analytes. The synergistic effect of nitro-substituted 3,3'-bis(indolyl)methane and multiwalled carbon nanotubes not only improved the surface-to-volume ratio but also enhanced multiple intermolecular interactions, such as hydrogen bonds, π-π, and hydrophobic interactions, between the new sorbent and the selected analytes. The as-established solid-phase extraction with high-performance liquid chromatography and diode array detection method was successfully applied to the simultaneous determination of flavonoids and aromatic organic acid preservatives in grape juices with recoveries ranging from 83.9 to 112% for all the selected analytes. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Perpetual extraction of work from a nonequilibrium dynamical system under Markovian feedback control

NASA Astrophysics Data System (ADS)

Kosugi, Taichi

2013-09-01

By treating both control parameters and dynamical variables as probabilistic variables, we develop a succinct theory of perpetual extraction of work from a generic classical nonequilibrium system subject to a heat bath via repeated measurements under a Markovian feedback control. It is demonstrated that a problem for perpetual extraction of work in a nonequilibrium system is reduced to a problem of Markov chain in the higher-dimensional phase space. We derive a version of the detailed fluctuation theorem, which was originally derived for classical nonequilibrium systems by Horowitz and Vaikuntanathan [Phys. Rev. EPLEEE81539-375510.1103/PhysRevE.82.061120 82, 061120 (2010)], in a form suitable for the analyses of perpetual extraction of work. Since our theory is formulated for generic dynamics of probability distribution function in phase space, its application to a physical system is straightforward. As simple applications of the theory, two exactly solvable models are analyzed. The one is a nonequilibrium two-state system and the other is a particle confined to a one-dimensional harmonic potential in thermal equilibrium. For the former example, it is demonstrated that the observer on the transitory steps to the stationary state can lose energy and that work larger than that achieved in the stationary state can be extracted. For the latter example, it is demonstrated that the optimal protocol for the extraction of work via repeated measurements can differ from that via a single measurement. The validity of our version of the detailed fluctuation theorem, which determines the upper bound of the expected work in the stationary state, is also confirmed for both examples. These observations provide useful insights into exploration for realistic modeling of a machine that extracts work from its environment.

VHR satellite multitemporal data to extract cultural landscape changes in the roman site of Grumentum

NASA Astrophysics Data System (ADS)

masini, nicola; Lasaponara, Rosa

2013-04-01

The papers deals with the use of VHR satellite multitemporal data set to extract cultural landscape changes in the roman site of Grumentum Grumentum is an ancient town, 50 km south of Potenza, located near the roman road of Via Herculea which connected the Venusia, in the north est of Basilicata, with Heraclea in the Ionian coast. The first settlement date back to the 6th century BC. It was resettled by the Romans in the 3rd century BC. Its urban fabric which evidences a long history from the Republican age to late Antiquity (III BC-V AD) is composed of the typical urban pattern of cardi and decumani. Its excavated ruins include a large amphitheatre, a theatre, the thermae, the Forum and some temples. There are many techniques nowadays available to capture and record differences in two or more images. In this paper we focus and apply the two main approaches which can be distinguished into : (i) unsupervised and (ii) supervised change detection methods. Unsupervised change detection methods are generally based on the transformation of the two multispectral images in to a single band or multiband image which are further analyzed to identify changes Unsupervised change detection techniques are generally based on three basic steps (i) the preprocessing step, (ii) a pixel-by-pixel comparison is performed, (iii). Identification of changes according to the magnitude an direction (positive /negative). Unsupervised change detection are generally based on the transformation of the two multispectral images into a single band or multiband image which are further analyzed to identify changes. Than the separation between changed and unchanged classes is obtained from the magnitude of the resulting spectral change vectors by means of empirical or theoretical well founded approaches Supervised change detection methods are generally based on supervised classification methods, which require the availability of a suitable training set for the learning process of the classifiers. Unsupervised change detection techniques are generally based on three basic steps (i) the preprocessing step, (ii) supervised classification is performed on the single dates or on the map obtained as the difference of two dates, (iii). Identification of changes according to the magnitude an direction (positive /negative). Supervised change detection are generally based on supervised classification methods, which require the availability of a suitable training set for the learning process of the classifiers, therefore these algorithms require a preliminary knowledge necessary: (i) to generate representative parameters for each class of interest; and (ii) to carry out the training stage Advantages and disadvantages of the supervised and unsupervised approaches are discuss. Finally results from the the satellite multitemporal dataset was also integrated with aerial photos from historical archive in order to expand the time window of the investigation and capture landscape changes occurred from the Agrarian Reform, in the 50s, up today.

Subcritical water extraction of organic matter from sedimentary rocks.

PubMed

Luong, Duy; Sephton, Mark A; Watson, Jonathan S

2015-06-16

Subcritical water extraction of organic matter containing sedimentary rocks at 300°C and 1500 psi produces extracts comparable to conventional solvent extraction. Subcritical water extraction of previously solvent extracted samples confirms that high molecular weight organic matter (kerogen) degradation is not occurring and that only low molecular weight organic matter (free compounds) are being accessed in analogy to solvent extraction procedures. The sedimentary rocks chosen for extraction span the classic geochemical organic matter types. A type I organic matter-containing sedimentary rock produces n-alkanes and isoprenoidal hydrocarbons at 300°C and 1500 psi that indicate an algal source for the organic matter. Extraction of a rock containing type II organic matter at the same temperature and pressure produces aliphatic hydrocarbons but also aromatic compounds reflecting the increased contributions from terrestrial organic matter in this sample. A type III organic matter-containing sample produces a range of non-polar and polar compounds including polycyclic aromatic hydrocarbons and oxygenated aromatic compounds at 300°C and 1500 psi reflecting a dominantly terrestrial origin for the organic materials. Although extraction at 300°C and 1500 psi produces extracts that are comparable to solvent extraction, lower temperature steps display differences related to organic solubility. The type I organic matter produces no products below 300°C and 1500 psi, reflecting its dominantly aliphatic character, while type II and type III organic matter contribute some polar components to the lower temperature steps, reflecting the chemical heterogeneity of their organic inventory. The separation of polar and non-polar organic compounds by using different temperatures provides the potential for selective extraction that may obviate the need for subsequent preparative chromatography steps. Our results indicate that subcritical water extraction can act as a suitable replacement for conventional solvent extraction of sedimentary rocks, but can also be used for any organic matter containing mineral matrix, including soils and recent sediments, and has the added benefit of tailored extraction for analytes of specific polarities. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Validation of lipolysis product extraction from aqueous/biological samples, separation and quantification by thin-layer chromatography with flame ionization detection analysis using O-cholesteryl ethylene glycol as a new internal standard.

PubMed

Cavalier, Jean-François; Lafont, Dominique; Boullanger, Paul; Houisse, David; Giallo, Jacqueline; Ballester, Jean-Michel; Carrière, Frédéric

2009-09-11

A general and easily accessible method for the extraction followed by the simultaneous separation and quantitative determination of triacylglycerols, diacylglycerols, monoacylglycerols and free fatty acids has been improved and optimized based on existing protocols using liquid-phase extraction and thin-layer chromatography coupled to flame ionization detection (TLC/FID Iatroscan). After lipid extraction in the presence of a suitable new synthetic internal standard, namely CholE1, a single elution step using n-heptane/diethyl ether/formic acid (55:45:1, v/v/v) was applied. This method was validated in line with international bioanalytical method validation guidelines using two different matrix systems: purified water and human gastro-intestinal fluid. Overall, the assay was found to have high levels of precision with coefficients of variation ranging from 1.48% to 11.0% and accuracy ranging from -13.3% to +5.79% RE. The confidence limits of the lipid mean recovery rates varied between 89.9% and 104%. This method is therefore highly suitable for quantifying the lipolysis products generated in vitro during the hydrolysis of various fats and oils by digestive lipases, as well as those collected from the gastro-intestinal tract in the course of human clinical studies on lipid digestion.

An efficient approach to selective electromembrane extraction of naproxen by means of molecularly imprinted polymer-coated multi-walled carbon nanotubes-reinforced hollow fibers.

PubMed

Tahmasebi, Zeinab; Davarani, Saied Saeed Hosseiny; Asgharinezhad, Ali Akbar

2016-10-28

In this work, a novel microextraction technique using molecularly imprinted polymer-coated multi-walled carbon nanotubes (MIP-MWCNTs) in electromembrane extraction (EME) procedure is described. The method in combination with HPLC-UV was utilized to determine naproxen, as an acidic model drug, in urine, plasma and wastewater samples. For this purpose, MIP-MWCNTs were placed in the pores of polypropylene hollow fiber. The MIP-MWCNTs-EME method has the advantages of high selectivity and cleanup of MIP along with high enrichment ability of the EME in a single step extraction. Continuing with the research, optimization of the factors affecting the migration of naproxen from sample solutions to MIP-MWCNTs sites and then into the lumen of hollow fiber was explored. Under the optimized conditions, the limit of detection (LOD) of the developed method was calculated to be 0.3μgL -1 . All relative standard deviations (RSDs) were lower than 3%. Linearity of the method was obtained within the range of 1-1000μgL -1 with the coefficient of determination (r 2 ) being higher than 0.999. Under the optimized conditions, an extraction recovery of 66% was obtained, which corresponded to a preconcentration factor of 88. Finally, the developed method was satisfactorily used to determine naproxen in urine, plasma and wastewater samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Methods for Integrated Air Sampling and DNA Analysis for Detection of Airborne Fungal Spores

PubMed Central

Williams, Roger H.; Ward, Elaine; McCartney, H. Alastair

2001-01-01

Integrated air sampling and PCR-based methods for detecting airborne fungal spores, using Penicillium roqueforti as a model fungus, are described. P. roqueforti spores were collected directly into Eppendorf tubes using a miniature cyclone-type air sampler. They were then suspended in 0.1% Nonidet P-40, and counted using microscopy. Serial dilutions of the spores were made. Three methods were used to produce DNA for PCR tests: adding untreated spores to PCRs, disrupting spores (fracturing of spore walls to release the contents) using Ballotini beads, and disrupting spores followed by DNA purification. Three P. roqueforti-specific assays were tested: single-step PCR, nested PCR, and PCR followed by Southern blotting and probing. Disrupting the spores was found to be essential for achieving maximum sensitivity of the assay. Adding untreated spores to the PCR did allow the detection of P. roqueforti, but this was never achieved when fewer than 1,000 spores were added to the PCR. By disrupting the spores, with or without subsequent DNA purification, it was possible to detect DNA from a single spore. When known quantities of P. roqueforti spores were added to air samples consisting of high concentrations of unidentified fungal spores, pollen, and dust, detection sensitivity was reduced. P. roqueforti DNA could not be detected using untreated or disrupted spore suspensions added to the PCRs. However, using purified DNA, it was possible to detect 10 P. roqueforti spores in a background of 4,500 other spores. For all DNA extraction methods, nested PCR was more sensitive than single-step PCR or PCR followed by Southern blotting. PMID:11375150

[Traditional Chinese medicine pairs (III)--effect of extract of Ginseng Radix et Rhizoma and Puerariae Lobatae Radix on intestinal absorption in rats].

PubMed

Chen, Yi-hang; Li, Meng-xuan; Meng, Zhao-qing; Yang, Jiao-jiao; Huang, Wen-zhe; Wang, Zhen-zhong; Wang, Yue-sheng; Xiao, Wei

2015-08-01

This study focused on the intestinal absorption of traditional Chinese medicines (TCM) to reveal the scientific connotation of the compatibility of TCM pairs. The single pass intestinal perfusion (SPIP) was used in rats to compare the absorption of single extracts from Puerariae Lobatae Radix, single extracts from Ginseng Radix et Rhizoma, combined extracts from Puerariae Lobatae Radix and Ginseng Radix et Rhizoma and Puerariae Lobatae Radix and Ginseng Radix et Rhizoma mixture in rats. The content of puerarin, ginsenoside Rg1, ginsenoside Re and ginsenoside Rb1 in liquid were tested by HPLC. The speed constant (Ka) and apparent permeability coefficients (Papp) were calculated and compared. Specifically, the order of puerarin Ka and Papp values from high to low was Ginseng Radix et Rhizoma and Puerariae Lobatae Radix mixture > single extracts from Puerariae Lobatae Radix > combined extracts from Ginseng Radix et Rhizoma and Puerariae Lobatae Radix; the order of ginsenosides Ka and Papp values from high to low was Ginseng Radix et Rhizoma and Puerariae Lobatae Radix mixture > single extracts from Ginseng Radix et Rhizoma > combined extracts from Ginseng Radix et Rhizoma and Puerariae Lobatae Radix. The combined administration of Ginseng Radix et Rhizoma and Puerariae Lobatae Radix may improve the absorption in the intestinal tract.

Step-to-step spatiotemporal variables and ground reaction forces of intra-individual fastest sprinting in a single session.

PubMed

Nagahara, Ryu; Mizutani, Mirai; Matsuo, Akifumi; Kanehisa, Hiroaki; Fukunaga, Tetsuo

2018-06-01

We aimed to investigate the step-to-step spatiotemporal variables and ground reaction forces during the acceleration phase for characterising intra-individual fastest sprinting within a single session. Step-to-step spatiotemporal variables and ground reaction forces produced by 15 male athletes were measured over a 50-m distance during repeated (three to five) 60-m sprints using a long force platform system. Differences in measured variables between the fastest and slowest trials were examined at each step until the 22nd step using a magnitude-based inferences approach. There were possibly-most likely higher running speed and step frequency (2nd to 22nd steps) and shorter support time (all steps) in the fastest trial than in the slowest trial. Moreover, for the fastest trial there were likely-very likely greater mean propulsive force during the initial four steps and possibly-very likely larger mean net anterior-posterior force until the 17th step. The current results demonstrate that better sprinting performance within a single session is probably achieved by 1) a high step frequency (except the initial step) with short support time at all steps, 2) exerting a greater mean propulsive force during initial acceleration, and 3) producing a greater mean net anterior-posterior force during initial and middle acceleration.

Controlling dental enamel-cavity ablation depth with optimized stepping parameters along the focal plane normal using a three axis, numerically controlled picosecond laser.

PubMed

Yuan, Fusong; Lv, Peijun; Wang, Dangxiao; Wang, Lei; Sun, Yuchun; Wang, Yong

2015-02-01

The purpose of this study was to establish a depth-control method in enamel-cavity ablation by optimizing the timing of the focal-plane-normal stepping and the single-step size of a three axis, numerically controlled picosecond laser. Although it has been proposed that picosecond lasers may be used to ablate dental hard tissue, the viability of such a depth-control method in enamel-cavity ablation remains uncertain. Forty-two enamel slices with approximately level surfaces were prepared and subjected to two-dimensional ablation by a picosecond laser. The additive-pulse layer, n, was set to 5, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70. A three-dimensional microscope was then used to measure the ablation depth, d, to obtain a quantitative function relating n and d. Six enamel slices were then subjected to three dimensional ablation to produce 10 cavities, respectively, with additive-pulse layer and single-step size set to corresponding values. The difference between the theoretical and measured values was calculated for both the cavity depth and the ablation depth of a single step. These were used to determine minimum-difference values for both the additive-pulse layer (n) and single-step size (d). When the additive-pulse layer and the single-step size were set 5 and 45, respectively, the depth error had a minimum of 2.25 μm, and 450 μm deep enamel cavities were produced. When performing three-dimensional ablating of enamel with a picosecond laser, adjusting the timing of the focal-plane-normal stepping and the single-step size allows for the control of ablation-depth error to the order of micrometers.

Ionic liquid-based dispersive liquid-liquid microextraction with back-extraction coupled with capillary electrophoresis to determine phenolic compounds.

PubMed

Zhou, Caihong; Tong, Shanshan; Chang, Yunxia; Jia, Qiong; Zhou, Weihong

2012-04-01

Ionic liquid (IL) based dispersive liquid-liquid microextraction (DLLME) with back-extraction coupled with capillary electrophoresis ultraviolet detection was developed to determine four phenolic compounds (bisphenol-A, β-naphthol, α-naphthol, 2, 4-dichlorophenol) in aqueous cosmetics. The developed method was used to preconcentrate and clean up the four phenolic compounds including two steps. The analytes were transferred into room temperature ionic liquid (1-octyl-3-methylimidazolium hexafluorophosphate, [C(8) MIM][PF(6) ]) rich-phase in the first step. In the second step, the analytes were back-extracted into the alkaline aqueous phase. The effects of extraction parameters, such as type and volume of extraction solvent, type and volume of disperser, extraction and centrifugal time, sample pH, salt addition, and concentration and volume of NaOH in back-extraction were investigated. Under the optimal experimental conditions, the preconcentration factors were 60.1 for bisphenol-A, 52.7 for β-naphthol, 49.2 for α-naphthol, and 18.0 for 2, 4-dichlorophenol. The limits of detection for bisphenol-A, β-naphthol, α-naphthol and 2, 4-dichlorophenol were 5, 5, 8, and 100 ng mL(-1), respectively. Four kinds of aqueous cosmetics including toner, soften lotion, make-up remover, and perfume were analyzed and yielded recoveries ranging from 81.6% to 119.4%. The main advantages of the proposed method are quick, easy, cheap, and effective. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Effects of Multiple-Step and Single-Step Directions on Fourth and Fifth Grade Students' Grammar Assessment Performance

ERIC Educational Resources Information Center

Mazerik, Matthew B.

2006-01-01

The mean scores of English Language Learners (ELL) and English Only (EO) students in 4th and 5th grade (N = 110), across the teacher-administered Grammar Skills Test, were examined for differences in participants' scores on assessments containing single-step directions and assessments containing multiple-step directions. The results indicated no…

Longevity of rAAV vector and plasmid DNA in blood after intramuscular injection in nonhuman primates: implications for gene doping.

PubMed

Ni, W; Le Guiner, C; Gernoux, G; Penaud-Budloo, M; Moullier, P; Snyder, R O

2011-07-01

Legitimate uses of gene transfer technology can benefit from sensitive detection methods to determine vector biodistribution in pre-clinical studies and in human clinical trials, and similar methods can detect illegitimate gene transfer to provide sports-governing bodies with the ability to maintain fairness. Real-time PCR assays were developed to detect a performance-enhancing transgene (erythropoietin, EPO) and backbone sequences in the presence of endogenous cellular sequences. In addition to developing real-time PCR assays, the steps involved in DNA extraction, storage and transport were investigated. By real-time PCR, the vector transgene is distinguishable from the genomic DNA sequence because of the absence of introns, and the vector backbone can be identified by heterologous gene expression control elements. After performance of the assays was optimized, cynomolgus macaques received a single dose by intramuscular (IM) injection of plasmid DNA, a recombinant adeno-associated viral vector serotype 1 (rAAV1) or a rAAV8 vector expressing cynomolgus macaque EPO. Macaques received a high plasmid dose intended to achieve a significant, but not life-threatening, increase in hematocrit. rAAV vectors were used at low doses to achieve a small increase in hematocrit and to determine the limit of sensitivity for detecting rAAV sequences by single-step PCR. DNA extracted from white blood cells (WBCs) was tested to determine whether WBCs can be collaterally transfected by plasmid or transduced by rAAV vectors in this context, and can be used as a surrogate marker for gene doping. We demonstrate that IM injection of a conventional plasmid and rAAV vectors results in the presence of DNA that can be detected at high levels in blood before rapid elimination, and that rAAV genomes can persist for several months in WBCs.

Evaluation of accuracy in implant site preparation performed in single- or multi-step drilling procedures.

PubMed

Marheineke, Nadine; Scherer, Uta; Rücker, Martin; von See, Constantin; Rahlf, Björn; Gellrich, Nils-Claudius; Stoetzer, Marcus

2018-06-01

Dental implant failure and insufficient osseointegration are proven results of mechanical and thermal damage during the surgery process. We herein performed a comparative study of a less invasive single-step drilling preparation protocol and a conventional multiple drilling sequence. Accuracy of drilling holes was precisely analyzed and the influence of different levels of expertise of the handlers and additional use of drill template guidance was evaluated. Six experimental groups, deployed in an osseous study model, were representing template-guided and freehanded drilling actions in a stepwise drilling procedure in comparison to a single-drill protocol. Each experimental condition was studied by the drilling actions of respectively three persons without surgical knowledge as well as three highly experienced oral surgeons. Drilling actions were performed and diameters were recorded with a precision measuring instrument. Less experienced operators were able to significantly increase the drilling accuracy using a guiding template, especially when multi-step preparations are performed. Improved accuracy without template guidance was observed when experienced operators were executing single-step versus multi-step technique. Single-step drilling protocols have shown to produce more accurate results than multi-step procedures. The outcome of any protocol can be further improved by use of guiding templates. Operator experience can be a contributing factor. Single-step preparations are less invasive and are promoting osseointegration. Even highly experienced surgeons are achieving higher levels of accuracy by combining this technique with template guidance. Hereby template guidance enables a reduction of hands-on time and side effects during surgery and lead to a more predictable clinical diameter.

Associations between bacteremia from oral sources and distant-site infections: tooth brushing versus single tooth extraction.

PubMed

Mougeot, Farah K Bahrani; Saunders, Sabrina E; Brennan, Michael T; Lockhart, Peter B

2015-04-01

To determine the impact of antibiotic prophylaxis (AP) on the incidence of bacteremia caused by oral bacterial species associated with infective endocarditis (IE) and prosthetic joint infections (PJIs) and to compare the incidence of following tooth brushing versus single tooth extraction. Bacterial species in blood following single tooth extraction, with or without AP, and tooth brushing(1) were compared with IE- and PJI-associated bacteria reported in the literature. Of the 98 bacterial species identified in blood following single tooth extraction and tooth brushing, 32(1) and 12 were species were associated with IE and PJI, respectively. AP decreased the frequency of IE- and PJI-causing oral bacterial species in blood; however, single tooth extraction versus brushing resulted in bacteremia with IE- and PJI-causing species with similar frequencies: 65% versus 56% for IE, and 31% versus 28% for PJI. Although AP significantly decreased the incidence of bacteremia, the similarity between the incidence of bacteremia following brushing and extraction undermines AP as an effective strategy for the prevention of these distant-site infections. Copyright © 2015 Elsevier Inc. All rights reserved.

Breast cancer mitosis detection in histopathological images with spatial feature extraction

NASA Astrophysics Data System (ADS)

Albayrak, Abdülkadir; Bilgin, Gökhan

2013-12-01

In this work, cellular mitosis detection in histopathological images has been investigated. Mitosis detection is very expensive and time consuming process. Development of digital imaging in pathology has enabled reasonable and effective solution to this problem. Segmentation of digital images provides easier analysis of cell structures in histopathological data. To differentiate normal and mitotic cells in histopathological images, feature extraction step is very crucial step for the system accuracy. A mitotic cell has more distinctive textural dissimilarities than the other normal cells. Hence, it is important to incorporate spatial information in feature extraction or in post-processing steps. As a main part of this study, Haralick texture descriptor has been proposed with different spatial window sizes in RGB and La*b* color spaces. So, spatial dependencies of normal and mitotic cellular pixels can be evaluated within different pixel neighborhoods. Extracted features are compared with various sample sizes by Support Vector Machines using k-fold cross validation method. According to the represented results, it has been shown that separation accuracy on mitotic and non-mitotic cellular pixels gets better with the increasing size of spatial window.

Extraction of toxic compounds from saliva by magnetic-stirring-assisted micro-solid-phase extraction step followed by headspace-gas chromatography-ion mobility spectrometry.

PubMed

Criado-García, Laura; Arce, Lourdes

2016-09-01

A new sample extraction procedure based on micro-solid-phase extraction (μSPE) using a mixture of sorbents of different polarities (polymeric reversed-phase sorbent HLB, silica-based sorbent C18, and multiwalled carbon nanotubes) was applied to extract benzene, toluene, butyraldehyde, benzaldehyde, and tolualdehyde present in saliva to avoid interference from moisture and matrix components and enhance sensitivity and selectivity of the ion mobility spectrometry (IMS) methodology proposed. The extraction of target analytes from saliva samples by using μSPE were followed by the desorption step carried out in the headspace vials placed in the autosampler of the IMS device. Then, 200 μL of headspace was injected into the GC column coupled to the IMS for its analysis. The method was fully validated in terms of sensitivity, precision, and recovery. The LODs and LOQs obtained, when analytes were dissolved in saliva samples to consider the matrix effect, were within the range of 0.38-0.49 and 1.26-1.66 μg mL(-1), respectively. The relative standard deviations were <3.5 % for retention time and drift time values, which indicate that the method proposed can be applied to determine toxic compounds in saliva samples. Graphical abstract Summary of steps followed in the experimental set up of this work.

Extraction of DNA from forensic-type sexual assault specimens using simple, rapid sonication procedures.

PubMed

Crouse, C A; Ban, J D; D'Alessio, J K

1993-10-01

Sonication procedures for the extraction of DNA from forensic-type semen specimens have been developed, which, when compared to currently utilized sperm DNA extraction techniques, are simple, rapid and result in comparable DNA yields. Sperm DNA extraction by sonication was performed on whole semen, seminal stains, buccal swabs and post-coital specimens. Ultrasound disruption of sperm cells and their ultimate release of cellular DNA has been conducted in the presence of sperm wash buffers followed by organic extraction or Chelex 100 with little or no compromise to DNA quality, quantity or amplifiability. Two advantages of sonication over currently used forensic techniques to extract sperm DNA include 1) sperm DNA extraction that occurs within five minutes of sonication compared with an hour or greater for water bath incubations in classic enzyme digestion DNA extractions and 2) one less preparatory step with the Chelex/sonication protocol and three less steps with the sonication/organic protocol compared with other procedures thus eliminating potential sample-to-sample cross-contamination. Sperm DNA extracted by optimum sonication procedures was used for forensic HLA DQ alpha typing and restriction fragment length polymorphisms analysis without any adverse effects on typing results.

Single-step electrochemical functionalization of double-walled carbon nanotube (DWCNT) membranes and the demonstration of ionic rectification

PubMed Central

2013-01-01

Carbon nanotube (CNT) membranes allow the mimicking of natural ion channels for applications in drug delivery and chemical separation. Double-walled carbon nanotube membranes were simply functionalized with dye in a single step instead of the previous two-step functionalization. Non-faradic electrochemical impedance spectra indicated that the functionalized gatekeeper by single-step modification can be actuated to mimic the protein channel under bias. This functional chemistry was proven by a highly efficient ion rectification, wherein the highest experimental rectification factor of ferricyanide was up to 14.4. One-step functionalization by electrooxidation of amine provides a simple and promising functionalization chemistry for the application of CNT membranes. PMID:23758999

Vessel extraction in retinal images using automatic thresholding and Gabor Wavelet.

PubMed

Ali, Aziah; Hussain, Aini; Wan Zaki, Wan Mimi Diyana

2017-07-01

Retinal image analysis has been widely used for early detection and diagnosis of multiple systemic diseases. Accurate vessel extraction in retinal image is a crucial step towards a fully automated diagnosis system. This work affords an efficient unsupervised method for extracting blood vessels from retinal images by combining existing Gabor Wavelet (GW) method with automatic thresholding. Green channel image is extracted from color retinal image and used to produce Gabor feature image using GW. Both green channel image and Gabor feature image undergo vessel-enhancement step in order to highlight blood vessels. Next, the two vessel-enhanced images are transformed to binary images using automatic thresholding before combined to produce the final vessel output. Combining the images results in significant improvement of blood vessel extraction performance compared to using individual image. Effectiveness of the proposed method was proven via comparative analysis with existing methods validated using publicly available database, DRIVE.

PROCESS FOR UTILIZING ORGANIC ORTHOPHOSPHATE EXTRACTANTS

DOEpatents

Grinstead, R.R.

1958-11-11

A process is presented for recovering uranium from its ores, the steps comprising producing the uranium in solution in the trivalent state, extracting the uranium from solution in an lmmiscible organic solvent extract phase which lncludes mono and dialkyl orthophosphorlc acid esters having a varying number of carbon atoms on the alkyl substituent, amd recovering the uranium from tbe extract phase.

Event-triggered logical flow control for comprehensive process integration of multi-step assays on centrifugal microfluidic platforms.

PubMed

Kinahan, David J; Kearney, Sinéad M; Dimov, Nikolay; Glynn, Macdara T; Ducrée, Jens

2014-07-07

The centrifugal "lab-on-a-disc" concept has proven to have great potential for process integration of bioanalytical assays, in particular where ease-of-use, ruggedness, portability, fast turn-around time and cost efficiency are of paramount importance. Yet, as all liquids residing on the disc are exposed to the same centrifugal field, an inherent challenge of these systems remains the automation of multi-step, multi-liquid sample processing and subsequent detection. In order to orchestrate the underlying bioanalytical protocols, an ample palette of rotationally and externally actuated valving schemes has been developed. While excelling with the level of flow control, externally actuated valves require interaction with peripheral instrumentation, thus compromising the conceptual simplicity of the centrifugal platform. In turn, for rotationally controlled schemes, such as common capillary burst valves, typical manufacturing tolerances tend to limit the number of consecutive laboratory unit operations (LUOs) that can be automated on a single disc. In this paper, a major advancement on recently established dissolvable film (DF) valving is presented; for the very first time, a liquid handling sequence can be controlled in response to completion of preceding liquid transfer event, i.e. completely independent of external stimulus or changes in speed of disc rotation. The basic, event-triggered valve configuration is further adapted to leverage conditional, large-scale process integration. First, we demonstrate a fluidic network on a disc encompassing 10 discrete valving steps including logical relationships such as an AND-conditional as well as serial and parallel flow control. Then we present a disc which is capable of implementing common laboratory unit operations such as metering and selective routing of flows. Finally, as a pilot study, these functions are integrated on a single disc to automate a common, multi-step lab protocol for the extraction of total RNA from mammalian cell homogenate.

Development of a rapid and sensitive one-step reverse transcription-nested polymerase chain reaction in a single tube using the droplet-polymerase chain reaction machine.

PubMed

Yamaguchi, Akemi; Matsuda, Kazuyuki; Sueki, Akane; Taira, Chiaki; Uehara, Masayuki; Saito, Yasunori; Honda, Takayuki

2015-08-25

Reverse transcription (RT)-nested polymerase chain reaction (PCR) is a time-consuming procedure because it has several handling steps and is associated with the risk of cross-contamination during each step. Therefore, a rapid and sensitive one-step RT-nested PCR was developed that could be performed in a single tube using a droplet-PCR machine. The K562 BCR-ABL mRNA-positive cell line as well as bone marrow aspirates from 5 patients with chronic myelogenous leukemia (CML) and 5 controls without CML were used. We evaluated one-step RT-nested PCR using the droplet-PCR machine. One-step RT-nested PCR performed in a single tube using the droplet-PCR machine enabled the detection of BCR-ABL mRNA within 40min, which was 10(3)-fold superior to conventional RT nested PCR using three steps in separate tubes. The sensitivity of the one-step RT-nested PCR was 0.001%, with sample reactivity comparable to that of the conventional assay. One-step RT-nested PCR was developed using the droplet-PCR machine, which enabled all reactions to be performed in a single tube accurately and rapidly and with high sensitivity. This one-step RT-nested PCR may be applicable to a wide spectrum of genetic tests in clinical laboratories. Copyright © 2015 Elsevier B.V. All rights reserved.

Characteristics of camel-gate structures with active doping channel profiles

NASA Astrophysics Data System (ADS)

Tsai, Jung-Hui; Lour, Wen-Shiung; Laih, Lih-Wen; Liu, Rong-Chau; Liu, Wen-Chau

1996-03-01

In this paper, we demonstrate the influence of channel doping profile on the performances of camel-gate field effect transistors (CAMFETs). For comparison, single and tri-step doping channel structures with identical doping thickness products are employed, while other parameters are kept unchanged. The results of a theoretical analysis show that the single doping channel FET with lightly doping active layer has higher barrier height and drain-source saturation current. However, the transconductance is decreased. For a tri-step doping channel structure, it is found that the output drain-source saturation current and the barrier height are enhanced. Furthermore, the relatively voltage independent performances are improved. Two CAMFETs with single and tri-step doping channel structures have been fabricated and discussed. The devices exhibit nearly voltage independent transconductances of 144 mS mm -1 and 222 mS mm -1 for single and tri-step doping channel CAMFETs, respectively. The operation gate voltage may extend to ± 1.5 V for a tri-step doping channel CAMFET. In addition, the drain current densities of > 750 and 405 mA mm -1 are obtained for the tri-step and single doping CAMFETs. These experimental results are inconsistent with theoretical analysis.

A highly sensitive and accurate gene expression analysis by sequencing ("bead-seq") for a single cell.

PubMed

Matsunaga, Hiroko; Goto, Mari; Arikawa, Koji; Shirai, Masataka; Tsunoda, Hiroyuki; Huang, Huan; Kambara, Hideki

2015-02-15

Analyses of gene expressions in single cells are important for understanding detailed biological phenomena. Here, a highly sensitive and accurate method by sequencing (called "bead-seq") to obtain a whole gene expression profile for a single cell is proposed. A key feature of the method is to use a complementary DNA (cDNA) library on magnetic beads, which enables adding washing steps to remove residual reagents in a sample preparation process. By adding the washing steps, the next steps can be carried out under the optimal conditions without losing cDNAs. Error sources were carefully evaluated to conclude that the first several steps were the key steps. It is demonstrated that bead-seq is superior to the conventional methods for single-cell gene expression analyses in terms of reproducibility, quantitative accuracy, and biases caused during sample preparation and sequencing processes. Copyright © 2014 Elsevier Inc. All rights reserved.

An Experimental Implementation of Chemical Subtraction

PubMed Central

Chen, Shao-Nong; Turner, Allison; Jaki, Birgit U.; Nikolic, Dejan; van Breemen, Richard B.; Friesen, J. Brent; Pauli, Guido F.

2008-01-01

A preparative analytical method was developed to selectively remove (“chemically subtract”) a single compound from a complex mixture, such as a natural extract or fraction, in a single step. The proof of concept is demonstrated by the removal of pure benzoic acid (BA) from cranberry (Vaccinium macrocarpon Ait.) juice fractions that exhibit anti-adhesive effects vs. uropathogenic E. coli. Chemical subtraction of BA, representing a major constituent of the fractions, eliminates the potential in vitro interference of the bacteriostatic effect of BA on the E. coli anti-adherence action measured in bioassays. Upon BA removal, the anti-adherent activity of the fraction was fully retained, 36% inhibition of adherence in the parent fraction at 100 ug/mL increased to 58% in the BA-free active fraction. The method employs countercurrent chromatography (CCC) and operates loss-free for both the subtracted and the retained portions as only liquid-liquid partitioning is involved. While the high purity (97.47% by quantitative 1H NMR) of the subtracted BA confirms the selectivity of the method, one minor impurity was determined to be scopoletin by HR-ESI-MS and (q)HNMR and represents the first coumarin reported from cranberries. A general concept for the selective removal of phytoconstituents by CCC is presented, which has potential broad applicability in the biological evaluation of medicinal plant extracts and complex pharmaceutical preparations. PMID:18234463

Development of the Fray-Farthing-Chen Cambridge Process: Towards the Sustainable Production of Titanium and Its Alloys

NASA Astrophysics Data System (ADS)

Hu, Di; Dolganov, Aleksei; Ma, Mingchan; Bhattacharya, Biyash; Bishop, Matthew T.; Chen, George Z.

2018-02-01

The Kroll process has been employed for titanium extraction since the 1950s. It is a labour and energy intensive multi-step semi-batch process. The post-extraction processes for making the raw titanium into alloys and products are also excessive, including multiple remelting steps. Invented in the late 1990s, the Fray-Farthing-Chen (FFC) Cambridge process extracts titanium from solid oxides at lower energy consumption via electrochemical reduction in molten salts. Its ability to produce alloys and powders, while retaining the cathode shape also promises energy and material efficient manufacturing. Focusing on titanium and its alloys, this article reviews the recent development of the FFC-Cambridge process in two aspects, (1) resource and process sustainability and (2) advanced post-extraction processing.

[A customized method for information extraction from unstructured text data in the electronic medical records].

PubMed

Bao, X Y; Huang, W J; Zhang, K; Jin, M; Li, Y; Niu, C Z

2018-04-18

There is a huge amount of diagnostic or treatment information in electronic medical record (EMR), which is a concrete manifestation of clinicians actual diagnosis and treatment details. Plenty of episodes in EMRs, such as complaints, present illness, past history, differential diagnosis, diagnostic imaging, surgical records, reflecting details of diagnosis and treatment in clinical process, adopt Chinese description of natural language. How to extract effective information from these Chinese narrative text data, and organize it into a form of tabular for analysis of medical research, for the practical utilization of clinical data in the real world, is a difficult problem in Chinese medical data processing. Based on the EMRs narrative text data in a tertiary hospital in China, a customized information extracting rules learning, and rule based information extraction methods is proposed. The overall method consists of three steps, which includes: (1) Step 1, a random sample of 600 copies (including the history of present illness, past history, personal history, family history, etc.) of the electronic medical record data, was extracted as raw corpora. With our developed Chinese clinical narrative text annotation platform, the trained clinician and nurses marked the tokens and phrases in the corpora which would be extracted (with a history of diabetes as an example). (2) Step 2, based on the annotated corpora clinical text data, some extraction templates were summarized and induced firstly. Then these templates were rewritten using regular expressions of Perl programming language, as extraction rules. Using these extraction rules as basic knowledge base, we developed extraction packages in Perl, for extracting data from the EMRs text data. In the end, the extracted data items were organized in tabular data format, for later usage in clinical research or hospital surveillance purposes. (3) As the final step of the method, the evaluation and validation of the proposed methods were implemented in the National Clinical Service Data Integration Platform, and we checked the extraction results using artificial verification and automated verification combined, proved the effectiveness of the method. For all the patients with diabetes as diagnosed disease in the Department of Endocrine in the hospital, the medical history episode of these patients showed that, altogether 1 436 patients were dismissed in 2015, and a history of diabetes medical records extraction results showed that the recall rate was 87.6%, the accuracy rate was 99.5%, and F-Score was 0.93. For all the 10% patients (totally 1 223 patients) with diabetes by the dismissed dates of August 2017 in the same department, the extracted diabetes history extraction results showed that the recall rate was 89.2%, the accuracy rate was 99.2%, F-Score was 0.94. This study mainly adopts the combination of natural language processing and rule-based information extraction, and designs and implements an algorithm for extracting customized information from unstructured Chinese electronic medical record text data. It has better results than existing work.

Isolation and characterization of antimicrobial food components.

PubMed

Papetti, Adele

2012-04-01

Nowadays there is an evident growing interest in natural antimicrobial compounds isolated from food matrices. According to the type of matrix, different isolation and purification steps are needed and as these active compounds belong to different chemical classes, also different chromatographic and electrophoretic methods coupled with various detectors (the most used diode array detector and mass spectrometer) have to be performed. This review covers recent steps made in the fundamental understanding of sample preparation methods as well as of analytical tools useful for the complete characterization of bioactive food compounds. The most commonly used methods for extraction of natural antimicrobial compounds are the conventional liquid-liquid or solid-liquid extraction and the modern techniques such as pressurized liquid extraction, microwave-assisted extraction, ultrasound-assisted extraction, solid-phase micro-extraction, supercritical fluid extraction, and matrix solid phase dispersion. The complete characterization of the compounds is achieved using both monodimensional chromatographic processes (LC, nano-LC, GC, and CE coupled with different type of detectors) and, recently, using comprehensive two-dimensional systems (LC×LC and GC×GC). Copyright © 2011 Elsevier Ltd. All rights reserved.

Aviation accident forensic assessment : comprehensive single-extraction urine screening procedure : final report.

DOT National Transportation Integrated Search

1996-05-01

This paper describes a new single extraction screening procedure that was developed to identify as many drugs as possible in urine, with minimal effort and cost. Urine specimens are hydrolyzed and the specimen is then extracted using commercially pur...

Precise turnaround time measurement of laboratory processes using radiofrequency identification technology.

PubMed

Mayer, Horst; Brümmer, Jens; Brinkmann, Thomas

2011-01-01

To implement Lean Six Sigma in our central laboratory we conducted a project to measure single pre-analytical steps influencing turnaround time (TAT) of emergency department (ED) serum samples. The traditional approach of extracting data from the Laboratory Information System (LIS) for a retrospective calculation of a mean TAT is not suitable. Therefore, we used radiofrequency identification (RFID) chips for real time tracking of individual samples at any pre-analytical step. 1,200 serum tubes were labelled with RFID chips and were provided to the emergency department. 3 RFID receivers were installed in the laboratory: at the outlet of the pneumatic tube system, at the centrifuge, and in the analyser area. In addition, time stamps of sample entry at the automated sample distributor and communication of results from the analyser were collected from LIS. 1,023 labelled serum tubes arrived at our laboratory. 899 RFID tags were used for TAT calculation. The following transfer times were determined (median 95th percentile in min:sec): pneumatic tube system --> centrifuge (01:25/04:48), centrifuge --> sample distributor (14:06/5:33), sample distributor --> analysis system zone (02:39/15:07), analysis system zone --> result communication (12:42/22:21). Total TAT was calculated at 33:19/57:40 min:sec. Manual processes around centrifugation were identified as a major part of TAT with 44%/60% (median/95th percentile). RFID is a robust, easy to use, and error-free technology and not susceptible to interferences in the laboratory environment. With this study design we were able to measure significant variations in a single manual sample transfer process. We showed that TAT is mainly influenced by manual steps around the centrifugation process and we concluded that centrifugation should be integrated in solutions for total laboratory automation.

Destruction-free procedure for the isolation of bacteria from sputum samples for Raman spectroscopic analysis.

PubMed

Kloß, Sandra; Lorenz, Björn; Dees, Stefan; Labugger, Ines; Rösch, Petra; Popp, Jürgen

2015-11-01

Lower respiratory tract infections are the fourth leading cause of death worldwide. Here, a timely identification of the causing pathogens is crucial to the success of the treatment. Raman spectroscopy allows for quick identification of bacterial cells without the need for time-consuming cultivation steps, which is the current gold standard to detect pathogens. However, before Raman spectroscopy can be used to identify pathogens, they have to be isolated from the sample matrix, i.e., sputum in case of lower respiratory tract infections. In this study, we report an isolation protocol for single bacterial cells from sputum samples for Raman spectroscopic identification. Prior to the isolation, a liquefaction step using the proteolytic enzyme mixture Pronase E is required in order to deal with the high viscosity of sputum. The extraction of the bacteria was subsequently performed via different filtration and centrifugation steps, whereby isolation ratios between 46 and 57 % were achieved for sputa spiked with 6·10(7) to 6·10(4) CFU/mL of Staphylococcus aureus. The compatibility of such a liquefaction and isolation procedure towards a Raman spectroscopic classification was shown for five different model species, namely S. aureus, Staphylococcus epidermidis, Streptococcus pneumoniae, Klebsiella pneumoniae, and Pseudomonas aeruginosa. A classification of single-cell Raman spectra of these five species with an accuracy of 98.5 % could be achieved on the basis of a principal component analysis (PCA) followed by a linear discriminant analysis (LDA). These classification results could be validated with an independent test dataset, where 97.4 % of all spectra were identified correctly. Graphical Abstract Development of an isolation protocol of bacterial cells out of sputum samples followed by Raman spectroscopic measurement and species identification using chemometrical models.

Proteomic analysis of formalin-fixed paraffin embedded tissue by MALDI imaging mass spectrometry

PubMed Central

Casadonte, Rita; Caprioli, Richard M

2012-01-01

Archived formalin-fixed paraffin-embedded (FFPE) tissue collections represent a valuable informational resource for proteomic studies. Multiple FFPE core biopsies can be assembled in a single block to form tissue microarrays (TMAs). We describe a protocol for analyzing protein in FFPE -TMAs using matrix-assisted laser desorption/ionization (MAL DI) imaging mass spectrometry (IMS). The workflow incorporates an antigen retrieval step following deparaffinization, in situ trypsin digestion, matrix application and then mass spectrometry signal acquisition. The direct analysis of FFPE -TMA tissue using IMS allows direct analysis of multiple tissue samples in a single experiment without extraction and purification of proteins. The advantages of high speed and throughput, easy sample handling and excellent reproducibility make this technology a favorable approach for the proteomic analysis of clinical research cohorts with large sample numbers. For example, TMA analysis of 300 FFPE cores would typically require 6 h of total time through data acquisition, not including data analysis. PMID:22011652

Purification Procedures for Single-Wall Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Gorelik, Olga P.; Nikolaev, Pavel; Arepalli, Sivaram

2001-01-01

This report summarizes the comparison of a variety of procedures used to purify carbon nanotubes. Carbon nanotube material is produced by the arc process and laser oven process. Most of the procedures are tested using laser-grown, single-wall nanotube (SWNT) material. The material is characterized at each step of the purification procedures by using different techniques including scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), transmission electron microscopy (TEM), Raman, X-ray diffractometry (XRD), thermogravimetric analysis (TGA), nuclear magnetic resonance (NMR), and high-performance liquid chromatography (HPLC). The identified impurities are amorphous and graphitic carbon, catalyst particle aggregates, fullerenes, and hydrocarbons. Solvent extraction and low-temperature annealing are used to reduce the amount of volatile hydrocarbons and dissolve fullerenes. Metal catalysts and amorphous as well as graphitic carbon are oxidized by reflux in acids including HCl, HNO3 and HF and other oxidizers such as H2O2. High-temperature annealing in vacuum and in inert atmosphere helps to improve the quality of SWNTs by increasing crystallinity and reducing intercalation.

Shape Adaptive, Robust Iris Feature Extraction from Noisy Iris Images

PubMed Central

Ghodrati, Hamed; Dehghani, Mohammad Javad; Danyali, Habibolah

2013-01-01

In the current iris recognition systems, noise removing step is only used to detect noisy parts of the iris region and features extracted from there will be excluded in matching step. Whereas depending on the filter structure used in feature extraction, the noisy parts may influence relevant features. To the best of our knowledge, the effect of noise factors on feature extraction has not been considered in the previous works. This paper investigates the effect of shape adaptive wavelet transform and shape adaptive Gabor-wavelet for feature extraction on the iris recognition performance. In addition, an effective noise-removing approach is proposed in this paper. The contribution is to detect eyelashes and reflections by calculating appropriate thresholds by a procedure called statistical decision making. The eyelids are segmented by parabolic Hough transform in normalized iris image to decrease computational burden through omitting rotation term. The iris is localized by an accurate and fast algorithm based on coarse-to-fine strategy. The principle of mask code generation is to assign the noisy bits in an iris code in order to exclude them in matching step is presented in details. An experimental result shows that by using the shape adaptive Gabor-wavelet technique there is an improvement on the accuracy of recognition rate. PMID:24696801

Shape adaptive, robust iris feature extraction from noisy iris images.

PubMed

Ghodrati, Hamed; Dehghani, Mohammad Javad; Danyali, Habibolah

2013-10-01

In the current iris recognition systems, noise removing step is only used to detect noisy parts of the iris region and features extracted from there will be excluded in matching step. Whereas depending on the filter structure used in feature extraction, the noisy parts may influence relevant features. To the best of our knowledge, the effect of noise factors on feature extraction has not been considered in the previous works. This paper investigates the effect of shape adaptive wavelet transform and shape adaptive Gabor-wavelet for feature extraction on the iris recognition performance. In addition, an effective noise-removing approach is proposed in this paper. The contribution is to detect eyelashes and reflections by calculating appropriate thresholds by a procedure called statistical decision making. The eyelids are segmented by parabolic Hough transform in normalized iris image to decrease computational burden through omitting rotation term. The iris is localized by an accurate and fast algorithm based on coarse-to-fine strategy. The principle of mask code generation is to assign the noisy bits in an iris code in order to exclude them in matching step is presented in details. An experimental result shows that by using the shape adaptive Gabor-wavelet technique there is an improvement on the accuracy of recognition rate.

Fast analysis of doping agents in urine by ultra-high-pressure liquid chromatography-quadrupole time-of-flight mass spectrometry. II: Confirmatory analysis.

PubMed

Badoud, F; Grata, E; Perrenoud, L; Saugy, M; Rudaz, S; Veuthey, J-L

2010-06-18

For doping control, analyses of samples are generally achieved in two steps: a rapid screening and, in the case of a positive result, a confirmatory analysis. A two-step methodology based on ultra-high-pressure liquid chromatography coupled to a quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) was developed to screen and confirm 103 doping agents from various classes (e.g., beta-blockers, stimulants, diuretics, and narcotics). The screening method was presented in a previous article as part I (i.e., Fast analysis of doping agents in urine by ultra-high-pressure liquid chromatography-quadrupole time-of-flight mass spectrometry. Part I: screening analysis). For the confirmatory method, basic, neutral and acidic compounds were extracted by a dedicated solid-phase extraction (SPE) in a 96-well plate format and detected by MS in the tandem mode to obtain precursor and characteristic product ions. The mass accuracy and the elemental composition of precursor and product ions were used for compound identification. After validation including matrix effect determination, the method was considered reliable to confirm suspect results without ambiguity according to the positivity criteria established by the World Anti-Doping Agency (WADA). Moreover, an isocratic method was developed to separate ephedrine from its isomer pseudoephedrine and cathine from phenylpropanolamine in a single run, what allowed their direct quantification in urine. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Droplet-based microfluidic washing module for magnetic particle-based assays

PubMed Central

Lee, Hun; Xu, Linfeng; Oh, Kwang W.

2014-01-01

In this paper, we propose a continuous flow droplet-based microfluidic platform for magnetic particle-based assays by employing in-droplet washing. The droplet-based washing was implemented by traversing functionalized magnetic particles across a laterally merged droplet from one side (containing sample and reagent) to the other (containing buffer) by an external magnetic field. Consequently, the magnetic particles were extracted to a parallel-synchronized train of washing buffer droplets, and unbound reagents were left in an original train of sample droplets. To realize the droplet-based washing function, the following four procedures were sequentially carried in a droplet-based microfluidic device: parallel synchronization of two trains of droplets by using a ladder-like channel network; lateral electrocoalescence by an electric field; magnetic particle manipulation by a magnetic field; and asymmetrical splitting of merged droplets. For the stable droplet synchronization and electrocoalescence, we optimized droplet generation conditions by varying the flow rate ratio (or droplet size). Image analysis was carried out to determine the fluorescent intensity of reagents before and after the washing step. As a result, the unbound reagents in sample droplets were significantly removed by more than a factor of 25 in the single washing step, while the magnetic particles were successfully extracted into washing buffer droplets. As a proof-of-principle, we demonstrate a magnetic particle-based immunoassay with streptavidin-coated magnetic particles and fluorescently labelled biotin in the proposed continuous flow droplet-based microfluidic platform. PMID:25379098

The lignol approach to biorefining of woody biomass to produce ethanol and chemicals.

PubMed

Arato, Claudio; Pye, E Kendall; Gjennestad, Gordon

2005-01-01

Processes that produce only ethanol from lignocellulosics display poor economics. This is generally overcome by constructing large facilities having satisfactory economies of scale, thus making financing onerous and hindering the development of suitable technologies. Lignol Innovations has developed a biorefining technology that employs an ethanol-based organosolv step to separate lignin, hemicellulose components, and extractives from the cellulosic fraction of woody biomass. The resultant cellulosic fraction is highly susceptible to enzymatic hydrolysis, generating very high yields of glucose (>90% in 12-24 h) with typical enzyme loadings of 10-20 FPU (filter paper units)/g. This glucose is readily converted to ethanol, or possibly other sugar platform chemicals, either by sequential or simultaneous saccharification and fermentation. The liquor from the organosolv step is processed by well-established unit operations to recover lignin, furfural, xylose, acetic acid, and a lipophylic extractives fraction. The process ethanol is recovered and recycled back to the process. The resulting recycled process water is of a very high quality, low BOD5, and suitable for overall system process closure. Significant benefits can be attained in greenhouse gas (GHG) emission reductions, as per the Kyoto Protocol. Revenues from the multiple products, particularly the lignin, ethanol and xylose fractions, ensure excellent economics for the process even in plants as small as 100 mtpd (metric tonnes per day) dry woody biomass input a scale suitable for processing wood residues produced by a single large sawmill.

EVIDENCE FOR AN EXOCELLULAR SITE FOR THE ACID PHOSPHATASE OF SACCHAROMYCES MELLIS1

PubMed Central

Weimberg, Ralph; Orton, William L.

1964-01-01

Weimberg, Ralph (Northern Regional Research Laboratory, Peoria, Ill.), and William L. Orton. Evidence for an exocellular site for the acid phosphatase of Saccharomyces mellis. J. Bacteriol. 88:1743–1754. 1964.—Evidence is presented which demonstrates an exocellular location for acid phosphatase in Saccharomyces mellis. Derepressed intact cells exhibit acid phosphatase activity. The properties of the system are similar to those shown by the enzyme in cell-free extracts. There is no increase in total activity when cell-free extracts are prepared. Enzymatically active cell walls were prepared by leaching acetone-dried cells of this yeast in dilute acetate buffer (pH 6.5) plus β-mercaptoethanol. The insoluble residue, consisting mainly of cell-wall material and containing the phosphatase, was treated with a variety of hydrolytic enzymes and other chemicals. Only papain and crude snail gut extracts dissociated the enzyme from the particulate fraction in nearly quantitative amounts. The mechanism of release by these two enzymes probably differs. Of all enzymes tested, only the snail gut extract digested the cell walls. By dividing the procedure for making protoplasts of S. mellis into two steps, acid phosphatase may be dissociated from resting cells and recovered as an active soluble enzyme. The first step is to pretreat the cells with a thiol reagent. The second step is to digest the cell wall by enzymes present in crude snail gut extracts. Arsenite must be included in the second step to protect the phosphatase from inactivation. The phosphatase is quantitatively released before the cell becomes osmotically fragile. Images PMID:14240965

SOLVENT EXTRACTION PROCESS FOR URANIUM FROM CHLORIDE SOLUTIONS

DOEpatents

Blake, C.A. Jr.; Brown, K.B.; Horner, D.E.

1960-05-24

An improvement was made in a uranium extraction process wherein the organic extractant is a phosphine oxide. An aqueous solution containing phosphate ions or sulfate ions together with uranium is provided with a source of chloride ions during the extraction step. The presence of the chloride ions enables a phosphine oxide to extract uranium in the presence of strong uranium- complexing ions such as phosphate or sulfate ions.

Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

DOEpatents

Soares, Marcelo Bento; Bonaldo, Maria de Fatima

1998-01-01

This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods.

Efficient and simpler method to construct normalized cDNA libraries with improved representations of full-length cDNAs

DOEpatents

Soares, M.B.; Fatima Bonaldo, M. de

1998-12-08

This invention provides a method to normalize a cDNA library comprising: (a) constructing a directionally cloned library containing cDNA inserts wherein the insert is capable of being amplified by polymerase chain reaction; (b) converting a double-stranded cDNA library into single-stranded DNA circles; (c) generating single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) by polymerase chain reaction with appropriate primers; (d) hybridizing the single-stranded DNA circles converted in step (b) with the complementary single-stranded nucleic acid molecules generated in step (c) to produce partial duplexes to an appropriate Cot; and (e) separating the unhybridized single-stranded DNA circles from the hybridized DNA circles, thereby generating a normalized cDNA library. This invention also provides a method to normalize a cDNA library wherein the generating of single-stranded nucleic acid molecules complementary to the single-stranded DNA circles converted in step (b) is by excising cDNA inserts from the double-stranded cDNA library; purifying the cDNA inserts from cloning vectors; and digesting the cDNA inserts with an exonuclease. This invention further provides a method to construct a subtractive cDNA library following the steps described above. This invention further provides normalized and/or subtractive cDNA libraries generated by the above methods. 25 figs.

Comparison of single extraction procedures and the application of an index for the assessment of heavy metal bioavailability in river sediments.

PubMed

Sakan, Sanja; Popović, Aleksandar; Škrivanj, Sandra; Sakan, Nenad; Đorđević, Dragana

2016-11-01

Metals in sediments are present in different chemical forms which affect their ability to transfer. The objective of this body of work was to compare different extraction methods for the bioavailability evaluation of some elements, such as Ba, Cd, Co, Cr, Cu, Fe, K, Mg, Mn, Ni, Pb, V and Zn from Serbian river sediments. A bioavailability risk assessment index (BRAI) was used for the quantification of heavy metal bioavailability in the sediments. Actual and potential element availability was assessed by single extractions with mild (CaCl 2 and CH 3 COONH 4 ) and acidic (CH 3 COOH) extractants and complexing agents (EDTA). Aqua regia extraction was used for the determination of the pseudo-total element content in river sediments. In different single extraction tests, higher extraction of Cd, Cu, Zn and Pb was observed than for the other elements. The results of the single extraction tests revealed that there is a considerable chance of metal leaching from the sediments assessed in this study. When the BRAI was applied, the results showed a high risk of heavy metal bioavailability in Serbian river sediments.

Increased knee valgus alignment and moment during single-leg landing after overhead stroke as a potential risk factor of anterior cruciate ligament injury in badminton.

PubMed

Kimura, Yuka; Ishibashi, Yasuyuki; Tsuda, Eiichi; Yamamoto, Yuji; Hayashi, Yoshimitsu; Sato, Shuichi

2012-03-01

In badminton, knees opposite to the racket-hand side received anterior cruciate ligament (ACL) injuries during single-leg landing after overhead stroke. Most of them occurred in the backhand-side of the rear court. Comparing lower limb biomechanics during single-leg landing after overhead stroke between the forehand-side and backhand-side court may help explain the different injury rates depending on court position. The knee kinematics and kinetics during single-leg landing after overhead stroke following back-stepping were different between the forehand-side and backhand-side court. Controlled laboratory study. Hip, knee and ankle joint kinematic and knee kinetic data were collected for 17 right-handed female college badminton players using a 3-dimensional motion analysis system. Subjects performed single-left-legged landing after an overhead stroke following left and right back-stepping. The kinematic and kinetic data of the left lower extremities during landing were measured and compared between left and right back-steps. Hip flexion and abduction and knee valgus at the initial contact, hip and knee flexion and knee valgus at the maximum knee flexion and the maximum knee valgus moment were significantly larger for the left back-step than the right back-step (p<0.05). Significant differences in joint kinematics and kinetics of the lower extremity during single-leg landing after overhead stroke were observed between different back-step directions. Increased knee valgus angle and moment following back-stepping to the backhand-side might be related to the higher incidence of ACL injury during single-leg landing after overhead stroke.

Single-step reinitialization and extending algorithms for level-set based multi-phase flow simulations

NASA Astrophysics Data System (ADS)

Fu, Lin; Hu, Xiangyu Y.; Adams, Nikolaus A.

2017-12-01

We propose efficient single-step formulations for reinitialization and extending algorithms, which are critical components of level-set based interface-tracking methods. The level-set field is reinitialized with a single-step (non iterative) "forward tracing" algorithm. A minimum set of cells is defined that describes the interface, and reinitialization employs only data from these cells. Fluid states are extrapolated or extended across the interface by a single-step "backward tracing" algorithm. Both algorithms, which are motivated by analogy to ray-tracing, avoid multiple block-boundary data exchanges that are inevitable for iterative reinitialization and extending approaches within a parallel-computing environment. The single-step algorithms are combined with a multi-resolution conservative sharp-interface method and validated by a wide range of benchmark test cases. We demonstrate that the proposed reinitialization method achieves second-order accuracy in conserving the volume of each phase. The interface location is invariant to reapplication of the single-step reinitialization. Generally, we observe smaller absolute errors than for standard iterative reinitialization on the same grid. The computational efficiency is higher than for the standard and typical high-order iterative reinitialization methods. We observe a 2- to 6-times efficiency improvement over the standard method for serial execution. The proposed single-step extending algorithm, which is commonly employed for assigning data to ghost cells with ghost-fluid or conservative interface interaction methods, shows about 10-times efficiency improvement over the standard method while maintaining same accuracy. Despite their simplicity, the proposed algorithms offer an efficient and robust alternative to iterative reinitialization and extending methods for level-set based multi-phase simulations.

Detecting Inspection Objects of Power Line from Cable Inspection Robot LiDAR Data

PubMed Central

Qin, Xinyan; Wu, Gongping; Fan, Fei

2018-01-01

Power lines are extending to complex environments (e.g., lakes and forests), and the distribution of power lines in a tower is becoming complicated (e.g., multi-loop and multi-bundle). Additionally, power line inspection is becoming heavier and more difficult. Advanced LiDAR technology is increasingly being used to solve these difficulties. Based on precise cable inspection robot (CIR) LiDAR data and the distinctive position and orientation system (POS) data, we propose a novel methodology to detect inspection objects surrounding power lines. The proposed method mainly includes four steps: firstly, the original point cloud is divided into single-span data as a processing unit; secondly, the optimal elevation threshold is constructed to remove ground points without the existing filtering algorithm, improving data processing efficiency and extraction accuracy; thirdly, a single power line and its surrounding data can be respectively extracted by a structured partition based on a POS data (SPPD) algorithm from “layer” to “block” according to power line distribution; finally, a partition recognition method is proposed based on the distribution characteristics of inspection objects, highlighting the feature information and improving the recognition effect. The local neighborhood statistics and the 3D region growing method are used to recognize different inspection objects surrounding power lines in a partition. Three datasets were collected by two CIR LIDAR systems in our study. The experimental results demonstrate that an average 90.6% accuracy and average 98.2% precision at the point cloud level can be achieved. The successful extraction indicates that the proposed method is feasible and promising. Our study can be used to obtain precise dimensions of fittings for modeling, as well as automatic detection and location of security risks, so as to improve the intelligence level of power line inspection. PMID:29690560

Detecting Inspection Objects of Power Line from Cable Inspection Robot LiDAR Data.

PubMed

Qin, Xinyan; Wu, Gongping; Lei, Jin; Fan, Fei; Ye, Xuhui

2018-04-22

Power lines are extending to complex environments (e.g., lakes and forests), and the distribution of power lines in a tower is becoming complicated (e.g., multi-loop and multi-bundle). Additionally, power line inspection is becoming heavier and more difficult. Advanced LiDAR technology is increasingly being used to solve these difficulties. Based on precise cable inspection robot (CIR) LiDAR data and the distinctive position and orientation system (POS) data, we propose a novel methodology to detect inspection objects surrounding power lines. The proposed method mainly includes four steps: firstly, the original point cloud is divided into single-span data as a processing unit; secondly, the optimal elevation threshold is constructed to remove ground points without the existing filtering algorithm, improving data processing efficiency and extraction accuracy; thirdly, a single power line and its surrounding data can be respectively extracted by a structured partition based on a POS data (SPPD) algorithm from "layer" to "block" according to power line distribution; finally, a partition recognition method is proposed based on the distribution characteristics of inspection objects, highlighting the feature information and improving the recognition effect. The local neighborhood statistics and the 3D region growing method are used to recognize different inspection objects surrounding power lines in a partition. Three datasets were collected by two CIR LIDAR systems in our study. The experimental results demonstrate that an average 90.6% accuracy and average 98.2% precision at the point cloud level can be achieved. The successful extraction indicates that the proposed method is feasible and promising. Our study can be used to obtain precise dimensions of fittings for modeling, as well as automatic detection and location of security risks, so as to improve the intelligence level of power line inspection.

Quantification of drugs in plasma without primary reference standards by liquid chromatography-chemiluminescence nitrogen detection: application to tramadol metabolite ratios.

PubMed

Ojanperä, Suvi; Rasanen, Ilpo; Sistonen, Johanna; Pelander, Anna; Vuori, Erkki; Ojanperä, Ilkka

2007-08-01

Lack of availability of reference standards for drug metabolites, newly released drugs, and illicit drugs hinders the analysis of these substances in biologic samples. To counter this problem, an approach is presented here for quantitative drug analysis in plasma without primary reference standards by liquid chromatography-chemiluminescence nitrogen detection (LC-CLND). To demonstrate the feasibility of the method, metabolic ratios of the opioid drug tramadol were determined in the setting of a pharmacogenetic study. Four volunteers were given a single 100-mg oral dose of tramadol, and a blood sample was collected from each subject 1 hour later. Tramadol, O-desmethyltramadol, and nortramadol were determined in plasma by LC-CLND without reference standards and by a gas chromatography-mass spectrometry reference method. In contrast to previous CLND studies lacking an extraction step, a liquid-liquid extraction system was created for 5-mL plasma samples using n-butyl chloride-isopropyl alcohol (98 + 2) at pH 10. Extraction recovery estimation was based on model compounds chosen according to their similar physicochemical characteristics (retention time, pKa, logD). Instrument calibration was performed with a single secondary standard (caffeine) using the equimolar response of the detector to nitrogen. The mean differences between the results of the LC-CLND and gas chromatography-mass spectrometry methods for tramadol, O-desmethyltramadol, and nortramadol were 8%, 32%, and 19%, respectively. The sensitivity of LC-CLND was sufficient for therapeutic concentrations of tramadol and metabolites. A good correlation was obtained between genotype, expressed by the number of functional genes, and the plasma metabolite ratios. This experiment suggests that a recovery-corrected LC-CLND analysis produces sufficiently accurate results to be useful in a clinical context, particularly in instances in which reference standards are not readily accessible.

Highly Sensitive Bacteriophage-Based Detection of Brucella abortus in Mixed Culture and Spiked Blood

PubMed Central

Sergueev, Kirill V.; Filippov, Andrey A.; Nikolich, Mikeljon P.

2017-01-01

For decades, bacteriophages (phages) have been used for Brucella species identification in the diagnosis and epidemiology of brucellosis. Traditional Brucella phage typing is a multi-day procedure including the isolation of a pure culture, a step that can take up to three weeks. In this study, we focused on the use of brucellaphages for sensitive detection of the pathogen in clinical and other complex samples, and developed an indirect method of Brucella detection using real-time quantitative PCR monitoring of brucellaphage DNA amplification via replication on live Brucella cells. This assay allowed the detection of single bacteria (down to 1 colony-forming unit per milliliter) within 72 h without DNA extraction and purification steps. The technique was equally efficient with Brucella abortus pure culture and with mixed cultures of B. abortus and α-proteobacterial near neighbors that can be misidentified as Brucella spp., Ochrobactrum anthropi and Afipia felis. The addition of a simple short sample preparation step enabled the indirect phage-based detection of B. abortus in spiked blood, with the same high sensitivity. This indirect phage-based detection assay enables the rapid and sensitive detection of live B. abortus in mixed cultures and in blood samples, and can potentially be applied for detection in other clinical samples and other complex sample types. PMID:28604602

Electro-kinetic Separation of Rare Earth Elements Using a Redox-Active Ligand.

PubMed

Fang, Huayi; Cole, Bren E; Qiao, Yusen; Bogart, Justin A; Cheisson, Thibault; Manor, Brian C; Carroll, Patrick J; Schelter, Eric J

2017-10-16

Purification of rare earth elements is challenging due to their chemical similarities. All of the deployed separation methods rely on thermodynamic properties, such as distribution equilibria in solvent extraction. Rare-earth-metal separations based on kinetic differences have not been examined. Herein, we demonstrate a new approach for rare-earth-element separations by exploiting differences in the oxidation rates within a series of rare earth compounds containing the redox-active ligand [{2-(tBuN(O))C 6 H 4 CH 2 } 3 N] 3- . Using this method, a single-step separation factor up to 261 was obtained for the separation of a 50:50 yttrium-lutetium mixture. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cloning and characterization of the human 5,10-methenyltetrahydrofolate synthetase-encoding cDNA.

PubMed

Dayan, A; Bertrand, R; Beauchemin, M; Chahla, D; Mamo, A; Filion, M; Skup, D; Massie, B; Jolivet, J

1995-11-20

Methenyltetrahydrofolate synthetase (MTHFS) catalyses the obligatory initial metabolic step in the intracellular conversion of 5-formyltetrahydrofolate to other reduced folates. We have isolated and sequenced a human MTHFS cDNA which is 872-bp long and codes for a 203-amino-acid protein of 23,229 Da. Escherichia coli BL21(DE3), transfected with pET11c plasmids containing an open reading frame encoding MTHFS, showed a 100-fold increase in MTHFS activity in bacterial extracts after IPTG induction. Northern blot studies of human tissues determined that the MTHFS mRNA was expressed preferentially in the liver and Southern blot analysis of human genomic DNA suggested the presence of a single-copy gene.

A modular computational framework for automated peak extraction from ion mobility spectra

PubMed Central

2014-01-01

Background An ion mobility (IM) spectrometer coupled with a multi-capillary column (MCC) measures volatile organic compounds (VOCs) in the air or in exhaled breath. This technique is utilized in several biotechnological and medical applications. Each peak in an MCC/IM measurement represents a certain compound, which may be known or unknown. For clustering and classification of measurements, the raw data matrix must be reduced to a set of peaks. Each peak is described by its coordinates (retention time in the MCC and reduced inverse ion mobility) and shape (signal intensity, further shape parameters). This fundamental step is referred to as peak extraction. It is the basis for identifying discriminating peaks, and hence putative biomarkers, between two classes of measurements, such as a healthy control group and a group of patients with a confirmed disease. Current state-of-the-art peak extraction methods require human interaction, such as hand-picking approximate peak locations, assisted by a visualization of the data matrix. In a high-throughput context, however, it is preferable to have robust methods for fully automated peak extraction. Results We introduce PEAX, a modular framework for automated peak extraction. The framework consists of several steps in a pipeline architecture. Each step performs a specific sub-task and can be instantiated by different methods implemented as modules. We provide open-source software for the framework and several modules for each step. Additionally, an interface that allows easy extension by a new module is provided. Combining the modules in all reasonable ways leads to a large number of peak extraction methods. We evaluate all combinations using intrinsic error measures and by comparing the resulting peak sets with an expert-picked one. Conclusions Our software PEAX is able to automatically extract peaks from MCC/IM measurements within a few seconds. The automatically obtained results keep up with the results provided by current state-of-the-art peak extraction methods. This opens a high-throughput context for the MCC/IM application field. Our software is available at http://www.rahmannlab.de/research/ims. PMID:24450533

A modular computational framework for automated peak extraction from ion mobility spectra.

PubMed

D'Addario, Marianna; Kopczynski, Dominik; Baumbach, Jörg Ingo; Rahmann, Sven

2014-01-22

An ion mobility (IM) spectrometer coupled with a multi-capillary column (MCC) measures volatile organic compounds (VOCs) in the air or in exhaled breath. This technique is utilized in several biotechnological and medical applications. Each peak in an MCC/IM measurement represents a certain compound, which may be known or unknown. For clustering and classification of measurements, the raw data matrix must be reduced to a set of peaks. Each peak is described by its coordinates (retention time in the MCC and reduced inverse ion mobility) and shape (signal intensity, further shape parameters). This fundamental step is referred to as peak extraction. It is the basis for identifying discriminating peaks, and hence putative biomarkers, between two classes of measurements, such as a healthy control group and a group of patients with a confirmed disease. Current state-of-the-art peak extraction methods require human interaction, such as hand-picking approximate peak locations, assisted by a visualization of the data matrix. In a high-throughput context, however, it is preferable to have robust methods for fully automated peak extraction. We introduce PEAX, a modular framework for automated peak extraction. The framework consists of several steps in a pipeline architecture. Each step performs a specific sub-task and can be instantiated by different methods implemented as modules. We provide open-source software for the framework and several modules for each step. Additionally, an interface that allows easy extension by a new module is provided. Combining the modules in all reasonable ways leads to a large number of peak extraction methods. We evaluate all combinations using intrinsic error measures and by comparing the resulting peak sets with an expert-picked one. Our software PEAX is able to automatically extract peaks from MCC/IM measurements within a few seconds. The automatically obtained results keep up with the results provided by current state-of-the-art peak extraction methods. This opens a high-throughput context for the MCC/IM application field. Our software is available at http://www.rahmannlab.de/research/ims.

Effect of humidity during artificial extraction on the subsequent vigor of pine pollen

Treesearch

Russell A. Ryker

1963-01-01

Controlled pollination of pines generally has been disappointing because cones contain too few seeds. We need to develop better techniques for collecting, extracting, and storing pollen, as well as better bagging procedures. A logical first step is to learn more about collecting and extracting pollen. In a recent study I found that extracting pollen of jack pine (Pinus...

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.

Pre-analytic evaluation of volumetric absorptive microsampling and integration in a mass spectrometry-based metabolomics workflow.

PubMed

Volani, Chiara; Caprioli, Giulia; Calderisi, Giovanni; Sigurdsson, Baldur B; Rainer, Johannes; Gentilini, Ivo; Hicks, Andrew A; Pramstaller, Peter P; Weiss, Guenter; Smarason, Sigurdur V; Paglia, Giuseppe

2017-10-01

Volumetric absorptive microsampling (VAMS) is a novel approach that allows single-drop (10 μL) blood collection. Integration of VAMS with mass spectrometry (MS)-based untargeted metabolomics is an attractive solution for both human and animal studies. However, to boost the use of VAMS in metabolomics, key pre-analytical questions need to be addressed. Therefore, in this work, we integrated VAMS in a MS-based untargeted metabolomics workflow and investigated pre-analytical strategies such as sample extraction procedures and metabolome stability at different storage conditions. We first evaluated the best extraction procedure for the polar metabolome and found that the highest number and amount of metabolites were recovered upon extraction with acetonitrile/water (70:30). In contrast, basic conditions (pH 9) resulted in divergent metabolite profiles mainly resulting from the extraction of intracellular metabolites originating from red blood cells. In addition, the prolonged storage of blood samples at room temperature caused significant changes in metabolome composition, but once the VAMS devices were stored at - 80 °C, the metabolome remained stable for up to 6 months. The time used for drying the sample did also affect the metabolome. In fact, some metabolites were rapidly degraded or accumulated in the sample during the first 48 h at room temperature, indicating that a longer drying step will significantly change the concentration in the sample. Graphical abstract Volumetric absorptive microsampling (VAMS) is a novel technology that allows single-drop blood collection and, in combination with mass spectrometry (MS)-based untargeted metabolomics, represents an attractive solution for both human and animal studies. In this work, we integrated VAMS in a MS-based untargeted metabolomics workflow and investigated pre-analytical strategies such as sample extraction procedures and metabolome stability at different storage conditions. The latter revealed that prolonged storage of blood samples at room temperature caused significant changes in metabolome composition, but if VAMS devices were stored at - 80 °C, the metabolome remained stable for up to 6 months.

Matrix solid-phase dispersion followed by liquid chromatography tandem mass spectrometry for the determination of selective ciclooxygenase-2 inhibitors in sewage sludge samples.

PubMed

Triñanes, Sara; Casais, M Carmen; Mejuto, M Carmen; Cela, Rafael

2016-09-02

A straightforward single-step extraction method based on matrix solid-phase dispersion (MSPD), followed by high-performance liquid chromatography with hybrid quadrupole time of flight mass spectrometry (LC-QTOF-MS), was developed and optimized to determine five non-steroidal anti-inflammatory drugs (Valdecoxib, Etoricoxib, Parecoxib, Celecoxib and 2,5-Dimethylcelecoxib) in sewage sludge samples. The influence of different operational parameters on the extraction efficiency a well as in the matrix effects of the produced extracts was evaluated in detail. Under final working conditions, freeze dried samples (0.2g) were first soaked with 100μL of aqueous potassium hydroxide solution (60%, w/v), mixed with 1g of anhydrous sodium sulfate and dispersed with 1g of Florisil. This blend was transferred to the top of a polypropylene column cartridge containing 3g of silica. Analytes were recovered using 15mL of hexane/acetone (1:2, v/v) mixture. The extracts were concentrated by evaporation and reconstituted with 1mL of methanol/water (1:1, v/v), filtered and injected in the LC system. Quantification limits from 0.005 and 0.05ngg(-1) and absolute recoveries between 86 and 105% were achieved. Results indicated the presence of two of the targeted COXIBs in real samples of sewage sludge, the highest average concentration (22ngg(-1)) corresponding to celecoxib. Moreover, the screening capabilities of the LC-QTOF-MS system demonstrated that the developed MSPD extraction procedure might be useful for the selective extraction of some other pharmaceuticals (e.g. amiodarone and their metabolite N-desethylamiodarone, miconazole, clotrimazole and ketoprofen) from sludge samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Clinical Efficacy Associated with Enhanced Antioxidant Enzyme Activities of Silver Nanoparticles Biosynthesized Using Moringa oleifera Leaf Extract, Against Cutaneous Leishmaniasis in a Murine Model of Leishmania major.

PubMed

El-Khadragy, Manal; Alolayan, Ebtesam M; Metwally, Dina M; El-Din, Mohamed F Serag; Alobud, Sara S; Alsultan, Nour I; Alsaif, Sarah S; Awad, Manal A; Abdel Moneim, Ahmed E

2018-05-22

Leishmaniasis is one of the most significant vector-borne syndromes of individuals. This parasitic infection can be affected by many species of Leishmania, most of which are zoonotic. Natural products have made and are continuing to make important contributions to the search for new antileishmanial agents. The use of plants in the production assembly of silver nanoparticles has drawn attention because of its rapid, eco-friendly, non-pathogenic, economical protocol and provides a single step technique for the biosynthetic process. Hence, we aimed to biosynthesize silver nanoparticles (Ag-NPs) using Moringa oleifera leaf extract and investigated the antileishmanial activity of these nanoparticles in a murine model of Leishmania major infection. A total of 50 mice were used and divided into five groups-healthy control, infected, infected mice treated with pentostam, infected mice treated with Ag-NPs and infected mice pretreated with Ag-NPs. In the present study, the leaf extract of the plant species Moringa oleifera was found to be a good source for the synthesis of silver nanoparticles, their formation being confirmed by color change and stability in solution. In the present murine model of Leishmania major infection, we found that oral treatment with silver nanoparticles biosynthesized using Moringa oleifera extract resulted in a significant reduction in the average size of leishmaniasis cutaneous lesions compared with untreated mice. Furthermore, the clinical efficacy of Moringa oleifera extract was associated with enhanced antioxidant enzyme activities. In conclusion, treatment with silver nanoparticles biosynthesized using Moringa oleifera extract has higher and faster clinical efficacy than standard pentavalent antimonial treatment, probably by boosting the endogenous antioxidant activity.

Clinical Efficacy Associated with Enhanced Antioxidant Enzyme Activities of Silver Nanoparticles Biosynthesized Using Moringa oleifera Leaf Extract, Against Cutaneous Leishmaniasis in a Murine Model of Leishmania major

PubMed Central

El-khadragy, Manal; Alolayan, Ebtesam M.; Metwally, Dina M.; El-Din, Mohamed F. Serag; Alobud, Sara S.; Alsultan, Nour I.; Alsaif, Sarah S.; Awad, Manal A.; Abdel Moneim, Ahmed E.

2018-01-01

Leishmaniasis is one of the most significant vector-borne syndromes of individuals. This parasitic infection can be affected by many species of Leishmania, most of which are zoonotic. Natural products have made and are continuing to make important contributions to the search for new antileishmanial agents. The use of plants in the production assembly of silver nanoparticles has drawn attention because of its rapid, eco-friendly, non-pathogenic, economical protocol and provides a single step technique for the biosynthetic process. Hence, we aimed to biosynthesize silver nanoparticles (Ag-NPs) using Moringa oleifera leaf extract and investigated the antileishmanial activity of these nanoparticles in a murine model of Leishmania major infection. A total of 50 mice were used and divided into five groups—healthy control, infected, infected mice treated with pentostam, infected mice treated with Ag-NPs and infected mice pretreated with Ag-NPs. In the present study, the leaf extract of the plant species Moringa oleifera was found to be a good source for the synthesis of silver nanoparticles, their formation being confirmed by color change and stability in solution. In the present murine model of Leishmania major infection, we found that oral treatment with silver nanoparticles biosynthesized using Moringa oleifera extract resulted in a significant reduction in the average size of leishmaniasis cutaneous lesions compared with untreated mice. Furthermore, the clinical efficacy of Moringa oleifera extract was associated with enhanced antioxidant enzyme activities. In conclusion, treatment with silver nanoparticles biosynthesized using Moringa oleifera extract has higher and faster clinical efficacy than standard pentavalent antimonial treatment, probably by boosting the endogenous antioxidant activity. PMID:29786651

Multiclass method for the determination of pharmaceuticals and personal care products in compost from sewage sludge using ultrasound and salt-assisted liquid-liquid extraction followed by ultrahigh performance liquid chromatography-tandem mass spectrometry analysis.

PubMed

Luque-Muñoz, A; Vílchez, J L; Zafra-Gómez, A

2017-07-21

An analytical method for the analysis of 16 pharmaceuticals and personal care products in compost from sewage sludge is successfully validated. Ultrasound assisted extraction with a mixture of acetonitrile:ethyl acetate (1:1, v/v) containing 10% (v/v) of acetic acid was carried out. Two cycles of extraction of 10min were applied. A clean-up of the extracts using salt-assisted liquid-liquid extraction (SALLE) was also included. Experimental design was used for the optimization of the main parameters involved in the extraction and cleaned-up steps. The chromatographic separation was carried out by ultrahigh performance liquid chromatography using a mobile phase gradient mixture of a 13mM buffer ammonium formate solution (pH 9.25) (solvent A) and methanol (solvent B). An ACQUITY UPLC ® BEH C18 column (1.7μm; 2.1×50mm) column was used. Analytes were separated in less than 11min. The compounds were detected and quantified using single reaction monitoring electrospray tandem mass spectrometry. The limits of detection calculated ranged from 0.5 to 4ngg -1 d.w., and the limits of quantification from 2 to 13ngg -1 d.w. Recoveries from 93% to 111%, with relative standar deviations lower than 11% in all cases, were obtained. The method was applied to natural compost samples. High concentrations of some analytes were found. Ketoprofen (510ngg -1 d.w.), methylparaben (240ngg -1 d.w.), diclofenac (175ngg -1 d.w.) and flufenamic acid (128ngg -1 d.w.) were the most abundant. Copyright © 2017 Elsevier B.V. All rights reserved.

Bond strength of one-step self-etch adhesives and their predecessors to ground versus unground enamel

PubMed Central

Yazici, A. Ruya; Yildirim, Zeren; Ertan, Atila; Ozgunaltay, Gül; Dayangac, Berrin; Antonson, Sibel A; Antonson, Donald E

2012-01-01

Objective The aim of this study was to compare the shear bond strength of several self-etch adhesives to their two-step predecessors to ground and unground enamel. Methods: Seventy-five extracted, non-carious human third molar teeth were selected for this study. The buccal surfaces of each tooth were mechanically ground to obtain flat enamel surfaces (ground enamel), while the lingual surfaces were left intact (unground enamel). The teeth were randomly divided into five groups according to the adhesive systems (n=15): one-step self-etch adhesive - Clearfil S3 Bond, its two-step predecessor - Clearfil SE Bond, one-step self-etch adhesive - AdheSE One, and its two-step predecessor - AdheSE, and a two-step etch-and-rinse adhesive - Adper Single Bond 2(control). After application of the adhesives to the buccal and lingual enamel surfaces of each tooth, a cylindrical capsule filled with a hybrid composite resin (TPH) was seated against the surfaces. The specimens were stored in distilled water at 37°C for 24 hours, followed by thermocy-cling (5°C–55°C/500 cycles). They were subjected to shear bond strength test in a universal testing machine at a crosshead speed of 1.0 mm/minute. The data were compared using a two-way ANOVA, followed by Bonferroni test at P<.05. Results: All adhesives exhibited statistically similar bond strengths to ground and unground enamel except for the etch-and-rinse adhesive that showed significantly higher bond strengths than the self-etch adhesives (P<.05). No significant differences in bond strength values were observed between ground and unground enamel for any of the adhesives tested (P=.17). Conclusion: Similar bond strengths to ground and unground enamel were achieved with one-step self-etch adhesives and their predecessors. Enamel preparation did not influence the bonding performance of the adhesives tested. PMID:22904656

Bond strength of one-step self-etch adhesives and their predecessors to ground versus unground enamel.

PubMed

Yazici, A Ruya; Yildirim, Zeren; Ertan, Atila; Ozgunaltay, Gül; Dayangac, Berrin; Antonson, Sibel A; Antonson, Donald E

2012-07-01

The aim of this study was to compare the shear bond strength of several self-etch adhesives to their two-step predecessors to ground and unground enamel. Seventy-five extracted, non-carious human third molar teeth were selected for this study. The buccal surfaces of each tooth were mechanically ground to obtain flat enamel surfaces (ground enamel), while the lingual surfaces were left intact (unground enamel). The teeth were randomly divided into five groups according to the adhesive systems (n=15): one-step self-etch adhesive - Clearfil S3 Bond, its two-step predecessor - Clearfil SE Bond, one-step self-etch adhesive - AdheSE One, and its two-step predecessor - AdheSE, and a two-step etch-and-rinse adhesive - Adper Single Bond 2(control). After application of the adhesives to the buccal and lingual enamel surfaces of each tooth, a cylindrical capsule filled with a hybrid composite resin (TPH) was seated against the surfaces. The specimens were stored in distilled water at 37°C for 24 hours, followed by thermocy-cling (5°C-55°C/500 cycles). They were subjected to shear bond strength test in a universal testing machine at a crosshead speed of 1.0 mm/minute. The data were compared using a two-way ANOVA, followed by Bonferroni test at P<.05. All adhesives exhibited statistically similar bond strengths to ground and unground enamel except for the etch-and-rinse adhesive that showed significantly higher bond strengths than the self-etch adhesives (P<.05). No significant differences in bond strength values were observed between ground and unground enamel for any of the adhesives tested (P=.17). Similar bond strengths to ground and unground enamel were achieved with one-step self-etch adhesives and their predecessors. Enamel preparation did not influence the bonding performance of the adhesives tested.

Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy.

PubMed

Moen, Aina E F; Tannæs, Tone M; Vatn, Simen; Ricanek, Petr; Vatn, Morten Harald; Jahnsen, Jørgen

2016-06-28

Nucleic acid purification methods are of importance when performing microbiota studies and especially when analysing the intestinal microbiota as we here find a wide range of different microbes. Various considerations must be taken to lyse the microbial cell wall of each microbe. In the present article, we compare several tissue lysis steps and commercial purification kits, to achieve a joint RNA and DNA purification protocol for the purpose of investigating the microbiota and the microbiota-host interactions in a single colonic mucosal tissue sample. A further optimised tissue homogenisation and lysis protocol comprising mechanical bead beating, lysis buffer replacement and enzymatic treatment, in combination with the AllPrep DNA/RNA Mini Kit (Qiagen, Hilden, Germany) resulted in efficient and simultaneous purification of microbial and human RNA and DNA from a single mucosal colonic tissue sample. The present work provides a unique possibility to study RNA and DNA from the same mucosal biopsy sample, making a direct comparison between metabolically active microbes and total microbial DNA. The protocol also offers an opportunity to investigate other members of a microbiota such as viruses, fungi and micro-eukaryotes, and moreover the possibility to extract data on microbiota and host interactions from one single mucosal biopsy.

Cellular and Biophysical Pipeline for the Screening of Peroxisome Proliferator-Activated Receptor Beta/Delta Agonists: Avoiding False Positives

PubMed Central

Batista, Fernanda Aparecida Heleno

2018-01-01

Peroxisome proliferator-activated receptor beta/delta (PPARß/δ) is considered a therapeutic target for metabolic disorders, cancer, and cardiovascular diseases. Here, we developed one pipeline for the screening of PPARß/δ agonists, which reduces the cost, time, and false-positive hits. The first step is an optimized 3-day long cellular transactivation assay based on reporter-gene technology, which is supported by automated liquid-handlers. This primary screening is followed by a confirmatory transactivation assay and by two biophysical validation methods (thermal shift assay (TSA) and (ANS) fluorescence quenching), which allow the calculation of the affinity constant, giving more information about the selected hits. All of the assays were validated using well-known commercial agonists providing trustworthy data. Furthermore, to validate and test this pipeline, we screened a natural extract library (560 extracts), and we found one plant extract that might be interesting for PPARß/δ modulation. In conclusion, our results suggested that we developed a cheaper and more robust pipeline that goes beyond the single activation screening, as it also evaluates PPARß/δ tertiary structure stabilization and the ligand affinity constant, selecting only molecules that directly bind to the receptor. Moreover, this approach might improve the effectiveness of the screening for agonists that target PPARß/δ for drug development.

Molecular Analyzer for Complex Refractory Organic-Rich Surfaces (MACROS)

NASA Technical Reports Server (NTRS)

Getty, Stephanie A.; Cook, Jamie E.; Balvin, Manuel; Brinckerhoff, William B.; Li, Xiang; Grubisic, Andrej; Cornish, Timothy; Ferrance, Jerome; Southard, Adrian

2017-01-01

The Molecular Analyzer for Complex Refractory Organic-rich Surfaces, MACROS, is a novel instrument package being developed at NASA Goddard Space Flight Center. MACROS enables the in situ characterization of a sample's composition by coupling two powerful techniques into one compact instrument package: (1) laser desorption/ionization time-of-flight mass spectrometry (LDMS) for broad detection of inorganic mineral composition and non-volatile organics, and (2) liquid-phase extraction methods to gently isolate the soluble organic and inorganic fraction of a planetary powder for enrichment and detailed analysis by liquid chromatographic separation coupled to LDMS. The LDMS is capable of positive and negative ion detection, precision mass selection, and fragment analysis. Two modes are included for LDMS: single laser LDMS as the broad survey mode and two step laser mass spectrometry (L2MS). The liquid-phase extraction will be done in a newly designed extraction module (EM) prototype, providing selectivity in the analysis of a complex sample. For the sample collection, a diamond drill front end will be used to collect rock/icy powder. With all these components and capabilities together, MACROS offers a versatile analytical instrument for a mission targeting an icy moon, carbonaceous asteroid, or comet, to fully characterize the surface composition and advance our understanding of the chemical inventory present on that body.

Determination of quinolones and fluoroquinolones, tetracyclines and sulfonamides in bovine, swine and poultry liver using LC-MS/MS.

PubMed

Martins, Magda Targa; Barreto, Fabiano; Hoff, Rodrigo Barcelos; Jank, Louise; Arsand, Juliana Bazzan; Feijó, Tiago Correa; Schapoval, Elfrides Eva Scherman

2015-01-01

Antibacterials are widely used in veterinary medicine. Residues of these drugs can remain in food of animal origin, including bovine liver. This paper describes a fast and simple analytical method for the determination of quinolones and fluoroquinolones, tetracyclines and sulfonamides in bovine liver samples. Deuterated enrofloxacin, sulfapyridine and demeclocycline were used as internal standards. The homogenised liver samples were extracted with acidified acetonitrile. Steps of non-solid-phase extraction (SPE) clean-up and concentration were used in the presented method. The final extracts were analysed by sensitive and selective detection of all components in a single run using LC-MS/MS. Acceptable recoveries between 66% and 110% were obtained. Good linearity (r(2)) above 0.96, considering three different days, for all drugs was achieved in concentrations ranging from 0.0 to 2.0 × the maximum residue limit (MRL). Intraday precision with coefficient of variation (CV%) (n = 6) lower than 14.7% and inter-day precision lower than 18.8% in agreement with European Commission Decision 2002/657/EC were obtained in concentrations ranging from 0.5 to 1.5 MRL. Accuracy was between 86% and 110%. Limits of detection and quantitation, as well as decision limit (CCα) and detection capability (CCβ), were also evaluated.

Semiquantitative Nucleic Acid Test with Simultaneous Isotachophoretic Extraction and Amplification.

PubMed

Bender, Andrew T; Borysiak, Mark D; Levenson, Amanda M; Lillis, Lorraine; Boyle, David S; Posner, Jonathan D

2018-06-19

Nucleic acid amplification tests (NAATs) provide high diagnostic accuracy for infectious diseases and quantitative results for monitoring viral infections. The majority of NAATs require complex equipment, cold chain dependent reagents, and skilled technicians to perform the tests. This largely confines NAATs to centralized laboratories and can significantly delay appropriate patient care. Low-cost, point-of-care (POC) NAATs are especially needed in low-resource settings to provide patients with diagnosis and treatment planning in a single visit to improve patient care. In this work, we present a rapid POC NAAT with integrated sample preparation and amplification using electrokinetics and paper substrates. We use simultaneous isotachophoresis (ITP) and recombinase polymerase amplification (RPA) to rapidly extract, amplify, and detect target nucleic acids from serum and whole blood in a paper-based format. We demonstrate simultaneous ITP and RPA can consistently detect 5 copies per reaction in buffer and 10 000 copies per milliliter of human serum with no intermediate user steps. We also show preliminary extraction and amplification of DNA from whole blood samples. Our test is rapid (results in less than 20 min) and made from low-cost materials, indicating its potential for detecting infectious diseases and monitoring viral infections at the POC in low resource settings.

Use of aluminum phosphate as the dehydration catalyst in single step dimethyl ether process

DOEpatents

Peng, Xiang-Dong; Parris, Gene E.; Toseland, Bernard A.; Battavio, Paula J.

1998-01-01

The present invention pertains to a process for the coproduction of methanol and dimethyl ether (DME) directly from a synthesis gas in a single step (hereafter, the "single step DME process"). In this process, the synthesis gas comprising hydrogen and carbon oxides is contacted with a dual catalyst system comprising a physical mixture of a methanol synthesis catalyst and a methanol dehydration catalyst. The present invention is an improvement to this process for providing an active and stable catalyst system. The improvement comprises the use of an aluminum phosphate based catalyst as the methanol dehydration catalyst. Due to its moderate acidity, such a catalyst avoids the coke formation and catalyst interaction problems associated with the conventional dual catalyst systems taught for the single step DME process.

Bone protein “extractomics”: comparing the efficiency of bone protein extractions of Gallus gallus in tandem mass spectrometry, with an eye towards paleoproteomics

PubMed Central

DeHart, Caroline J.; Schweitzer, Mary H.; Thomas, Paul M.; Kelleher, Neil L.

2016-01-01

Proteomic studies of bone require specialized extraction protocols to demineralize and solubilize proteins from within the bone matrix. Although various protocols exist for bone protein recovery, little is known about how discrete steps in each protocol affect the subset of the bone proteome recovered by mass spectrometry (MS) analyses. Characterizing these different “extractomes” will provide critical data for development of novel and more efficient protein extraction methodologies for fossils. Here, we analyze 22 unique sub-extractions of chicken bone and directly compare individual extraction components for their total protein yield and diversity and coverage of bone proteins identified by MS. We extracted proteins using different combinations and ratios of demineralizing reagents, protein-solubilizing reagents, and post-extraction buffer removal methods, then evaluated tryptic digests from 20 µg aliquots of each fraction by tandem MS/MS on a 12T FT-ICR mass spectrometer. We compared total numbers of peptide spectral matches, peptides, and proteins identified from each fraction, the redundancy of protein identifications between discrete steps of extraction methods, and the sequence coverage obtained for select, abundant proteins. Although both alpha chains of collagen I (the most abundant protein in bone) were found in all fractions, other collagenous and non-collagenous proteins (e.g., apolipoprotein, osteonectin, hemoglobin) were differentially identified. We found that when a standardized amount of extracted proteins was analyzed, extraction steps that yielded the most protein (by weight) from bone were often not the ones that produced the greatest diversity of bone proteins, or the highest degree of protein coverage. Generally, the highest degrees of diversity and coverage were obtained from demineralization fractions, and the proteins found in the subsequent solubilization fractions were highly redundant with those in the previous fraction. Based on these data, we identify future directions and parameters to consider (e.g., proteins targeted, amount of sample required) when applying discrete parts of these protocols to fossils. PMID:27812413

[Study on biopharmaceutics classification system for Chinese materia medica of extract of Huanglian].

PubMed

Liu, Yang; Yin, Xiu-Wen; Wang, Zi-Yu; Li, Xue-Lian; Pan, Meng; Li, Yan-Ping; Dong, Ling

2017-11-01

One of the advantages of biopharmaceutics classification system of Chinese materia medica (CMMBCS) is expanding the classification research level from single ingredient to multi-components of Chinese herb, and from multi-components research to holistic research of the Chinese materia medica. In present paper, the alkaloids of extract of huanglian were chosen as the main research object to explore their change rules in solubility and intestinal permeability of single-component and multi-components, and to determine the biopharmaceutical classification of extract of Huanglian from holistic level. The typical shake-flask method and HPLC were used to detect the solubility of single ingredient of alkaloids from extract of huanglian. The quantitative research of alkaloids in intestinal absorption was measured in single-pass intestinal perfusion experiment while permeability coefficient of extract of huanglian was calculated by self-defined weight coefficient method. Copyright© by the Chinese Pharmaceutical Association.

Voluntary stepping behavior under single- and dual-task conditions in chronic stroke survivors: A comparison between the involved and uninvolved legs.

PubMed

Melzer, Itshak; Goldring, Melissa; Melzer, Yehudit; Green, Elad; Tzedek, Irit

2010-12-01

If balance is lost, quick step execution can prevent falls. Research has shown that speed of voluntary stepping was able to predict future falls in old adults. The aim of the study was to investigate voluntary stepping behavior, as well as to compare timing and leg push-off force-time relation parameters of involved and uninvolved legs in stroke survivors during single- and dual-task conditions. We also aimed to compare timing and leg push-off force-time relation parameters between stroke survivors and healthy individuals in both task conditions. Ten stroke survivors performed a voluntary step execution test with their involved and uninvolved legs under two conditions: while focusing only on the stepping task and while a separate attention-demanding task was performed simultaneously. Temporal parameters related to the step time were measured including the duration of the step initiation phase, the preparatory phase, the swing phase, and the total step time. In addition, force-time parameters representing the push-off power during stepping were calculated from ground reaction data and compared with 10 healthy controls. The involved legs of stroke survivors had a significantly slower stepping time than uninvolved legs due to increased swing phase duration during both single- and dual-task conditions. For dual compared to single task, the stepping time increased significantly due to a significant increase in the duration of step initiation. In general, the force time parameters were significantly different in both legs of stroke survivors as compared to healthy controls, with no significant effect of dual compared with single-task conditions in both groups. The inability of stroke survivors to swing the involved leg quickly may be the most significant factor contributing to the large number of falls to the paretic side. The results suggest that stroke survivors were unable to rapidly produce muscle force in fast actions. This may be the mechanism of delayed execution of a fast step when balance is lost, thus increasing the likelihood of falls in stroke survivors. Copyright © 2010 Elsevier Ltd. All rights reserved.

Hemoglobin binding and catalytic heme extraction by IsdB near iron transporter domains.

PubMed

Bowden, Catherine F M; Verstraete, Meghan M; Eltis, Lindsay D; Murphy, Michael E P

2014-04-15

The Isd (iron-regulated surface determinant) system is a multiprotein transporter that allows bacterium Staphylococcus aureus to take up iron from hemoglobin (Hb) during human infection. In this system, IsdB is a cell wall-anchored surface protein that contains two near iron transporter (NEAT) domains, one of which binds heme. IsdB rapidly extracts heme from Hb and transfers it to IsdA for relay into the bacterial cell. Using a series of recombinant IsdB constructs that included at least one NEAT domain, we demonstrated that both domains are required to bind Hb with high affinity (KD = 0.42 ± 0.05 μM) and to extract heme from Hb. Moreover, IsdB extracted heme only from oxidized metHb, although it also bound oxyHb and the Hb-CO complex. In a reconstituted model of the biological heme relay pathway, IsdB catalyzed the transfer of heme from metHb to IsdA with a Km for metHb of 0.75 ± 0.07 μN and a kcat of 0.22 ± 0.01 s(-1). The latter is consistent with the transfer of heme from metHb to IsdB being the rate-limiting step. With both NEAT domains and the linker region present in a single contiguous polypeptide, high-affinity Hb binding was achieved, rapid heme uptake was observed, and multiple turnovers of heme extraction from metHb and transfer to IsdA were conducted, representing all known Hb-heme uptake functions of the full-length IsdB protein.

Understanding Medical Words Tutorial: Download Instructions

MedlinePlus

... are compressed into a zip format, not all software packages will follow the step-by-step directions ... http://www.winzip.com/aboutzip.htm) or similar software and be sure to extract ALL the files ...

U-EXTRACTION--IMPROVEMENTS IN ELIMINATION OF Mo BY USE OF FERRIC ION

DOEpatents

Clark, H.M.; Duffey, D.

1958-06-10

An improved solvent extraction process is described whereby U may be extracted by a water immiscible organic solvent from an aqueous solution of uranyl nitrate. It has been found that Mo in the presence of phosphate ions appears to form a complex with the phosphate which extracts along with the U. This extraction of Mo may be suppressed by providing ferric ion in the solution prior to the extraction step. The ferric ion is preferably provided in the form of ferric nitrate.

Direct LiT Electrolysis in a Metallic Fusion Blanket

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

Olson, Luke

2016-09-30

A process that simplifies the extraction of tritium from molten lithium-based breeding blankets was developed. The process is based on the direct electrolysis of lithium tritide using a ceramic Li ion conductor that replaces the molten salt extraction step. Extraction of tritium in the form of lithium tritide in the blankets/targets of fusion/fission reactors is critical in order to maintain low concentrations. This is needed to decrease the potential tritium permeation to the surroundings and large releases from unforeseen accident scenarios. Extraction is complicated due to required low tritium concentration limits and because of the high affinity of tritium formore » the blanket. This work identified, developed and tested the use of ceramic lithium ion conductors capable of recovering hydrogen and deuterium through an electrolysis step at high temperatures.« less

Direct Lit Electrolysis In A Metallic Lithium Fusion Blanket

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

Colon-Mercado, H.; Babineau, D.; Elvington, M.

2015-10-13

A process that simplifies the extraction of tritium from molten lithium based breeding blankets was developed.  The process is based on the direct electrolysis of lithium tritide using a ceramic Li ion conductor that replaces the molten salt extraction step. Extraction of tritium in the form of lithium tritide in the blankets/targets of fission/fusion reactors is critical in order to maintained low concentrations.  This is needed to decrease the potential tritium permeation to the surroundings and large releases from unforeseen accident scenarios. Because of the high affinity of tritium for the blanket, extraction is complicated at the required low levels. This workmore » identified, developed and tested the use of ceramic lithium ion conductors capable of recovering the hydrogen and deuterium thru an electrolysis step at high temperatures. « less

Alternative sorbents for the dispersive solid-phase extraction step in quick, easy, cheap, effective, rugged and safe method for extraction of pesticides from rice paddy soils with determination by liquid chromatography tandem mass spectrometry.

PubMed

Arias, Jean Lucas de Oliveira; Rombaldi, Caroline; Caldas, Sergiane Souza; Primel, Ednei Gilberto

2014-09-19

The clean-up step is essential to reduce interferences, improve quantification and help to maintain the integrity of the chromatographic system when working with complex matrices. In this study, alternative materials were evaluated as sorbents in the dispersive solid-phase extraction (D-SPE) for the determination and extraction of seventeen pesticides from rice paddy soil samples by the quick, easy, cheap, effective, rugged and safe (QuEChERS) method coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Chitin, chitosan, diatomaceous earth and PSA were compared in terms of extraction efficiency and matrix effect. The best results were achieved when chitosan was used. Quantification limits ranged from 0.1 to 100μgkg(-1). Calibration curves showed correlation coefficient values higher than 0.98. Results of accuracy and precision in the spiked soil samples between 60% and 120%, with a relative standard deviation lower than 20%, were reached for 15 out of 17 pesticides. The matrix effect was evaluated and only one compound was influenced by the matrix components, showing medium effect. Results showed that alternative materials are more effective and less expensive than traditional sorbents which have been usually employed, i.e., they may be used in the D-SPE step during the extraction of pesticides from rice paddy soils. Copyright © 2014 Elsevier B.V. All rights reserved.

Hydrophilic 2,9-bis-triazolyl-1,10-phenanthroline ligands enable selective Am(iii) separation: a step further towards sustainable nuclear energy.

PubMed

Edwards, Alyn C; Mocilac, Pavle; Geist, Andreas; Harwood, Laurence M; Sharrad, Clint A; Burton, Neil A; Whitehead, Roger C; Denecke, Melissa A

2017-05-02

The first hydrophilic, 1,10-phenanthroline derived ligands consisting of only C, H, O and N atoms for the selective extraction of Am(iii) from spent nuclear fuel are reported herein. One of these 2,9-bis-triazolyl-1,10-phenanthroline (BTrzPhen) ligands combined with a non-selective extracting agent, was found to exhibit process-suitable selectivity for Am(iii) over Eu(iii) and Cm(iii), providing a clear step forward.

Economic Methods of Ginger Protease'sextraction and Purification

NASA Astrophysics Data System (ADS)

Qiao, Yuanyuan; Tong, Junfeng; Wei, Siqing; Du, Xinyong; Tang, Xiaozhen

This article reports the ginger protease extraction and purification methods from fresh ginger rhizome. As to ginger protease extraction, we adapt the steps of organic solvent dissolving, ammonium sulfate depositing and freeze-drying, and this method can attain crude enzyme powder 0.6% weight of fresh ginger rhizome. The purification part in this study includes two steps: cellulose ion exchange (DEAE-52) and SP-Sephadex 50 chromatography, which can purify crude ginger protease through ion and molecular weight differences respectively.

Effects of dual task on turning ability in stroke survivors and older adults.

PubMed

Hollands, K L; Agnihotri, D; Tyson, S F

2014-09-01

Turning is an integral component of independent mobility in which stroke survivors frequently fall. This study sought to measure the effects of competing cognitive demands on the stepping patterns of stroke survivors, compared to healthy age-match adults, during turning as a putative mechanism for falls. Walking and turning (90°) was assessed under single (walking and turning alone) and dual task (subtracting serial 3s while walking and turning) conditions using an electronic, pressure-sensitive walkway. Dependent measures were time to turn, variability in time to turn, step length, step width and single support time during three steps of the turn. Turning ability in single and dual task conditions was compared between stroke survivors (n=17, mean ± SD: 59 ± 113 months post-stroke, 64 ± 10 years of age) and age-matched healthy counterparts (n=15). Both groups took longer, were more variable, tended to widen the second step and, crucially, increased single support time on the inside leg of the turn while turning and distracted. Increased single support time during turning may represent biomechanical mechanism, within stepping patterns of turning under distraction, for increased risk of falls for both stroke survivors and older adults. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Comparison of phosphorus recovery from incineration and gasification sewage sludge ash.

PubMed

Parés Viader, Raimon; Jensen, Pernille Erland; Ottosen, Lisbeth M; Thomsen, Tobias P; Ahrenfeldt, Jesper; Hauggaard-Nielsen, Henrik

2017-03-01

Incineration of sewage sludge is a common practice in many western countries. Gasification is an attractive option because of its high energy efficiency and flexibility in the usage of the produced gas. However, they both unavoidably produce sewage sludge ashes, a material that is rich in phosphorus, but which is commonly landfilled or used in construction materials. With current uncertainty in phosphate rock supply, phosphorus recovery from sewage sludge ashes has become interesting. In the present work, ashes from incineration and gasification of the same sewage sludge were compared in terms of phosphorus extractability using electrodialytic (ED) methods. The results show that comparable recovery rates of phosphorus were achieved with a single ED step for incineration ashes and a sequential combination of two ED steps for gasification ashes, which was due to a higher influence of iron and/or aluminium in phosphorus solubility for the latter. A product with lower level of metallic impurities and comparable to wet process phosphoric acid was eventually obtained from gasification ashes. Thus, gasification becomes an interesting alternative to incineration also in terms of phosphorus separation.

An Accelerated Analytical Process for the Development of STR Profiles for Casework Samples.

PubMed

Laurin, Nancy; Frégeau, Chantal J

2015-07-01

Significant efforts are being devoted to the development of methods enabling rapid generation of short tandem repeat (STR) profiles in order to reduce turnaround times for the delivery of human identification results from biological evidence. Some of the proposed solutions are still costly and low throughput. This study describes the optimization of an analytical process enabling the generation of complete STR profiles (single-source or mixed profiles) for human identification in approximately 5 h. This accelerated process uses currently available reagents and standard laboratory equipment. It includes a 30-min lysis step, a 27-min DNA extraction using the Promega Maxwell(®) 16 System, DNA quantification in <1 h using the Qiagen Investigator(®) Quantiplex HYres kit, fast amplification (<26 min) of the loci included in AmpFℓSTR(®) Identifiler(®), and analysis of the profiles on the 3500-series Genetic Analyzer. This combination of fast individual steps produces high-quality profiling results and offers a cost-effective alternative approach to rapid DNA analysis. © 2015 American Academy of Forensic Sciences.

A study on the stability and green synthesis of silver nanoparticles using Ziziphora tenuior (Zt) extract at room temperature.

PubMed

Sadeghi, Babak; Gholamhoseinpoor, F

2015-01-05

Biomolecules present in plant extracts can be used to reduce metal ions to nanoparticles in a single-step green synthesis process. This biogenic reduction of metal ion to base metal is quite rapid, readily conducted at room temperature and pressure, and easily scaled up. Mediated Synthesis by plant extracts is environmentally benign. The involved reducing agents include the various water soluble plant metabolites (e.g. alkaloids, phenolic compounds, terpenoids) and co-enzymes. Silver (Ag) nanoparticles have the particular focus of plant-based syntheses. Extracts of a diverse range of Ziziphora tenuior (Zt) have been successfully used in making nanoparticles. The aim of this study was to investigate the antioxidant properties of this plant and its ability to synthesize silver nanoparticles. Z.tenuior leaves were used to prepare the aqueous extract for this study. Silver nanoparticles were characterized with different techniques such as UV-vis spectroscopy, Fourier transform infrared (FT-IR) spectroscopy, X-ray diffraction (XRD), Scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Transmission electron microscopy experiments showed that these nanoparticles are spherical and uniformly distributed and its size is from 8 to 40 nm. FT-IR spectroscopy revealed that silver nanoparticles were functionalized with biomolecules that have primary amine group (NH₂), carbonyl group, -OH groups and other stabilizing functional groups. X-ray diffraction pattern showed high purity and face centered cubic structure of silver nanoparticles with size of 38 nm. In addition to plant extracts, live plants can be used for the synthesis. Here were view the methods of making nanoparticles using plant extracts. The scanning electron microscopy (SEM) implies the right of forming silver nanoparticles. The results of TEM, SEM, FT-IR, UV-VIS and XRD confirm that the leaves extract of Zt can synthesis silver nanoparticles. Copyright © 2014 Elsevier B.V. All rights reserved.

Leaching behavior of rare earth elements in fort union lignite coals of North America

DOE PAGES

Laudal, Daniel A.; Benson, Steven A.; Addleman, Raymond Shane; ...

2018-03-30

Fort Union lignite coal samples were subjected to a series of aqueous leaching experiments to understand the extraction behavior of the rare earth elements (REE). This testing was aimed at understanding the modes of occurrence of the REE in the lignite coals, as well as to provide foundational data for development of rare earth extraction processes. In a first series of tests, a sequential leaching process was used to investigate modes of occurrence of the REE of select lignite coals. The tests involved sequential exposure to solvents consisting of water, ammonium acetate and dilute hydrochloric acid (HCl). The results indicatedmore » that water and ammonium acetate extracted very little of the REE, indicating the REE are not present as water soluble or ion-exchangeable forms. However, the data shows that a large percentage of the REE were extracted with the hydrochloric acid (80–95 wt%), suggesting presence in HCl-soluble mineral forms such as carbonates, and/or presence as organic complexes. A second series of tests was performed involving single-step leaching with dilute acids and various operating parameters, including acid type, acid concentration, acid/coal contact time and coal particle size. For select samples, additional tests were performed to understand the results of leaching, including float-sink density separations and humic acid extraction. The results have shown that the majority of REE in Fort Union lignites appear to be associated weakly with the organic matrix of the coals, most likely as coordination complexes of carboxylic acid groups. The light REE and heavy REE exhibit different behaviors, however. The extractable light REE appear to have association both in acid-soluble mineral forms and as organic complexes, whereas the extractable heavy REE appear to be almost solely associated with the organics. In conclusion, scandium behavior was notably different than yttrium and the lanthanides, and the data suggests the extractable content is primarily associated as acid-soluble mineral forms.« less

Dispersive liquid-phase microextraction with solidification of floating organic droplet coupled with high-performance liquid chromatography for the determination of Sudan dyes in foodstuffs and water samples.

PubMed

Chen, Bo; Huang, Yuming

2014-06-25

Dispersive liquid-phase microextraction with solidification of floating organic drop (SFO-DLPME) is one of the most interesting sample preparation techniques developed in recent years. In this paper, a new, rapid, and efficient SFO-DLPME coupled with high-performance liquid chromatography (HPLC) was established for the extraction and sensitive detection of banned Sudan dyes, namely, Sudan I, Sudan II, Sudan III, and Sudan IV, in foodstuff and water samples. Various factors, such as the type and volume of extractants and dispersants, pH and volume of sample solution, extraction time and temperature, ion strength, and humic acid concentration, were investigated and optimized to achieve optimal extraction of Sudan dyes in one single step. After optimization of extraction conditions using 1-dodecanol as an extractant and ethanol as a dispersant, the developed procedure was applied for extraction of the target Sudan dyes from 2 g of food samples and 10 mL of the spiked water samples. Under the optimized conditions, all Sudan dyes could be easily extracted by the proposed SFO-DLPME method. Limits of detection of the four Sudan dyes obtained were 0.10-0.20 ng g(-1) and 0.03 μg L(-1) when 2 g of foodstuff samples and 10 mL of water samples were adopted, respectively. The inter- and intraday reproducibilities were below 4.8% for analysis of Sudan dyes in foodstuffs. The method was satisfactorily used for the detection of Sudan dyes, and the recoveries of the target for the spiked foodstuff and water samples ranged from 92.6 to 106.6% and from 91.1 to 108.6%, respectively. These results indicated that the proposed method is simple, rapid, sensitive, and suitable for the pre-concentration and detection of the target dyes in foodstuff samples.

Leaching behavior of rare earth elements in fort union lignite coals of North America

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

Laudal, Daniel A.; Benson, Steven A.; Addleman, Raymond Shane

Fort Union lignite coal samples were subjected to a series of aqueous leaching experiments to understand the extraction behavior of the rare earth elements (REE). This testing was aimed at understanding the modes of occurrence of the REE in the lignite coals, as well as to provide foundational data for development of rare earth extraction processes. In a first series of tests, a sequential leaching process was used to investigate modes of occurrence of the REE of select lignite coals. The tests involved sequential exposure to solvents consisting of water, ammonium acetate and dilute hydrochloric acid (HCl). The results indicatedmore » that water and ammonium acetate extracted very little of the REE, indicating the REE are not present as water soluble or ion-exchangeable forms. However, the data shows that a large percentage of the REE were extracted with the hydrochloric acid (80–95 wt%), suggesting presence in HCl-soluble mineral forms such as carbonates, and/or presence as organic complexes. A second series of tests was performed involving single-step leaching with dilute acids and various operating parameters, including acid type, acid concentration, acid/coal contact time and coal particle size. For select samples, additional tests were performed to understand the results of leaching, including float-sink density separations and humic acid extraction. The results have shown that the majority of REE in Fort Union lignites appear to be associated weakly with the organic matrix of the coals, most likely as coordination complexes of carboxylic acid groups. The light REE and heavy REE exhibit different behaviors, however. The extractable light REE appear to have association both in acid-soluble mineral forms and as organic complexes, whereas the extractable heavy REE appear to be almost solely associated with the organics. In conclusion, scandium behavior was notably different than yttrium and the lanthanides, and the data suggests the extractable content is primarily associated as acid-soluble mineral forms.« less

Bond durability of adhesives containing modified-monomer with/without-fluoride after aging in artificial saliva and under intrapulpal pressure simulation.

PubMed

El-Deeb, H A; Al Sherbiney, H H; Mobarak, E H

2013-01-01

To evaluate the dentin bond strength durability of adhesives containing modified-monomer with/without-fluoride after storage in artificial saliva and under intrapulpal pressure simulation (IPPS). The occlusal enamel of 48 freshly extracted teeth was trimmed to expose midcoronal dentin. Roots were sectioned to expose the pulp chamber and to connect the specimens to the pulpal-pressure assembly. Specimens were assigned into four groups (n=12) according to adhesive system utilized: a two-step etch-and-rinse adhesive system (SB, Adper Single Bond 2, 3M ESPE), a two-step self-etch adhesive system (CSE, Clearfil SE Bond, Kuraray Medical Inc), and two single-step self-etch adhesives with the same modified monomer (bis-acrylamide)-one with fluoride (AOF, AdheSE One F, Ivoclar-Vivadent) and the other without (AO, AdheSE One, Ivoclar-Vivadent). Bonding was carried out while the specimens were subjected to 15-mm Hg IPPS. Resin composite (Valux Plus, 3M ESPE) buildups were made. After curing, specimens were aged in artificial saliva and under 20-mm Hg IPPS at 37°C in a specially constructed incubator either for 24 hours or six months prior to testing. Bonded specimens (n=6/group) were sectioned into sticks (n=24/group) with a cross section of 0.9 ± 0.01 mm(2) and subjected to microtensile bond strength (μTBS) testing using a universal testing machine. Data were statistically analyzed using two-way analysis of variance (ANOVA) with repeated measures, one-way ANOVA tests, and a t-test (p<0.05). Failure modes were determined using a scanning electron microscope. The μTBS values of SB and CSE fell significantly after six-month storage in artificial saliva and under IPPS, yet these values remained significantly higher than those for the other two adhesives with modified monomers. There was no significant difference in the bond strength values between fluoride-containing and fluoride-free self-etch adhesive systems (AOF and AO) after 24 hours or six months. Modes of failure were mainly adhesive and mixed. Based on the results of this study, 1) Fluoride addition did not affect dentin bond durability; and 2) despite the fact that the single-step adhesive system with modified monomer showed stability, bond strengths associated with these systems remained lower than those of multistep adhesive systems.

Bond Strength and Interfacial Morphology of Different Dentin Adhesives in Primary Teeth

PubMed Central

Vashisth, Pallavi; Mittal, Mudit; Goswami, Mousumi; Chaudhary, Seema; Dwivedi, Swati

2014-01-01

Objective: To evaluate the interfacial morphology and the bond strength produced by the three-step, two-step and single-step bonding systems in primary teeth. Materials and Methods: Occlusal surfaces of 72 extracted human deciduous teeth were ground to expose the dentin. The teeth were divided into four groups: (a) Scotchbond Multipurpose (3M, ESPE), (b) Adh Se (Vivadent), (d) OptiBond All-in-One (Kerr) and (e)Futurabond NR (VOCO, Cuxhaven, Germany). The adhesives were applied to each group following the manufacturer’s instructions. Then, teeth from each group were divided into two groups: (A) For viewing interfacial morphology (32 teeth), with 8 teeth in each group, and (B) For measurement of bond strength (40 teeth), with 10 teeth in each group. All the samples were prepared for viewing under SEM. The statistical analysis was done using SPSS version 15.0 software. Results: Observational measurement of tag length in different adhesives revealed that Scotchbond had the most widely spread values with a range from 12.20 to 89.10μm while OptiBond AIO had the narrowest range (0 to 22.50). The bond strength of Scotchbond Multipurpose was significantly higher (7.4744±1.88763) (p<0.001) as compared to Futurabond NR (3.8070±1.61345), Adhe SE (4.4478 ± 1.3820) and OptiBond-all-in-one (4.4856±1.07925). Conclusion: The three-step bonding system showed better results as compared to simplified studied bonding systems PMID:24910694

Toward automated denoising of single molecular Förster resonance energy transfer data

NASA Astrophysics Data System (ADS)

Lee, Hao-Chih; Lin, Bo-Lin; Chang, Wei-Hau; Tu, I.-Ping

2012-01-01

A wide-field two-channel fluorescence microscope is a powerful tool as it allows for the study of conformation dynamics of hundreds to thousands of immobilized single molecules by Förster resonance energy transfer (FRET) signals. To date, the data reduction from a movie to a final set containing meaningful single-molecule FRET (smFRET) traces involves human inspection and intervention at several critical steps, greatly hampering the efficiency at the post-imaging stage. To facilitate the data reduction from smFRET movies to smFRET traces and to address the noise-limited issues, we developed a statistical denoising system toward fully automated processing. This data reduction system has embedded several novel approaches. First, as to background subtraction, high-order singular value decomposition (HOSVD) method is employed to extract spatial and temporal features. Second, to register and map the two color channels, the spots representing bleeding through the donor channel to the acceptor channel are used. Finally, correlation analysis and likelihood ratio statistic for the change point detection (CPD) are developed to study the two channels simultaneously, resolve FRET states, and report the dwelling time of each state. The performance of our method has been checked using both simulation and real data.

Human Movement Recognition Based on the Stochastic Characterisation of Acceleration Data

PubMed Central

Munoz-Organero, Mario; Lotfi, Ahmad

2016-01-01

Human activity recognition algorithms based on information obtained from wearable sensors are successfully applied in detecting many basic activities. Identified activities with time-stationary features are characterised inside a predefined temporal window by using different machine learning algorithms on extracted features from the measured data. Better accuracy, precision and recall levels could be achieved by combining the information from different sensors. However, detecting short and sporadic human movements, gestures and actions is still a challenging task. In this paper, a novel algorithm to detect human basic movements from wearable measured data is proposed and evaluated. The proposed algorithm is designed to minimise computational requirements while achieving acceptable accuracy levels based on characterising some particular points in the temporal series obtained from a single sensor. The underlying idea is that this algorithm would be implemented in the sensor device in order to pre-process the sensed data stream before sending the information to a central point combining the information from different sensors to improve accuracy levels. Intra- and inter-person validation is used for two particular cases: single step detection and fall detection and classification using a single tri-axial accelerometer. Relevant results for the above cases and pertinent conclusions are also presented. PMID:27618063

Inverse finite element methods for extracting elastic-poroviscoelastic properties of cartilage and other soft tissues from indentation

NASA Astrophysics Data System (ADS)

Namani, Ravi

Mechanical properties are essential for understanding diseases that afflict various soft tissues, such as osteoarthritic cartilage and hypertension which alters cardiovascular arteries. Although the linear elastic modulus is routinely measured for hard materials, standard methods are not available for extracting the nonlinear elastic, linear elastic and time-dependent properties of soft tissues. Consequently, the focus of this work is to develop indentation methods for soft biological tissues; since analytical solutions are not available for the general context, finite element simulations are used. First, parametric studies of finite indentation of hyperelastic layers are performed to examine if indentation has the potential to identify nonlinear elastic behavior. To answer this, spherical, flat-ended conical and cylindrical tips are examined and the influence of thickness is exploited. Also the influence of the specimen/substrate boundary condition (slip or non-slip) is clarified. Second, a new inverse method---the hyperelastic extraction algorithm (HPE)---was developed to extract two nonlinear elastic parameters from the indentation force-depth data, which is the basic measurement in an indentation test. The accuracy of the extracted parameters and the influence of noise in measurements on this accuracy were obtained. This showed that the standard Berkovitch tip could only extract one parameter with sufficient accuracy, since the indentation force-depth curve has limited sensitivity to both nonlinear elastic parameters. Third, indentation methods for testing tissues from small animals were explored. New methods for flat-ended conical tips are derived. These account for practical test issues like the difficulty in locating the surface or soft specimens. Also, finite element simulations are explored to elucidate the influence of specimen curvature on the indentation force-depth curve. Fourth, the influence of inhomogeneity and material anisotropy on the extracted "average" linear elastic modulus was studied. The focus here is on murine tibial cartilage, since recent experiments have shown that the modulus measured by a 15 mum tip is considerably larger than that obtained from a 90 mum tip. It is shown that a depth-dependent modulus could give rise to such a size effect. Lastly, parametric studies were performed within the small strain setting to understand the influence of permeability and viscoelastic properties on the indentation stress-relaxation response. The focus here is on cartilage, and specific test protocols (single-step vs. multi-step stress relaxation) are explored. An inverse algorithm was developed to extract the poroviscoelastic parameters. A sensitivity study using this algorithm shows that the instantaneous elastic modulus (which is a measure of the viscous relaxation) can be extracted with very good accuracy, but the permeability and long-time relaxation constant cannot be extracted with good accuracy. The thesis concludes with implications of these studies. The potential and limitations of indentation tests for studying cartilage and other soft tissues is discussed.

Age and gender estimation using Region-SIFT and multi-layered SVM

NASA Astrophysics Data System (ADS)

Kim, Hyunduk; Lee, Sang-Heon; Sohn, Myoung-Kyu; Hwang, Byunghun

2018-04-01

In this paper, we propose an age and gender estimation framework using the region-SIFT feature and multi-layered SVM classifier. The suggested framework entails three processes. The first step is landmark based face alignment. The second step is the feature extraction step. In this step, we introduce the region-SIFT feature extraction method based on facial landmarks. First, we define sub-regions of the face. We then extract SIFT features from each sub-region. In order to reduce the dimensions of features we employ a Principal Component Analysis (PCA) and a Linear Discriminant Analysis (LDA). Finally, we classify age and gender using a multi-layered Support Vector Machines (SVM) for efficient classification. Rather than performing gender estimation and age estimation independently, the use of the multi-layered SVM can improve the classification rate by constructing a classifier that estimate the age according to gender. Moreover, we collect a dataset of face images, called by DGIST_C, from the internet. A performance evaluation of proposed method was performed with the FERET database, CACD database, and DGIST_C database. The experimental results demonstrate that the proposed approach classifies age and performs gender estimation very efficiently and accurately.

A Featured-Based Strategy for Stereovision Matching in Sensors with Fish-Eye Lenses for Forest Environments

PubMed Central

Herrera, Pedro Javier; Pajares, Gonzalo; Guijarro, Maria; Ruz, José J.; Cruz, Jesús M.; Montes, Fernando

2009-01-01

This paper describes a novel feature-based stereovision matching process based on a pair of omnidirectional images in forest stands acquired with a stereovision sensor equipped with fish-eye lenses. The stereo analysis problem consists of the following steps: image acquisition, camera modelling, feature extraction, image matching and depth determination. Once the depths of significant points on the trees are obtained, the growing stock volume can be estimated by considering the geometrical camera modelling, which is the final goal. The key steps are feature extraction and image matching. This paper is devoted solely to these two steps. At a first stage a segmentation process extracts the trunks, which are the regions used as features, where each feature is identified through a set of attributes of properties useful for matching. In the second step the features are matched based on the application of the following four well known matching constraints, epipolar, similarity, ordering and uniqueness. The combination of the segmentation and matching processes for this specific kind of sensors make the main contribution of the paper. The method is tested with satisfactory results and compared against the human expert criterion. PMID:22303134

Border preserving skin lesion segmentation

NASA Astrophysics Data System (ADS)

Kamali, Mostafa; Samei, Golnoosh

2008-03-01

Melanoma is a fatal cancer with a growing incident rate. However it could be cured if diagnosed in early stages. The first step in detecting melanoma is the separation of skin lesion from healthy skin. There are particular features associated with a malignant lesion whose successful detection relies upon accurately extracted borders. We propose a two step approach. First, we apply K-means clustering method (to 3D RGB space) that extracts relatively accurate borders. In the second step we perform an extra refining step for detecting the fading area around some lesions as accurately as possible. Our method has a number of novelties. Firstly as the clustering method is directly applied to the 3D color space, we do not overlook the dependencies between different color channels. In addition, it is capable of extracting fine lesion borders up to pixel level in spite of the difficulties associated with fading areas around the lesion. Performing clustering in different color spaces reveals that 3D RGB color space is preferred. The application of the proposed algorithm to an extensive data-base of skin lesions shows that its performance is superior to that of existing methods both in terms of accuracy and computational complexity.

Determination of fluoroquinolone antibiotics via ionic-liquid-based, salt-induced, dual microextraction in swine feed.

PubMed

Wang, Huili; Gao, Ming; Gao, Jiajia; Yu, Nana; Huang, Hong; Yu, Qing; Wang, Xuedong

2016-09-01

In conventional microextraction procedures, the disperser (organic solvent or ionic liquid) is left in the aqueous phase and discarded after finishing the microextraction process. Because the disperser is water-soluble, it results in low extraction recovery for polar compounds. In this investigation, an ionic-liquid-based microextraction (ILBME) was integrated with salting-out assisted liquid-liquid microextraction (SALLME) to build an ionic-liquid-based, salt-induced, dual microextraction (ILSDME) for isolation of five fluoroquinolone antibiotics (FQs) with high polarity (log P, -1.0 to 1.0). The proposed ILSDME method incorporates a dual microextraction by converting the disperser in the ILBME to the extractor in the SALLME. Optimization of key factors was conducted by integrating single-factor experiments and central composite design. The optimized experimental parameters were 80 μL [C8MIM][PF6] as extractor, 505 μL acetone as disperser, pH = 2.0, 4.1 min extraction time, and 4.2 g of Na2SO4. Under optimized conditions, high ERs (90.6-103.2 %) and low LODs (0.07-0.61 μg kg(-1)) were determined for five FQs in swine feed. Experimental precision based on RSDs was 1.4-5.2 % for intra-day and 2.4-6.9 % for inter-day analyses. The combination of ILBME with SALLME increased FQ recoveries by 15-20 % as compared with SALLME, demonstrating that the ILSDME method can enhance extraction efficiency for polar compounds compared to single-step microextraction. Therefore, the ILSDME method developed in this study has wide application for pretreatment of moderately to highly polar pollutants in complex matrices. Graphical Abstract A dual microextraction was developed by integrating ionic-liquid-based microextraction with salting-out assisted liquid-liquid microextraction for isolation of five fluoroquinolone antibiotics (FQs) with high polarity (log P = -1.0 to 1.0). The principle of dual microextraction is based on converting the remaining disperser from the first microextraction into an extractor in the second microextraction. Single-factor experiment and central composite design were applied for optimizing operational parameters using 3D response surfaces and contour lines. Under optimized conditions, the method provided high extraction recoveries and low LODs for five FQs in swine feed. The prominent advantage of the dual microextraction is rapid and highly efficient extraction of moderately to highly polar fluoroquinolones from complex matrices.

A Comparative Study of Chemically and Biologically Synthesized MgO Nanomaterial for Liquefied Petroleum Gas Detection

NASA Astrophysics Data System (ADS)

Thirupathi, Rampelly; Solleti, Goutham; Sreekanth, Tirumala; Sadasivuni, Kishor Kumar; Venkateswara Rao, Kalagadda

2018-03-01

The exceptional chemical and physical properties of nanostructured materials are extremely suitable for designing new and enhanced sensing devices, particularly gas sensors and biosensors. The present work describes the synthesis of magnesium oxide (MgO) nanoparticles through two methods: a green synthesis using aloe vera plant extract and a chemical method using a glycine-based solution combustion route. In a single step, the extracted organic molecules from aloe vera plants were used to reduce metal ions by the green method. MgO nanoparticles were coated onto the interdigital electrode using the drop-drying method. The dynamic gas-sensing characteristics were measured for liquefied petroleum gas (LPG) at different concentrations and various temperatures. The MgO nanoparticles were characterized by using x-ray diffraction, field emission scanning electron microscopy, and high-resolution transmission electron microscopy to determine the size and structure of the particles. The product's functional properties were analyzed by Fourier transform-infrared spectroscopy and UV-visible spectroscopy. We found that the LPG sensing behavior of biologically synthesized MgO registers excellent sensitivity at various operating temperatures.

A Comparative Study of Chemically and Biologically Synthesized MgO Nanomaterial for Liquefied Petroleum Gas Detection

NASA Astrophysics Data System (ADS)

Thirupathi, Rampelly; Solleti, Goutham; Sreekanth, Tirumala; Sadasivuni, Kishor Kumar; Venkateswara Rao, Kalagadda

2018-07-01

The exceptional chemical and physical properties of nanostructured materials are extremely suitable for designing new and enhanced sensing devices, particularly gas sensors and biosensors. The present work describes the synthesis of magnesium oxide (MgO) nanoparticles through two methods: a green synthesis using aloe vera plant extract and a chemical method using a glycine-based solution combustion route. In a single step, the extracted organic molecules from aloe vera plants were used to reduce metal ions by the green method. MgO nanoparticles were coated onto the interdigital electrode using the drop-drying method. The dynamic gas-sensing characteristics were measured for liquefied petroleum gas (LPG) at different concentrations and various temperatures. The MgO nanoparticles were characterized by using x-ray diffraction, field emission scanning electron microscopy, and high-resolution transmission electron microscopy to determine the size and structure of the particles. The product's functional properties were analyzed by Fourier transform-infrared spectroscopy and UV-visible spectroscopy. We found that the LPG sensing behavior of biologically synthesized MgO registers excellent sensitivity at various operating temperatures.

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.

Determination of supplemental feeding needs for astaxanthin and canthaxanthin in salmonids by supramolecular solvent-based microextraction and liquid chromatography-UV/VIS spectroscopy.

PubMed

Caballo, Carmen; Costi, Esther María; Sicilia, María Dolores; Rubio, Soledad

2012-09-15

Development of simple and rapid analytical methods for predicting supplemental feeding requirements in aquaculture is a need to reduce production costs. In this article, a supramolecular solvent (SUPRAS) made up of decanoic acid (DeA) assemblies was proposed to simplify sample treatment in the total and individual determination of carotenoids (red-pink pigments) in farmed salmonids. The analytes were quantitatively extracted in a single step that spends a few minutes using a small volume of SUPRAS (i.e. 800 μL) and directly determined in extracts without the interference from fats or other matrix components. The methods based on the combination of microextraction with SUPRAS and photometry or HPLC-UV/VIS spectroscopy were developed for the determination of total and individual carotenoids, respectively. The applicability of the methods was demonstrated by analysing non-fortified and fortified samples of farmed Atlantic salmons and rainbow trouts. Recoveries obtained by photometry and HPLC-UV/VIS spectroscopy were within the intervals 98-104% and 94-106%, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

Plant nuclear pore complex proteins are modified by novel oligosaccharides with terminal N-acetylglucosamine.

PubMed Central

Heese-Peck, A; Cole, R N; Borkhsenious, O N; Hart, G W; Raikhel, N V

1995-01-01

Only a few nuclear pore complex (NPC) proteins, mainly in vertebrates and yeast but none in plants, have been well characterized. As an initial step to identify plant NPC proteins, we examined whether NPC proteins from tobacco are modified by N-acetylglucosamine (GlcNAc). Using wheat germ agglutinin, a lectin that binds specifically to GlcNAc in plants, specific labeling was often found associated with or adjacent to NPCs. Nuclear proteins containing GlcNAc can be partially extracted by 0.5 M salt, as shown by a wheat germ agglutinin blot assay, and at least eight extracted proteins were modified by terminal GlcNAc, as determined by in vitro galactosyltransferase assays. Sugar analysis indicated that the plant glycans with terminal GlcNAc differ from the single O-linked GlcNAc of vertebrate NPC proteins in that they consist of oligosaccharides that are larger in size than five GlcNAc residues. Most of these appear to be bound to proteins via a hydroxyl group. This novel oligosaccharide modification may convey properties to the plant NPC that are different from those of vertebrate NPCs. PMID:8589629

An efficient one-pot synthesis of 1,4-disubstituted 1,2,3-triazoles at room temperature by green synthesized Cu NPs using Otostegia persica leaf extract.

PubMed

Nasrollahzadeh, Mahmoud; Sajadi, S Mohammad; Mirzaei, Yousef

2016-04-15

In this study, copper nanoparticles (Cu NPs) were synthesized using a rapid, single step and completely green biosynthetic method by reduction of CuCl2 · 2H2O solution with aqueous extract of leaves of Otostegia persica containing flavonoid and other phenolics as a main factor which acts as reducing agent and efficient stabilizer. UV-vis spectra gave surface plasmon resonance (SPR) at 560 nm. The Cu NPs were characterized by transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR) and X-ray diffraction (XRD). A possible synthesis mechanism of Cu NPs was presented. In addition, we investigated the catalytic activity of Cu NPs for the one-pot synthesis of 1,4-disubstituted 1,2,3-triazoles under mild reaction conditions with good to excellent yields. The catalyst could be easily recovered by centrifugation and reused at least five recycles with no significant decreases in the yields. Copyright © 2016 Elsevier Inc. All rights reserved.

Effect of Phenolic Compounds on the Synthesis of Gold Nanoparticles and Its Catalytic Activity in the Reduction of Nitro Compounds

PubMed Central

Mendes, Marta; Pombeiro, Armando J. L.

2018-01-01

Gold nanoparticles (AuNPs) were prepared using an eco-friendly approach in a single step by reduction of HAuCl4 with polyphenols from tea extracts, which act as both reducing and capping agents. The obtained AuNPs were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), ultraviolet–visible spectroscopy (UV–vis), and X-ray photoelectron spectroscopy (XPS). They act as highly efficient catalysts in the reduction of various aromatic nitro compounds in aqueous solution. The effects of a variety of factors (e.g., reaction time, type and amount of reducing agent, shape, size, or amount of AuNPs) were studied towards the optimization of the processes. The total polyphenol content (TPC) was determined before and after the catalytic reaction and the results are discussed in terms of the tea extract percentage, the size of the AuNPs, and their catalytic activity. The reusability of the AuNP catalyst in the reduction of 4-nitrophenol was also tested. The reactions follow pseudo first-order kinetics. PMID:29748502

Effect of Phenolic Compounds on the Synthesis of Gold Nanoparticles and its Catalytic Activity in the Reduction of Nitro Compounds.

PubMed

Alegria, Elisabete C B A; Ribeiro, Ana P C; Mendes, Marta; Ferraria, Ana M; do Rego, Ana M Botelho; Pombeiro, Armando J L

2018-05-10

Gold nanoparticles (AuNPs) were prepared using an eco-friendly approach in a single step by reduction of HAuCl₄ with polyphenols from tea extracts, which act as both reducing and capping agents. The obtained AuNPs were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), ultraviolet⁻visible spectroscopy (UV⁻vis), and X-ray photoelectron spectroscopy (XPS). They act as highly efficient catalysts in the reduction of various aromatic nitro compounds in aqueous solution. The effects of a variety of factors (e.g., reaction time, type and amount of reducing agent, shape, size, or amount of AuNPs) were studied towards the optimization of the processes. The total polyphenol content (TPC) was determined before and after the catalytic reaction and the results are discussed in terms of the tea extract percentage, the size of the AuNPs, and their catalytic activity. The reusability of the AuNP catalyst in the reduction of 4-nitrophenol was also tested. The reactions follow pseudo first-order kinetics.

Single-Rooted Extraction Sockets: Classification and Treatment Protocol.

PubMed

El Chaar, Edgar; Oshman, Sarah; Fallah Abed, Pooria

2016-09-01

Clinicians have many treatment techniques from which to choose when extracting a failing tooth and replacing it with an implant-supported restoration and when successful management of an extraction socket during the course of tooth replacement is necessary to achieve predictable and esthetic outcomes. This article presents a straightforward, yet thorough, classification for extraction sockets of single-rooted teeth and provides guidance to clinicians in the selection of appropriate and predictable treatment. The presented classification of extraction sockets for single-rooted teeth focuses on the topography of the extraction socket, while the protocol for treatment of each socket type factors in the shape of the remaining bone, the biotype, and the location of the socket whether it be in the mandible or maxilla. This system is based on the biologic foundations of wound healing and can help guide clinicians to successful treatment outcomes.

Automatic Rooftop Extraction in Stereo Imagery Using Distance and Building Shape Regularized Level Set Evolution

NASA Astrophysics Data System (ADS)

Tian, J.; Krauß, T.; d'Angelo, P.

2017-05-01

Automatic rooftop extraction is one of the most challenging problems in remote sensing image analysis. Classical 2D image processing techniques are expensive due to the high amount of features required to locate buildings. This problem can be avoided when 3D information is available. In this paper, we show how to fuse the spectral and height information of stereo imagery to achieve an efficient and robust rooftop extraction. In the first step, the digital terrain model (DTM) and in turn the normalized digital surface model (nDSM) is generated by using a newly step-edge approach. In the second step, the initial building locations and rooftop boundaries are derived by removing the low-level pixels and high-level pixels with higher probability to be trees and shadows. This boundary is then served as the initial level set function, which is further refined to fit the best possible boundaries through distance regularized level-set curve evolution. During the fitting procedure, the edge-based active contour model is adopted and implemented by using the edges indicators extracted from panchromatic image. The performance of the proposed approach is tested by using the WorldView-2 satellite data captured over Munich.

Metal fractionation in olive oil and urban sewage sludges using the three-stage BCR sequential extraction method and microwave single extractions.

PubMed

Pérez Cid, B; Fernández Alborés, A; Fernández Gómez, E; Faliqé López, E

2001-08-01

The conventional three-stage BCR sequential extraction method was employed for the fractionation of heavy metals in sewage sludge samples from an urban wastewater treatment plant and from an olive oil factory. The results obtained for Cu, Cr, Ni, Pb and Zn in these samples were compared with those attained by a simplified extraction procedure based on microwave single extractions and using the same reagents as employed in each individual BCR fraction. The microwave operating conditions in the single extractions (heating time and power) were optimized for all the metals studied in order to achieve an extraction efficiency similar to that of the conventional BCR procedure. The measurement of metals in the extracts was carried out by flame atomic absorption spectrometry. The results obtained in the first and third fractions by the proposed procedure were, for all metals, in good agreement with those obtained using the BCR sequential method. Although in the reducible fraction the extraction efficiency of the accelerated procedure was inferior to that of the conventional method, the overall metals leached by both microwave single and sequential extractions were basically the same (recoveries between 90.09 and 103.7%), except for Zn in urban sewage sludges where an extraction efficiency of 87% was achieved. Chemometric analysis showed a good correlation between the results given by the two extraction methodologies compared. The application of the proposed approach to a certified reference material (CRM-601) also provided satisfactory results in the first and third fractions, as it was observed for the sludge samples analysed.

Auxotonic to isometric contraction transitioning in a beating heart causes myosin step-size to down shift

PubMed Central

Sun, Xiaojing; Wang, Yihua; Ajtai, Katalin

2017-01-01

Myosin motors in cardiac ventriculum convert ATP free energy to the work of moving blood volume under pressure. The actin bound motor cyclically rotates its lever-arm/light-chain complex linking motor generated torque to the myosin filament backbone and translating actin against resisting force. Previous research showed that the unloaded in vitro motor is described with high precision by single molecule mechanical characteristics including unitary step-sizes of approximately 3, 5, and 8 nm and their relative step-frequencies of approximately 13, 50, and 37%. The 3 and 8 nm unitary step-sizes are dependent on myosin essential light chain (ELC) N-terminus actin binding. Step-size and step-frequency quantitation specifies in vitro motor function including duty-ratio, power, and strain sensitivity metrics. In vivo, motors integrated into the muscle sarcomere form the more complex and hierarchically functioning muscle machine. The goal of the research reported here is to measure single myosin step-size and step-frequency in vivo to assess how tissue integration impacts motor function. A photoactivatable GFP tags the ventriculum myosin lever-arm/light-chain complex in the beating heart of a live zebrafish embryo. Detected single GFP emission reports time-resolved myosin lever-arm orientation interpreted as step-size and step-frequency providing single myosin mechanical characteristics over the active cycle. Following step-frequency of cardiac ventriculum myosin transitioning from low to high force in relaxed to auxotonic to isometric contraction phases indicates that the imposition of resisting force during contraction causes the motor to down-shift to the 3 nm step-size accounting for >80% of all the steps in the near-isometric phase. At peak force, the ATP initiated actomyosin dissociation is the predominant strain inhibited transition in the native myosin contraction cycle. The proposed model for motor down-shifting and strain sensing involves ELC N-terminus actin binding. Overall, the approach is a unique bottom-up single molecule mechanical characterization of a hierarchically functional native muscle myosin. PMID:28423017

Comparison of Stepped Care Delivery Against a Single, Empirically Validated Cognitive-Behavioral Therapy Program for Youth With Anxiety: A Randomized Clinical Trial.

PubMed

Rapee, Ronald M; Lyneham, Heidi J; Wuthrich, Viviana; Chatterton, Mary Lou; Hudson, Jennifer L; Kangas, Maria; Mihalopoulos, Cathrine

2017-10-01

Stepped care is embraced as an ideal model of service delivery but is minimally evaluated. The aim of this study was to evaluate the efficacy of cognitive-behavioral therapy (CBT) for child anxiety delivered via a stepped-care framework compared against a single, empirically validated program. A total of 281 youth with anxiety disorders (6-17 years of age) were randomly allocated to receive either empirically validated treatment or stepped care involving the following: (1) low intensity; (2) standard CBT; and (3) individually tailored treatment. Therapist qualifications increased at each step. Interventions did not differ significantly on any outcome measures. Total therapist time per child was significantly shorter to deliver stepped care (774 minutes) compared with best practice (897 minutes). Within stepped care, the first 2 steps returned the strongest treatment gains. Stepped care and a single empirically validated program for youth with anxiety produced similar efficacy, but stepped care required slightly less therapist time. Restricting stepped care to only steps 1 and 2 would have led to considerable time saving with modest loss in efficacy. Clinical trial registration information-A Randomised Controlled Trial of Standard Care Versus Stepped Care for Children and Adolescents With Anxiety Disorders; http://anzctr.org.au/; ACTRN12612000351819. Copyright © 2017 American Academy of Child and Adolescent Psychiatry. Published by Elsevier Inc. All rights reserved.

High-resolution melt PCR analysis for genotyping of Ureaplasma parvum isolates directly from clinical samples.

PubMed

Payne, Matthew S; Tabone, Tania; Kemp, Matthew W; Keelan, Jeffrey A; Spiller, O Brad; Newnham, John P

2014-02-01

Ureaplasma sp. infection in neonates and adults underlies a variety of disease pathologies. Of the two human Ureaplasma spp., Ureaplasma parvum is clinically the most common. We have developed a high-resolution melt (HRM) PCR assay for the differentiation of the four serovars of U. parvum in a single step. Currently U. parvum strains are separated into four serovars by sequencing the promoter and coding region of the multiple-banded antigen (MBA) gene. We designed primers to conserved sequences within this region for PCR amplification and HRM analysis to generate reproducible and distinct melt profiles that distinguish clonal representatives of serovars 1, 3, 6, and 14. Furthermore, our HRM PCR assay could classify DNA extracted from 74 known (MBA-sequenced) test strains with 100% accuracy. Importantly, HRM PCR was also able to identify U. parvum serovars directly from 16 clinical swabs. HRM PCR performed with DNA consisting of mixtures of combined known serovars yielded profiles that were easily distinguished from those for single-serovar controls. These profiles mirrored clinical samples that contained mixed serovars. Unfortunately, melt curve analysis software is not yet robust enough to identify the composition of mixed serovar samples, only that more than one serovar is present. HRM PCR provides a single-step, rapid, cost-effective means to differentiate the four serovars of U. parvum that did not amplify any of the known 10 serovars of Ureaplasma urealyticum tested in parallel. Choice of reaction reagents was found to be crucial to allow sufficient sensitivity to differentiate U. parvum serovars directly from clinical swabs rather than requiring cell enrichment using microbial culture techniques.

Development and Evaluation of a Single-Step Duplex PCR for Simultaneous Detection of Fasciola hepatica and Fasciola gigantica (Family Fasciolidae, Class Trematoda, Phylum Platyhelminthes)

PubMed Central

Nguyen, Khue Thi; Nguyen, Nga Thi Bich; Doan, Huong Thi Thanh; Le, Xuyen Thi Kim; Hoang, Chau Thi Minh; De, Nguyen Van

2012-01-01

A single-step multiplex PCR (here referred to as a duplex PCR) has been developed for simultaneous detection and diagnosis of Fasciola hepatica and F. gigantica. These species overlap in distribution in many countries of North and East Africa and Central and Southeast Asia and are similar in egg morphology, making identification from fecal samples difficult. Based on a comparative alignment of mitochondrial DNA (mtDNA) spanning the region of cox1-trnT-rrnL, two species-specific forward primers were designed, FHF (for F. hepatica) and FGF (for F. gigantica), and a single reverse primer, FHGR (common for both species). Conventional PCR followed by sequencing was applied using species-specific primer pairs to verify the specificity of primers and the identity of Fasciola DNA templates. Duplex PCR (using three primers) was used for testing with the DNA extracted from adult worms, miracidia, and eggs, producing amplicons of 1,031 bp for F. hepatica and 615 bp for F. gigantica. The duplex PCR failed to amplify from DNA of other common liver and intestinal trematodes, including two opisthorchiids, three heterophyids, an echinostomid, another fasciolid, and a taeniid cestode. The sensitivity assay showed that the duplex PCR limit of detection for each Fasciola species was between 0.012 ng and 0.006 ng DNA. Evaluation using DNA templates from 32 Fasciola samples (28 adults and 4 eggs) and from 25 field-collected stools of ruminants and humans revealed specific bands of the correct size and the presence of Fasciola species. This novel mtDNA duplex PCR is a sensitive and fast tool for accurate identification of Fasciola species in areas of distributional and zonal overlap. PMID:22692744

Development and evaluation of a single-step duplex PCR for simultaneous detection of Fasciola hepatica and Fasciola gigantica (family Fasciolidae, class Trematoda, phylum Platyhelminthes).

PubMed

Le, Thanh Hoa; Nguyen, Khue Thi; Nguyen, Nga Thi Bich; Doan, Huong Thi Thanh; Le, Xuyen Thi Kim; Hoang, Chau Thi Minh; De, Nguyen Van

2012-08-01

A single-step multiplex PCR (here referred to as a duplex PCR) has been developed for simultaneous detection and diagnosis of Fasciola hepatica and F. gigantica. These species overlap in distribution in many countries of North and East Africa and Central and Southeast Asia and are similar in egg morphology, making identification from fecal samples difficult. Based on a comparative alignment of mitochondrial DNA (mtDNA) spanning the region of cox1-trnT-rrnL, two species-specific forward primers were designed, FHF (for F. hepatica) and FGF (for F. gigantica), and a single reverse primer, FHGR (common for both species). Conventional PCR followed by sequencing was applied using species-specific primer pairs to verify the specificity of primers and the identity of Fasciola DNA templates. Duplex PCR (using three primers) was used for testing with the DNA extracted from adult worms, miracidia, and eggs, producing amplicons of 1,031 bp for F. hepatica and 615 bp for F. gigantica. The duplex PCR failed to amplify from DNA of other common liver and intestinal trematodes, including two opisthorchiids, three heterophyids, an echinostomid, another fasciolid, and a taeniid cestode. The sensitivity assay showed that the duplex PCR limit of detection for each Fasciola species was between 0.012 ng and 0.006 ng DNA. Evaluation using DNA templates from 32 Fasciola samples (28 adults and 4 eggs) and from 25 field-collected stools of ruminants and humans revealed specific bands of the correct size and the presence of Fasciola species. This novel mtDNA duplex PCR is a sensitive and fast tool for accurate identification of Fasciola species in areas of distributional and zonal overlap.

New sorbent in the dispersive solid phase extraction step of quick, easy, cheap, effective, rugged, and safe for the extraction of organic contaminants in drinking water treatment sludge.

PubMed

Cerqueira, Maristela B R; Caldas, Sergiane S; Primel, Ednei G

2014-04-04

Recent studies have shown a decrease in the concentration of pesticides, pharmaceuticals and personal care products (PCPs) in water after treatment. A possible explanation for this phenomenon is that these compounds may adhere to the sludge; however, investigation of these compounds in drinking water treatment sludge has been scarce. The sludge generated by drinking water treatment plants during flocculation and decantation steps should get some special attention not only because it has been classified as non-inert waste but also because it is a very complex matrix, consisting essentially of inorganic (sand, argil and silt) and organic (humic substances) compounds. In the first step of this study, three QuEChERS methods were used, and then compared, for the extraction of pesticides (atrazine, simazine, clomazone and tebuconazole), pharmaceuticals (amitriptyline, caffeine, diclofenac and ibuprofen) and PCPs (methylparaben, propylparaben, triclocarban and bisphenol A) from drinking water treatment sludge. Afterwards, the study of different sorbents in the dispersive solid phase extraction (d-SPE) step was evaluated. Finally, a new QuEChERS method employing chitin, obtained from shrimp shell waste, was performed in the d-SPE step. After having been optimized, the method showed limits of quantification (LOQ) between 1 and 50 μg kg(-1) and the analytical curves showed r values higher than 0.98, when liquid chromatography tandem mass spectrometry was employed. Recoveries ranged between 50 and 120% with RSD≤15%. The matrix effect was evaluated and compensated with matrix-matched calibration. The method was applied to drinking water treatment sludge samples and methylparaben and tebuconazole were found in concentration

Step Forward. Single Parent/Homemaker Annual Report for the Fiscal Year 1990-1991.

ERIC Educational Resources Information Center

Kentucky Tech Region 5, Elizabethtown.

The Step Forward Single Parent/Homemaker Program in Elizabethtown, Kentucky, was developed to provide information on career opportunities and assist the target individuals in career assessment, career counseling, and goal setting in order to develop self-esteem and time management skills. During the second year of the Step Forward program in…

Methods for producing extracted and digested products from pretreated lignocellulosic biomass

DOEpatents

Chundawat, Shishir; Sousa, Leonardo Da Costa; Cheh, Albert M.; Balan; , Venkatesh; Dale, Bruce

2017-05-16

Methods for producing extracted and digested products from pretreated lignocellulosic biomass are provided. The methods include converting native cellulose I.sub..beta. to cellulose III.sub.I by pretreating the lignocellulosic biomass with liquid ammonia under certain conditions, and performing extracting or digesting steps on the pretreated/converted lignocellulosic biomass.

Cardiac and Vascular Synergic Protective Effect of Olea europea L. Leaves and Hibiscus sabdariffa L. Flower Extracts.

PubMed

Micucci, Matteo; Malaguti, Marco; Toschi, Tullia Gallina; Di Lecce, Giuseppe; Aldini, Rita; Angeletti, Andrea; Chiarini, Alberto; Budriesi, Roberta; Hrelia, Silvana

2015-01-01

This study was aimed at investigating the cardiovascular effects of an Olea europea L. leaf extract (OEE), of a Hibiscus sabdariffa L. flower extract (HSE), and of their 13 : 2 w/w mixture in order to assess their cardiac and vascular activity. Both extracts were fully characterized in their bioactive compounds by HPLC-MS/MS analysis. The study was performed using primary vascular endothelial cells (HUVECs) to investigate the antioxidant and cytoprotective effect of the extracts and their mixture and isolated guinea-pig left and right atria and aorta to evaluate the inotropic and chronotropic activities and vasorelaxant properties. In cultured HUVECs, OEE and HSE reduced intracellular reactive oxygen species formation and improved cell viability, following oxidative stress in dose-dependent manner. OEE and HSE exerted negative inotropic and vasorelaxant effects without any chronotropic property. Interestingly, the mixture exerted higher cytoprotective effects and antioxidant activities. Moreover, the mixture exerted an inotropic effect similar to each single extract, while it revealed an intrinsic negative chronotropic activity different from the single extract; its relaxant activity was higher than that of each single extract. In conclusion OEE and HSE mixture has a good potential for pharmaceutical and nutraceutical application, thanks to the synergistic effects of the single phytochemicals.

Cardiac and Vascular Synergic Protective Effect of Olea europea L. Leaves and Hibiscus sabdariffa L. Flower Extracts

PubMed Central

Micucci, Matteo; Gallina Toschi, Tullia; Di Lecce, Giuseppe; Aldini, Rita; Angeletti, Andrea; Chiarini, Alberto

2015-01-01

This study was aimed at investigating the cardiovascular effects of an Olea europea L. leaf extract (OEE), of a Hibiscus sabdariffa L. flower extract (HSE), and of their 13 : 2 w/w mixture in order to assess their cardiac and vascular activity. Both extracts were fully characterized in their bioactive compounds by HPLC-MS/MS analysis. The study was performed using primary vascular endothelial cells (HUVECs) to investigate the antioxidant and cytoprotective effect of the extracts and their mixture and isolated guinea-pig left and right atria and aorta to evaluate the inotropic and chronotropic activities and vasorelaxant properties. In cultured HUVECs, OEE and HSE reduced intracellular reactive oxygen species formation and improved cell viability, following oxidative stress in dose-dependent manner. OEE and HSE exerted negative inotropic and vasorelaxant effects without any chronotropic property. Interestingly, the mixture exerted higher cytoprotective effects and antioxidant activities. Moreover, the mixture exerted an inotropic effect similar to each single extract, while it revealed an intrinsic negative chronotropic activity different from the single extract; its relaxant activity was higher than that of each single extract. In conclusion OEE and HSE mixture has a good potential for pharmaceutical and nutraceutical application, thanks to the synergistic effects of the single phytochemicals. PMID:26180582

Algorithm-enabled partial-angular-scan configurations for dual-energy CT.

PubMed

Chen, Buxin; Zhang, Zheng; Xia, Dan; Sidky, Emil Y; Pan, Xiaochuan

2018-05-01

We seek to investigate an optimization-based one-step method for image reconstruction that explicitly compensates for nonlinear spectral response (i.e., the beam-hardening effect) in dual-energy CT, to investigate the feasibility of the one-step method for enabling two dual-energy partial-angular-scan configurations, referred to as the short- and half-scan configurations, on standard CT scanners without involving additional hardware, and to investigate the potential of the short- and half-scan configurations in reducing imaging dose and scan time in a single-kVp-switch full-scan configuration in which two full rotations are made for collection of dual-energy data. We use the one-step method to reconstruct images directly from dual-energy data through solving a nonconvex optimization program that specifies the images to be reconstructed in dual-energy CT. Dual-energy full-scan data are generated from numerical phantoms and collected from physical phantoms with the standard single-kVp-switch full-scan configuration, whereas dual-energy short- and half-scan data are extracted from the corresponding full-scan data. Besides visual inspection and profile-plot comparison, the reconstructed images are analyzed also in quantitative studies based upon tasks of linear-attenuation-coefficient and material-concentration estimation and of material differentiation. Following the performance of a computer-simulation study to verify that the one-step method can reconstruct numerically accurately basis and monochromatic images of numerical phantoms, we reconstruct basis and monochromatic images by using the one-step method from real data of physical phantoms collected with the full-, short-, and half-scan configurations. Subjective inspection based upon visualization and profile-plot comparison reveals that monochromatic images, which are used often in practical applications, reconstructed from the full-, short-, and half-scan data are largely visually comparable except for some differences in texture details. Moreover, quantitative studies based upon tasks of linear-attenuation-coefficient and material-concentration estimation and of material differentiation indicate that the short- and half-scan configurations yield results in close agreement with the ground-truth information and that of the full-scan configuration. The one-step method considered can compensate effectively for the nonlinear spectral response in full- and partial-angular-scan dual-energy CT. It can be exploited for enabling partial-angular-scan configurations on standard CT scanner without involving additional hardware. Visual inspection and quantitative studies reveal that, with the one-step method, partial-angular-scan configurations considered can perform at a level comparable to that of the full-scan configuration, thus suggesting the potential of the two partial-angular-scan configurations in reducing imaging dose and scan time in the standard single-kVp-switch full-scan CT in which two full rotations are performed. The work also yields insights into the investigation and design of other nonstandard scan configurations of potential practical significance in dual-energy CT. © 2018 American Association of Physicists in Medicine.

Extraction of endoscopic images for biomedical figure classification

NASA Astrophysics Data System (ADS)

Xue, Zhiyun; You, Daekeun; Chachra, Suchet; Antani, Sameer; Long, L. R.; Demner-Fushman, Dina; Thoma, George R.

2015-03-01

Modality filtering is an important feature in biomedical image searching systems and may significantly improve the retrieval performance of the system. This paper presents a new method for extracting endoscopic image figures from photograph images in biomedical literature, which are found to have highly diverse content and large variability in appearance. Our proposed method consists of three main stages: tissue image extraction, endoscopic image candidate extraction, and ophthalmic image filtering. For tissue image extraction we use image patch level clustering and MRF relabeling to detect images containing skin/tissue regions. Next, we find candidate endoscopic images by exploiting the round shape characteristics that commonly appear in these images. However, this step needs to compensate for images where endoscopic regions are not entirely round. In the third step we filter out the ophthalmic images which have shape characteristics very similar to the endoscopic images. We do this by using text information, specifically, anatomy terms, extracted from the figure caption. We tested and evaluated our method on a dataset of 115,370 photograph figures, and achieved promising precision and recall rates of 87% and 84%, respectively.

Vigi4Med Scraper: A Framework for Web Forum Structured Data Extraction and Semantic Representation

PubMed Central

Audeh, Bissan; Beigbeder, Michel; Zimmermann, Antoine; Jaillon, Philippe; Bousquet, Cédric

2017-01-01

The extraction of information from social media is an essential yet complicated step for data analysis in multiple domains. In this paper, we present Vigi4Med Scraper, a generic open source framework for extracting structured data from web forums. Our framework is highly configurable; using a configuration file, the user can freely choose the data to extract from any web forum. The extracted data are anonymized and represented in a semantic structure using Resource Description Framework (RDF) graphs. This representation enables efficient manipulation by data analysis algorithms and allows the collected data to be directly linked to any existing semantic resource. To avoid server overload, an integrated proxy with caching functionality imposes a minimal delay between sequential requests. Vigi4Med Scraper represents the first step of Vigi4Med, a project to detect adverse drug reactions (ADRs) from social networks founded by the French drug safety agency Agence Nationale de Sécurité du Médicament (ANSM). Vigi4Med Scraper has successfully extracted greater than 200 gigabytes of data from the web forums of over 20 different websites. PMID:28122056

The optimization of essential oils supercritical CO2 extraction from Lavandula hybrida through static-dynamic steps procedure and semi-continuous technique using response surface method

PubMed Central

Kamali, Hossein; Aminimoghadamfarouj, Noushin; Golmakani, Ebrahim; Nematollahi, Alireza

2015-01-01

Aim: The aim of this study was to examine and evaluate crucial variables in essential oils extraction process from Lavandula hybrida through static-dynamic and semi-continuous techniques using response surface method. Materials and Methods: Essential oil components were extracted from Lavandula hybrida (Lavandin) flowers using supercritical carbon dioxide via static-dynamic steps (SDS) procedure, and semi-continuous (SC) technique. Results: Using response surface method the optimum extraction yield (4.768%) was obtained via SDS at 108.7 bar, 48.5°C, 120 min (static: 8×15), 24 min (dynamic: 8×3 min) in contrast to the 4.620% extraction yield for the SC at 111.6 bar, 49.2°C, 14 min (static), 121.1 min (dynamic). Conclusion: The results indicated that a substantial reduction (81.56%) solvent usage (kg CO2/g oil) is observed in the SDS method versus the conventional SC method. PMID:25598636

Sequential Extraction Results and Mineralogy of Mine Waste and Stream Sediments Associated With Metal Mines in Vermont, Maine, and New Zealand

USGS Publications Warehouse

Piatak, N.M.; Seal, R.R.; Sanzolone, R.F.; Lamothe, P.J.; Brown, Z.A.; Adams, M.

2007-01-01

We report results from sequential extraction experiments and the quantitative mineralogy for samples of stream sediments and mine wastes collected from metal mines. Samples were from the Elizabeth, Ely Copper, and Pike Hill Copper mines in Vermont, the Callahan Mine in Maine, and the Martha Mine in New Zealand. The extraction technique targeted the following operationally defined fractions and solid-phase forms: (1) soluble, adsorbed, and exchangeable fractions; (2) carbonates; (3) organic material; (4) amorphous iron- and aluminum-hydroxides and crystalline manganese-oxides; (5) crystalline iron-oxides; (6) sulfides and selenides; and (7) residual material. For most elements, the sum of an element from all extractions steps correlated well with the original unleached concentration. Also, the quantitative mineralogy of the original material compared to that of the residues from two extraction steps gave insight into the effectiveness of reagents at dissolving targeted phases. The data are presented here with minimal interpretation or discussion and further analyses and interpretation will be presented elsewhere.

Single-step reinforced microextraction of polycyclic aromatic hydrocarbons from soil samples using an inside needle capillary adsorption trap with electropolymerized aniline/multi-walled carbon nanotube sorbent.

PubMed

Ghiasvand, Ali Reza; Yazdankhah, Fatemeh

2017-03-03

A polyaniline/multi-wall carbon nanotubes (PANI/MWCNT) composite was electrodeposited on the interior surface of a platinized stainless steel capillary needle and used to prepare an inside needle capillary adsorption trap (INCAT) device. The platinization expanded the interior adsorbing surface of the needle and made it more porous and cohesive for nanocomposite film. The nanocomposite was characterized using scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FT-IR). The fabricated INCAT was fixed into a cooling capsule to fabricate a cooling-assisted INCAT (CA-INCAT) system. The CA-INCAT device was used to extract polycyclic aromatic hydrocarbons (PAHs) from solid samples followed by gas chromatography-flame ionization detection (GC-FID) determination. To obtain the best extraction efficiency, the important experimental variables were studied and optimized. Under the optimal conditions, the limits of detection (LODs) for the studied PAHs were in the range of 0.002-0.02ngg -1 . Linear dynamic ranges (LDRs) for the calibration curves were found to be 0.1-30,000ngg -1 . Relative standard deviations (RSDs%) for six replicated analysis of 1ngg -1 PAHs were obtained 7.7-11%. The CA-INCAT-GC-FID method was successfully applied for the extraction and determination of PAHs in contaminated soil samples. The results were in agreement with those obtained by a validated ultrasound-assisted solvent extraction (UA-SE) method. Copyright © 2017 Elsevier B.V. All rights reserved.

Multiresidue analysis of endocrine-disrupting compounds and perfluorinated sulfates and carboxylic acids in sediments by ultra-high-performance liquid chromatography-tandem mass spectrometry.

PubMed

Cavaliere, Chiara; Capriotti, Anna Laura; Ferraris, Francesca; Foglia, Patrizia; Samperi, Roberto; Ventura, Salvatore; Laganà, Aldo

2016-03-18

A multiresidue analytical method for the determination of 11 perfluorinated compounds and 22 endocrine-disrupting compounds (ECDs) including 13 natural and synthetic estrogens (free and conjugated forms), 2 alkylphenols, 1 plasticiser, 2 UV-filters, 1 antimicrobial, and 2 organophosphorus compounds in sediments has been developed. Ultrasound-assisted extraction followed by solid phase extraction (SPE) with graphitized carbon black (GCB) cartridge as clean-up step were used. The extraction process yield was optimized in terms of solvent composition. Then, a 3(2) experimental design was used to optimize solvent volume and sonication time by response surface methodology, which simplifies the optimization procedure. The final extract was analyzed by ultra-high performance liquid chromatography coupled with tandem mass spectrometry. The optimized sample preparation method is simple and robust, and allows recovery of ECDs belonging to different classes in a complex matrix such as sediment. The use of GCB for SPE allowed to obtain with a single clean-up procedure excellent recoveries ranging between 75 and 110% (relative standard deviation <16%). The developed methodology has been successfully applied to the analysis of ECDs in sediments from different rivers and lakes of the Lazio Region (Italy). These analyses have shown the ubiquitous presence of chloro-substituted organophosphorus flame retardants and bisphenol A, while other analyzed compounds were occasionally found at concentration between the limit of detection and quantification. Copyright © 2016 Elsevier B.V. All rights reserved.

Mercury removal from aqueous streams utilizing microemulsion liquid membranes

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

Larson, K.A.; Wiencek, J.M.

1994-11-01

The goal of this work is the removal of mercury ion from wastewater using thermodynamically stable microemulsions as liquid membranes. The research focuses on identification and modeling of the appropriate aqueous and organic phase equilibrium reactions for mercury extraction and stripping, comparison of extraction kinetics between coarse emulsions and microemulsions, and demulsification and recovery of the emulsion components. An oleic acid microemulsion liquid membrane (water-in-oil) containing sulfuric acid as the internal phase reduces the feed phase mercury concentration from 460 mg/l to 0.84 mg/l in a single contacting. This compares favorably with a control extraction (oleic acid/no internal phase) whichmore » results in a final concentration of 20 mg/l Hg{sup +2}. Microemulsions can be demulsified using butanol as an additive. The demulsification kinetics are proportional to butanol concentration and temperature and inversely proportional to surfactant concentration. The demulsification rate is second order with respect to water concentration which implies that the rate-limiting step in the process is the rate of internal phase droplet encounters. Proof-of-principle experiments demonstrate the ability to extract mercury ion using microemulsions formulated with recycled organic phase, albeit at a somewhat reduced efficiency. The reduced efficiency is attributed to increased internal phase leakage due to residual butanol in the oil phase. Finally, the cycle is brought around full circle by recovering metallic mercury from the internal phase by electroplating. 27 refs., 11 figs., 1 tab.« less

A procedure for quantitation of total oxidized uranium for bioremediation studies

USGS Publications Warehouse

Elias, Dwayne A.; Senko, John M.; Krumholz, Lee R.

2003-01-01

A procedure was developed for the quantitation of complexed U(VI) during studies on U(VI) bioremediation. These studies typically involve conversion of soluble or complexed U(VI) (oxidized) to U(IV) (the reduced form which is much less soluble). Since U(VI) freely exchanges between material adsorbed to the solid phase and the dissolved phase, uranium bioremediation experiments require a mass balance of U in both its soluble and adsorbed forms as well as in the reduced sediment bound phase. We set out to optimize a procedure for extraction and quantitation of sediment bound U(VI). Various extractant volumes to sediment ratios were tested and it was found that between 1:1 to 8:1 ratios (v/w) there was a steady increase in U(VI) recovered, but no change with further increases in v/w ratio.Various strengths of NaHCO3, Na-EDTA, and Na-citrate were used to evaluate complexed U(VI) recovery, while the efficiency of a single versus repeated extraction steps was compared with synthesized uranyl-phosphate and uranyl-hydroxide. Total recovery with 1 M NaHCO3 was 95.7% and 97.9% from uranyl-phosphate and uranyl-hydroxide, respectively, compared to 80.7% and 89.9% using 450 mM NaHCO3. Performing the procedure once yielded an efficiency of 81.1% and 92.3% for uranyl-phosphate and uranyl-hydroxide, respectively, as compared to three times. All other extractants yielded 7.9–82.0% in both experiments.

A Procedure for the supercritical fluid extraction of coal samples, with subsequent analysis of extracted hydrocarbons

USGS Publications Warehouse

Kolak, Jonathan J.

2006-01-01

Introduction: This report provides a detailed, step-by-step procedure for conducting extractions with supercritical carbon dioxide (CO2) using the ISCO SFX220 supercritical fluid extraction system. Protocols for the subsequent separation and analysis of extracted hydrocarbons are also included in this report. These procedures were developed under the auspices of the project 'Assessment of Geologic Reservoirs for Carbon Dioxide Sequestration' (see http://pubs.usgs.gov/fs/fs026-03/fs026-03.pdf) to investigate possible environmental ramifications associated with CO2 storage (sequestration) in geologic reservoirs, such as deep (~1 km below land surface) coal beds. Supercritical CO2 has been used previously to extract contaminants from geologic matrices. Pressure-temperature conditions within deep coal beds may render CO2 supercritical. In this context, the ability of supercritical CO2 to extract contaminants from geologic materials may serve to mobilize noxious compounds from coal, possibly complicating storage efforts. There currently exists little information on the physicochemical interactions between supercritical CO2 and coal in this setting. The procedures described herein were developed to improve the understanding of these interactions and provide insight into the fate of CO2 and contaminants during simulated CO2 injections.

Optimisation of olive oil phenol extraction conditions using a high-power probe ultrasonication.

PubMed

Jerman Klen, T; Mozetič Vodopivec, B

2012-10-15

A new method of ultrasound probe assisted liquid-liquid extraction (US-LLE) combined with a freeze-based fat precipitation clean-up and HPLC-DAD-FLD-MS detection is described for extra virgin olive oil (EVOO) phenol analysis. Three extraction variables (solvent type; 100%, 80%, 50% methanol, sonication time; 5, 10, 20 min, extraction steps; 1-5) and two clean-up methods (n-hexane washing vs. low temperature fat precipitation) were studied and optimised with aim to maximise extracts' phenol recoveries. A three-step extraction of 10 min with pure methanol (5 mL) resulted in the highest phenol content of freeze-based defatted extracts (667 μg GAE g(-1)) from 10 g of EVOO, providing much higher efficiency (up to 68%) and repeatability (up to 51%) vs. its non-sonicated counterpart (LLE-agitation) and n-hexane washing. In addition, the overall method provided high linearity (r(2)≥0.97), precision (RSD: 0.4-9.3%) and sensitivity with LODs/LOQs ranging from 0.03 to 0.16 μg g(-1) and 0.10-0.51 μg g(-1) of EVOO, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

Optimization of Milk-Based Medium for Efficient Cultivation of Bifidobacterium pseudocatenulatum G4 Using Face-Centered Central Composite-Response Surface Methodology

PubMed Central

Abdul Khalil, Khalilah; Mustafa, Shuhaimi; Mohammad, Rosfarizan; Bin Ariff, Arbakariya; Shaari, Yamin; Abdul Manap, Yazid; Dahalan, Farrah Aini

2014-01-01

This study was undertaken to optimize skim milk and yeast extract concentration as a cultivation medium for optimal Bifidobacteria pseudocatenulatum G4 (G4) biomass and β-galactosidase production as well as lactose and free amino nitrogen (FAN) balance after cultivation period. Optimization process in this study involved four steps: screening for significant factors using 23 full factorial design, steepest ascent, optimization using FCCD-RSM, and verification. From screening steps, skim milk and yeast extract showed significant influence on the biomass production and, based on the steepest ascent step, middle points of skim milk (6% wt/vol) and yeast extract (1.89% wt/vol) were obtained. A polynomial regression model in FCCD-RSM revealed that both factors were found significant and the strongest influence was given by skim milk concentration. Optimum concentrations of skim milk and yeast extract for maximum biomass G4 and β-galactosidase production meanwhile low in lactose and FAN balance after cultivation period were 5.89% (wt/vol) and 2.31% (wt/vol), respectively. The validation experiments showed that the predicted and experimental values are not significantly different, indicating that the FCCD-RSM model developed is sufficient to describe the cultivation process of G4 using skim-milk-based medium with the addition of yeast extract. PMID:24527457

Gradient x Isocratic Elution CCC on the Isolation of Verbascoside and Other Phenylethanoids: Influence of the Complexity of the Matrix.

PubMed

Leitão, Gilda Guimarães; Pinto, Shaft Correa; de Oliveira, Danilo Ribeiro; Timoteo, Patrícia; Guimarães, Michelle Guedes; Cordova, Wilmer H Perera; Leitão, Suzana Guimarães

2015-11-01

Verbascoside is a phenylethanoid glycoside widely distributed in nature, especially among the order Lamiales, occurring in numerous plants that are constituents of folk medicine preparations. This natural compound, previously isolated by our group from the ethyl acetate extract of Lantana trifolia using the gradient approach in countercurrent chromatography, was now isolated from the butanol extract of the same plant and from Lippia alba f. intermedia (Verbenaceae) using countercurrent chromatography in either gradient or isocratic elution modes. The ethyl acetate extract of L. alba, rich in phenylethanoids and flavonoids, was fractionated using countercurrent chromatography in the step-gradient elution approach. The four-step solvent system was composed of n-hexane-ethyl acetate-n-butanol-water (4 : 10 : X : 10), where X = 1 (solvent system A), 3 (solvent system B), 5 (solvent system C), and 7 (solvent system D), and allowed for the isolation of verbascoside along with other phenylethanoids and flavonoids from both plants. Verbascoside and 2'-O-β-apiosylverbascoside were further isolated from the n-butanol extract of L. trifolia using the solvent system ethyl acetate-n-butanol-water 10 : 2 : 10 on an isocratic run. The difference in the complexity of the two plant extracts demanded different purification steps, which included a second high-speed countercurrent chromatography purification using the isocratic elution mode. Georg Thieme Verlag KG Stuttgart · New York.

Changes in step-width during dual-task walking predicts falls.

PubMed

Nordin, E; Moe-Nilssen, R; Ramnemark, A; Lundin-Olsson, L

2010-05-01

The aim was to evaluate whether gait pattern changes between single- and dual-task conditions were associated with risk of falling in older people. Dual-task cost (DTC) of 230 community living, physically independent people, 75 years or older, was determined with an electronic walkway. Participants were followed up each month for 1 year to record falls. Mean and variability measures of gait characteristics for 5 dual-task conditions were compared to single-task walking for each participant. Almost half (48%) of the participants fell at least once during follow-up. Risk of falling increased in individuals where DTC for performing a subtraction task demonstrated change in mean step-width compared to single-task walking. Risk of falling decreased in individuals where DTC for carrying a cup and saucer demonstrated change compared to single-task walking in mean step-width, mean step-time, and step-length variability. Degree of change in gait characteristics related to a change in risk of falling differed between measures. Prognostic guidance for fall risk was found for the above DTCs in mean step-width with a negative likelihood ratio of 0.5 and a positive likelihood ratio of 2.3, respectively. Findings suggest that changes in step-width, step-time, and step-length with dual tasking may be related to future risk of falling. Depending on the nature of the second task, DTC may indicate either an increased risk of falling, or a protective strategy to avoid falling. Copyright 2010. Published by Elsevier B.V.

Method of upgrading oils containing hydroxyaromatic hydrocarbon compounds to highly aromatic gasoline

DOEpatents

Baker, Eddie G.; Elliott, Douglas C.

1993-01-01

The present invention is a multi-stepped method of converting an oil which is produced by various biomass and coal conversion processes and contains primarily single and multiple ring hydroxyaromatic hydrocarbon compounds to highly aromatic gasoline. The single and multiple ring hydroxyaromatic hydrocarbon compounds in a raw oil material are first deoxygenated to produce a deoxygenated oil material containing single and multiple ring aromatic compounds. Then, water is removed from the deoxygenated oil material. The next step is distillation to remove the single ring aromatic compouns as gasoline. In the third step, the multiple ring aromatics remaining in the deoxygenated oil material are cracked in the presence of hydrogen to produce a cracked oil material containing single ring aromatic compounds. Finally, the cracked oil material is then distilled to remove the single ring aromatics as gasoline.

Method of upgrading oils containing hydroxyaromatic hydrocarbon compounds to highly aromatic gasoline

DOEpatents

Baker, E.G.; Elliott, D.C.

1993-01-19

The present invention is a multi-stepped method of converting an oil which is produced by various biomass and coal conversion processes and contains primarily single and multiple ring hydroxyaromatic hydrocarbon compounds to highly aromatic gasoline. The single and multiple ring hydroxyaromatic hydrocarbon compounds in a raw oil material are first deoxygenated to produce a deoxygenated oil material containing single and multiple ring aromatic compounds. Then, water is removed from the deoxygenated oil material. The next step is distillation to remove the single ring aromatic compounds as gasoline. In the third step, the multiple ring aromatics remaining in the deoxygenated oil material are cracked in the presence of hydrogen to produce a cracked oil material containing single ring aromatic compounds. Finally, the cracked oil material is then distilled to remove the single ring aromatics as gasoline.

Single molecule thermodynamics in biological motors.

PubMed

Taniguchi, Yuichi; Karagiannis, Peter; Nishiyama, Masayoshi; Ishii, Yoshiharu; Yanagida, Toshio

2007-04-01

Biological molecular machines use thermal activation energy to carry out various functions. The process of thermal activation has the stochastic nature of output events that can be described according to the laws of thermodynamics. Recently developed single molecule detection techniques have allowed each distinct enzymatic event of single biological machines to be characterized providing clues to the underlying thermodynamics. In this study, the thermodynamic properties in the stepping movement of a biological molecular motor have been examined. A single molecule detection technique was used to measure the stepping movements at various loads and temperatures and a range of thermodynamic parameters associated with the production of each forward and backward step including free energy, enthalpy, entropy and characteristic distance were obtained. The results show that an asymmetry in entropy is a primary factor that controls the direction in which the motor will step. The investigation on single molecule thermodynamics has the potential to reveal dynamic properties underlying the mechanisms of how biological molecular machines work.

Genomic prediction in a nuclear population of layers using single-step models.

PubMed

Yan, Yiyuan; Wu, Guiqin; Liu, Aiqiao; Sun, Congjiao; Han, Wenpeng; Li, Guangqi; Yang, Ning

2018-02-01

Single-step genomic prediction method has been proposed to improve the accuracy of genomic prediction by incorporating information of both genotyped and ungenotyped animals. The objective of this study is to compare the prediction performance of single-step model with a 2-step models and the pedigree-based models in a nuclear population of layers. A total of 1,344 chickens across 4 generations were genotyped by a 600 K SNP chip. Four traits were analyzed, i.e., body weight at 28 wk (BW28), egg weight at 28 wk (EW28), laying rate at 38 wk (LR38), and Haugh unit at 36 wk (HU36). In predicting offsprings, individuals from generation 1 to 3 were used as training data and females from generation 4 were used as validation set. The accuracies of predicted breeding values by pedigree BLUP (PBLUP), genomic BLUP (GBLUP), SSGBLUP and single-step blending (SSBlending) were compared for both genotyped and ungenotyped individuals. For genotyped females, GBLUP performed no better than PBLUP because of the small size of training data, while the 2 single-step models predicted more accurately than the PBLUP model. The average predictive ability of SSGBLUP and SSBlending were 16.0% and 10.8% higher than the PBLUP model across traits, respectively. Furthermore, the predictive abilities for ungenotyped individuals were also enhanced. The average improvements of prediction abilities were 5.9% and 1.5% for SSGBLUP and SSBlending model, respectively. It was concluded that single-step models, especially the SSGBLUP model, can yield more accurate prediction of genetic merits and are preferable for practical implementation of genomic selection in layers. © 2017 Poultry Science Association Inc.

Single-Run Single-Mask Inductively-Coupled-Plasma Reactive-Ion-Etching Process for Fabricating Suspended High-Aspect-Ratio Microstructures

NASA Astrophysics Data System (ADS)

Yang, Yao-Joe; Kuo, Wen-Cheng; Fan, Kuang-Chao

2006-01-01

In this work, we present a single-run single-mask (SRM) process for fabricating suspended high-aspect-ratio structures on standard silicon wafers using an inductively coupled plasma-reactive ion etching (ICP-RIE) etcher. This process eliminates extra fabrication steps which are required for structure release after trench etching. Released microstructures with 120 μm thickness are obtained by this process. The corresponding maximum aspect ratio of the trench is 28. The SRM process is an extended version of the standard process proposed by BOSCH GmbH (BOSCH process). The first step of the SRM process is a standard BOSCH process for trench etching, then a polymer layer is deposited on trench sidewalls as a protective layer for the subsequent structure-releasing step. The structure is released by dry isotropic etching after the polymer layer on the trench floor is removed. All the steps can be integrated into a single-run ICP process. Also, only one mask is required. Therefore, the process complexity and fabrication cost can be effectively reduced. Discussions on each SRM step and considerations for avoiding undesired etching of the silicon structures during the release process are also presented.

Optimizing Fungal DNA Extraction Methods from Aerosol Filters

NASA Astrophysics Data System (ADS)

Jimenez, G.; Mescioglu, E.; Paytan, A.

2016-12-01

Fungi and fungal spores can be picked up from terrestrial ecosystems, transported long distances, and deposited into marine ecosystems. It is important to study dust-borne fungal communities, because they can stay viable and effect the ambient microbial populations, which are key players in biogeochemical cycles. One of the challenges of studying dust-borne fungal populations is that aerosol samples contain low biomass, making extracting good quality DNA very difficult. The aim of this project was to increase DNA yield by optimizing DNA extraction methods. We tested aerosol samples collected from Haifa, Israel (polycarbonate filter), Monterey Bay, CA (quartz filter) and Bermuda (quartz filter). Using the Qiagen DNeasy Plant Kit, we tested the effect of altering bead beating times and incubation times, adding three freeze and thaw steps, initially washing the filters with buffers for various lengths of time before using the kit, and adding a step with 30 minutes of sonication in 65C water. Adding three freeze/thaw steps, adding a sonication step, washing with a phosphate buffered saline overnight, and increasing incubation time to two hours, in that order, resulted in the highest increase in DNA for samples from Israel (polycarbonate). DNA yield of samples from Monterey (quart filter) increased about 5 times when washing with buffers overnight (phosphate buffered saline and potassium phophate buffer), adding a sonication step, and adding three freeze and thaw steps. Samples collected in Bermuda (quartz filter) had the highest increase in DNA yield from increasing incubation to 2 hours, increasing bead beating time to 6 minutes, and washing with buffers overnight (phosphate buffered saline and potassium phophate buffer). Our results show that DNA yield can be increased by altering various steps of the Qiagen DNeasy Plant Kit protocol, but different types of filters collected at different sites respond differently to alterations. These results can be used as preliminary results to continue developing fungi DNA extraction methods. Developing these methods will be important as dust storms are predicted to increase due to increased draughts and anthropogenic activity, and the fungal communities of these dust-storms are currently relatively understudied.

Sulfur K-edge XANES and acid volatile sulfide analyses of changes in chemical speciation of S and Fe during sequential extraction of trace metals in anoxic sludge from biogas reactors.

PubMed

Shakeri Yekta, Sepehr; Gustavsson, Jenny; Svensson, Bo H; Skyllberg, Ulf

2012-01-30

The effect of sequential extraction of trace metals on sulfur (S) speciation in anoxic sludge samples from two lab-scale biogas reactors augmented with Fe was investigated. Analyses of sulfur K-edge X-ray absorption near edge structure (S XANES) spectroscopy and acid volatile sulfide (AVS) were conducted on the residues from each step of the sequential extraction. The S speciation in sludge samples after AVS analysis was also determined by S XANES. Sulfur was mainly present as FeS (≈ 60% of total S) and reduced organic S (≈ 30% of total S), such as organic sulfide and thiol groups, in the anoxic solid phase. Sulfur XANES and AVS analyses showed that during first step of the extraction procedure (the removal of exchangeable cations), a part of the FeS fraction corresponding to 20% of total S was transformed to zero-valent S, whereas Fe was not released into the solution during this transformation. After the last extraction step (organic/sulfide fraction) a secondary Fe phase was formed. The change in chemical speciation of S and Fe occurring during sequential extraction procedure suggests indirect effects on trace metals associated to the FeS fraction that may lead to incorrect results. Furthermore, by S XANES it was verified that the AVS analysis effectively removed the FeS fraction. The present results identified critical limitations for the application of sequential extraction for trace metal speciation analysis outside the framework for which the methods were developed. Copyright © 2011 Elsevier B.V. All rights reserved.

Integrated feature extraction and selection for neuroimage classification

NASA Astrophysics Data System (ADS)

Fan, Yong; Shen, Dinggang

2009-02-01

Feature extraction and selection are of great importance in neuroimage classification for identifying informative features and reducing feature dimensionality, which are generally implemented as two separate steps. This paper presents an integrated feature extraction and selection algorithm with two iterative steps: constrained subspace learning based feature extraction and support vector machine (SVM) based feature selection. The subspace learning based feature extraction focuses on the brain regions with higher possibility of being affected by the disease under study, while the possibility of brain regions being affected by disease is estimated by the SVM based feature selection, in conjunction with SVM classification. This algorithm can not only take into account the inter-correlation among different brain regions, but also overcome the limitation of traditional subspace learning based feature extraction methods. To achieve robust performance and optimal selection of parameters involved in feature extraction, selection, and classification, a bootstrapping strategy is used to generate multiple versions of training and testing sets for parameter optimization, according to the classification performance measured by the area under the ROC (receiver operating characteristic) curve. The integrated feature extraction and selection method is applied to a structural MR image based Alzheimer's disease (AD) study with 98 non-demented and 100 demented subjects. Cross-validation results indicate that the proposed algorithm can improve performance of the traditional subspace learning based classification.

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.

Comparison of four extraction/methylation analytical methods to measure fatty acid composition by gas chromatography in meat.

PubMed

Juárez, M; Polvillo, O; Contò, M; Ficco, A; Ballico, S; Failla, S

2008-05-09

Four different extraction-derivatization methods commonly used for fatty acid analysis in meat (in situ or one-step method, saponification method, classic method and a combination of classic extraction and saponification derivatization) were tested. The in situ method had low recovery and variation. The saponification method showed the best balance between recovery, precision, repeatability and reproducibility. The classic method had high recovery and acceptable variation values, except for the polyunsaturated fatty acids, showing higher variation than the former methods. The combination of extraction and methylation steps had great recovery values, but the precision, repeatability and reproducibility were not acceptable. Therefore the saponification method would be more convenient for polyunsaturated fatty acid analysis, whereas the in situ method would be an alternative for fast analysis. However the classic method would be the method of choice for the determination of the different lipid classes.

Scale-up and economic analysis of biodiesel production from municipal primary sewage sludge.

PubMed

Olkiewicz, Magdalena; Torres, Carmen M; Jiménez, Laureano; Font, Josep; Bengoa, Christophe

2016-08-01

Municipal wastewater sludge is a promising lipid feedstock for biodiesel production, but the need to eliminate the high water content before lipid extraction is the main limitation for scaling up. This study evaluates the economic feasibility of biodiesel production directly from liquid primary sludge based on experimental data at laboratory scale. Computational tools were used for the modelling of the process scale-up and the different configurations of lipid extraction to optimise this step, as it is the most expensive. The operational variables with a major influence in the cost were the extraction time and the amount of solvent. The optimised extraction process had a break-even price of biodiesel of 1232 $/t, being economically competitive with the current cost of fossil diesel. The proposed biodiesel production process from waste sludge eliminates the expensive step of sludge drying, lowering the biodiesel price. Copyright © 2016 Elsevier Ltd. All rights reserved.

Needle-free nasal delivery of glucagon for treatment of diabetes-related severe hypoglycemia: toxicology of polypropylene resin used in delivery device.

PubMed

Reno, Frederick E; Edwards, C Nicholas; Bendix Jensen, Morten; Török-Bathó, Magdolna; Esdaile, David J; Piché, Claude; Triest, Myriam; Carballo, Dolorès

2016-09-01

The intranasal route is a promising route of administration for several emergency rescue drugs including naloxone and glucagon. Glucagon nasal powder (GNP) is a novel, needle-free delivery system for intranasal administration of glucagon for the treatment of severe hypoglycemia, an infrequent but serious complication of insulin use in patients with diabetes. The GNP delivery device is a compact, highly portable, single-use nasal powder dosing device constructed of polypropylene that allows for simple, single-step administration. To evaluate the toxicological profile of the polypropylene resin used in the actuator part of the delivery device that will contact skin and nasal mucosal membranes of the patient, we performed an in vitro cytotoxicity study, a skin sensitization study and an irritation (intracutaneous reactivity) study in animal models. Extracts of the actuator of the GNP device were generated from HAM F12 medium with 10% fetal bovine serum, 0.9% sodium chloride (NaCl) or sesame oil. The in vitro cytotoxicity test was performed in cultured L929 mouse fibroblasts. Skin sensitization analysis was performed in 10 guinea pigs according to the Magnusson-Kligman method, using a maximization method with Freund's Complete Adjuvant. Irritation following intracutaneous/intradermal treatment with device extracts (NaCl and sesame oil extractants) was assessed in three New Zealand White rabbits. In vitro cytotoxicity test: Both undiluted and diluted extract showed no toxicity (i.e. no abnormal morphology, cell death or cell lysis) toward L929 fibroblasts (cytotoxicity grade 0). Sensitization test in guinea pigs: Challenge with device extracts did not evoke positive responses in test animals previously induced with device extracts. The net response value represented an incidence rate of 0% and a net dermal irritation score value of 0.00. Irritation (intracutaneous/intradermal) test in New Zealand White rabbits: Device extracts and corresponding vehicle controls caused similar irritation reactions. The difference between the mean scores for the device extracts and the corresponding vehicle controls was less than 1.0. Extracts of the polypropylene resin of the GNP delivery device are not cytotoxic, do not result in dermal sensitization and do not cause irritation when applied topically or intracutaneously. Given the infrequent use and very short duration of exposure to the nasal mucosa during administration of GNP, the polypropylene resin of the GNP device actuator will likely not cause adverse dermal sensitization effects or irritation effects in humans and can, therefore, be considered for use as a delivery device in clinical trials assessing the efficacy and safety of GNP for the treatment of insulin-using patients experiencing episodes of severe hypoglycemia.